@article {pmid39620136, year = {2024}, author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, ÅJ and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD}, title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111076}, pmid = {39620136}, issn = {2589-0042}, abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.}, } @article {pmid39612613, year = {2024}, author = {Ferrando-Bernal, M and Brand, CM and Capra, JA}, title = {Inferring human phenotypes using ancient DNA: from molecules to populations.}, journal = {Current opinion in genetics & development}, volume = {90}, number = {}, pages = {102283}, doi = {10.1016/j.gde.2024.102283}, pmid = {39612613}, issn = {1879-0380}, abstract = {The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes - from the molecular to population scale - with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data.}, } @article {pmid39613690, year = {2024}, author = {Gaul, E and Spyrou, MA}, title = {Historical plague pandemics: perspectives from ancient DNA.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.10.008}, pmid = {39613690}, issn = {1878-4380}, abstract = {Ancient DNA research has provided important insights into the evolutionary history of Yersinia pestis during the historical plague pandemics. Future work should prioritise a more diversified approach to sampling, to ensure a broader understanding of the factors underlying pandemic onset, spread, and impact across different regions and hosts.}, } @article {pmid39606698, year = {2024}, author = {Zagorc, B and Blanz, M and Gelabert, P and Sawyer, S and Oberreiter, V and Cheronet, O and Chen, HS and Carić, M and Visković, E and Olalde, I and Ivanova-Bieg, M and Novak, M and Reich, D and Pinhasi, R}, title = {Bioarchaeological Perspectives on Late Antiquity in Dalmatia: Paleogenetic, Dietary, and Population Studies of the Hvar - Radošević burial site.}, journal = {Archaeological and anthropological sciences}, volume = {16}, number = {9}, pages = {150}, pmid = {39606698}, issn = {1866-9557}, abstract = {Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of those in that region. The Late Antique burial site of Hvar - Radošević, spanning the 3[rd] to 5[th] centuries CE, is located on the Croatian Dalmatian island of Hvar. Given the time frame and location on a busy marine trade route, the study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb and the remaining individuals buried in separate locations in the tomb's proximity. The study aims to provide a new perspective on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. The genetic analysis of the ancestral origins of the individuals buried at Hvar - Radošević revealed a diverse population reflective of the era's genetic variability. The identification of genetic outliers suggests a range of ancestries from distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis (δ[13]C and δ[15]N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties among this specific buried population.}, } @article {pmid39592000, year = {2024}, author = {Martínez-García, L and Pulido, A and Ferrari, G and Hufthammer, AK and Vedeler, M and Hirons, A and Kneale, C and Barrett, JH and Star, B}, title = {Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2035}, pages = {20242019}, doi = {10.1098/rspb.2024.2019}, pmid = {39592000}, issn = {1471-2954}, support = {//European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement, SeaChanges/ ; //Research Council of Norway projects 'FOODIMPACT'/ ; //4-OCEANS Synergy grant agreement/ ; }, mesh = {*Gadus morhua/genetics ; *DNA, Ancient/analysis ; Norway ; Animals ; History, Medieval ; Carbon Isotopes/analysis ; Fisheries ; Nitrogen Isotopes/analysis ; Archaeology ; History, 17th Century ; }, abstract = {Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ[13]C, δ[15]N, non-exchangeable δ[2]H and δ[34]S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ[13]C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries.}, } @article {pmid39586186, year = {2024}, author = {Zavala, EI and Rohlfs, RV and Moorjani, P}, title = {Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations.}, journal = {Forensic science international. Genetics}, volume = {75}, number = {}, pages = {103177}, doi = {10.1016/j.fsigen.2024.103177}, pmid = {39586186}, issn = {1878-0326}, abstract = {Advancements in sequencing and laboratory technologies have enabled forensic genetic analysis on increasingly low quality and degraded DNA samples. However, existing computational methods applied to genotyping and imputation for generating DNA profiles from degraded DNA have not been tested for forensic applications. Here we simulated sequencing data of varying qualities-coverage, fragment lengths, and deamination patterns-from forty individuals of diverse genetic ancestries. We used this dataset to test the performance of commonly used genotype and imputation methods (SAMtools, GATK, ATLAS, Beagle, and GLIMPSE) on five different SNP panels (MPS-plex, FORCE, two extended kinship panels, and the Human Origins array) that are used for forensic and population genetics applications. For genome mapping and variant calling with degraded DNA, we find use of parameters and methods (such as ATLAS) developed for ancient DNA analysis provides a marked improvement over conventional standards used for next generation sequencing analysis. We find that ATLAS outperforms GATK and SAMtools, achieving over 90 % genotyping accuracy for the four largest SNP panels with coverages greater than 10X. For lower coverages, decreased concordance rates are correlated with increased rates of heterozygosity. Genotype refinement and imputation improve the accuracy at lower coverages by leveraging population reference data. For all five SNP panels, we find that using a population reference panel representative of worldwide populations (e.g., the 1000 Genomes Project) results in increased genotype accuracies across genetic ancestries, compared to ancestry-matched population reference panels. Importantly, we find that the low SNP density of commonly used forensics SNP panels can impact the reliability and performance of genotype refinement and imputation. This highlights a critical trade-off between enhancing privacy by using panels with fewer SNPs and maintaining the effectiveness of genomic tools. We provide benchmarks and recommendations for analyzing degraded DNA from diverse populations with widely used genomic methods in forensic casework.}, } @article {pmid39584937, year = {2024}, author = {Bragazzi, NL and Lehr, T}, title = {Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {5}, number = {4}, pages = {669-691}, doi = {10.3390/epidemiologia5040047}, pmid = {39584937}, issn = {2673-3986}, abstract = {Big Epidemiology represents an innovative framework that extends the interdisciplinary approach of Big History to understand disease patterns, causes, and effects across human history on a global scale. This comprehensive methodology integrates epidemiology, genetics, environmental science, sociology, history, and data science to address contemporary and future public health challenges through a broad historical and societal lens. The foundational research agenda involves mapping the historical occurrence of diseases and their impact on societies over time, utilizing archeological findings, biological data, and historical records. By analyzing skeletal remains, ancient DNA, and artifacts, researchers can trace the origins and spread of diseases, such as Yersinia pestis in the Black Death. Historical documents, including chronicles and medical treatises, provide contextual narratives and quantitative data on past disease outbreaks, societal responses, and disruptions. Modern genetic studies reveal the evolution and migration patterns of pathogens and human adaptations to diseases, offering insights into co-evolutionary dynamics. This integrative approach allows for temporal and spatial mapping of disease patterns, linking them to social upheavals, population changes, and economic transformations. Big Epidemiology also examines the roles of environmental changes and socioeconomic factors in disease emergence and re-emergence, incorporating climate science, urban development, and economic history to inform public health strategies. The framework reviews historical and contemporary policy responses to pandemics, aiming to enhance future global health governance. By addressing ethical, legal, and societal implications, Big Epidemiology seeks to ensure responsible and effective epidemiological research and interventions. This approach aims to profoundly impact how we understand, prevent, and respond to diseases, leveraging historical perspectives to enrich modern scientific inquiry and global public health strategies.}, } @article {pmid39582673, year = {2023}, author = {Armit, I and Fischer, CE and Koon, H and Nicholls, R and Olalde, I and Rohland, N and Buckberry, J and Montgomery, J and Mason, P and Črešnar, M and Büster, L and Reich, D}, title = {Kinship practices in Early Iron Age southeast Europe: genetic and isotopic analysis of burials from the Dolge njive barrow cemetery, Dolenjska, Slovenia.}, journal = {Antiquity}, volume = {97}, number = {392}, pages = {403-418}, pmid = {39582673}, issn = {0003-598X}, abstract = {DNA analysis demonstrates that all seven individuals buried in an Early Iron Age barrow at Dolge njive, southeast Slovenia, are close biological relatives. Although group composition does not suggest strict adherence to a patrilineal or matrilineal kinship system, the funerary tradition appears highly gendered, with family links through both the male and female line being important in structuring communities. We explore the implications for our understandings of kinship and funerary practices in Early Iron Age southeast Europe.}, } @article {pmid39577594, year = {2024}, author = {Majewski, W and Szczuciński, W and Pawłowska, J and Szymczak-Żyła, M and Lubecki, L and Niedzielski, P}, title = {Environmental degradation and recovery after termination of whaling in sub-Antarctic fjord, South Georgia.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {177536}, doi = {10.1016/j.scitotenv.2024.177536}, pmid = {39577594}, issn = {1879-1026}, abstract = {Polar ecosystems are considered very fragile, however, due to the short observation record it is hard to assess the recovery processes of the coastal and fjord environments after a major disturbance. Here, we provide a unique case study from South Georgia (sub-Antarctic), an area seriously affected by the whaling industry. The study focuses on King Edward Cove, serving as a sheltered harbor for the former whaling station at Grytviken, as well as other parts of Cumberland Bay considered to represent generally pristine areas. We studied [210]Pb dated sediment cores, which were subjected to analysis of sediment geochemical composition, concentrations of anthropogenic organic markers and biomarkers, foraminiferal assemblage changes, as well as sedimentary ancient DNA. Three distinct phases have been identified. The oldest one, predating ca. 1970, recorded the whaling period, and was characterized by anoxic conditions, high organic carbon content, contamination with heavy metals, organic markers, distinct DNA signature and lack of foraminiferal microfossils. It took only a few years to establish a new ecosystem with a fully developed foraminiferal assemblage and decreased contamination characteristic for the middle phase (c. 1970-2000). Ancient DNA suggests macro-zoobenthic recovery being delayed by a several years in comparison to benthic foraminifera. In the youngest period, around Cumberland Bay, the increase of iceberg rafted debris from rapidly retreating tidewater glaciers was noted, while the improved oxygen availability in bottom waters in King Edward Cove can be likely ascribed to frequent water mixing due to increasing traffic of large cruise vessels. The recorded pace of ecosystem recovery from major anthropogenic disturbance appears similar to that observed in the temperate fjords from the Northern Hemisphere, however, the effects of new anthropogenic threat and the ongoing climate change are already resulting in the new ecosystem disturbance.}, } @article {pmid39574513, year = {2020}, author = {Catalano, G and Vetro, DL and Fabbri, PF and Mallick, S and Reich, D and Rohland, N and Sineo, L and Mathieson, I and Martini, F}, title = {Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily).}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {537}, number = {}, pages = {24-32}, pmid = {39574513}, issn = {1040-6182}, abstract = {Grotta d'Oriente, a small coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. The individual known as Oriente C was found in the lower portion of an anthropogenic deposit containing typical local Late Upper Palaeolithic (Late Epigravettian) stone assemblages. Two radiocarbon dates on charcoal from the deposit containing the burial are consistent with the archaeological context and refer Oriente C to a period spanning about 14,200-13,800 cal. BP. Anatomical features are similar to those of Late Upper Palaeolithic populations of the Mediterranean and show some affinity with Palaeolithic individuals of San Teodoro (Messina, Sicily). Here we present new ancient DNA data from Oriente C. Our results, confirming previous genetic analysis, suggest a substantial genetic homogeneity among Late Epigravettian hunter-gatherer populations of Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the Last Glacial Maximum (LGM).}, } @article {pmid39302159, year = {2024}, author = {Leppälä, K and da Silva Coelho, FA and Richter, M and Albert, VA and Lindqvist, C}, title = {Five-leaf Generalizations of the D-statistic Reveal the Directionality of Admixture.}, journal = {Molecular biology and evolution}, volume = {41}, number = {11}, pages = {}, doi = {10.1093/molbev/msae198}, pmid = {39302159}, issn = {1537-1719}, mesh = {*Models, Genetic ; Polymorphism, Single Nucleotide ; Hybridization, Genetic ; Animals ; Phylogeny ; Genetic Introgression ; Alleles ; }, abstract = {Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use five leaves to evaluate admixture. Among these, the DFOIL method ("FOIL", a mnemonic for "First-Outer-Inner-Last"), which tests allelic patterns on the "symmetric" tree S=(((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the "asymmetric" tree A=((((1,2),3),4),5) and the "quasisymmetric" tree Q=(((1,2),3),(4,5)), which can considerably supplement the "symmetric" S=(((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently, DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality.}, } @article {pmid39567978, year = {2024}, author = {Ravasini, F and Kabral, H and Solnik, A and de Gennaro, L and Montinaro, F and Hui, R and Delpino, C and Finocchi, S and Giroldini, P and Mei, O and Beck De Lotto, MA and Cilli, E and Hajiesmaeil, M and Pistacchia, L and Risi, F and Giacometti, C and Scheib, CL and Tambets, K and Metspalu, M and Cruciani, F and D'Atanasio, E and Trombetta, B}, title = {The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {292}, pmid = {39567978}, issn = {1474-760X}, abstract = {BACKGROUND: The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9[th] and the 3[rd] century BCE, until the Roman colonization.

RESULTS: More than 50 samples are reported, spanning more than 1000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to different population dynamics in the two sides of Italy and/or genetic contacts across the Adriatic Sea. Additionally, we identify several individuals with ancestries deviating from their general population. Lastly, in our Late Antiquity site, we observe a drastic change in the genetic landscape of the Middle Adriatic region, indicating a relevant influx from the Near East, possibly as a consequence of Romanization.

CONCLUSIONS: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula.}, } @article {pmid39567925, year = {2024}, author = {Lv, M and Ma, H and Wang, R and Li, H and Zhang, X and Zhang, W and Zeng, Y and Qin, Z and Zhai, H and Lou, Y and Lin, Y and Tao, L and He, H and Yang, X and Zhu, K and Zhou, Y and Wang, CC}, title = {Ancient genomes from the Tang Dynasty capital reveal the genetic legacy of trans-Eurasian communication at the eastern end of Silk Road.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {267}, pmid = {39567925}, issn = {1741-7007}, abstract = {BACKGROUND: Ancient Chang'an in the Tang Dynasty (618-907 AD) was one of the world's largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang'an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city.

RESULTS: Here, we present seven genomes from Xingfulindai (XFLD) sites dating to the Tang Dynasty in Chang'an. We observed that four of seven XFLD individuals (XFLD_1) were genetically homogenous with the Late Neolithic Wadian, Pingliangtai, and Haojiatai populations from the middle reaches of the Yellow River Basin (YR_LN), with no genetic influence from the Western Eurasian or other non-Yellow River-related lineages. The remaining three XFLD individuals were a mixture of YR_LN-related ancestry and ~ 3-15% Western Eurasian-related ancestry. Mixtures of XFLD_1 and Western Eurasian-related ancestry drove the main gradient of genetic variation in northern and central Shaanxi Province today.

CONCLUSIONS: Our study underlined the widespread distribution of the YR_LN-related ancestry alongside the Silk Road within the territory of China during the historical era and provided direct evidence of trans-Eurasian communication in Chang'an from a genetic perspective.}, } @article {pmid39567757, year = {2024}, author = {Mathov, Y and Nissim-Rafinia, M and Leibson, C and Galun, N and Marques-Bonet, T and Kandel, A and Liebergal, M and Meshorer, E and Carmel, L}, title = {Inferring DNA methylation in non-skeletal tissues of ancient specimens.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {39567757}, issn = {2397-334X}, support = {61739//John Templeton Foundation (JTF)/ ; }, abstract = {Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.}, } @article {pmid39564545, year = {2019}, author = {Spriggs, M and Reich, D}, title = {AN ANCIENT DNA PACIFIC JOURNEY: A CASE STUDY OF COLLABORATION BETWEEN ARCHAEOLOGISTS AND GENETICISTS.}, journal = {World archaeology}, volume = {51}, number = {4}, pages = {620-639}, pmid = {39564545}, issn = {0043-8243}, abstract = {We present a case-study of a collaboration between archaeologists and geneticists that has helped settle a long-standing controversy and opened up new research questions for the Pacific region. The work provided insights into the history of human settlement and cultural changes in Vanuatu in the western Pacific, which in turn shed light on the origins of the cultural and linguistic diversity that characterizes the archipelago. Close interdisciplinary collaborations like this maximize the potential of ancient DNA to contribute to our understanding of the past and advance the scholarship of practitioners in both disciplines.}, } @article {pmid39532856, year = {2024}, author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM}, title = {Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9772}, pmid = {39532856}, issn = {2041-1723}, mesh = {*DNA, Ancient/analysis ; *Selection, Genetic ; Humans ; Europe ; *Genetic Drift ; *Gene Frequency ; Haplotypes/genetics ; Animals ; Lactase/genetics ; Genetics, Population/methods ; Evolution, Molecular ; Genotype ; }, abstract = {Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.}, } @article {pmid39529860, year = {2019}, author = {Spriggs, M and Valentin, F and Bedford, S and Pinhasi, R and Skoglund, P and Reich, D and Lipson, M}, title = {Revisiting ancient DNA insights into the human history of the Pacific Islands.}, journal = {Oceania; a journal devoted to the study of the native peoples of Australia, New Guinea, and the Islands of the Pacific}, volume = {54}, number = {1}, pages = {53-56}, doi = {10.1002/arco.5180}, pmid = {39529860}, issn = {0029-8077}, abstract = {We respond to issues raised in the recent Forum on "Ancient DNA and its contribution to understanding the human history of the Pacific Islands" in AO (Bedford et al. 2018). We first present an emerging model for the early peopling of Vanuatu combining the genetic and archaeological evidence. Secondly, we respond specifically to the criticisms of two contributors: Matisoo-Smith and Sand. We discuss various misconceptions about the Teouma Lapita cemetery and about sampling issues in DNA research.}, } @article {pmid39515325, year = {2024}, author = {Pilli, E and Vai, S and Moses, VC and Morelli, S and Lari, M and Modi, A and Diroma, MA and Amoretti, V and Zuchtriegel, G and Osanna, M and Kennett, DJ and George, RJ and Krigbaum, J and Rohland, N and Mallick, S and Caramelli, D and Reich, D and Mittnik, A}, title = {Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.10.007}, pmid = {39515325}, issn = {1879-0445}, abstract = {The eruption of Somma-Vesuvius in 79 CE buried several nearby Roman towns, killing the inhabitants and burying under pumice lapilli and ash deposits a unique set of civil and private buildings, monuments, sculptures, paintings, and mosaics that provide a rich picture of life in the empire. The eruption also preserved the forms of many of the dying as the ash compacted around their bodies. Although the soft tissue decayed, the outlines of the bodies remained and were recovered by excavators centuries later by filling the cavities with plaster. From skeletal material embedded in the casts, we generated genome-wide ancient DNA and strontium isotopic data to characterize the genetic relationships, sex, ancestry, and mobility of five individuals. We show that the individuals' sexes and family relationships do not match traditional interpretations, exemplifying how modern assumptions about gendered behaviors may not be reliable lenses through which to view data from the past. For example, an adult wearing a golden bracelet with a child on their lap-often interpreted as mother and child-is genetically an adult male biologically unrelated to the child. Similarly, a pair of individuals who were thought to have died in an embrace-often interpreted as sisters-included at least one genetic male. All Pompeiians with genome-wide data consistently derive their ancestry largely from recent immigrants from the eastern Mediterranean, as has also been seen in contemporaneous ancient genomes from the city of Rome, underscoring the cosmopolitanism of the Roman Empire in this period.}, } @article {pmid39514086, year = {2024}, author = {Geršak, ŽM and Golob, A and Kravanja, P and Concato, M and Leskovar, T and Pajnič, IZ}, title = {Patellae as a source of DNA in forensic and archaeological analysis.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {39514086}, issn = {1437-1596}, support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, abstract = {Analysing genetic material from skeletonised human remains has become valuable in forensic and archaeological contexts. While the petrous bone is often preferred for DNA extraction, its availability is not guaranteed, and because of destructive sampling, it is not frequently used in forensic cases. This study explores the potential of patellae as an alternative source of bone material for genetic investigations. Forty-five patellae were sampled from a post-World War II mass grave and an archaeological Christian cemetery dated from the 13th to 19th centuries. A full demineralisation extraction method was used to obtain the DNA, and real-time PCR quantification was used to determine the quantity and quality of DNA. To evaluate the suitability of patellae for forensic and archaeological analyses, short tandem repeat (STR) typing was performed using the ESI17 Fast PCR amplification kit (Promega). To explore the difference in DNA yield, DNA degradation and STR typing success between the post-World War II and archaeological patellae, statistical analysis was performed. The results revealed significantly higher DNA yield and STR typing success in WWII patellae and higher degradation of DNA in archaeological patellae, highlighting the impact of environmental exposure time on genetic material preservation. Almost all WWII patellae achieved a high success rate in STR typing with full profiles generated. More than half of the archaeological patellae showed high STR typing performance and highly informative partial profiles were obtained, indicating the suitability of patellae not only for forensic purposes but also for archaeological genetic analyses.}, } @article {pmid39509486, year = {2024}, author = {Chandrashekhar, V}, title = {India looks to ancient DNA to track migrations.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6722}, pages = {607}, doi = {10.1126/science.adu4090}, pmid = {39509486}, issn = {1095-9203}, mesh = {Humans ; Bone and Bones ; *DNA, Ancient/analysis ; *Human Migration/history ; India ; *South Asian People/history ; }, abstract = {Findings from analyses of human bones could be politically sensitive.}, } @article {pmid39500721, year = {2024}, author = {Hong, JH and Fujita, H and Kim, J and Shin, DH}, title = {Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis.}, journal = {Anatomy & cell biology}, volume = {}, number = {}, pages = {}, doi = {10.5115/acb.24.125}, pmid = {39500721}, issn = {2093-3665}, abstract = {Ancient DNA (aDNA) analysis has developed rapidly since it first emerged in the 1980s, becoming an almost indispensable tool in anthropological and archaeological sciences. Earlier aDNA study was based on the polymerase chain reaction (PCR) technique, with which, unfortunately, modern DNA contamination and other authenticity issues were often incurred. These technical hurdles were soon overcome by application of advancements in the forms of the next generation sequencing (NGS) technique and others. However, since NGS requires money, time, and, in the case of large projects, manpower as well, genetic analysis of some ancient samples considered to be insignificant is commonly delayed or, in the worst cases, neglected entirely. We acknowledge that as a diagnostic tool in aDNA analysis, PCR is less accurate than NGS and more easily affected by modern DNA contamination; but it also has advantages, such as simplicity, time-saving, and greater ease of interpretation, among others. The role of PCR in aDNA analysis, then, should be reconsidered.}, } @article {pmid39493412, year = {2024}, author = {Sedig, J and Snow, M and Searcy, M and Diaz, JLP and LeBlanc, S and Ramos, F and Eccles, L and Reich, D}, title = {High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico.}, journal = {Antiquity}, volume = {98}, number = {400}, pages = {1023-1039}, pmid = {39493412}, issn = {0003-598X}, abstract = {This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.}, } @article {pmid39481771, year = {2024}, author = {Brambilla, L and Ibarra, DA and Barboza, MC and Bresso, EG and Rosano, G and Pérez, G and Straccia, P and Scian, RD and Brun, LR}, title = {Mitochondrial genome of Neuryurus rudis (Xenarthra, Cingulata); contribution to phylogeny and origin of glyptodonts.}, journal = {Gene}, volume = {}, number = {}, pages = {149059}, doi = {10.1016/j.gene.2024.149059}, pmid = {39481771}, issn = {1879-0038}, abstract = {The remarkable glyptodonts have sparked the interest of evolutionary biologists since the 19th century, in their attempts to elucidate the phylogenetic relationships among the various species of these armored giants and their relationship with other xenarthrans. In recent years, the molecular analysis of the first glyptodont has included them within the cingulates, as a special group of armadillos that lost the mobility of the bands of their armor during their evolutionary history. In this research, we obtained the mitochondrial DNA sequence of the elusive and poorly known glyptodont Neuryurus rudis, inferring its phylogenetic position with respect to the glyptodont Doedicurus sp. and extant armadillos. This study reaffirms glyptodonts as a subgroup of cingulates, with Neuryurus and Doedicurus sharing a common ancestor from the late Oligocene or early Miocene and traces the group's origin back to an armadillo ancestor in the Eocene.}, } @article {pmid39478221, year = {2024}, author = {Ghalichi, A and Reinhold, S and Rohrlach, AB and Kalmykov, AA and Childebayeva, A and Yu, H and Aron, F and Semerau, L and Bastert-Lamprichs, K and Belinskiy, AB and Berezina, NY and Berezin, YB and Broomandkhoshbacht, N and Buzhilova, AP and Erlikh, VR and Fehren-Schmitz, L and Gambashidze, I and Kantorovich, AR and Kolesnichenko, KB and Lordkipanidze, D and Magomedov, RG and Malek-Custodis, K and Mariaschk, D and Maslov, VE and Mkrtchyan, L and Nagler, A and Fazeli Nashli, H and Ochir, M and Piotrovskiy, YY and Saribekyan, M and Sheremetev, AG and Stöllner, T and Thomalsky, J and Vardanyan, B and Posth, C and Krause, J and Warinner, C and Hansen, S and Haak, W}, title = {The rise and transformation of Bronze Age pastoralists in the Caucasus.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39478221}, issn = {1476-4687}, abstract = {The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age[1] and the birthplace of the earliest steppe pastoralist societies[2]. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies[3-5]. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry[4,6] in the north, and a distinct Caucasus hunter-gatherer ancestry[7] with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex[8]. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.}, } @article {pmid39478147, year = {2024}, author = {Yavuz, OE and Oxilia, G and Silvestrini, S and Tassoni, L and Reiter, E and Drucker, DG and Talamo, S and Fontana, F and Benazzi, S and Posth, C}, title = {Biomolecular analysis of the Epigravettian human remains from Riparo Tagliente in northern Italy.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1415}, pmid = {39478147}, issn = {2399-3642}, mesh = {Italy ; Humans ; *Radiometric Dating ; Fossils ; Male ; Body Remains/chemistry ; Femur/chemistry/metabolism ; }, abstract = {The Epigravettian human remains from Riparo Tagliente in northern Italy represent some of the earliest evidence of human occupation in the southern Alpine slopes after the Last Glacial Maximum. Genomic analyses of the 17,000-year-old Tagliente 2 mandible revealed the oldest presence of a genetic profile with affinities to the Near East in the Italian peninsula, which later became the most widespread hunter-gatherer ancestry across Europe. However, a comparable biomolecular characterization of the Tagliente 1 burial remains unavailable, preventing us from defining its biological relationships with Tagliente 2. Here, we apply paleogenomic, isotopic, and radiocarbon dating analyses on a femur fragment of Tagliente 1 and compare the reconstructed data with previously reported results from Tagliente 2. Despite their different isotopic signatures and non-overlapping radiocarbon dates, we reveal that the two human remains belong to the same male individual. We determine that the distinct isotopic values can be explained by different dietary practices during lifetime, whereas the non-overlapping radiocarbon dates can be caused by minimal radiocarbon contamination, possibly deriving from chemical treatments for conservation purposes. These findings highlight the importance of interdisciplinary biomolecular studies in offering new perspectives on the Palaeolithic fossil record and addressing long-standing bioarchaeological questions.}, } @article {pmid39468234, year = {2024}, author = {Słowakiewicz, M and Borkowski, A and Perri, E and Działak, P and Tagliasacchi, E and Gradziński, M and Kele, S and Reuning, L and Kibblewhite, T and Whitaker, F and Reid, RP and Tucker, ME}, title = {Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25889}, pmid = {39468234}, issn = {2045-2322}, support = {2019/35/B/ST10/02190//Narodowe Centrum Nauki/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; }, mesh = {*Biofilms/growth & development ; *Fresh Water/microbiology/virology ; *Calcium Carbonate/metabolism/chemistry ; Geologic Sediments/microbiology/virology ; Viruses/genetics/metabolism ; Principal Component Analysis ; Metagenomics/methods ; }, abstract = {Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.}, } @article {pmid39440313, year = {2024}, author = {Malyarchuk, BA}, title = {Genetic aspects of lactase deficiency in indigenous populations of Siberia.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {28}, number = {6}, pages = {650-658}, doi = {10.18699/vjgb-24-72}, pmid = {39440313}, issn = {2500-0462}, abstract = {The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.}, } @article {pmid39439471, year = {2024}, author = {Verry, AJF and Lubbe, P and Mitchell, KJ and Rawlence, NJ}, title = {Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions.}, journal = {Journal of the Royal Society of New Zealand}, volume = {54}, number = {1}, pages = {75-97}, pmid = {39439471}, issn = {1175-8899}, abstract = {Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many - often unexpected - insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.}, } @article {pmid39438503, year = {2024}, author = {Feinauer, IS and Lord, E and von Seth, J and Xenikoudakis, G and Ersmark, E and Dalén, L and Meleg, IN}, title = {Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24917}, pmid = {39438503}, issn = {2045-2322}, mesh = {*Ursidae/genetics ; Animals ; Scandinavian and Nordic Countries ; *Genome, Mitochondrial ; *Haplotypes ; *Genetic Variation ; *Phylogeny ; Female ; DNA, Mitochondrial/genetics ; Genetics, Population ; }, abstract = {Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.}, } @article {pmid39437846, year = {2024}, author = {Kaptan, D and Atağ, G and Vural, KB and Morell Miranda, P and Akbaba, A and Yüncü, E and Buluktaev, A and Abazari, MF and Yorulmaz, S and Kazancı, DD and Küçükakdağ Doğu, A and Çakan, YG and Özbal, R and Gerritsen, F and De Cupere, B and Duru, R and Umurtak, G and Arbuckle, BS and Baird, D and Çevik, Ö and Bıçakçı, E and Gündem, CY and Pişkin, E and Hachem, L and Canpolat, K and Fakhari, Z and Ochir-Goryaeva, M and Kukanova, V and Valipour, HR and Hoseinzadeh, J and Küçük Baloğlu, F and Götherström, A and Hadjisterkotis, E and Grange, T and Geigl, EM and Togan, İZ and Günther, T and Somel, M and Özer, F}, title = {The Population History of Domestic Sheep Revealed by Paleogenomes.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, doi = {10.1093/molbev/msae158}, pmid = {39437846}, issn = {1537-1719}, support = {772390/ERC_/European Research Council/International ; //University Paris Diderot/ ; DGE20111123014//Fondation pour la Recherche Médicale/ ; 11015901//Région Ile-de-France/ ; 2017-05267//Swedish Research Council Vetenskapsrådet/ ; F20-0274//Helge Ax:son Johnson Stiftelse/ ; 075-15-2019-1879//Government of Russian Federation/ ; BCS-0530699//National Science Foundation/ ; }, mesh = {Animals ; *Sheep, Domestic/genetics ; *Domestication ; Sheep/genetics ; Genome ; DNA, Ancient/analysis ; Europe ; }, abstract = {Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not.}, } @article {pmid39432055, year = {2024}, author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS}, title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14029}, doi = {10.1111/1755-0998.14029}, pmid = {39432055}, issn = {1755-0998}, support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; }, abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.}, } @article {pmid39429655, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Tuberculosis in Human Bones from 4000 Years Ago, Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {9}, pages = {2103-2112}, pmid = {39429655}, issn = {2251-6093}, abstract = {BACKGROUND: Tuberculosis is caused by a bacterium called Mycobacterium tuberculosis, which is a contagious and infectious disease; in the first stage, it destroys the lungs and in the next stage other body organs, such as the spine and long bones. This disease is transmitted through an infected person and due to the weakness of the immune system, the infection intensifies. Tuberculosis has two stages: low activity and high activity. In this article, we have discussed the signs of tuberculosis destruction with high intensity on the bones of prehistory human remains.

METHODS: The examples of our research are related to human remains from the ancient cemetery of 4000 years ago from Sagezabad region of Qazvin Province of Iran. That period of history coincides with the Iron Age 2 and 3 in the region. People inside the Sagezabad cemetery were very near to early urban (the late rural) society.

RESULTS: By matching the form of bone destruction with international atlases for tuberculosis, we have reached a satisfactory result in this article. Due to the strong penetration of the infection into the bones, destruction in the remains was high, so it has simplified the diagnosis for us.

CONCLUSION: We found tuberculosis among the bones. This common ancient disease existed even among Neanderthals.}, } @article {pmid39415996, year = {2024}, author = {Rubin, J and van Waaij, J and Kraft, L and Sirén, J and Sackett, PW and Renaud, G}, title = {SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.08.12.607489}, pmid = {39415996}, issn = {2692-8205}, abstract = {Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C→T and G→A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI , an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.}, } @article {pmid39408629, year = {2024}, author = {Herbert, A}, title = {A Compendium of G-Flipon Biological Functions That Have Experimental Validation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, doi = {10.3390/ijms251910299}, pmid = {39408629}, issn = {1422-0067}, mesh = {*G-Quadruplexes ; Animals ; Humans ; Transcription Factors/metabolism/genetics ; DNA/metabolism/genetics ; RNA, Untranslated/genetics/metabolism ; DNA Repair ; Caenorhabditis elegans/genetics/metabolism ; }, abstract = {As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G3N1-7)3G3, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate.}, } @article {pmid39395415, year = {2024}, author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS}, title = {Compacted hair in broken teeth reveals dietary prey of historic lions.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.09.029}, pmid = {39395415}, issn = {1879-0445}, abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.}, } @article {pmid39390557, year = {2024}, author = {Sawyer, S and Gelabert, P and Yakir, B and Llanos-Lizcano, A and Sperduti, A and Bondioli, L and Cheronet, O and Neugebauer-Maresch, C and Teschler-Nicola, M and Novak, M and Pap, I and Szikossy, I and Hajdu, T and Moiseyev, V and Gromov, A and Zariņa, G and Meshorer, E and Carmel, L and Pinhasi, R}, title = {Improved detection of methylation in ancient DNA.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {261}, pmid = {39390557}, issn = {1474-760X}, abstract = {Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.}, } @article {pmid39383567, year = {2024}, author = {Wu, Y and Ma, Q and Han, B and Shen, Y and Wen, S}, title = {Familial hypodontia in bronze age Northwest China (1046-771BC).}, journal = {Archives of oral biology}, volume = {169}, number = {}, pages = {106104}, doi = {10.1016/j.archoralbio.2024.106104}, pmid = {39383567}, issn = {1879-1506}, abstract = {OBJECTIVE: This research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals.

DESIGN: In this study, dental anomalies were observed on a human skeletal sample (n = 45) uncovered from Yaoheyuan, China. Ancient DNA analysis was subsequently employed on a subsample of the Yaoheyuan individuals (n = 15), including individuals observed hypodontia and individuals randomly sampled from the cemetery for preliminary investigation on the cemetery demography. Kinship estimation tests (READ, TKGWV2, KIN, and F3 test) were subsequently employed.

RESULTS: The Yaoheyuan elite population had a prevalence (n = 7, 15 %) of tooth agenesis in either the maxilla or mandible, with one to two teeth missing. All missing teeth were incisors, except for one individual missing maxillary second molar. Preliminary ancient DNA results indicate that several kinship groups existed among interred individuals, including those with hypodontia, indicating the hereditary origin of these cases.

CONCLUSIONS: The prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals.}, } @article {pmid39357284, year = {2024}, author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C}, title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.}, journal = {Journal of human evolution}, volume = {196}, number = {}, pages = {103599}, doi = {10.1016/j.jhevol.2024.103599}, pmid = {39357284}, issn = {1095-8606}, abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.}, } @article {pmid39345259, year = {2024}, author = {Wu, X and Ding, B and Nie, L and Zhong, C and Liu, P and Liang, J and Wang, L and Gao, X and Wei, J and Zhou, Y}, title = {Genomic insights into the complex demographic history and inbreeding phenomena during Zhou Dynasty on the Central Plains of China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1471740}, pmid = {39345259}, issn = {1664-302X}, abstract = {In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population's genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization's multiethnic.}, } @article {pmid39343094, year = {2024}, author = {Wei, X and Zhang, M and Min, R and Jiang, Z and Xue, J and Zhu, Z and Yuan, H and Li, X and Zhao, D and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Wu, X and Hu, C and Ma, M and Liu, X and Wan, Y and Yang, F and Zhou, R and Kang, L and Dong, G and Ping, W and Wang, T and Miao, B and Bai, F and Zheng, Y and Liu, Y and Yang, MA and Wang, W and Bennett, EA and Fu, Q}, title = {Neolithic to Bronze Age human maternal genetic history in Yunnan, China.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.09.013}, pmid = {39343094}, issn = {1673-8527}, abstract = {Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Tibet, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 to 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.}, } @article {pmid39333293, year = {2024}, author = {Petrova, TV and Panitsina, VA and Bodrov, SY and Abramson, NI}, title = {The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22259}, pmid = {39333293}, issn = {2045-2322}, support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; *Phylogeny ; *Genome, Mitochondrial ; Endangered Species ; Rodentia/genetics/classification ; }, abstract = {Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.}, } @article {pmid39326418, year = {2024}, author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q}, title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.08.008}, pmid = {39326418}, issn = {1097-4172}, abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.}, } @article {pmid39322456, year = {2024}, author = {Hou, J and Guan, X and Xia, X and Lyu, Y and Liu, X and Mazei, Y and Xie, P and Chang, F and Zhang, X and Chen, J and Li, X and Zhang, F and Jin, L and Luo, X and Sinding, MS and Sun, X and Achilli, A and Migliore, NR and Zhang, D and Lenstra, JA and Han, J and Fu, Q and Liu, X and Zhang, X and Chen, N and Lei, C and Zhang, H}, title = {Evolution and legacy of East Asian aurochs.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2024.09.016}, pmid = {39322456}, issn = {2095-9281}, abstract = {Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.}, } @article {pmid39314480, year = {2024}, author = {Akbari, A and Barton, AR and Gazal, S and Li, Z and Kariminejad, M and Perry, A and Zeng, Y and Mittnik, A and Patterson, N and Mah, M and Zhou, X and Price, AL and Lander, ES and Pinhasi, R and Rohland, N and Mallick, S and Reich, D}, title = {Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.14.613021}, pmid = {39314480}, issn = {2692-8205}, abstract = {We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ∼0% to ∼20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1 ; a rise from ∼0% to ∼8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ∼2% to ∼9% from ∼5500 to ∼3000 years ago before dropping to ∼3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.}, } @article {pmid39305897, year = {2024}, author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M}, title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.08.047}, pmid = {39305897}, issn = {1879-0445}, abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."}, } @article {pmid39300260, year = {2024}, author = {Gretzinger, J and Gibbon, VE and Penske, SE and Sealy, JC and Rohrlach, AB and Salazar-García, DC and Krause, J and Schiffels, S}, title = {9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {39300260}, issn = {2397-334X}, abstract = {Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 BP, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.}, } @article {pmid39294129, year = {2024}, author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS}, title = {Towards predicting the geographical origin of ancient samples with metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21794}, pmid = {39294129}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; }, abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.}, } @article {pmid39292210, year = {2024}, author = {Atağ, G and Waldman, S and Carmi, S and Somel, M}, title = {An explanation for the sister repulsion phenomenon in Patterson's f-statistics.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae144}, pmid = {39292210}, issn = {1943-2631}, support = {772390//H2020 ERC Consolidator/ ; 952317//H2020-WIDESPREAD-05-2020 TWINNING/ ; //Scientific and Technological Research Council of Turkey (TÜBİTAK)/ ; }, abstract = {Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.}, } @article {pmid39291130, year = {2024}, author = {Song, G and Wang, Y and Ruan, Q and Cai, DE}, title = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {9}, number = {9}, pages = {1232-1236}, pmid = {39291130}, issn = {2380-2359}, abstract = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.}, } @article {pmid39280844, year = {2024}, author = {Modina, SA and Kusliy, MA and Malikov, DG and Molodtseva, AS}, title = {Phylogeography of the woolly mammoth (Mammuthus primigenius) in the Minusinsk Depression of southern Siberia in the Late Pleistocene.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {28}, number = {5}, pages = {571-577}, doi = {10.18699/vjgb-24-63}, pmid = {39280844}, issn = {2500-0462}, abstract = {To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100-150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.}, } @article {pmid39279684, year = {2024}, author = {Pan, J and Liu, X and Baca, M and Calvière-Tonasso, L and Schiavinato, S and Chauvey, L and Tressières, G and Perdereau, A and Aury, JM and Oliveira, PH and Wincker, P and Abdykanova, A and Arsuaga, JL and Bayarsaikhan, J and Belinskiy, AB and Carbonell, E and Davoudi, H and Lira Garrido, J and Gilbert, AS and Hermes, T and Warinner, C and Kalmykov, AA and Lordkipanidze, D and Mackiewicz, P and Mohaseb, AF and Richter, K and Sayfullaev, N and Shapiro, B and Shnaider, S and Southon, J and Stefaniak, K and Summers, GD and van Asperen, EN and Vanishvili, N and Hill, EA and Kuznetsov, P and Reinhold, S and Hansen, S and Mashkour, M and Berthon, R and Taylor, WTT and Houle, JL and Hekkala, E and Popović, D and Orlando, L}, title = {Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17527}, doi = {10.1111/mec.17527}, pmid = {39279684}, issn = {1365-294X}, support = {101027750//European Union's Horizon 2020 research and innovation programme/ ; 101062645//European Union's Horizon 2020 research and innovation programme/ ; //Agricultural Science and Technology Innovation Program (ASTIP-05)/ ; //CNRS and University Paul Sabatier (AnimalFarm IRP)/ ; //Spanish Ministerio de Educación, Cultura y Deporte (Archaeological Projects Abroad 2017)/ ; //Wroclaw Centre of Biotechnology programme ('The Leading National Research Center [KNOW]')/ ; 681605//HORIZON EUROPE European Research Council/ ; 834616//HORIZON EUROPE European Research Council/ ; 101071707//HORIZON EUROPE European Research Council/ ; ANR-10-INBS-09//Agence Nationale pour la Recherche/ ; 19-78-10053//Russian Science Foundation/ ; 22-18-00194//Russian Science Foundation/ ; }, abstract = {The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.}, } @article {pmid39278943, year = {2024}, author = {Sun, Y and Lorenzen, ED and Westbury, MV}, title = {Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {826}, pmid = {39278943}, issn = {1471-2164}, support = {37352//Villum Fonden/ ; 9064-00025B//Danmarks Frie Forskningsfond/ ; }, mesh = {*Ursidae/genetics ; Animals ; Arctic Regions ; *Alleles ; *Genome ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; }, abstract = {The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.}, } @article {pmid39268685, year = {2024}, author = {Scheib, CL and Hui, R and Rose, AK and D'Atanasio, E and Inskip, SA and Dittmar, J and Cessford, C and Griffith, SJ and Solnik, A and Wiseman, R and Neil, B and Biers, T and Harknett, SJ and Sasso, S and Biagini, SA and Runfeldt, G and Duhig, C and Evans, C and Metspalu, M and Millett, MJ and O'Connell, TC and Robb, JE and Kivisild, T}, title = {Low Genetic Impact of the Roman Occupation of Britain in Rural Communities.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, doi = {10.1093/molbev/msae168}, pmid = {39268685}, issn = {1537-1719}, support = {2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; //St John's College, Cambridge/ ; PRG243//Estonian Research Council/ ; 2014-2020.4.01.16-0030//European Union through the European Regional Development Fund/ ; 2014-2020.4.01.15-0012//European Regional Development Fund/ ; }, mesh = {Humans ; United Kingdom ; *Human Migration ; *Rural Population ; History, Ancient ; DNA, Ancient/analysis ; Genetics, Population ; }, abstract = {The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.}, } @article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, doi = {10.12688/f1000research.134798.2}, pmid = {39262445}, issn = {2046-1402}, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, } @article {pmid39261697, year = {2024}, author = {Thompson, B and Petrić Howe, N}, title = {Ancient DNA debunks Rapa Nui 'ecological suicide' theory.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-02963-9}, pmid = {39261697}, issn = {1476-4687}, } @article {pmid39261696, year = {2024}, author = {Callaway, E}, title = {Famed Pacific island's population 'crash' debunked by ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39261696}, issn = {1476-4687}, } @article {pmid39261607, year = {2024}, author = {Schiffels, S and Nägele, K}, title = {Rapa Nui's population history rewritten using ancient DNA.}, journal = {Nature}, volume = {633}, number = {8029}, pages = {290-291}, pmid = {39261607}, issn = {1476-4687}, } @article {pmid39261501, year = {2024}, author = {Canesin, LEC and Vilaça, ST and Oliveira, RRM and Al-Ajli, F and Tracey, A and Sims, Y and Formenti, G and Fedrigo, O and Banhos, A and Sanaiotti, TM and Farias, IP and Jarvis, ED and Oliveira, G and Hrbek, T and Solferini, V and Aleixo, A}, title = {A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19925}, pmid = {39261501}, issn = {2045-2322}, support = {316531/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 316532/2023-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Genome ; *Eagles/genetics ; Female ; DNA Transposable Elements/genetics ; Phylogeny ; Evolution, Molecular ; Retroelements/genetics ; Genomics/methods ; }, abstract = {The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.}, } @article {pmid39235046, year = {2024}, author = {de la Fuente Castro, C and Cortés, C and Raghavan, M and Castillo, D and Castro, M and Verdugo, RA and Moraga, M}, title = {The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evae196}, pmid = {39235046}, issn = {1759-6653}, abstract = {The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly-generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies the Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.}, } @article {pmid39233501, year = {2024}, author = {Pavlova, SV and Romanenko, SA and Matveevsky, SN and Kuksin, AN and Dvoyashov, IA and Kovalskaya, YM and Proskuryakova, AA and Serdyukova, NA and Petrova, TV}, title = {Supernumerary Chromosomes Enhance Karyotypic Diversification of Narrow-Headed Voles of the Subgenus Stenocranius (Rodentia, Mammalia).}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.23273}, pmid = {39233501}, issn = {1552-5015}, support = {//This study was supported by Russian Science Foundation (Grant 22-24-00513)./ ; }, abstract = {The subgenus Stenocranius contains two cryptic species: Lasiopodomys gregalis (subdivided into three allopatrically distributed and genetically well-isolated lineages A, B, and C) and Lasiopodomys raddei. To identify karyotype characteristics of this poorly studied cryptic species complex, we used comparative cytogenetic analysis of 138 individuals from 41 localities in South Siberia and Mongolia. A detailed description of the L. raddei karyotype and of the L. gregalis lineage С karyotype is presented for the first time. The A chromosome complement of all examined narrow-headed voles consisted of 2n = 36 and a fundamental number of autosomal arms (FNa) of 50. Between species, patterns of differential staining were similar, though additional C-heterochromatic blocks were found in L. gregalis lineages; Ag-positive nucleolar organizers and ribosomal DNA (rDNA) clusters are located on eight and nine acrocentric pairs, respectively. No B chromosomes (Bs) were found in the Early Pleistocene relic L. raddei, while one to five small heterochromatic acrocentric Bs were detected in all L. gregalis lineages; the number and frequency of Bs varied considerably within lineages, but no intraindividual variation was observed. In both species, telomeric repeats were visualized at termini of all chromosomes, including Bs. The number and localization of rDNA clusters on Bs varied among B-carriers. Immunodetection of several meiotic proteins indicated that meio-Bs are transcriptionally inactive and have a pattern of meiotic behavior similar to that of sex chromosomes (some homology of Bs to sex chromosomes is supposed). The nature, mechanisms of inheritance and stability of Bs in L. gregalis require further investigation.}, } @article {pmid39222521, year = {2024}, author = {Garcia-Heras, J}, title = {The Discovery of Common Chromosome Aneuploidies with Medical Implications Through Innovative Analysis of Ancient DNA (aDNA).}, journal = {Journal of the Association of Genetic Technologists}, volume = {50}, number = {3}, pages = {96-99}, pmid = {39222521}, issn = {1523-7834}, abstract = {Two recent studies that re-examined through novel approaches previous shotgun sequencing data from prehistoric/historic Europeans uncovered several autosomal and sex chromosome aneuploidies (Anastasiadou et al., 2024; Rohrlach et al., 2024). These disorders, which are common in contemporary humans, were trisomies 18 and 21, Klinefelter syndrome (47,XXY), 47,XYY syndrome, and mosaic Turner syndrome X/XX. These discoveries about prehistoric/historic occurrence of constitutional chromosomal syndromes with high clinical significance in modern medical genetics are an important breakthrough. They contribute to a more comprehensive genetic delineation of past human populations and give impetus to perform more historic/prehistoric studies to discover other contemporary genetic disorders. A molecular profiling of ancient DNA (aDNA) from human remains added to anthropological and archaeological data may also give a broader picture of the social and historical contexts of individuals who were affected by genetic diseases. These advances in the detection of chromosome aneuploidies and previous discoveries of current monogenic syndromes in archaic hominins also highlight the possibility of detecting other genetic diseases of present-day occurrence in our ancestors. As a result, it might be feasible to delineate the evolutionary history of modern genetic diseases, establishing a timeline of their emergence, patterns of mutations, putative mechanisms of selection, and genomic mechanisms involved.}, } @article {pmid39215552, year = {2024}, author = {Laval, G and Patin, E and Quintana-Murci, L and Kerner, G}, title = {Deep estimation of the intensity and timing of natural selection from ancient genomes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14015}, doi = {10.1111/1755-0998.14015}, pmid = {39215552}, issn = {1755-0998}, abstract = {Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.}, } @article {pmid39191285, year = {2024}, author = {Arzelier, A and De Belvalet, H and Pemonge, MH and Garberi, P and Binder, D and Duday, H and Deguilloux, MF and Pruvost, M}, title = {Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2029}, pages = {rspb20241215}, doi = {10.1098/rspb.2024.1215}, pmid = {39191285}, issn = {1471-2954}, support = {DFG-HA-5407/4-1//Deutsche Forschungsgemeinschaft/ ; ANR22-CE27-0012, ANR15-CE27-0001, ANR17-FRAL-0010//Agence Nationale de la Recherche/ ; }, mesh = {*DNA, Ancient/analysis ; France ; Humans ; *Burial/history ; *Archaeology ; Male ; Bayes Theorem ; Female ; History, Ancient ; }, abstract = {The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.}, } @article {pmid39169089, year = {2024}, author = {Oberreiter, V and Gelabert, P and Brück, F and Franz, S and Zelger, E and Szedlacsek, S and Cheronet, O and Cano, FT and Exler, F and Zagorc, B and Karavanić, I and Banda, M and Gasparyan, B and Straus, LG and Gonzalez Morales, MR and Kappelman, J and Stahlschmidt, M and Rattei, T and Kraemer, SM and Sawyer, S and Pinhasi, R}, title = {Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19388}, pmid = {39169089}, issn = {2045-2322}, support = {1111111//Research Platform MINERVA, University of Vienna/ ; CA19141-8d068698//COST iNEAL STSM Grant/ ; NECEM, HRZZ-IP-2019-04-6649//Hrvatska Zaklada za Znanost/ ; No. 101042570//European Research Council (ERC) MicroStratDNA project/ ; M3108-G//Austrian Science Fund/ ; }, mesh = {*DNA, Ancient/analysis ; *Geologic Sediments ; Humans ; Animals ; Archaeology/methods ; Fossils ; High-Throughput Nucleotide Sequencing/methods ; Hominidae/genetics ; Europe ; Africa ; }, abstract = {In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.}, } @article {pmid39165395, year = {2024}, author = {Armbrecht, L and Bolch, CJS and Paine, B and Cooper, A and McMinn, A and Woodward, C and Hallegraeff, G}, title = {Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae098}, pmid = {39165395}, issn = {2730-6151}, abstract = {Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.}, } @article {pmid39159385, year = {2024}, author = {Tian, Y and Koncz, I and Defant, S and Giostra, C and Vyas, DN and Sołtysiak, A and Pejrani Baricco, L and Fetner, R and Posth, C and Brandt, G and Bedini, E and Modi, A and Lari, M and Vai, S and Francalacci, P and Fernandes, R and Steinhof, A and Pohl, W and Caramelli, D and Krause, J and Izdebski, A and Geary, PJ and Veeramah, KR}, title = {The role of emerging elites in the formation and development of communities after the fall of the Roman Empire.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {36}, pages = {e2317868121}, doi = {10.1073/pnas.2317868121}, pmid = {39159385}, issn = {1091-6490}, support = {856453//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 426551838//Deutsche Forschungsgemeinschaft (DFG)/ ; 2018/31/G/HS3/01159//Narodowe Centrum Nauki (NCN)/ ; }, mesh = {Humans ; *Archaeology ; *Roman World/history ; Italy ; History, Medieval ; Human Migration/history ; History, Ancient ; }, abstract = {Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups.}, } @article {pmid39158588, year = {2024}, author = {Van Emmenis, L}, title = {Sarah Gaffen: I thrive on turning my vision for the lab into reality.}, journal = {The Journal of experimental medicine}, volume = {221}, number = {9}, pages = {}, doi = {10.1084/jem.20241418}, pmid = {39158588}, issn = {1540-9538}, mesh = {Humans ; History, 20th Century ; History, 21st Century ; *Interleukin-17/metabolism ; Autoimmunity ; }, abstract = {Sarah Gaffen, PhD, is a professor of medicine and rheumatology and holds the Gerald P. Rodnan endowed chair at the University of Pittsburgh. Her lab explores the biological function of IL-17 and its receptor in the context of fungal host defense and autoimmunity. We spoke to Sarah about where her interest in cytokines began, the importance of saying no in your career, and her interest in paleogenetics.}, } @article {pmid39151011, year = {2024}, author = {Rathmann, H and Vizzari, MT and Beier, J and Bailey, SE and Ghirotto, S and Harvati, K}, title = {Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn8129}, doi = {10.1126/sciadv.adn8129}, pmid = {39151011}, issn = {2375-2548}, mesh = {Humans ; *Fossils ; Europe ; *Phenotype ; *Tooth/anatomy & histology ; *Population Dynamics ; Bayes Theorem ; Archaeology ; }, abstract = {Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.}, } @article {pmid39149515, year = {2024}, author = {Rbbani, G and Murshed, R and Siriyappagouder, P and Sharko, F and Nedoluzhko, A and Joshi, R and Galindo-Villegas, J and Raeymaekers, JAM and Fernandes, JMO}, title = {Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1369758}, doi = {10.3389/fcell.2024.1369758}, pmid = {39149515}, issn = {2296-634X}, abstract = {Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture.}, } @article {pmid39146937, year = {2024}, author = {Du, P and Zhu, K and Wang, M and Sun, Z and Tan, J and Sun, B and Sun, B and Wang, P and He, G and Xiong, J and Huang, Z and Meng, H and Sun, C and Xie, S and Wang, B and Ge, D and Ma, Y and Sheng, P and Ren, X and Tao, Y and Xu, Y and Qin, X and Allen, E and Zhang, B and Chang, X and Wang, K and Bao, H and Yu, Y and Wang, L and Ma, X and Du, Z and Guo, J and Yang, X and Wang, R and Ma, H and Li, D and Pan, Y and Li, B and Zhang, Y and Zheng, X and Han, S and Jin, L and Chen, G and Li, H and Wang, CC and Wen, S}, title = {Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.07.063}, pmid = {39146937}, issn = {1879-0445}, abstract = {The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.}, } @article {pmid39140291, year = {2024}, author = {de la Fuente, J}, title = {Catastrophic selection: the other side of the coin.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2391014}, doi = {10.1080/07853890.2024.2391014}, pmid = {39140291}, issn = {1365-2060}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Peptides/pharmacology ; Machine Learning ; Drug Resistance, Bacterial ; Proteomics/methods ; }, abstract = {Recently, a machine learning molecular de-extinction paleoproteomic approach was used to recover inactivated antimicrobial peptides to overcome the challenges posed by antibiotic-resistant pathogens. The authors showed the possibility of identifying lost molecules with antibacterial capacity, but the other side of the coin associated with catastrophic selection should be considered for the development of new pharmaceuticals.}, } @article {pmid39136992, year = {2024}, author = {Skovrind, M and Louis, M and Ferguson, SH and Glazov, DM and Litovka, DI and Loseto, L and Meschersky, IG and Miller, MM and Petr, M and Postma, L and Rozhnov, VV and Scott, M and Westbury, MV and Szpak, P and Friesen, TM and Lorenzen, ED}, title = {Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {34}, pages = {e2405993121}, doi = {10.1073/pnas.2405993121}, pmid = {39136992}, issn = {1091-6490}, support = {37352//Villum Fonden YIP+/ ; 9064-00025B//Independent research fund, Sapre Aude/ ; CF23-1061//Carlsberg Foundation Semper Ardens Accelerate/ ; 435-2012-0641//Canadian Government | Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; 61914//Polar Continental Shelf Program/ ; 62816//Polar Continental Shelf Program/ ; 000//Aurora Research Institute (ARI)/ ; }, mesh = {Animals ; *Beluga Whale/genetics ; Northwest Territories ; Female ; Male ; Hunting ; Nitrogen Isotopes/analysis ; Carbon Isotopes/analysis ; DNA, Mitochondrial/genetics ; Inuit ; }, abstract = {Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ[13]C and δ[15]N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ[13]C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.}, } @article {pmid39135339, year = {2024}, author = {Tseng, YH and Kuo, LY and Borokini, I and Fawcett, S}, title = {The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e16388}, doi = {10.1002/ajb2.16388}, pmid = {39135339}, issn = {1537-2197}, abstract = {PREMISE: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.

METHODS: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.

RESULTS: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.

CONCLUSIONS: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.}, } @article {pmid39078618, year = {2024}, author = {Vaughn, AH and Nielsen, R}, title = {Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, doi = {10.1093/molbev/msae156}, pmid = {39078618}, issn = {1537-1719}, mesh = {*Selection, Genetic ; Humans ; *DNA, Ancient/analysis ; *Models, Genetic ; *Gene Frequency ; Likelihood Functions ; Markov Chains ; Algorithms ; Evolution, Molecular ; Alleles ; Computer Simulation ; }, abstract = {We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.}, } @article {pmid39135108, year = {2024}, author = {Alaçamlı, E and Naidoo, T and Güler, MN and Sağlıcan, E and Aktürk, Ş and Mapelli, I and Vural, KB and Somel, M and Malmström, H and Günther, T}, title = {READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {216}, pmid = {39135108}, issn = {1474-760X}, support = {P21-0266//Riksbankens Jubileumsfond/ ; 772390//HORIZON EUROPE European Research Council/ ; }, abstract = {The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.}, } @article {pmid39114968, year = {2024}, author = {Moriano, J and Leonardi, O and Vitriolo, A and Testa, G and Boeckx, C}, title = {A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution.}, journal = {Development (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1242/dev.202390}, pmid = {39114968}, issn = {1477-9129}, support = {2021-SGR-313; FI-SDUR 2020//Generalitat de Catalunya/ ; PID2019-107042GB-I00//Ministerio de Ciencia e Innovacion/ ; }, abstract = {The definition of molecular and cellular mechanisms contributing to brain ontogenetic trajectories is essential to investigate the evolution of our species. Yet their functional dissection at an appropriate level of granularity remains challenging. Capitalizing on recent efforts that have extensively profiled neural stem cells from the developing human cortex, we develop an integrative computational framework to perform (i) trajectory inference and gene regulatory network reconstruction, (ii) (pseudo)time-informed non-negative matrix factorization for learning the dynamics of gene expression programs, and (iii) paleogenomic analysis for a higher-resolution mapping of derived regulatory variants in our species in comparison to our closest relatives. We provide evidence for cell type-specific regulation of gene expression programs during indirect neurogenesis. In particular, our analysis uncovers a key role for a cholesterol program in outer radial glia, regulated by zinc-finger transcription factor KLF6. A cartography of the regulatory landscape impacted by Homo sapiens-derived variants reveals signals of selection clustering around regulatory regions associated with GLI3, a well-known regulator of radial glial cell cycle, and impacting KLF6 regulation. Our study contributes to the evidence of significant changes in metabolic pathways in recent human brain evolution.}, } @article {pmid39114174, year = {2024}, author = {Civáň, P and Fricano, A and Russell, J and Pont, C and Özkan, H and Kilian, B and Brown, TA}, title = {Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity.}, journal = {Ecology and evolution}, volume = {14}, number = {8}, pages = {e70068}, pmid = {39114174}, issn = {2045-7758}, abstract = {Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.}, } @article {pmid39113775, year = {2024}, author = {Furness, LH and Kersten, O and Boilard, A and Keith-Diagne, L and Brito, C and Barrett, JH and Kitchener, A and Sabin, R and Lavery, S and Plön, S and Star, B}, title = {Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes.}, journal = {Royal Society open science}, volume = {11}, number = {8}, pages = {240599}, pmid = {39113775}, issn = {2054-5703}, abstract = {Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.}, } @article {pmid39105137, year = {2024}, author = {de Vos, JM and Streiff, SJR and Bachelier, JB and Epitawalage, N and Maurin, O and Forest, F and Baker, WJ}, title = {Phylogenomics of the pantropical Connaraceae: revised infrafamilial classification and the evolution of heterostyly.}, journal = {Plant systematics and evolution = Entwicklungsgeschichte und Systematik der Pflanzen}, volume = {310}, number = {4}, pages = {29}, pmid = {39105137}, issn = {0378-2697}, abstract = {UNLABELLED: Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.}, } @article {pmid39098141, year = {2024}, author = {Golob, A and Kravanja, P and Concato, M and Leskovar, T and Zupanič Pajnič, I}, title = {Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains.}, journal = {Forensic science international}, volume = {362}, number = {}, pages = {112184}, doi = {10.1016/j.forsciint.2024.112184}, pmid = {39098141}, issn = {1872-6283}, abstract = {The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations.}, } @article {pmid39091721, year = {2024}, author = {Gyuris, B and Vyazov, L and Türk, A and Flegontov, P and Szeifert, B and Langó, P and Mende, BG and Csáky, V and Chizhevskiy, AA and Gazimzyanov, IR and Khokhlov, AA and Kolonskikh, AG and Matveeva, NP and Ruslanova, RR and Rykun, MP and Sitdikov, A and Volkova, EV and Botalov, SG and Bugrov, DG and Grudochko, IV and Komar, O and Krasnoperov, AA and Poshekhonova, OE and Chikunova, I and Sungatov, F and Stashenkov, DA and Zubov, S and Zelenkov, AS and Ringbauer, H and Cheronet, O and Pinhasi, R and Akbari, A and Rohland, N and Mallick, S and Reich, D and Szécsényi-Nagy, A}, title = {Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39091721}, issn = {2692-8205}, abstract = {During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.}, } @article {pmid39088604, year = {2024}, author = {Kukutai, T and Black, A}, title = {CARE-ing for Indigenous nonhuman genomic data - rethinking our approach.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6708}, pages = {eadr2493}, doi = {10.1126/science.adr2493}, pmid = {39088604}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; *Birds/genetics ; DNA, Ancient/analysis ; *Fossils ; *Genome ; *Genomics/ethics ; New Zealand ; Sequence Analysis, DNA ; }, abstract = {Earlier this year, an international group of scientists published a paper in ScienceAdvances on the draft genome of the little bush moa (Anomalopteryx didiformis), one of about nine species of extinct flightless birds endemic to Aotearoa (New Zealand). The genome was sequenced from the ancient DNA of a "poorly provenanced" fossil bone acquired by the Royal Ontario Museum. It held important clues about the moa's evolutionary history and aspects of its biology.}, } @article {pmid39086419, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Tracking of Infectious Diseases and Deadly Injuries through Signs Observed in Excavated Human Skeletons of 2000 BC/Iron Age in Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {7}, pages = {1598-1611}, pmid = {39086419}, issn = {2251-6093}, abstract = {BACKGROUND: Throughout history, many wars have occurred for various reasons, and many empires and kings have fallen or many people killed by wars. Wars were not always due to the conquest of the country. in the Iron Age, societies were governed by tribes at the head of the tribe, and war was only for to seize property, slaves, and food. Our research area is the same period as the Medes Kingdom, which included the union of small, large tribes, wars between tribes existed in that period, and their signs can be seen on the remains of the people of that period.

METHODS: Our research is related to human remains from Sagezabad cemetery, Qazvin plain, which dates back to 2000 BC (Iron Age 2 and 3) in Iran.

RESULTS: The blows on the remains were very serious and caused death. We have discussed how to kill by "considering the injured body".

CONCLUSION: Our investigation of how people were killed in war based on injury marks and bullet holes in bones, and simulating those injuries to body tissues and organs also, people who had bone cuts from the war and survived and had bone repair and died due to lack of nutrients and infection were also discussed.}, } @article {pmid39080329, year = {2024}, author = {Boggi, B and Sharpen, JDA and Taylor, G and Drosou, K}, title = {A novel integrated extraction protocol for multi-omic studies in heavily degraded samples.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17477}, pmid = {39080329}, issn = {2045-2322}, mesh = {Animals ; Brain/metabolism ; DNA/isolation & purification ; Genomics/methods ; Lipids/analysis ; Metabolomics/methods ; *Multiomics/methods ; Proteins/isolation & purification/metabolism ; Proteomics/methods ; Swine ; }, abstract = {The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.}, } @article {pmid39078610, year = {2024}, author = {Nagel, AA and Flouri, T and Yang, Z and Rannala, B}, title = {Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syae047}, pmid = {39078610}, issn = {1076-836X}, abstract = {Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.}, } @article {pmid39067763, year = {2024}, author = {Bragazzi, NL and Del Rio, D and Mayer, EA and Mena, P}, title = {We are what, when, and how we eat: the evolutionary impact of dietary shifts on physical and cognitive development, health, and disease.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100280}, doi = {10.1016/j.advnut.2024.100280}, pmid = {39067763}, issn = {2156-5376}, abstract = {"We are what, when, and how we eat": the evolution of human dietary habits mirrors the evolution of humans themselves. Key developments in human history, such as the advent of stone tool technology, the shift to a meat-based diet, control of fire, advancements in cooking and fermentation techniques, the domestication of plants and animals, have significantly influenced human anatomical, physiological, social, cognitive, and behavioral changes. Advancements in scientific methods, such as the analysis of microfossils like starch granules, plant-derived phytoliths, and coprolites, have yielded unprecedented insights into past diets. Nonetheless, the isolation of ancient food matrices remains analytically challenging. Future technological breakthroughs and a more comprehensive integration of paleogenomics, paleoproteomics, paleoglycomics, and paleometabolomics will enable a more nuanced understanding of early human ancestors' diets, which holds the potential to guide contemporary dietary recommendations and tackle modern health challenges, with far-reaching implications for human well-being, and ecological impact on the planet.}, } @article {pmid39050717, year = {2024}, author = {Monnereau, A and Ughi, A and Orecchioni, P and Hagan, R and Talbot, HM and Nikita, E and Hamilton, D and Le Roux, P and Molinari, A and Carver, M and Craig, OE and Speller, CF and Alexander, MM and Wales, N}, title = {Multi-proxy bioarchaeological analysis of skeletal remains shows genetic discontinuity in a Medieval Sicilian community.}, journal = {Royal Society open science}, volume = {11}, number = {7}, pages = {240436}, pmid = {39050717}, issn = {2054-5703}, abstract = {The medieval period in Sicily was turbulent, involving successive regime changes, from Byzantine (Greek Christian), Aghlabid (Sunni Muslim), Fatimid (Shī'a Muslim), to Normans and Swabians (Latin Christian). To shed new light on the local implications of regime changes, we conducted a multidisciplinary analysis of 27 individuals buried in adjacent Muslim and Christian cemeteries at the site of Segesta, western Sicily. By combining radiocarbon dating, genome-wide sequencing, stable and radiogenic isotopic data, and archaeological records, we uncover genetic differences between the two communities but find evidence of continuity in other aspects of life. Historical and archaeological evidence shows a Muslim community was present by the 12th century during Norman governance, with the Christian settlement appearing in the 13th century under Swabian governance. A Bayesian analysis of radiocarbon dates from the burials finds the abandonment of the Muslim cemetery likely occurred after the establishment of the Christian cemetery, indicating that individuals of both faiths were present in the area in the first half of the 13th century. The biomolecular results suggest the Christians remained genetically distinct from the Muslim community at Segesta while following a substantially similar diet. This study demonstrates that medieval regime changes had major impacts beyond the political core, leading to demographic changes while economic systems persisted and new social relationships emerged.}, } @article {pmid39044634, year = {2024}, author = {Rivera Rosas, DE and Geraldi, NR and Glud, RN and Oguri, K and Haond, SA and Duarte, CM}, title = {A sedimentary DNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17412}, doi = {10.1111/gcb.17412}, pmid = {39044634}, issn = {1365-2486}, support = {JP20H02013//Japan Society for the Promotion of Science/ ; 669947//ERC Advanced Grant "Benthic diagenesis and microbiology of hadal trenches"/ ; DNRF145//Danmarks Grundforskningsfond/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {*Geologic Sediments/analysis ; *Biodiversity ; *DNA, Environmental/analysis ; *RNA, Ribosomal, 18S/genetics ; *Ecosystem ; Chile ; Animals ; DNA Barcoding, Taxonomic ; Eukaryota/genetics ; Aquatic Organisms/genetics ; }, abstract = {The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment environmental DNA (eDNA) can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open-ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000 m. The chronologies of the sedimentary record were determined using [210]Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rRNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events and extensive fishing efforts during the time. We find a direct impact of sea surface temperature on the community composition over time. Fish and cnidarian read abundance was examined separately to determine whether fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes an important step toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.}, } @article {pmid39028337, year = {2024}, author = {Çubukcu, H and Kılınç, GM}, title = {Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {}, number = {}, pages = {}, pmid = {39028337}, issn = {1432-1777}, abstract = {Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.}, } @article {pmid39026955, year = {2024}, author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S}, title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11584}, pmid = {39026955}, issn = {2045-7758}, abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.}, } @article {pmid39018301, year = {2024}, author = {Del Papa, M and De Los Reyes, M and Poiré, DG and Rascovan, N and Jofré, G and Delgado, M}, title = {Anthropic cut marks in extinct megafauna bones from the Pampean region (Argentina) at the last glacial maximum.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0304956}, pmid = {39018301}, issn = {1932-6203}, mesh = {*Fossils ; Animals ; Argentina ; *Bone and Bones/anatomy & histology ; Humans ; *Extinction, Biological ; Xenarthra/anatomy & histology ; Paleontology ; Archaeology ; }, abstract = {The initial peopling of South America is a topic of intense archaeological debate. Among the most contentious issues remain the nature of the human-megafauna interaction and the possible role of humans, along with climatic change, in the extinction of several megamammal genera at the end of the Pleistocene. In this study, we present the analysis of fossil remains with cutmarks belonging to a specimen of Neosclerocalyptus (Xenarthra, Glyptodontidae), found on the banks of the Reconquista River, northeast of the Pampean region (Argentina), whose AMS 14C dating corresponds to the Last Glacial Maximum (21,090-20,811 cal YBP). Paleoenvironmental reconstructions, stratigraphic descriptions, absolute chronological dating of bone materials, and deposits suggest a relatively rapid burial event of the bone assemblage in a semi-dry climate during a wet season. Quantitative and qualitative analyses of the cut marks, reconstruction of butchering sequences, and assessments of the possible agents involved in the observed bone surface modifications indicate anthropic activities. Our results provide new elements for discussing the earliest peopling of southern South America and specifically for the interaction between humans and local megafauna in the Pampean region during the Last Glacial Maximum.}, } @article {pmid39013011, year = {2024}, author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD}, title = {Testing Times: Disentangling Admixture Histories in Recent and Complex Demographies using ancient DNA.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae110}, pmid = {39013011}, issn = {1943-2631}, abstract = {Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches - firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes - and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We observe population differentiation is the primary factor driving qpAdm performance. Notably, whilst complex gene-flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible amongst a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.}, } @article {pmid39009303, year = {2024}, author = {Shen, Q and Wu, Z and Zan, J and Yang, X and Guo, J and Ji, Z and Wang, B and Liu, Y and Mao, X and Wang, X and Zou, X and Zhou, H and Peng, Y and Ma, H and He, H and Bai, T and Xu, M and Wen, S and Jin, L and Zhang, Q and Wang, CC}, title = {Ancient genomes illuminate the demographic history of Shandong over the past two millennia.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.008}, pmid = {39009303}, issn = {1673-8527}, abstract = {Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.}, } @article {pmid39009302, year = {2024}, author = {Yu, Y and Yang, X and Liu, D and Du, P and Meng, H and Huang, Z and Xiong, J and Ding, Y and Ren, X and Allen, E and Wang, H and Han, S and Jin, L and Wang, CC and Wen, S}, title = {Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.009}, pmid = {39009302}, issn = {1673-8527}, abstract = {China's Northern and Southern Dynasties period (3[rd]-6[th] centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.}, } @article {pmid39002897, year = {2024}, author = {Du, S and Chen, J and Li, J and Qian, W and Wu, S and Peng, Q and Liu, Y and Pan, T and Li, Y and Hadi, SS and Tan, J and Yuan, Z and Wang, J and Tang, K and Wang, Z and Wen, Y and Dong, X and Zhou, W and Ruiz-Linares, A and Shi, Y and Jin, L and Liu, F and Zhang, M and Wang, S}, title = {A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.005}, pmid = {39002897}, issn = {1673-8527}, abstract = {Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of Genome-Wide Association Study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited significant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA, and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovan. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.}, } @article {pmid38996487, year = {2024}, author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL}, title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3541-3562.e51}, doi = {10.1016/j.cell.2024.06.002}, pmid = {38996487}, issn = {1097-4172}, support = {R35 GM147467/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; }, abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.}, } @article {pmid38996465, year = {2024}, author = {Sawchuk, EA and Sirak, KA and Manthi, FK and Ndiema, EK and Ogola, CA and Prendergast, ME and Reich, D and Aluvaala, E and Ayodo, G and Badji, L and Bird, N and Black, W and Fregel, R and Gachihi, N and Gibbon, VE and Gidna, A and Goldstein, ST and Hamad, R and Hassan, HY and Hayes, VM and Hellenthal, G and Kebede, S and Kurewa, A and Kusimba, C and Kyazike, E and Lane, PJ and MacEachern, S and Massilani, D and Mbua, E and Morris, AG and Mutinda, C and M'Mbogori, FN and Reynolds, AW and Tishkoff, S and Vilar, M and Yimer, G}, title = {Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.}, journal = {American journal of human genetics}, volume = {111}, number = {7}, pages = {1243-1251}, pmid = {38996465}, issn = {1537-6605}, mesh = {Humans ; *DNA, Ancient/analysis ; *Genetics, Population ; Africa ; Genomics ; Black People/genetics ; }, abstract = {Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.}, } @article {pmid38993187, year = {2023}, author = {Meng, XY and Wang, QL and Shi, MJ and Zhang, HY}, title = {Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.}, journal = {Bladder cancer (Amsterdam, Netherlands)}, volume = {9}, number = {3}, pages = {211-216}, pmid = {38993187}, issn = {2352-3735}, abstract = {BACKGROUND: The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences.

METHODS: We calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs.

RESULTS: We validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution.

CONCLUSIONS: It is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.}, } @article {pmid38987254, year = {2024}, author = {Bergström, A}, title = {Improving data archiving practices in ancient genomics.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {754}, pmid = {38987254}, issn = {2052-4463}, mesh = {*Genomics ; Humans ; *DNA, Ancient/analysis ; Animals ; Metadata ; }, abstract = {Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.}, } @article {pmid38986104, year = {2024}, author = {Jordan, B}, title = {[Ancient DNA speaks].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {6-7}, pages = {563-565}, doi = {10.1051/medsci/2024070}, pmid = {38986104}, issn = {1958-5381}, mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Pedigree ; }, abstract = {Many human DNA sequences have been obtained from ancient remains dating back from several millennia. However, these have low coverage and may contain many errors; this has limited their usefulness for many analyses, in particular the search for Identical By Descent (IBD) segments that is very powerful for detection of kinship. A new method, using imputation from database data and sophisticated statistical analysis, proves able to detect IBD segments (and thus parenthood) in low-quality DNA sequences from individuals linked only by sixth degree parenthood, opening a whole new field of investigation using ancient DNA.}, } @article {pmid38981530, year = {2024}, author = {Goldstein, ST and Mueller, NG and Janzen, A and Ogola, C and Dal Martello, R and Fernandes, R and Li, S and Iminjili, V and Juengst, S and Odera Otwani, A and Sawchuk, EA and Wang, K and Ndiema, E and Boivin, N}, title = {Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2026}, pages = {20232747}, doi = {10.1098/rspb.2023.2747}, pmid = {38981530}, issn = {1471-2954}, support = {//Max-Planck-Institut für Menschheitsgeschichte/ ; }, mesh = {*Crops, Agricultural ; Kenya ; *Archaeology ; *Agriculture ; Animals ; Radiometric Dating ; Africa, Eastern ; }, abstract = {The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.}, } @article {pmid38976766, year = {2024}, author = {Souilmi, Y and Wasef, S and Williams, MP and Conroy, G and Bar, I and Bover, P and Dann, J and Heiniger, H and Llamas, B and Ogbourne, S and Archer, M and Ballard, JWO and Reed, E and Tobler, R and Koungoulos, L and Walshe, K and Wright, JL and Balme, J and O'Connor, S and Cooper, A and Mitchell, KJ}, title = {Ancient genomes reveal over two thousand years of dingo population structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {30}, pages = {e2407584121}, pmid = {38976766}, issn = {1091-6490}, support = {CE170100015//Department of Education and Training | Australian Research Council (ARC)/ ; DP210101960//Department of Education and Training | Australian Research Council (ARC)/ ; FL140100260//Department of Education and Training | Australian Research Council (ARC)/ ; 2021/GNT2011277//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Animals ; Australia ; *Genome ; Dogs/genetics ; Wolves/genetics ; DNA, Ancient/analysis ; Genetics, Population ; }, abstract = {Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.}, } @article {pmid38969261, year = {2024}, author = {Wang, M and Chen, H and Luo, L and Huang, Y and Duan, S and Yuan, H and Tang, R and Liu, C and He, G}, title = {Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.06.016}, pmid = {38969261}, issn = {1673-8527}, abstract = {Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent, to understand kinship, migration patterns, and population dynamics. Within forensic science, forensic investigative genetic genealogy (FIGG) has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources, opening new investigative avenues. In this review, we synthesize current knowledge, underscore recent advancements, and discuss the growing role of FIGG in forensic genomics. FIGG has been pivotal in revitalizing dormant inquiries and offering new genetic leads in numerous cold cases. Its effectiveness relies on the extensive SNP profiles contributed by individuals from diverse populations to specialized genomic databases. Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics, anthropology, and ancient DNA studies. As the field progresses, FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline, shaping the future of forensic investigations.}, } @article {pmid38965340, year = {2024}, author = {Gibbon, VE and Thompson, JC and Alves, S}, title = {Informed proxy consent for ancient DNA research.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {815}, pmid = {38965340}, issn = {2399-3642}, mesh = {Humans ; *Informed Consent ; *DNA, Ancient/analysis ; }, abstract = {We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people the research affects. Embracing the underlying principles and process of informed proxy consent has the potential to transform research by (1) enriching outcomes by learning from and collaborating with interested and affected persons; (2) empowering people potentially impacted by research to stipulate evidence for information flow; (3) guarding researchers against actual or perceived violations by providing a common set of guidelines; and (4) highlighting the essential nature of long-term consultation and community partnerships to research outcome success.}, } @article {pmid38963678, year = {2024}, author = {Coppola Bove, L and Kirkpatrick, CL and Vigil-Escalera Guirado, A and Botella López, MC and Bos, KI}, title = {A morphological and molecular approach to investigating infectious disease in early medieval Iberia: The necropolis of La Olmeda (Palencia, Spain).}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {e24994}, doi = {10.1002/ajpa.24994}, pmid = {38963678}, issn = {2692-7691}, support = {805268/ERC_/European Research Council/International ; //Erasmus+ Traineeship Program Scholarship/ ; //Junta de Andalucía and SEPIE/ ; 756-2023-0246//Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship/ ; }, abstract = {OBJECTIVE: Here we investigate infectious diseases that potentially contribute to osteological lesions in individuals from the early medieval necropolis of La Olmeda (6th-11th c. CE) in North Iberia.

MATERIALS AND METHODS: We studied a minimum number of 268 individuals (33 adult females; 38 adult males, 77 unknown/indeterminate sex; and 120 non-adults), including articulated and commingled remains. Individuals with differential diagnoses suggesting chronic systemic infectious diseases were sampled and bioinformatically screened for ancient pathogen DNA.

RESULTS: Five non-adults (and no adults) presented skeletal evidence of chronic systemic infectious disease (1.87% of the population; 4.67% of non-adults). The preferred diagnoses for these individuals included tuberculosis, brucellosis, and malaria. Ancient DNA fragments assigned to the malaria-causing pathogen, Plasmodium spp., were identified in three of the five individuals. Observed pathology includes lesions generally consistent with malaria; however, additional lesions in two of the individuals may represent hitherto unknown variation in the skeletal manifestation of this disease or co-infection with tuberculosis or brucellosis. Additionally, spondylolysis was observed in one individual with skeletal lesions suggestive of infectious disease.

CONCLUSIONS: This study sheds light on the pathological landscape in Iberia during a time of great social, demographic, and environmental change. Genetic evidence challenges the hypothesis that malaria was absent from early medieval Iberia and demonstrates the value of combining osteological and archaeogenetic methods. Additionally, all of the preferred infectious diagnoses for the individuals included in this study (malaria, tuberculosis, and brucellosis) could have contributed to the febrile cases described in historical sources from this time.}, } @article {pmid38960861, year = {2024}, author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD}, title = {Unravelling reference bias in ancient DNA datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38960861}, issn = {1367-4811}, support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.

RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).}, } @article {pmid38957694, year = {2024}, author = {Mousavi-Derazmahalleh, M and Haue, N and Kanstrup, M and Laursen, JT and Lukehurst, SS and Kveiborg, J and Allentoft, ME}, title = {Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11680}, pmid = {38957694}, issn = {2045-7758}, abstract = {An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.}, } @article {pmid38957308, year = {2024}, author = {Çokoğlu, SS and Koptekin, D and Fidan, FR and Somel, M}, title = {Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.}, journal = {Evolutionary applications}, volume = {17}, number = {7}, pages = {e13743}, pmid = {38957308}, issn = {1752-4571}, abstract = {The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.}, } @article {pmid38948161, year = {2024}, author = {Özdoğan, KT and Gelabert, P and Hammers, N and Altınışık, NE and de Groot, A and Plets, G}, title = {Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past.}, journal = {Archaeological and anthropological sciences}, volume = {16}, number = {7}, pages = {108}, pmid = {38948161}, issn = {1866-9557}, abstract = {Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.}, } @article {pmid38946459, year = {2024}, author = {Özkan, M and Gürün, K and Yüncü, E and Vural, KB and Atağ, G and Akbaba, A and Fidan, FR and Sağlıcan, E and Altınışık, EN and Koptekin, D and Pawłowska, K and Hodder, I and Adcock, SE and Arbuckle, BS and Steadman, SR and McMahon, G and Erdal, YS and Bilgin, CC and Togan, İ and Geigl, EM and Götherström, A and Grange, T and Özer, F and Somel, M}, title = {The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).}, journal = {Molecular ecology}, volume = {33}, number = {14}, pages = {e17440}, doi = {10.1111/mec.17440}, pmid = {38946459}, issn = {1365-294X}, support = {772390//European Research Council Consolidator Grant H2020/ ; 952317//European Commission Horizon 2020 TWINNING Programme/ ; 117Z991//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Haplotypes/genetics ; *Phylogeny ; *Gene Flow ; Equidae/genetics ; Genome, Mitochondrial ; Extinction, Biological ; Fossils ; Genetics, Population ; Genetic Variation ; }, abstract = {We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.}, } @article {pmid38942016, year = {2024}, author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L}, title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3531-3540.e13}, doi = {10.1016/j.cell.2024.05.033}, pmid = {38942016}, issn = {1097-4172}, mesh = {Animals ; *Mammoths/genetics ; *Extinction, Biological ; *Genome/genetics ; *Mutation ; Siberia ; Phylogeny ; Evolution, Molecular ; Time Factors ; }, abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.}, } @article {pmid38932149, year = {2024}, author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS}, title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932149}, issn = {1999-4915}, support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation & purification ; Fossils/virology ; }, abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.}, } @article {pmid38929847, year = {2024}, author = {Puga, M and Serrano, JG and García, EL and González Carracedo, MA and Jiménez-Canino, R and Pino-Yanes, M and Karlsson, R and Sullivan, PF and Fregel, R}, title = {El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population.}, journal = {Journal of personalized medicine}, volume = {14}, number = {6}, pages = {}, pmid = {38929847}, issn = {2075-4426}, support = {D0886501//Swedish Research Council/ ; PID2021-123080NB-I00//Spanish Ministry of Science, Innovation, and Universities/ ; RYC-2015-17205//Spanish Ministry of Science, Innovation, and Universities/ ; }, abstract = {El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.}, } @article {pmid38927726, year = {2024}, author = {Zhu, S and Zhang, N and Zhang, J and Shao, X and Guo, Y and Cai, D}, title = {Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927726}, issn = {2073-4425}, support = {NO.17ZDA221//Major Project of the National Social Science Foundation of China/ ; NO.2020YFC1521606//National Key Research and Development Program of China/ ; NO. 2022M722460//Project funded by China Postdoctoral Science Foundation/ ; NO. 2022CXTD17//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial/genetics ; China ; *DNA, Ancient/analysis ; *Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; History, Ancient ; High-Throughput Nucleotide Sequencing ; Domestication ; }, abstract = {This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.}, } @article {pmid38927608, year = {2024}, author = {Di Stefano, B and Zupanič Pajnič, I and Concato, M and Bertoglio, B and Calvano, MG and Sorçaburu Ciglieri, S and Bosetti, A and Grignani, P and Addoum, Y and Vetrini, R and Introna, F and Bonin, S and Previderè, C and Fattorini, P}, title = {Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927608}, issn = {2073-4425}, support = {no available//Comunità di Lussino, Trieste, Italy/ ; }, mesh = {Humans ; *Bone and Bones/chemistry ; World War II ; DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats/genetics ; DNA/genetics/isolation & purification ; DNA, Ancient/analysis ; }, abstract = {Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell[®] FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.}, } @article {pmid38926415, year = {2024}, author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA}, title = {Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14720}, pmid = {38926415}, issn = {2045-2322}, support = {Pre-doctoral Fellowship//Smithsonian Institution, National Museum of Natural History, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; }, mesh = {*Dental Calculus/microbiology/history ; Humans ; *Metagenomics/methods ; *Paleopathology/methods ; *Tuberculosis/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation & purification ; DNA, Bacterial/genetics ; Male ; Treponema pallidum/genetics/isolation & purification ; Syphilis/diagnosis/microbiology/history ; Female ; Adult ; Metagenome/genetics ; Middle Aged ; }, abstract = {Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.}, } @article {pmid38916350, year = {2024}, author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G}, title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0266223}, pmid = {38916350}, issn = {2165-0497}, abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.}, } @article {pmid38913897, year = {2024}, author = {Sasso, S and Saag, L and Spros, R and Beneker, O and Molinaro, L and Biagini, SA and Lehouck, A and Van De Vijver, K and Hui, R and D'Atanasio, E and Kushniarevich, A and Kabral, H and Metspalu, E and Guellil, M and Ali, MQA and Geypen, J and Hoebreckx, M and Berk, B and De Winter, N and Driesen, P and Pijpelink, A and Van Damme, P and Scheib, CL and Deschepper, E and Deckers, P and Snoeck, C and Dewilde, M and Ervynck, A and Tambets, K and Larmuseau, MHD and Kivisild, T}, title = {Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {27}, pages = {e2406734121}, pmid = {38913897}, issn = {1091-6490}, support = {NA//agentschap Onroerend Erfgoed Archeologie syntheseproject/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; STG/18/021//KU Leuven start-up grant/ ; ZKD6488 C24M/19/075//KU Leuven BOF-C24/ ; NA//EWI-Vlaanderen citizien science project "MamaMito"/ ; PRG1027//Estonian Research fundation grant/ ; NA//Sapienza University Rome fellowship/ ; }, mesh = {Humans ; History, Medieval ; *Pedigree ; Belgium ; Burial/history ; Genetics, Population/methods ; Female ; Male ; DNA, Ancient/analysis ; England ; Human Migration ; Archaeology ; Netherlands ; Genome, Human ; }, abstract = {The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.}, } @article {pmid38912151, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Oral Infections in Ancient Human Skulls in 2000 BC/Iron Age, Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {5}, pages = {1115-1127}, pmid = {38912151}, issn = {2251-6093}, abstract = {BACKGROUND: Oral infections have been seen in humans since ancient times. Excessive penetration of this infection can cause human death. Most of these infections are gum cysts and abscesses. The cyst creates large hard lumps in the gums, which is causes loose, and protruding teeth and abscesses, causing cavities in the jawbone and teeth. In this article, we have discussed for this infectious disease in 4000 - year - old ancient humans from Qazvin Province, Iran. The bone remains of our research are related to Sagezabad ancient cemetery in Qazvin plain.

METHODS: We tried to use reliable international atlases to get detailed information about ancient oral infections. The bones were extracted from the 2019 excavation of the Ghara Tappe area of Sagezabad for the Iron Age 2[nd] and 3[rd] Qazvin plains of Iran. This cemetery belongs to the period of the Medes Kingdom (pre - Achaemenian kingdom) in Iran.

RESULTS: We have discussed one of the ancient cemeteries with a large number of ancient populations. In this cemetery, there are signs of war and infectious diseases on the bones, which can be clearly seen. We have specially mentioned the abscess as the cause of oral infection from Sagezabad cemetery.

CONCLUSION: Oral infection existed in Iran since 2000 BC. Of course, this infection was common in ancient times and even Paleolithic period, like Homo Heidelbergensis.}, } @article {pmid38903121, year = {2024}, author = {Bougiouri, K and Aninta, SG and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F}, title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38903121}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R[2]>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.}, } @article {pmid38891676, year = {2024}, author = {Abdelmanova, AA and Deniskova, TE and Kharzinova, VR and Chinarov, RY and Boronetskaya, OI and Sölkner, J and Brem, G and Ai, H and Huang, L and Trukhachev, VI and Zinovieva, NA}, title = {Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {11}, pages = {}, pmid = {38891676}, issn = {2076-2615}, support = {23-46-00014//Russian Science Foundation/ ; }, abstract = {The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.}, } @article {pmid38886480, year = {2024}, author = {Laffranchi, Z and Zingale, S and Indra, L and Coia, V and Salazar García, DC and Paladin, A and Kaeser, MA and Delley, G and Szidat, S and Lösch, S and Zink, A and Milella, M}, title = {Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12180}, pmid = {38886480}, issn = {2045-2322}, support = {10531FL_197103 / 1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Funding Decree n.9/2021//Autonomous Province of Bolzano-Alto Adige - Department of Innovation, Research, University and Museums/ ; CIDEGENT/2019/061//Generalitat Valenciana/ ; }, mesh = {Humans ; Switzerland ; Male ; History, Ancient ; Adult ; Female ; *Archaeology ; Fossils ; Bone and Bones ; Radiometric Dating ; }, abstract = {Cornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.}, } @article {pmid38885310, year = {2024}, author = {Wang, M and Huang, Y and Liu, K and Wang, Z and Zhang, M and Yuan, H and Duan, S and Wei, L and Yao, H and Sun, Q and Zhong, J and Tang, R and Chen, J and Sun, Y and Li, X and Su, H and Yang, Q and Hu, L and Yun, L and Yang, J and Nie, S and Cai, Y and Yan, J and Zhou, K and Wang, C and , and Zhu, B and Liu, C and He, G}, title = {Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage.}, journal = {Molecular biology and evolution}, volume = {41}, number = {7}, pages = {}, pmid = {38885310}, issn = {1537-1719}, support = {82202078//National Natural Science Foundation of China/ ; 23&ZD203//Major Project of the National Social Science Foundation of China/ ; }, mesh = {Humans ; *Human Migration ; China ; *Asian People/genetics ; Male ; *Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; Paternal Inheritance ; Phylogeny ; East Asian People ; }, abstract = {Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.}, } @article {pmid38883810, year = {2024}, author = {Pathak, AK and Simonian, H and Ibrahim, IAA and Hrechdakian, P and Behar, DM and Ayub, Q and Arsanov, P and Metspalu, E and Yepiskoposyan, L and Rootsi, S and Endicott, P and Villems, R and Sahakyan, H}, title = {Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.}, journal = {iScience}, volume = {27}, number = {6}, pages = {110016}, pmid = {38883810}, issn = {2589-0042}, abstract = {West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.}, } @article {pmid38881417, year = {2024}, author = {Green, MH}, title = {The Pandemic Arc: Expanded Narratives in the History of Global Health.}, journal = {Journal of the history of medicine and allied sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhmas/jrae008}, pmid = {38881417}, issn = {1468-4373}, abstract = {Using the examples of plague, smallpox, and HIV/AIDS, the present essay argues for the benefits of incorporating the evolutionary histories of pathogens, beyond visible epidemic spikes within human populations, into our understanding of what pandemics actually are as epidemiological phenomena. The pandemic arc - which takes the pathogen as the defining "actor" in a pandemic, from emergence to local proliferation to globalization - offers a framework capable of bringing together disparate aspects not only of the manifestations of disease but also of human involvement in the pandemic process. Pathogens may differ, but there are common patterns in disease emergence and proliferation that distinguish those diseases that become pandemic, dispersed through human communities regionally or globally. The same methods of genomic analysis that allow tracking the evolutionary development of a modern pathogen such as SARS-CoV-2 also allow us to trace pandemics into the past. Reconstruction of these pandemic arcs brings new elements of these stories into view, recovering the experiences of regions and populations hitherto overlooked by Eurocentric narratives. This expanded global history of infectious diseases, in turn, lays a groundwork for reconceiving what ambitions a truly global health might aim for.}, } @article {pmid38871872, year = {2024}, author = {Callaway, E}, title = {Ancient DNA from Maya ruins tells story of ritual human sacrifices.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38871872}, issn = {1476-4687}, } @article {pmid38870299, year = {2024}, author = {Curry, A}, title = {Sacrificed Maya boys tied to myth of 'Hero Twins'.}, journal = {Science (New York, N.Y.)}, volume = {384}, number = {6701}, pages = {1160-1161}, doi = {10.1126/science.adr0288}, pmid = {38870299}, issn = {1095-9203}, mesh = {Female ; Humans ; Male ; *DNA, Ancient ; History, Ancient ; *Twins/history ; Child ; *Ceremonial Behavior ; *Civilization/history ; }, abstract = {Ancient DNA shows continuity between living and ancient Maya communities.}, } @article {pmid38845985, year = {2024}, author = {Tejero, JM and Cheronet, O and Gelabert, P and Zagorc, B and Álvarez-Fernández, E and Arias, P and Averbouh, A and Bar-Oz, G and Barzilai, O and Belfer-Cohen, A and Bosch, MD and Brück, F and Cueto, M and Dockner, M and Fullola, JM and Gárate, D and Giannakoulis, M and González, C and Jakeli, N and Mangado, X and Meshveliani, T and Neruda, P and Nigst, P and Ontañón, R and Shemer, M and Šimková, PG and Tapia, J and Sánchez de la Torre, M and Schwab, C and Weber, G and Pinhasi, R}, title = {Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e31858}, pmid = {38845985}, issn = {2405-8440}, abstract = {Antler is one of the primary animal raw materials exploited for technical purposes by the hunter-gatherer groups of the Eurasian Upper Palaeolithic (UP) all over the ecological range of deers, and beyond. It was exhaustively employed to produce one of the most critical tools for the survival of the UP societies: hunting weapons. However, antler implements can be made from diverse deer taxa, with different ecological requirements and ethological behaviours. Identifying the antler's origin at a taxonomic level is thus essential in improving our knowledge of humans' functional, practical and symbolic choices, as well as the human-animal interface during Prehistoric times. Nevertheless, palaeogenetics analyses have focused mainly on bone and teeth, with genetic studies of antler generally focused on modern deer conservation. Here we present the results of the first whole mitochondrial genome ancient DNA (aDNA) analysis by means of in-solution hybridisation capture of antlers from pre-Holocene archaeological contexts. We analysed a set of 50 Palaeolithic and Neolithic (c. 34-8ka) antler and osseous objects from South-Western Europe, Central Europe, South-Western Asia and the Caucasus. We successfully obtained aDNA, allowing us to identify the exploited taxa and demonstrate the archaeological relevance of those finds. Moreover, as most of the antlers were sampled using a minimally-invasive method, further analyses (morphometric, technical, genetic, radiometric and more) remain possible on these objects.}, } @article {pmid38830089, year = {2024}, author = {Fordham, DA and Brown, SC and Canteri, E and Austin, JJ and Lomolino, MV and Haythorne, S and Armstrong, E and Bocherens, H and Manica, A and Rey-Iglesia, A and Rahbek, C and Nogués-Bravo, D and Lorenzen, ED}, title = {52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {24}, pages = {e2316419121}, pmid = {38830089}, issn = {1091-6490}, support = {DP180102392//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {Animals ; *Extinction, Biological ; *Perissodactyla ; *Population Dynamics ; *Fossils ; Ecosystem ; DNA, Ancient/analysis ; Paleontology ; }, abstract = {The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.}, } @article {pmid38813936, year = {2024}, author = {Arsuaga, JL and Martínez, I and Gracia-Téllez, A and Carretero, JM and Esquivel, A and García, N and Lorenzo, C and Quam, R and Aramburu, A and Sala, N and Trueba, J}, title = {How the Sima de los Huesos was won.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2225-2245}, doi = {10.1002/ar.25509}, pmid = {38813936}, issn = {1932-8494}, support = {PID2021-122355NB-C31 supported by MCIN/AEI/10.1303//Government of Spain/ ; //Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá)/ ; EPU-INV-UAH/2022/006//Universidad de Alcalá/ ; }, mesh = {Humans ; *Fossils ; Animals ; *Biological Evolution ; Female ; Male ; Hominidae/anatomy & histology ; Spain ; }, abstract = {Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.}, } @article {pmid38806487, year = {2024}, author = {Bagnasco, G and Marzullo, M and Cattaneo, C and Biehler-Gomez, L and Mazzarelli, D and Ricciardi, V and Müller, W and Coppa, A and McLaughlin, R and Motta, L and Prato, O and Schmidt, F and Gaveriaux, F and Marras, GB and Millet, MA and Madgwick, R and Ballantyne, R and Makarewicz, CA and Trentacoste, A and Reimer, P and Mattiangeli, V and Bradley, DG and Malone, C and Esposito, C and Breslin, EM and Stoddart, S}, title = {Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11895}, pmid = {38806487}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Italy ; Humans ; *Archaeology ; History, Ancient ; Male ; DNA, Ancient/analysis ; Female ; }, abstract = {Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.}, } @article {pmid38798346, year = {2024}, author = {Fine, AG and Steinrücken, M}, title = {A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38798346}, issn = {2692-8205}, support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; }, abstract = {Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Thus, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which heterozygote and homozygote fitnesses are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, as well as a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years, and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.}, } @article {pmid38796876, year = {2024}, author = {Psonis, N and Vassou, D and Nafplioti, A and Tabakaki, E and Pavlidis, P and Stamatakis, A and Poulakakis, N}, title = {Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes.}, journal = {Forensic science international. Genetics}, volume = {71}, number = {}, pages = {103060}, doi = {10.1016/j.fsigen.2024.103060}, pmid = {38796876}, issn = {1878-0326}, mesh = {Humans ; *DNA, Ancient/analysis ; *World War II ; Male ; Greece ; *DNA Fingerprinting ; Skull ; Genome, Human ; Forensic Anthropology ; Whole Genome Sequencing ; }, abstract = {In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.}, } @article {pmid38795367, year = {2024}, author = {Larsson, MNA and Morell Miranda, P and Pan, L and Başak Vural, K and Kaptan, D and Rodrigues Soares, AE and Kivikero, H and Kantanen, J and Somel, M and Özer, F and Johansson, AM and Storå, J and Günther, T}, title = {Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.}, journal = {Genome biology and evolution}, volume = {16}, number = {6}, pages = {}, pmid = {38795367}, issn = {1759-6653}, support = {2017-05267//Vetenskapsrådet/ ; P21-0266//Riksbankens Jubileumsfond/ ; CTS 18:129//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; //Knut and Alice Wallenberg Foundation/ ; //National Academic Infrastructure for Supercomputing in Sweden/ ; //Swedish National Infrastructure for Computing/ ; }, mesh = {Animals ; *Genome ; Sheep/genetics ; Genetic Variation ; Sheep, Domestic/genetics ; DNA, Ancient/analysis ; }, abstract = {Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.}, } @article {pmid38781957, year = {2024}, author = {Bai, F and Liu, Y and Wangdue, S and Wang, T and He, W and Xi, L and Tsho, Y and Tsering, T and Cao, P and Dai, Q and Liu, F and Feng, X and Zhang, M and Ran, J and Ping, W and Payon, D and Mao, X and Tong, Y and Tsring, T and Chen, Z and Fu, Q}, title = {Ancient genomes revealed the complex human interactions of the ancient western Tibetans.}, journal = {Current biology : CB}, volume = {34}, number = {12}, pages = {2594-2605.e7}, doi = {10.1016/j.cub.2024.04.068}, pmid = {38781957}, issn = {1879-0445}, mesh = {Humans ; *DNA, Ancient/analysis ; East Asian People/genetics ; Genetics, Population ; *Genome, Human ; *Human Migration/history ; Tibet ; }, abstract = {The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.}, } @article {pmid38781323, year = {2024}, author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ}, title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.}, journal = {Science advances}, volume = {10}, number = {21}, pages = {eadj6823}, doi = {10.1126/sciadv.adj6823}, pmid = {38781323}, issn = {2375-2548}, mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; }, abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.}, } @article {pmid38769390, year = {2024}, author = {Borbély, N and Dudás, D and Tapasztó, A and Dudás-Boda, E and Csáky, V and Szeifert, B and Mende, BG and Egyed, B and Szécsényi-Nagy, A and Pamjav, H}, title = {Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11480}, pmid = {38769390}, issn = {2045-2322}, support = {FK 127938//Hungarian National Research, Development, and Innovation Office/ ; }, mesh = {Humans ; *Phylogeny ; *Chromosomes, Human, Y/genetics ; Hungary ; *Genome, Mitochondrial ; Male ; Genetics, Population ; Female ; DNA, Mitochondrial/genetics ; DNA, Ancient/analysis ; Microsatellite Repeats/genetics ; Haplotypes ; }, abstract = {This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.}, } @article {pmid38756579, year = {2024}, author = {Wang, Z and Wang, M and Hu, L and He, G and Nie, S}, title = {Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives.}, journal = {Heliyon}, volume = {10}, number = {9}, pages = {e30067}, pmid = {38756579}, issn = {2405-8440}, abstract = {Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.}, } @article {pmid38754423, year = {2024}, author = {Yuan, J and Hu, J and Liu, W and Chen, S and Zhang, F and Wang, S and Zhang, Z and Wang, L and Xiao, B and Li, F and Hofreiter, M and Lai, X and Westbury, MV and Sheng, G}, title = {Camelus knoblochi genome reveals the complex evolutionary history of Old World camels.}, journal = {Current biology : CB}, volume = {34}, number = {11}, pages = {2502-2508.e5}, doi = {10.1016/j.cub.2024.04.050}, pmid = {38754423}, issn = {1879-0445}, mesh = {Animals ; *Camelus/genetics ; *Phylogeny ; Genome ; Biological Evolution ; }, abstract = {Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.[1][,][2] Although many remains have been unearthed,[3][,][4][,][5] we know neither whether the prevalent hybridization observed between extant Camelus species[2][,][6][,][7] also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.}, } @article {pmid38750053, year = {2024}, author = {Cabrera, VM}, title = {New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11150}, pmid = {38750053}, issn = {2045-2322}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *DNA, Ancient/analysis ; *Phylogeography ; Spain ; Phylogeny ; Genetics, Population ; Indigenous Peoples/genetics ; Archaeology ; Human Migration ; History, Ancient ; High-Throughput Nucleotide Sequencing ; }, abstract = {Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.}, } @article {pmid38745401, year = {2024}, author = {Ekram, MA and Campbell, M and Kose, SH and Plet, C and Hamilton, R and Bijaksana, S and Grice, K and Russell, J and Stevenson, J and Vogel, H and Coolen, MJL}, title = {A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).}, journal = {Geobiology}, volume = {22}, number = {3}, pages = {e12599}, doi = {10.1111/gbi.12599}, pmid = {38745401}, issn = {1472-4669}, support = {DP15102587//Australian Research Council/ ; //International Continental Scientific Drilling Program (ICDP)/ ; //U.S. National Science Foundation (NSF)/ ; 200021_153053/SNSF_/Swiss National Science Foundation/Switzerland ; //PT Vale Indonesia/ ; //Ministry of Research, Education, and Higher Technology of Indonesia (RISTEK)/ ; //Brown University/ ; //The Institute for Geoscience Research (TIGeR)/ ; //Research Office at Curtin University (ROC)/ ; }, mesh = {*Lakes/chemistry ; *Geologic Sediments ; Indonesia ; *DNA, Ancient/analysis ; Plants ; Tropical Climate ; Ecosystem ; DNA, Plant/genetics ; }, abstract = {Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.}, } @article {pmid38742634, year = {2024}, author = {Harris, KD and Greenbaum, G}, title = {DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W54-W60}, pmid = {38742634}, issn = {1362-4962}, mesh = {Humans ; *DNA, Ancient/analysis ; *Software ; Genomics/methods ; Genome, Human ; Genotype ; User-Computer Interface ; Genetics, Population/methods ; }, abstract = {The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.}, } @article {pmid38739117, year = {2024}, author = {Dahlquist-Axe, G and Standeven, FJ and Speller, CF and Tedder, A and Meehan, CJ}, title = {Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.}, journal = {Microbial genomics}, volume = {10}, number = {5}, pages = {}, pmid = {38739117}, issn = {2057-5858}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Anti-Bacterial Agents/pharmacology ; History, Ancient ; Diet ; Bacteria/genetics/classification/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; History, Medieval ; History, 17th Century ; History, 18th Century ; History, 16th Century ; }, abstract = {The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.}, } @article {pmid38703773, year = {2024}, author = {Urban, C and Blom, AA and Avanzi, C and Walker-Meikle, K and Warren, AK and White-Iribhogbe, K and Turle, R and Marter, P and Dawson-Hobbis, H and Roffey, S and Inskip, SA and Schuenemann, VJ}, title = {Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host.}, journal = {Current biology : CB}, volume = {34}, number = {10}, pages = {2221-2230.e8}, doi = {10.1016/j.cub.2024.04.006}, pmid = {38703773}, issn = {1879-0445}, mesh = {Animals ; *Mycobacterium leprae/genetics/isolation & purification ; *Sciuridae/microbiology ; *Leprosy/microbiology/history ; Humans ; *Genome, Bacterial ; *Phylogeny ; England ; DNA, Ancient/analysis ; Archaeology ; History, Medieval ; }, abstract = {Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.[1][,][2] Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,[3][,][4][,][5] the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.[6][,][7] However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.}, } @article {pmid38691462, year = {2024}, author = {Zhu, K and He, H and Tao, L and Ma, H and Yang, X and Wang, R and Guo, J and Wang, CC}, title = {Protocol for a comprehensive pipeline to study ancient human genomes.}, journal = {STAR protocols}, volume = {5}, number = {2}, pages = {102985}, pmid = {38691462}, issn = {2666-1667}, mesh = {Humans ; *Genome, Human/genetics ; *DNA, Ancient/analysis ; *Genomics/methods ; Sequence Analysis, DNA/methods ; Gene Library ; Genetics, Population/methods ; }, abstract = {Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.[1].}, } @article {pmid38676702, year = {2024}, author = {Aktürk, Ş and Mapelli, I and Güler, MN and Gürün, K and Katırcıoğlu, B and Vural, KB and Sağlıcan, E and Çetin, M and Yaka, R and Sürer, E and Atağ, G and Çokoğlu, SS and Sevkar, A and Altınışık, NE and Koptekin, D and Somel, M}, title = {Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13960}, doi = {10.1111/1755-0998.13960}, pmid = {38676702}, issn = {1755-0998}, mesh = {*Pedigree ; *Benchmarking/methods ; *Polymorphism, Single Nucleotide ; Humans ; Gene Frequency ; DNA, Ancient/analysis ; Computer Simulation ; Genetics, Population/methods ; Computational Biology/methods ; }, abstract = {There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.}, } @article {pmid38671208, year = {2024}, author = {Taurozzi, AJ and Rüther, PL and Patramanis, I and Koenig, C and Sinclair Paterson, R and Madupe, PP and Harking, FS and Welker, F and Mackie, M and Ramos-Madrigal, J and Olsen, JV and Cappellini, E}, title = {Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.}, journal = {Nature protocols}, volume = {19}, number = {7}, pages = {2085-2116}, pmid = {38671208}, issn = {1750-2799}, support = {17649//Villum Fonden (Villum Foundation)/ ; 722606//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 948365//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PROTEIOS (DNRF128)//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {*Phylogeny ; *Dental Enamel/chemistry/metabolism ; *Proteomics/methods ; Animals ; Humans ; Paleontology/methods ; Mass Spectrometry/methods ; Fossils ; }, abstract = {In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.}, } @article {pmid38659893, year = {2024}, author = {Lazaridis, I and Patterson, N and Anthony, D and Vyazov, L and Fournier, R and Ringbauer, H and Olalde, I and Khokhlov, AA and Kitov, EP and Shishlina, NI and Ailincăi, SC and Agapov, DS and Agapov, SA and Batieva, E and Bauyrzhan, B and Bereczki, Z and Buzhilova, A and Changmai, P and Chizhevsky, AA and Ciobanu, I and Constantinescu, M and Csányi, M and Dani, J and Dashkovskiy, PK and Évinger, S and Faifert, A and Flegontov, PN and Frînculeasa, A and Frînculeasa, MN and Hajdu, T and Higham, T and Jarosz, P and Jelínek, P and Khartanovich, VI and Kirginekov, EN and Kiss, V and Kitova, A and Kiyashko, AV and Koledin, J and Korolev, A and Kosintsev, P and Kulcsár, G and Kuznetsov, P and Magomedov, R and Malikovich, MA and Melis, E and Moiseyev, V and Molnár, E and Monge, J and Negrea, O and Nikolaeva, NA and Novak, M and Ochir-Goryaeva, M and Pálfi, G and Popovici, S and Rykun, MP and Savenkova, TM and Semibratov, VP and Seregin, NN and Šefčáková, A and Serikovna, MR and Shingiray, I and Shirokov, VN and Simalcsik, A and Sirak, K and Solodovnikov, KN and Tárnoki, J and Tishkin, AA and Trifonov, V and Vasilyev, S and Akbari, A and Brielle, ES and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Flegontova, O and Iliev, L and Kearns, A and Keating, D and Lawson, AM and Mah, M and Micco, A and Michel, M and Oppenheimer, J and Qiu, L and Noah Workman, J and Zalzala, F and Szécsényi-Nagy, A and Palamara, PF and Mallick, S and Rohland, N and Pinhasi, R and Reich, D}, title = {The Genetic Origin of the Indo-Europeans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38659893}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.}, } @article {pmid38658749, year = {2024}, author = {Gnecchi-Ruscone, GA and Rácz, Z and Samu, L and Szeniczey, T and Faragó, N and Knipper, C and Friedrich, R and Zlámalová, D and Traverso, L and Liccardo, S and Wabnitz, S and Popli, D and Wang, K and Radzeviciute, R and Gulyás, B and Koncz, I and Balogh, C and Lezsák, GM and Mácsai, V and Bunbury, MME and Spekker, O and le Roux, P and Szécsényi-Nagy, A and Mende, BG and Colleran, H and Hajdu, T and Geary, P and Pohl, W and Vida, T and Krause, J and Hofmanová, Z}, title = {Network of large pedigrees reveals social practices of Avar communities.}, journal = {Nature}, volume = {629}, number = {8011}, pages = {376-383}, pmid = {38658749}, issn = {1476-4687}, mesh = {Adult ; Female ; Humans ; Male ; *Archaeology/methods ; Asia/ethnology ; Cemeteries/history ; Consanguinity ; *DNA, Ancient/analysis ; Europe/ethnology ; *Family Characteristics/ethnology/history ; Genomics ; *Grassland ; History, Medieval ; *Pedigree ; Politics ; Adolescent ; Young Adult ; }, abstract = {From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years[1]. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies[2]. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.}, } @article {pmid38658715, year = {2024}, author = {Cassidy, LM}, title = {Ancient DNA traces family lines and political shifts in the Avar empire.}, journal = {Nature}, volume = {629}, number = {8011}, pages = {287-288}, pmid = {38658715}, issn = {1476-4687}, mesh = {*DNA, Ancient/analysis ; Humans ; *Politics ; History, Ancient ; Female ; }, } @article {pmid38642939, year = {2024}, author = {Zhu, S and Chen, Z and Hu, S and Wang, W and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Fu, Q}, title = {Corrigendum to "Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis)" [Journal of Genetics and Genomics (2022) 49, 1076-1079].}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {4}, pages = {466}, doi = {10.1016/j.jgg.2024.03.002}, pmid = {38642939}, issn = {1673-8527}, } @article {pmid38640342, year = {2024}, author = {Lin, Q and Zhang, K and Giguet-Covex, C and Arnaud, F and McGowan, S and Gielly, L and Capo, E and Huang, S and Ficetola, GF and Shen, J and Dearing, JA and Meadows, ME}, title = {Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {17}, pages = {e2321303121}, pmid = {38640342}, issn = {1091-6490}, support = {2022YFF0801101//MOST | National Key Research and Development Program of China (NKPs)/ ; 42230507//MOST | National Natural Science Foundation of China (NSFC)/ ; 42361144717//MOST | National Natural Science Foundation of China (NSFC)/ ; 42111530229//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20201099//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {*Ecosystem ; *Rivers ; Eutrophication ; Conservation of Natural Resources/methods ; }, abstract = {Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.}, } @article {pmid38636619, year = {2024}, author = {Sun, Z and Pan, L and Tian, A and Chen, P}, title = {Critically-ill COVID-19 susceptibility gene CCR3 shows natural selection in sub-Saharan Africans.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {121}, number = {}, pages = {105594}, doi = {10.1016/j.meegid.2024.105594}, pmid = {38636619}, issn = {1567-7257}, mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; *Selection, Genetic ; *Polymorphism, Single Nucleotide ; *Receptors, CCR3/genetics ; *Genetic Predisposition to Disease ; Africa South of the Sahara/epidemiology ; *Critical Illness ; *SARS-CoV-2/genetics ; Gene Frequency ; Haplotypes ; Black People/genetics ; Mendelian Randomization Analysis ; Sub-Saharan African People ; }, abstract = {The prevalence of COVID-19 critical illness varies across ethnicities, with recent studies suggesting that genetic factors may contribute to this variation. The aim of this study was to investigate natural selection signals of genes associated with critically-ill COVID-19 in sub-Saharan Africans. Severe COVID-19 SNPs were obtained from the HGI website. Selection signals were assessed in 661 sub-Sahara Africans from 1000 Genomes Project using integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and fixation index (Fst). Allele frequency trajectory analysis of ancient DNA samples were used to validate the existing of selection in sub-Sahara Africans. We also used Mendelian randomization to decipher the correlation between natural selection and critically-ill COVID-19. We identified that CCR3 exhibited significant natural selection signals in sub-Sahara Africans. Within the CCR3 gene, rs17217831-A showed both high iHS (Standardized iHS = 2) and high XP-EHH (Standardized XP-EHH = 2.5) in sub-Sahara Africans. Allele frequency trajectory of CCR3 rs17217831-A revealed natural selection occurring in the recent 1,500 years. Natural selection resulted in increased CCR3 expression in sub-Sahara Africans. Mendelian Randomization provided evidence that increased blood CCR3 expression and eosinophil counts lowered the risk of critically ill COVID-19. Our findings suggest that sub-Saharan Africans are resistant to critically ill COVID-19 due to natural selection and identify CCR3 as a potential novel therapeutic target.}, } @article {pmid38626302, year = {2024}, author = {Ghimire, P and Palacios, C and Trimble, J and Lamichhaney, S}, title = {Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, doi = {10.1093/g3journal/jkae081}, pmid = {38626302}, issn = {2160-1836}, support = {//Kent State University/ ; }, mesh = {*Museums ; Animals ; *Genomics/methods ; *Phylogeny ; *Birds/genetics/classification ; Biological Evolution ; Genome ; Evolution, Molecular ; Genetic Variation ; }, abstract = {The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.}, } @article {pmid38623594, year = {2024}, author = {Meijer, H}, title = {Janus faced: The co-evolution of war and peace in the human species.}, journal = {Evolutionary anthropology}, volume = {33}, number = {3}, pages = {e22027}, doi = {10.1002/evan.22027}, pmid = {38623594}, issn = {1520-6505}, mesh = {Humans ; Animals ; *Warfare ; Cultural Evolution ; Biological Evolution ; Social Behavior ; Cooperative Behavior ; Hominidae/physiology ; Violence ; }, abstract = {The human species presents a paradox. No other species possesses the propensity to carry out coalitionary lethal attacks on adult conspecifics coupled with the inclination to establish peaceful relations with genetically unrelated groups. What explains this seemingly contradictory feature? Existing perspectives, the "deep roots" and "shallow roots" of war theses, fail to capture the plasticity of human intergroup behaviors, spanning from peaceful cooperation to warfare. By contrast, this article argues that peace and war have both deep roots, and they co-evolved through an incremental process over several million years. On the one hand, humans inherited the propensity for coalitionary lethal violence from their chimpanzee-like ancestor. Specifically, having first inherited the skills to engage in cooperative hunting, they gradually repurposed such capacity to execute coalitionary killings of adult conspecifics and subsequently enhanced it through tech`nological innovations like the use of weapons. On the other hand, they underwent a process of cumulative cultural evolution and, subsequently, of self-domestication which led to heightened cooperative communication and increased prosocial behavior within and between groups. The combination of these two biocultural evolutionary processes-coupled with feedback loop effects between self-domestication and Pleistocene environmental variability-considerably broadened the human intergroup behavioral repertoire, thereby producing the distinctive combination of conflictual and peaceful intergroup relations that characterizes our species. To substantiate this argument, the article synthesizes and integrates the findings from a variety of disciplines, leveraging evidence from evolutionary anthropology, primatology, archeology, paleo-genetics, and paleo-climatology.}, } @article {pmid38617445, year = {2024}, author = {Zhang, J and Li, X and Li, L and Chen, A and Zhang, S}, title = {Y-STR analysis of highly degraded DNA from skeletal remains over 70 years old.}, journal = {Forensic sciences research}, volume = {9}, number = {2}, pages = {owae020}, pmid = {38617445}, issn = {2471-1411}, abstract = {The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery. Considering that information about distant relatives is more relevant for long-term missing persons and alleged family members are male, Y-STR loci analysis is considered the most appropriate and informative approach for determining paternal lineage relationship. In this study, Y-STR genotypes obtained from these alleged relatives were identical to each other and to the alleles of missing persons' consensus profiles at more than 22 loci examined, whilst not being found in Y-STR population database from Y-Chromosome STR Haplotype Reference Database. Therefore, Missing Person No.7 and Missing Person No.18 have a patrilineal relationship with reference samples from Family1 and Family2, respectively. In addition, the fact that Y-STR haplotypes obtained from skeletal remains of missing persons and reference samples are not found in the Han Chinese people from East Asian demonstrates its rarity and further supports a paternal lineage relationship amongst them.}, } @article {pmid38614080, year = {2024}, author = {Hempel, E and Faith, JT and Preick, M and de Jager, D and Barish, S and Hartmann, S and Grau, JH and Moodley, Y and Gedman, G and Pirovich, KM and Bibi, F and Kalthoff, DC and Bocklandt, S and Lamm, B and Dalén, L and Westbury, MV and Hofreiter, M}, title = {Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.}, journal = {Current biology : CB}, volume = {34}, number = {9}, pages = {2020-2029.e6}, doi = {10.1016/j.cub.2024.03.051}, pmid = {38614080}, issn = {1879-0445}, mesh = {*Extinction, Biological ; Animals ; *Antelopes/genetics/physiology ; *Population Density ; Genetic Variation ; Gene Flow ; Adaptation, Physiological/genetics ; Ecosystem ; Genome ; }, abstract = {Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.[1][,][2][,][3][,][4][,][5][,][6] Moreover, small population size may promote gene flow with congeners and outbreeding depression.[7][,][8][,][9][,][10][,][11][,][12][,][13] Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,[14][,][15] populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.[16][,][17][,][18] However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.}, } @article {pmid38612593, year = {2024}, author = {Ferreira, RC and Rodrigues, CR and Broach, JR and Briones, MRS}, title = {Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612593}, issn = {1422-0067}, support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; *Genome, Mitochondrial ; Mutation ; *Alzheimer Disease ; Nucleotides ; }, abstract = {The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.}, } @article {pmid38601034, year = {2024}, author = {Abbona, CC and Lebrasseur, O and Prevosti, FJ and Peralta, E and González Venanzi, L and Frantz, L and Larson, G and Gil, AF and Neme, GA}, title = {Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities.}, journal = {Royal Society open science}, volume = {11}, number = {4}, pages = {231835}, pmid = {38601034}, issn = {2054-5703}, abstract = {The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ[13]Ccol and δ[15]N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.}, } @article {pmid38589385, year = {2024}, author = {Mills, KK and Hildebrandt, KPB and Everson, KM and Horstmann, L and Misarti, N and Olson, LE}, title = {Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8257}, pmid = {38589385}, issn = {2045-2322}, support = {Walrus Adaptability and Long-term Responses; Using multi-proxy data to project Sustainability, Award #1263848//National Science Foundation/ ; OIA-1826801//National Science Foundation/ ; }, mesh = {Animals ; *Walruses/genetics ; DNA, Ancient ; *Caniformia ; Ecosystem ; Genetic Variation ; }, abstract = {Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.}, } @article {pmid38586998, year = {2024}, author = {Brack, J and Biran, M and Amitai, R}, title = {Plague and the Mongol conquest of Baghdad (1258)? A reevaluation of the sources.}, journal = {Medical history}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/mdh.2023.38}, pmid = {38586998}, issn = {2048-8343}, abstract = {This paper reexamines the sources used by N. Fancy and M.H. Green in "Plague and the Fall of Baghdad (1258)" (Medical History, 65/2 (2021), 157-177). Fancy and Green argued that the Arabic and Persian descriptions of the Mongol sieges in Iran and Iraq, and in particular, in the conquest of Baghdad in 1258, indicate that the besieged fortresses and cities were struck by Plague after the Mongol sieges were lifted. This, they suggested, is part of a recurrent pattern of the outbreak of Plague transmitted by the Mongol expansion across Eurasia. Fancy and Green concluded that the primary sources substantiate the theory driven by recent paleogenetic studies indicating that the Mongol conquests of the thirteenth century set the stage for the massive pandemic of the mid-fourteenth century. The link between the Plague outbreak and the Mongol siege of Baghdad relies on three near-contemporaneous historical accounts. However, our re-examination of the sources shows that the main text (in Persian) has been significantly misunderstood, and that the two other texts (in Syriac and Arabic) have been mis-contextualized, and thus not understood properly. They do not support the authors' claim regarding Plague epidemic in Baghdad in 1258, nor do other contemporary and later Arabic texts from Syria and Egypt adduced by them, which we re-examine in detail here. We conclude that there is no evidence for the appearance of Plague during or immediately after the Mongol conquests in the Middle East, certainly not for its transmission by the Mongols.}, } @article {pmid38583481, year = {2024}, author = {Alsos, IG and Boussange, V and Rijal, DP and Beaulieu, M and Brown, AG and Herzschuh, U and Svenning, JC and Pellissier, L}, title = {Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1902}, pages = {20230017}, pmid = {38583481}, issn = {1471-2970}, mesh = {Animals ; *Ecosystem ; *DNA, Ancient ; Climate Change ; Biodiversity ; Pollen ; Mammals ; }, abstract = {Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.}, } @article {pmid38567866, year = {2024}, author = {Miles, LS and Waterman, H and Ayoub, NA and Garb, JE and Haney, RA and Rosenberg, MS and Krabbenhoft, TJ and Verrelli, BC}, title = {Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.}, journal = {The Journal of heredity}, volume = {115}, number = {3}, pages = {241-252}, doi = {10.1093/jhered/esae018}, pmid = {38567866}, issn = {1465-7333}, support = {//Virginia Commonwealth University/ ; //University at Buffalo/ ; }, mesh = {Animals ; *Black Widow Spider/genetics ; *Gene Duplication ; *Evolution, Molecular ; *Genome ; Chromosomes/genetics ; Phylogeny ; Transcriptome ; Spiders/genetics ; Biological Evolution ; Molecular Sequence Annotation ; Selection, Genetic ; }, abstract = {Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.}, } @article {pmid38559769, year = {2024}, author = {Bellini, G and Schrieber, K and Kirleis, W and Erfmeier, A}, title = {Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1307364}, pmid = {38559769}, issn = {1664-462X}, abstract = {Pre-adaptation to anthropogenic disturbance is broadly considered key for plant invasion success. Nevertheless, empirical evidence remains scarce and fragmentary, given the multifaceted nature of anthropogenic disturbance itself and the complexity of other evolutionary forces shaping the (epi)-genomes of recent native and invasive plant populations. Here, we review and critically revisit the existing theory and empirical evidence in the field of evolutionary ecology and highlight novel integrative research avenues that work at the interface with archaeology to solve open questions. The approaches suggested so far focus on contemporary plant populations, although their genomes have rapidly changed since their initial introduction in response to numerous selective and stochastic forces. We elaborate that a role of pre-adaptation to anthropogenic disturbance in plant invasion success should thus additionally be validated based on the analyses of archaeobotanical remains. Such materials, in the light of detailed knowledge on past human societies could highlight fine-scale differences in the type and timing of past disturbances. We propose a combination of archaeobotanical, ancient DNA and morphometric analyses of plant macro- and microremains to assess past community composition, and species' functional traits to unravel the timing of adaptation processes, their drivers and their long-term consequences for invasive species. Although such methodologies have proven to be feasible for numerous crop plants, they have not been yet applied to wild invasive species, which opens a wide array of insights into their evolution.}, } @article {pmid38552628, year = {2024}, author = {Du, P and Zhu, K and Qiao, H and Zhang, J and Meng, H and Huang, Z and Yu, Y and Xie, S and Allen, E and Xiong, J and Zhang, B and Chang, X and Ren, X and Xu, Y and Zhou, Q and Han, S and Jin, L and Wei, P and Wang, CC and Wen, S}, title = {Ancient genome of the Chinese Emperor Wu of Northern Zhou.}, journal = {Current biology : CB}, volume = {34}, number = {7}, pages = {1587-1595.e5}, doi = {10.1016/j.cub.2024.02.059}, pmid = {38552628}, issn = {1879-0445}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Asian People/genetics ; Genome ; Polymorphism, Single Nucleotide ; China ; Genetics, Population ; }, abstract = {Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.[1][,][2] Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.}, } @article {pmid38552260, year = {2024}, author = {Rmoutilová, R and Brůžek, J and Gómez-Olivencia, A and Madelaine, S and Couture-Veschambre, C and Holliday, T and Maureille, B}, title = {Sex estimation of the adult Neandertal Regourdou 1 (Montignac, France): Implications for sexing human fossil remains.}, journal = {Journal of human evolution}, volume = {189}, number = {}, pages = {103470}, doi = {10.1016/j.jhevol.2023.103470}, pmid = {38552260}, issn = {1095-8606}, mesh = {Animals ; Humans ; Male ; *Neanderthals/anatomy & histology ; Fossils ; Genomics ; Paleontology ; *Hominidae ; France ; }, abstract = {Sex is a biological trait fundamental to the study of hominin fossils. Among the many questions that can be addressed are those related to taxonomy, biological variability, sexual dimorphism, paleoobstetrics, funerary selection, and paleodemography. While new methodologies such as paleogenomics or paleoproteomics can be used to determine sex, they have not been systematically applied to Pleistocene human remains due to their destructive nature. Therefore, we estimated sex from the coxal bone of the newly discovered pelvic remains of the Regourdou 1 Neandertal (Southwest France, MIS 5) based on morphological and metric data employing two methods that have been recently revised and shown to be reliable in multiple studies. Both methods calculate posterior probabilities of the estimate. The right coxal bone of Regourdou 1 was partially reconstructed providing additional traits for sex estimation. These methods were cross validated on 14 sufficiently preserved coxal bones of specimens from the Neandertal lineage. Our results show that the Regourdou 1 individual, whose postcranial skeleton is not robust, is a male, and that previous sex attributions of comparative Neandertal specimens are largely in agreement with those obtained here. Our results encourage additional morphological research of fossil hominins in order to develop a set of methods that are applicable, reliable, and reproducible.}, } @article {pmid38552017, year = {2024}, author = {Boilard, A and Walker, SJ and Lødøen, TK and Henriksen, M and Takken Beijersbergen, LM and Star, B and Robu, M and Tøssebro, C and Albrektsen, CM and Soleng, Y and Aksnes, S and Jørgensen, R and Hufthammer, AK and van Kolfschoten, T and Lauritzen, SE and Boessenkool, S}, title = {Ancient DNA and osteological analyses of a unique paleo-archive reveal Early Holocene faunal expansion into the Scandinavian Arctic.}, journal = {Science advances}, volume = {10}, number = {13}, pages = {eadk3032}, pmid = {38552017}, issn = {2375-2548}, mesh = {Arctic Regions ; Climate ; *DNA, Ancient ; *Ecosystem ; Norway ; }, abstract = {Paleo-archives are essential for our understanding of species responses to climate warming, yet such archives are extremely rare in the Arctic. Here, we combine morphological analyses and bulk-bone metabarcoding to investigate a unique chronology of bone deposits sealed in the high-latitude Storsteinhola cave system (68°50' N 16°22' E) in Norway. This deposit dates to a period of climate warming from the end of the Late Glacial [~13 thousand calibrated years before the present (ka cal B.P.)] to the Holocene thermal maximum (~5.6 ka cal B.P.). Paleogenetic analyses allow us to exploit the 1000s of morphologically unidentifiable bone fragments resulting in a high-resolution sequence with 40 different taxa, including species not previously found here. Our record reveals borealization in both the marine and terrestrial environments above the Arctic Circle as a naturally recurring phenomenon in past periods of warming, providing fundamental insights into the ecosystem-wide responses that are ongoing today.}, } @article {pmid38533900, year = {2024}, author = {Jackson, I and Woodman, P and Dowd, M and Fibiger, L and Cassidy, LM}, title = {Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38533900}, issn = {1537-1719}, support = {IRCLA/2022/126//Wellcome Trust Institutional Strategic Support Fund/ ; 18/CRT/6214//Science Foundation Ireland Centre for Research Training in Genomics Data Science/ ; }, mesh = {Humans ; Phylogeny ; *Streptococcus mutans/genetics ; Genomics ; Metagenome ; *Microbiota ; }, abstract = {Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.}, } @article {pmid38530148, year = {2024}, author = {Yaka, R and Maja Krzewińska, and Lagerholm, VK and Linderholm, A and Özer, F and Somel, M and Götherström, A}, title = {Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.}, journal = {BioTechniques}, volume = {76}, number = {5}, pages = {216-223}, doi = {10.2144/btn-2023-0107}, pmid = {38530148}, issn = {1940-9818}, support = {STF 7909//EMBO (short-term fellowship)/ ; 772390//ERC (consolidator grant)/ ; 117Z229//TUBITAK of Turkey/ ; NAISS 2023/22-504, NAISS 2023/23-262//Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, mesh = {*DNA, Ancient/analysis/isolation & purification ; Humans ; *Genome, Human/genetics ; Gene Library ; Sequence Analysis, DNA/methods ; Silicon Dioxide/chemistry ; }, abstract = {Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.}, } @article {pmid38526010, year = {2024}, author = {Gill, H and Lee, J and Jeong, C}, title = {Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38526010}, issn = {1759-6653}, support = {RS-2023-00212640//National Research Foundation of Korea/ ; }, mesh = {Humans ; Siberia ; *Genome, Human ; *Genetics, Population ; *North Asian People ; }, abstract = {Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.}, } @article {pmid38517967, year = {2024}, author = {Pryor, AJE and Ameen, C and Liddiard, R and Baker, G and Kanne, KS and Milton, JA and Standish, CD and Hambach, B and Orlando, L and Chauvey, L and Schiavinato, S and Calvière-Tonasso, L and Tressières, G and Wagner, S and Southon, J and Shapiro, B and Pipe, A and Creighton, OH and Outram, AK}, title = {Isotopic biographies reveal horse rearing and trading networks in medieval London.}, journal = {Science advances}, volume = {10}, number = {12}, pages = {eadj5782}, pmid = {38517967}, issn = {2375-2548}, mesh = {Humans ; Middle Aged ; Male ; Female ; Horses ; Animals ; London ; *Commerce ; *Bone and Bones/chemistry ; Oxygen Isotopes/analysis ; Strontium Isotopes/analysis ; Internationality ; }, abstract = {This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites.}, } @article {pmid38507661, year = {2024}, author = {Zhang, M and Song, Y and Wang, C and Sun, G and Zhuang, L and Guo, M and Ren, L and Wangdue, S and Dong, G and Dai, Q and Cao, P and Yang, R and Liu, F and Feng, X and Bennett, EA and Zhang, X and Chen, X and Wang, F and Luan, F and Dong, W and Lu, G and Hao, D and Hou, H and Wang, H and Qiao, H and Wang, Z and Hu, X and He, W and Xi, L and Wang, W and Shao, J and Sun, Z and Yue, L and Ding, Y and Tashi, N and Tsho, Y and Tong, Y and Yang, Y and Zhu, S and Miao, B and Wang, W and Zhang, L and Hu, S and Ni, X and Fu, Q}, title = {Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38507661}, issn = {1537-1719}, support = {41925009//National Natural Science Foundation of China/ ; 2022YFE0203800//National Key R&D Program of China/ ; 2024RS-CXTD-74//Science and Technology Innovation Team of Shaanxi Province/ ; XDB26000000//Chinese Academy of Sciences/ ; //Ministry of Finance of the People's/ ; YSBR-019//Republic of China/ ; //new Cornerstone Science Foundation/ ; }, mesh = {Animals ; Dogs ; Animals, Domestic/genetics ; Asia, Eastern ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Mammals/genetics ; Phylogeny ; }, abstract = {Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.}, } @article {pmid38486065, year = {2024}, author = {Garrido Marques, A and Rubinacci, S and Malaspinas, AS and Delaneau, O and Sousa da Mota, B}, title = {Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6227}, pmid = {38486065}, issn = {2045-2322}, support = {679330/ERC_/European Research Council/International ; 679330/ERC_/European Research Council/International ; 679330/ERC_/European Research Council/International ; }, mesh = {*DNA, Ancient ; Genotype ; *Genome ; Genome-Wide Association Study/methods ; Polymorphism, Single Nucleotide ; }, abstract = {Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.}, } @article {pmid38466119, year = {2024}, author = {Poyraz, L and Colbran, LL and Mathieson, I}, title = {Predicting Functional Consequences of Recent Natural Selection in Britain.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38466119}, issn = {1537-1719}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; R35GM133708/GM/NIGMS NIH HHS/United States ; grant T32HG009495/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; United Kingdom ; *Selection, Genetic ; Genome ; Genotype ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; }, abstract = {Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.}, } @article {pmid38462159, year = {2024}, author = {Ahlawat, B and Kumar, L and Ambekar, A and Singh Sehrawat, J and Rawat, YS and Rai, N}, title = {Ancient mitogenomes suggest complex maternal history of one of the oldest settlements of western India.}, journal = {Mitochondrion}, volume = {76}, number = {}, pages = {101871}, doi = {10.1016/j.mito.2024.101871}, pmid = {38462159}, issn = {1872-8278}, mesh = {Humans ; India ; *Genome, Mitochondrial ; DNA, Ancient/analysis ; History, Medieval ; Human Migration ; Archaeology ; Female ; DNA, Mitochondrial/genetics ; Haplotypes ; History, Ancient ; }, abstract = {The ancient township of Vadnagar tells a story of a long chain of cultural diversity and exchange. Vadnagar has been continuously habituated and shows a presence of rich cultural amalgamation and continuous momentary sequences between the 2th century BCE and present-day. Seven cultural periods developed a complex and enriched settlement at Vadnagar in spatio-temporality. Although archaeological studies done on this oldest settlement suggested a rich cultural heritage, the genetic studies to pinpoint the genetic ancestry was lacking till date. In our current study we have for the first time reconstructed the complete mitogenomes of medieval individuals of the Vadnagar archaeological site in Gujarat. The study aimed to investigate the cosmopolitan nature of the present population as well as the migratory pattern and the inflow of different groups through trade, cultural and religious practices. Our analysis suggests heterogeneous nature of the medieval population of Vadnagar with presence of deeply rooted local ancestral components as well as central Asian genetic ancestry. This Central Asian component associated with mitochondrial haplotype U2e was not shared with any individual from India, but rather with individuals from the Bronze Age of Tajikistan and with an earlier age of coalescence. In summary, we propose that the medieval site of Vadnagar in western India was rich in cultural and genetic aspects, with both local and western Eurasian components.}, } @article {pmid38458749, year = {2024}, author = {Geier, A and Trost, J and Wang, K and Schmid, C and Krawczyk, M and Schiffels, S}, title = {PNPLA3 fatty liver allele was fixed in Neanderthals and segregates neutrally in humans.}, journal = {Gut}, volume = {73}, number = {6}, pages = {1008-1014}, doi = {10.1136/gutjnl-2023-331594}, pmid = {38458749}, issn = {1468-3288}, support = {851511/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Acyltransferases/genetics ; *Alleles ; DNA, Ancient/analysis ; *Fatty Liver/genetics ; Gene Frequency ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; *Neanderthals/genetics ; *Phospholipases A2, Calcium-Independent/genetics ; }, abstract = {OBJECTIVE: Fat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identified PNPLA3 p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date.

DESIGN: Here we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls for PNPLA3 p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed.

RESULTS: We find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixed PNPLA3 risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15 000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10 000 years.

CONCLUSION: Archaic human individuals exclusively carried a fixed PNPLA3 allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case of PNPLA3 p.I148M.}, } @article {pmid38453993, year = {2024}, author = {Bergfeldt, N and Kırdök, E and Oskolkov, N and Mirabello, C and Unneberg, P and Malmström, H and Fraser, M and Sanchez-Quinto, F and Jorgensen, R and Skar, B and Lidén, K and Jakobsson, M and Storå, J and Götherström, A}, title = {Identification of microbial pathogens in Neolithic Scandinavian humans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5630}, pmid = {38453993}, issn = {2045-2322}, support = {2017-02503//Vetenskapsrådet/ ; 2019-00849//Vetenskapsrådet/ ; P21-0266//Riksbankens Jubileumsfond/ ; P19.0740:1//Riksbankens Jubileumsfond/ ; }, mesh = {Humans ; Agriculture ; *DNA, Mitochondrial/genetics ; Europe ; History, Ancient ; *Yersinia/classification/isolation & purification ; *Microbiota ; }, abstract = {With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.}, } @article {pmid38452965, year = {2024}, author = {Galaktionov, KV and Gonchar, A and Postanogova, D and Miroliubov, A and Bodrov, SY}, title = {Parvatrema spp. (Digenea, Gymnophallidae) with parthenogenetic metacercariae: diversity, distribution and host specificity in the palaearctic.}, journal = {International journal for parasitology}, volume = {54}, number = {7}, pages = {333-355}, doi = {10.1016/j.ijpara.2024.02.002}, pmid = {38452965}, issn = {1879-0135}, mesh = {Animals ; *Trematoda/genetics/physiology/classification/growth & development ; *Host Specificity ; *Metacercariae/physiology/genetics/growth & development ; *Trematode Infections/parasitology/veterinary/transmission ; Phylogeny ; Parthenogenesis ; Life Cycle Stages ; Birds/parasitology ; Biodiversity ; Bivalvia/parasitology ; }, abstract = {There are several species of gymnophallid digeneans in the genus Parvatrema that are unique in developing metacercariae that reproduce by parthenogenesis in the second intermediate host. Transmission of these digeneans takes place in coastal ecosystems of the North Pacific and North Atlantic seas. The first intermediate hosts are bivalves, the second ones are gastropods, and the definitive hosts are migratory birds. We integrated data accumulated over 25 years of research and differentiated a complex of five closely related species. They differ in the molluscan second intermediate hosts, distribution ranges, and life cycles patterns. The type I life cycle includes two generations of parthenogenetic metacercariae, followed by development of metacercariae which are invasive for the definitive host. In the type II life cycle, the number of generations of parthenogenetic metacercariae is unlimited, and they can also produce cercariae. These cercariae emerge into the environment and can infect new individuals of the second intermediate host. We conclude that the type I life cycle is a derived option that has evolved as a better fit to transmission in the unstable conditions in the intertidal zone. Another evolutionary trend in Parvatrema is transition from inhabiting the extrapallial space of the gastropod second intermediate host to endoparasitism in its mantle and internal organs. rDNA sequence analysis highlighted that Parvatrema spp. with parthenogenetic metacercariae form a monophyletic clade and suggested the Pacific origin of the group, with two transfers to the North Atlantic and colonisation of new second intermediate host species. Apparently the group formed in the late Pliocene-Pleistocene and diversified as a result of recurrent isolation in inshore refugia during glacial periods. We argue that parthenogenetic metacercariae in Parvatrema may serve as a model for early digenean evolution, demonstrating the first steps of adopting the molluscan first intermediate host and becoming tissue parasites.}, } @article {pmid38447923, year = {2024}, author = {Mokrousov, I}, title = {Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration.}, journal = {Molecular phylogenetics and evolution}, volume = {195}, number = {}, pages = {108045}, doi = {10.1016/j.ympev.2024.108045}, pmid = {38447923}, issn = {1095-9513}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Phylogeny ; *Tuberculosis/microbiology ; Human Migration ; Genotype ; }, abstract = {The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.}, } @article {pmid38446809, year = {2024}, author = {MacRoberts, RA and Liberato, M and Roca-Rada, X and Valente, MJ and Relvado, C and Matos Fernandes, T and Barrocas Dias, C and Llamas, B and Vasconcelos Vilar, H and Schöne, BR and Ribeiro, S and Santos, JF and Teixeira, JC and Maurer, AF}, title = {Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD).}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299958}, pmid = {38446809}, issn = {1932-6203}, mesh = {Humans ; Adult ; Female ; Male ; Portugal ; *Islam ; *Strontium Isotopes ; Carbon ; }, abstract = {In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel. The results of this study revealed a dietary pattern of predominantly C3-plant and domestic C3-fed herbivore consumption during adulthood (δ13Ccol and δ15N, respectively) but a higher proportion of C4-plant input during childhood (δ13Cen) for some individuals-interpreted as possible childhood consumption of millet porridge, a common practice in North Africa-in those with unorthodox burial types (Groups 1 and 2) that was not practiced in the individuals with canonical burials (Group 3). In this first mobility study of a medieval Muslim population in Portugal, δ18ODW values revealed greater heterogeneity in Groups 1 and 2, consistent with diverse origins, some in more humid regions than Santarém when compared to regional precipitation δ18O data, contrasting the more homogenous Group 3, consistent with the local precipitation δ18O range. Ancient DNA analysis conducted on three individuals revealed maternal (mtDNA) and paternal (Y-chromosome) lineages compatible with a North African origin for (at least) some of the individuals. Additionally, mobility of females in this population was higher than males, potentially resulting from a patrilocal social system, practiced in Berber and Arab communities. These results serve to offer a more detailed insight into the ancestry and cultural practices of early Muslim populations in Iberia.}, } @article {pmid38440408, year = {2024}, author = {Eisenhofer, R and Wright, S and Weyrich, L}, title = {Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16770}, pmid = {38440408}, issn = {2167-8359}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Genes, rRNA ; Dental Calculus ; *Microbiota ; DNA, Ancient ; }, abstract = {The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.}, } @article {pmid38428387, year = {2024}, author = {Bennett, EA and Fu, Q}, title = {Ancient genomes and the evolutionary path of modern humans.}, journal = {Cell}, volume = {187}, number = {5}, pages = {1042-1046}, doi = {10.1016/j.cell.2024.01.047}, pmid = {38428387}, issn = {1097-4172}, mesh = {Animals ; Humans ; *Biological Evolution ; *DNA, Ancient ; Genome, Human ; *Hominidae/genetics ; }, abstract = {Growing evidence from archaic and early modern human genomes brings new insights to the emergence of modern humans. We recount recent information collected from ancient DNA studies that inform us about the evolutionary pathway to modern humanity. These findings point to both individual- and population-level advantages underlying modern human expansion.}, } @article {pmid38423916, year = {2024}, author = {Meiri, M and Bar-Oz, G}, title = {Unraveling the diversity and cultural heritage of fruit crops through paleogenomics.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {5}, pages = {398-409}, pmid = {38423916}, issn = {0168-9525}, mesh = {*Crops, Agricultural/genetics ; *Fruit/genetics ; Genomics/methods ; Domestication ; Plant Breeding/methods ; Genetic Variation ; Genome, Plant/genetics ; Vitis/genetics ; Solanum lycopersicum/genetics ; Phoeniceae/genetics ; }, abstract = {Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.}, } @article {pmid38418841, year = {2024}, author = {Huang, J and Chen, J and Shi, M and Zheng, J and Chen, M and Wu, L and Zhu, H and Zheng, Y and Wu, Q and Wu, F}, title = {Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4867}, pmid = {38418841}, issn = {2045-2322}, support = {2018KJCX023//Forestry Science and Technology Innovation Project of Guangdong province/ ; 2021B1212040015//Guangdong Provincial Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products/ ; QD202122//school-level projects of Hanshan Normal University/ ; QD202123//school-level projects of Hanshan Normal University/ ; 060302052305//the program for scientific research start-up funds of Guangdong Ocean University/ ; }, mesh = {*Genome, Plant ; China ; Repetitive Sequences, Nucleic Acid ; *Malpighiales ; Evolution, Molecular ; Phylogeny ; }, abstract = {Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat-retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.}, } @article {pmid38417515, year = {2024}, author = {Thomson-Laing, G and Howarth, JD and Atalah, J and Vandergoes, MJ and Li, X and Pearman, JK and Fitzsimons, S and Moy, C and Moody, A and Shepherd, C and McKay, N and Wood, SA}, title = {Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake.}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171266}, doi = {10.1016/j.scitotenv.2024.171266}, pmid = {38417515}, issn = {1879-1026}, mesh = {Animals ; Humans ; *DNA, Ancient ; *Lakes ; Biodiversity ; DNA ; Fishes ; Ruminants ; Ecosystem ; }, abstract = {Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes.}, } @article {pmid38417441, year = {2024}, author = {Martiniano, R and Haber, M and Almarri, MA and Mattiangeli, V and Kuijpers, MCM and Chamel, B and Breslin, EM and Littleton, J and Almahari, S and Aloraifi, F and Bradley, DG and Lombard, P and Durbin, R}, title = {Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.}, journal = {Cell genomics}, volume = {4}, number = {3}, pages = {100507}, pmid = {38417441}, issn = {2666-979X}, support = {205072/WT_/Wellcome Trust/United Kingdom ; 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 207492/WT_/Wellcome Trust/United Kingdom ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Arabs/genetics ; Bahrain ; *DNA, Ancient ; *Genetics, Population ; *Genome, Human ; }, abstract = {The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.}, } @article {pmid38415845, year = {2024}, author = {Emery, MV and Bolhofner, K and Spake, L and Ghafoor, S and Versoza, CJ and Rawls, EM and Winingear, S and Buikstra, JE and Loreille, O and Fulginiti, LC and Stone, AC}, title = {Targeted enrichment of whole-genome SNPs from highly burned skeletal remains.}, journal = {Journal of forensic sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/1556-4029.15482}, pmid = {38415845}, issn = {1556-4029}, support = {2016-DN-BX-0158//National Institute of Justice/ ; }, abstract = {Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.}, } @article {pmid38412309, year = {2024}, author = {McComish, BJ and Charleston, MA and Parks, M and Baroni, C and Salvatore, MC and Li, R and Zhang, G and Millar, CD and Holland, BR and Lambert, DM}, title = {Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time.}, journal = {Genome biology and evolution}, volume = {16}, number = {3}, pages = {}, pmid = {38412309}, issn = {1759-6653}, support = {RGP0036/2011//Human Frontier Science Program/ ; 2157200//Australian Research Council Linkage/ ; //Australia-India Strategic Research Fund/ ; //Griffith University/ ; //University of Tasmania/ ; PNRA-4.2/2004//Italian National Program on Antarctic Research/ ; //Antarctica New Zealand/ ; }, mesh = {Humans ; *Genome ; *Genetics, Population ; Mutation ; Microsatellite Repeats ; Polymorphism, Genetic ; }, abstract = {Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.}, } @article {pmid38407438, year = {2024}, author = {Shao, W and Wang, J and Zhang, Y and Zhang, C and Chen, J and Chen, Y and Fei, Z and Ma, Z and Sun, X and Jiao, C}, title = {The jet-like chromatin structure defines active secondary metabolism in fungi.}, journal = {Nucleic acids research}, volume = {52}, number = {9}, pages = {4906-4921}, pmid = {38407438}, issn = {1362-4962}, support = {2022YFD1400100//National Key Research and Development Program of China/ ; U21A20219//National Natural Science Foundation of China/ ; CARS-03-29//Earmarked Fund for China Agriculture Research System/ ; //National Excellent Young Scientists (overseas) Fund of NSFC/ ; }, mesh = {Acetylation ; *Chromatin/metabolism/genetics ; *Chromosomes, Fungal/genetics/metabolism ; Fungal Proteins/metabolism/genetics ; *Fusarium/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Histone Acetyltransferases/metabolism/genetics ; Histones/metabolism/genetics ; Multigene Family ; *Secondary Metabolism/genetics ; Transcription, Genetic ; }, abstract = {Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.}, } @article {pmid38378781, year = {2024}, author = {Rohrlach, AB and Rivollat, M and de-Miguel-Ibáñez, P and Moilanen, U and Liira, AM and Teixeira, JC and Roca-Rada, X and Armendáriz-Martija, J and Boyadzhiev, K and Boyadzhiev, Y and Llamas, B and Tiliakou, A and Mötsch, A and Tuke, J and Prevedorou, EA and Polychronakou-Sgouritsa, N and Buikstra, J and Onkamo, P and Stockhammer, PW and Heyne, HO and Lemke, JR and Risch, R and Schiffels, S and Krause, J and Haak, W and Prüfer, K}, title = {Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1294}, pmid = {38378781}, issn = {2041-1723}, support = {771234//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Down Syndrome/genetics ; Trisomy/genetics ; Trisomy 18 Syndrome/genetics ; *Chromosome Disorders/genetics ; DNA, Ancient ; Trisomy 13 Syndrome ; }, abstract = {Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice.}, } @article {pmid38365253, year = {2024}, author = {Buchwald, SZ and Herzschuh, U and Nürnberg, D and Harms, L and Stoof-Leichsenring, KR}, title = {Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365253}, issn = {1751-7370}, support = {03G0672A//German Ministry of Education and Research/ ; }, mesh = {Plankton/genetics ; DNA, Ancient ; Oceans and Seas ; Phytoplankton/genetics ; *Diatoms/genetics ; *Cyanobacteria/genetics ; Carbon ; Ecosystem ; }, abstract = {Current global warming results in rising sea-water temperatures, and the loss of sea ice in Arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon sequencing data from sedimentary ancient DNA of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial-interglacial cycles, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by picosized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic picosized chlorophytes and Triparmaceae. By contrast, the glacial period is characterized by microsized phototrophic protists, including sea ice-associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift toward the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community's potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea's function as an effective carbon sink.}, } @article {pmid38363870, year = {2024}, author = {Simon, A and Coop, G}, title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2312377121}, pmid = {38363870}, issn = {1091-6490}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; R35 GM136290/GF/NIH HHS/United States ; }, mesh = {Humans ; *Gene Flow ; *Selection, Genetic ; DNA, Ancient ; Gene Frequency ; Genetic Drift ; Genetics, Population ; }, abstract = {Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.}, } @article {pmid38362924, year = {2024}, author = {Taylor, GM and White-Iribhogbe, K and Cole, G and Ashby, D and Stewart, GR and Dawson-Hobbis, H}, title = {Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK.}, journal = {Journal of medical microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/jmm.0.001806}, pmid = {38362924}, issn = {1473-5644}, mesh = {Adult ; Child ; Humans ; Male ; Female ; Adolescent ; X-Ray Microtomography ; *Leprosy/microbiology ; Mycobacterium leprae/genetics ; DNA, Bacterial/genetics ; *Leprosy, Multibacillary ; United Kingdom ; }, abstract = {Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.}, } @article {pmid38354185, year = {2024}, author = {Laffranchi, Z and Zingale, S and Tecchiati, U and Amato, A and Coia, V and Paladin, A and Salzani, L and Thompson, SR and Bersani, M and Dori, I and Szidat, S and Lösch, S and Ryan-Despraz, J and Arenz, G and Zink, A and Milella, M}, title = {"Until death do us part". A multidisciplinary study on human- Animal co- burials from the Late Iron Age necropolis of Seminario Vescovile in Verona (Northern Italy, 3rd-1st c. BCE).}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0293434}, pmid = {38354185}, issn = {1932-6203}, mesh = {Humans ; Animals ; Horses ; Dogs ; *Body Remains ; *Burial/methods ; Italy ; Anthropology ; Culture ; Archaeology ; }, abstract = {Animal remains are a common find in prehistoric and protohistoric funerary contexts. While taphonomic and osteological data provide insights about the proximate (depositional) factors responsible for these findings, the ultimate cultural causes leading to this observed mortuary behavior are obscured by the opacity of the archaeological record and the lack of written sources. Here, we apply an interdisciplinary suite of analytical approaches (zooarchaeological, anthropological, archaeological, paleogenetic, and isotopic) to explore the funerary deposition of animal remains and the nature of joint human-animal burials at Seminario Vescovile (Verona, Northern Italy 3rd-1st c. BCE). This context, culturally attributed to the Cenomane culture, features 161 inhumations, of which only 16 included animal remains in the form of full skeletons, isolated skeletal parts, or food offerings. Of these, four are of particular interest as they contain either horses (Equus caballus) or dogs (Canis lupus familiaris)-animals that did not play a dietary role. Analyses show no demographic, dietary, funerary similarities, or genetic relatedness between individuals buried with animals. Isotopic data from two analyzed dogs suggest differing management strategies for these animals, possibly linked to economic and/or ritual factors. Overall, our results point to the unsuitability of simple, straightforward explanations for the observed funerary variability. At the same time, they connect the evidence from Seminario Vescovile with documented Transalpine cultural traditions possibly influenced by local and Roman customs.}, } @article {pmid38350445, year = {2024}, author = {Laine, J and Mak, SST and Martins, NFG and Chen, X and Gilbert, MTP and Jones, FC and Pedersen, MW and Romundset, A and Foote, AD}, title = {Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.}, journal = {Current biology : CB}, volume = {34}, number = {5}, pages = {1142-1147.e6}, doi = {10.1016/j.cub.2024.01.056}, pmid = {38350445}, issn = {1879-0445}, mesh = {Animals ; *Ecosystem ; Adaptation, Physiological/genetics ; *Smegmamorpha/genetics ; Retrospective Studies ; Lakes ; }, abstract = {Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms[1][,][2][,][3] and to thereby potentially provide an understanding of the evolutionary histories of past populations.[4][,][5] To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.[6][,][7] Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies[1][,][2][,][3] to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)[8] were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches[9][,][10][,][11] and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.}, } @article {pmid38348756, year = {2024}, author = {Vincenti, G and Molinaro, L and Sajjadi, SMS and Moradi, H and Pagani, L and Fabbri, PF}, title = {Female biased adult sex ratio in the Bronze Age cemetery of Shahr-i Sokhta (Iran) as an indicator of long distance trade and matrilocality.}, journal = {American journal of biological anthropology}, volume = {183}, number = {4}, pages = {e24911}, doi = {10.1002/ajpa.24911}, pmid = {38348756}, issn = {2692-7691}, support = {//Ministero degli Affari Esteri e della Cooperazione Internazionale/ ; //University of Salento/ ; }, mesh = {Adult ; Male ; Middle Aged ; Humans ; Female ; Iran ; *Cemeteries ; Sex Ratio ; Middle East ; Anthropology ; *Polygonaceae ; }, abstract = {OBJECTIVES: This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr-i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site.

METHODS: We computed the SR (pelvis-based sex determination) in a random unpublished adult sample from the cemetery of Shahr-i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi-chronological sample of sites, n = 47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n = 10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men.

RESULTS: Adult SR in a sample (n = 549) from Shahr-i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR = 72.09) and Indus Valley (SR = 67.54). On the contrary, in a larger Supra Regional multi-chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society.

CONCLUSIONS: Indicators suggest that Bronze Age Shahr-ì Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery.}, } @article {pmid38341426, year = {2024}, author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D}, title = {The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {182}, pmid = {38341426}, issn = {2052-4463}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; *Genome, Human ; *Genomics ; Paleontology ; }, abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.}, } @article {pmid38308451, year = {2024}, author = {Navarro-Romero, MT and Muñoz, ML and Krause-Kyora, B and Cervini-Silva, J and Alcalá-Castañeda, E and David, RE}, title = {Bioanthropological analysis of human remains from the archaic and classic period discovered in Puyil cave, Mexico.}, journal = {American journal of biological anthropology}, volume = {184}, number = {2}, pages = {e24903}, doi = {10.1002/ajpa.24903}, pmid = {38308451}, issn = {2692-7691}, support = {2015-Marzo 2016-290936//Consejo Nacional de Ciencia y Tecnología/ ; 2014_Primer Periodo-380118//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Humans ; Mexico ; *Caves ; *DNA, Mitochondrial/genetics ; *Body Remains/chemistry/anatomy & histology ; Radiometric Dating ; Male ; History, Ancient ; Female ; Anthropology, Physical ; Archaeology ; }, abstract = {OBJECTIVES: Determine the geographic place of origin and maternal lineage of prehistoric human skeletal remains discovered in Puyil Cave, Tabasco State, Mexico, located in a region currently populated by Olmec, Zoque and Maya populations.

MATERIALS AND METHODS: All specimens were radiocarbon ([14]C) dated (beta analytic), had dental modifications classified, and had an analysis of 13 homologous reference points conducted to evaluate artificial cranial deformation (ACD). Following DNA purification, hypervariable region I (HVR-1) of the mitogenome was amplified and Sanger sequenced. Finally, Next Generation Sequencing (NGS) was performed for total DNA. Mitochondrial DNA (mtDNA) variants and haplogroups were determined using BioEdit 7.2 and IGV software and confirmed with MITOMASTER and WebHome softwares.

RESULTS: Radiocarbon dating ([14]C) demonstrated that the inhabitants of Puyil Cave lived during the Archaic and Classic Periods and displayed tabular oblique and tabular mimetic ACD. These pre-Hispanic remains exhibited five mtDNA lineages: A, A2, C1, C1c and D4. Network analysis revealed a close genetic affinity between pre-Hispanic Puyil Cave inhabitants and contemporary Maya subpopulations from Mexico and Guatemala, as well as individuals from Bolivia, Brazil, the Dominican Republic, and China.

CONCLUSIONS: Our results elucidate the dispersal of pre-Hispanic Olmec and Maya ancestors and suggest that ACD practices are closely related to Olmec and Maya practices. Additionally, we conclude that ACD has likely been practiced in the region since the Middle-Archaic Period.}, } @article {pmid38302698, year = {2024}, author = {Petrić Howe, N and Bundell, S}, title = {Ancient DNA solves the mystery of who made a set of stone tools.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-00290-7}, pmid = {38302698}, issn = {1476-4687}, } @article {pmid38288729, year = {2024}, author = {Antonio, ML and Weiß, CL and Gao, Z and Sawyer, S and Oberreiter, V and Moots, HM and Spence, JP and Cheronet, O and Zagorc, B and Praxmarer, E and Özdoğan, KT and Demetz, L and Gelabert, P and Fernandes, D and Lucci, M and Alihodžić, T and Amrani, S and Avetisyan, P and Baillif-Ducros, C and Bedić, Ž and Bertrand, A and Bilić, M and Bondioli, L and Borówka, P and Botte, E and Burmaz, J and Bužanić, D and Candilio, F and Cvetko, M and De Angelis, D and Drnić, I and Elschek, K and Fantar, M and Gaspari, A and Gasperetti, G and Genchi, F and Golubović, S and Hukeľová, Z and Jankauskas, R and Vučković, KJ and Jeremić, G and Kaić, I and Kazek, K and Khachatryan, H and Khudaverdyan, A and Kirchengast, S and Korać, M and Kozlowski, V and Krošláková, M and Kušan Špalj, D and La Pastina, F and Laguardia, M and Legrand, S and Leleković, T and Leskovar, T and Lorkiewicz, W and Los, D and Silva, AM and Masaryk, R and Matijević, V and Cherifi, YMS and Meyer, N and Mikić, I and Miladinović-Radmilović, N and Milošević Zakić, B and Nacouzi, L and Natuniewicz-Sekuła, M and Nava, A and Neugebauer-Maresch, C and Nováček, J and Osterholtz, A and Paige, J and Paraman, L and Pieri, D and Pieta, K and Pop-Lazić, S and Ruttkay, M and Sanader, M and Sołtysiak, A and Sperduti, A and Stankovic Pesterac, T and Teschler-Nicola, M and Teul, I and Tončinić, D and Trapp, J and Vulović, D and Waliszewski, T and Walter, D and Živanović, M and Filah, MEM and Čaušević-Bully, M and Šlaus, M and Borić, D and Novak, M and Coppa, A and Pinhasi, R and Pritchard, JK}, title = {Stable population structure in Europe since the Iron Age, despite high mobility.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {38288729}, issn = {2050-084X}, support = {R01 HG011432/HG/NHGRI NIH HHS/United States ; HG011432/NH/NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; *Genome, Human ; Europe ; France ; Genetics, Population ; Population Dynamics ; Human Migration ; }, abstract = {Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.}, } @article {pmid38287404, year = {2024}, author = {Lei, H and Li, J and Zhao, B and Kou, SH and Xiao, F and Chen, T and Wang, SM}, title = {Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {5}, pmid = {38287404}, issn = {1479-7364}, support = {2019YFE0198800//National Key Research-Development Program of China/ ; 2021R52020//Ten-Thousand Talents Plan of Zhejiang Province/ ; 085/2017/A2//Macau Science and Technology Development Fund/ ; 0077/2019/AMJ//Macau Science and Technology Development Fund/ ; 0032/2022/A1//Macau Science and Technology Development Fund/ ; SRG2017-00097-FHS//University of Macau/ ; MYRG2019-00018-FHS//University of Macau/ ; MYRG2020-00094-FHS//University of Macau/ ; FHSIG/SW/0007/2020P, MOE Frontiers Science Center for Precision Oncology pilot grant and a startup fund//Faculdade de Ciências da Saúde, Universidade de Macau/ ; }, mesh = {Humans ; *DNA Mismatch Repair/genetics ; Phylogeny ; *Neoplastic Syndromes, Hereditary ; Germ-Line Mutation/genetics ; Germ Cells ; *Brain Neoplasms ; *Colorectal Neoplasms ; }, abstract = {BACKGROUND: Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs.

METHODS: We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis.

RESULTS: Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns.

CONCLUSION: Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.}, } @article {pmid38284317, year = {2024}, author = {Śledziński, ŁJ and Zamerska, A and Jędrychowska-Dańska, K and Strózik, T and Wasiak, T and Płoszaj, T and Witas, P and Witas, HW and Borowiec, M and Agier, J}, title = {Suggested mechanism of CCR5Δ32, CCR2-64I and SDF 1-3'A allele frequency change in Polish and Lithuanian gene pools from the perspective of passing time.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {81}, number = {3}, pages = {261-280}, doi = {10.1127/anthranz/2024/1637}, pmid = {38284317}, issn = {0003-5548}, mesh = {Humans ; Lithuania ; *Receptors, CCR5/genetics ; *Receptors, CCR2/genetics ; Poland ; *Gene Frequency ; *Chemokine CXCL12/genetics ; Haplotypes ; DNA, Mitochondrial/genetics ; Polymorphism, Genetic ; }, abstract = {The study aimed to determine the frequency of the alleles associated with hereditary immune response in 16 historical populations and assess which evolutionary forces may have contributed to the observed frequency fluctuation. The analysed polymorphic sites are located in three genes - CCR5, CCR2 and SDF 1 (CXCL12). Protein products are involved in the innate immune response and are also involved in various types of infections, autoimmune diseases and tumours. The frequency of the alleles found in the DNA of the studied individuals was determined by the Sanger methodology and was compared with the data obtained for modern populations. To confirm the authenticity of the obtained results, mtDNA HVRI haplotypes of all the studied samples were obtained and compared with the genetic database of the laboratory personnel who came into contact with the studied material. Based on the variability of allele frequency, advanced biostatistical analysis was used to distinguish the effect of natural selection from genetic drift, i.e. the forces operating on the polymorphic sites studied. All procedures were performed according to the guidelines for working with ancient DNA to avoid contamination with modern DNA molecules. 681 samples from 39 archaeological sites in Poland and Lithuania dated to the 40[th] century BC and the 19[th] century were studied. The biostatistical analysis showed that the fluctuations in the frequency of CCR5Δ32 in the analysed time interval could be mainly the effect of genetic drift. Nevertheless, for CCR2-64I and SDF 1-3'A, the results confirm the suggestion of negative selection as the mechanism involved. Since all the polymorphic sites encode the elements of innate immune response that are indirectly associated with the process of an HPV infection and the development of cervical cancer, the human papillomavirus may be a good candidate for a selection coefficient affecting the frequency of CCR2-64I and SDF 1-3'A. However, for CCR5Δ32, selection was not detected despite its proven role in the molecular mechanism involved in the response to an HPV infection. The presented work seems to be the first in which the problem of the pattern of CCR5Δ32, CCR2-64I and SDF 1-3'A frequency fluctuations in a temporal perspective was discussed, proposing HPV as a factor influencing the occurrence of the CCR2 and SDF1 alleles.}, } @article {pmid38279681, year = {2024}, author = {Kellner, FL and Le Moullec, M and Ellegaard, MR and Rosvold, J and Peeters, B and Burnett, HA and Pedersen, ÅØ and Brealey, JC and Dussex, N and Bieker, VC and Hansen, BB and Martin, MD}, title = {A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17274}, doi = {10.1111/mec.17274}, pmid = {38279681}, issn = {1365-294X}, support = {14/137//Svalbard Environmental Protection Fund/ ; 15/105//Svalbard Environmental Protection Fund/ ; 223257//Norwegian Research Council/ ; 276080//Norwegian Research Council/ ; 325589//Norwegian Research Council/ ; 235652//Arctic Field Grant/ ; 246054//Arctic Field Grant/ ; 257173//Arctic Field Grant/ ; }, mesh = {Animals ; *Reindeer/genetics ; Animals, Wild ; Gene Frequency ; Genetic Drift ; Svalbard ; }, abstract = {Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.}, } @article {pmid38273870, year = {2024}, author = {Wurst, C and Maixner, F and Paladin, A and Mussauer, A and Valverde, G and Narula, J and Thompson, R and Zink, A}, title = {Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Remains.}, journal = {Annals of global health}, volume = {90}, number = {1}, pages = {6}, pmid = {38273870}, issn = {2214-9996}, mesh = {Humans ; *Cardiovascular Diseases ; Genome-Wide Association Study ; Body Remains ; *Atherosclerosis/genetics ; Genetic Predisposition to Disease ; Risk Factors ; Risk Assessment ; }, abstract = {BACKGROUND: Several computed tomographic studies have shown the presence of atherosclerosis in ancient human remains. However, while it is important to understand the development of atherosclerotic cardiovascular disease (ASCVD), genetic data concerning the prevalence of the disease-associated single nucleotide polymorphisms (SNPs) in our ancestors are scarce.

OBJECTIVE: For a better understanding of the role of genetics in the evolution of ASCVD, we applied an enrichment capture sequencing approach to mummified human remains from different geographic regions and time periods.

METHODS: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.

FINDINGS: Five out of 22 ancient individuals passed all filter steps for calculating a weighted polygenic risk score (PRS) based on 87 SNPs in 56 genes. PRSs were correlated to scores obtained from contemporary people from around the world and cover their complete range. The genetic results of the ancient individuals reflect their phenotypic results, given that the only two mummies showing calcified atherosclerotic arterial plaques on computed tomography scans are the ones exhibiting the highest calculated PRSs.

CONCLUSIONS: These data show that alleles associated with ASCVD have been widespread for at least 5,000 years. Despite some limitations due to the nature of aDNA, our approach has the potential to lead to a better understanding of the interaction between environmental and genetic influences on the development of ASCVD.}, } @article {pmid38267579, year = {2024}, author = {Majander, K and Pla-Díaz, M and du Plessis, L and Arora, N and Filippini, J and Pezo-Lanfranco, L and Eggers, S and González-Candelas, F and Schuenemann, VJ}, title = {Redefining the treponemal history through pre-Columbian genomes from Brazil.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {182-188}, pmid = {38267579}, issn = {1476-4687}, mesh = {Humans ; Brazil/epidemiology/ethnology ; Europe/epidemiology ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; History, 15th Century ; History, Ancient ; Syphilis/epidemiology/history/microbiology/transmission ; *Treponema pallidum/classification/genetics/isolation & purification ; *Treponemal Infections/epidemiology/history/microbiology/transmission ; }, abstract = {The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions[1,2]. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico[3-6]. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.}, } @article {pmid38266614, year = {2024}, author = {Delezene, LK and Scott, JE and Irish, JD and Villaseñor, A and Skinner, MM and Hawks, J and Berger, LR}, title = {Sex-biased sampling may influence Homo naledi tooth size variation.}, journal = {Journal of human evolution}, volume = {187}, number = {}, pages = {103490}, doi = {10.1016/j.jhevol.2023.103490}, pmid = {38266614}, issn = {1095-8606}, mesh = {Humans ; Animals ; *Hominidae ; Fossils ; *Tooth ; Genetic Drift ; Molar ; Tooth, Deciduous ; }, abstract = {A frequent source of debate in paleoanthropology concerns the taxonomic unity of fossil assemblages, with many hominin samples exhibiting elevated levels of variation that can be interpreted as indicating the presence of multiple species. By contrast, the large assemblage of hominin fossils from the Rising Star cave system, assigned to Homo naledi, exhibits a remarkably low degree of variation for most skeletal elements. Many factors can contribute to low sample variation, including genetic drift, strong natural selection, biased sex ratios, and sampling of closely related individuals. In this study, we tested for potential sex-biased sampling in the Rising Star dental sample. We compared coefficients of variation for the H. naledi teeth to those for eight extant hominoid samples. We used a resampling procedure that generated samples from the extant taxa that matched the sample size of the fossil sample for each possible Rising Star dental sex ratio. We found that variation at four H. naledi tooth positions-I2, M1, P[4], M1-is so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded. Additional evidence is needed to corroborate this inference, such as ancient DNA or enamel proteome data, and our study design does not address other potential factors that would account for low sample variation. Nevertheless, our results highlight the importance of considering the taphonomic history of a hominin assemblage and suggest that sex-biased sampling is a plausible explanation for the low level of phenotypic variation found in some aspects of the current H. naledi assemblage.}, } @article {pmid38261973, year = {2024}, author = {Barouch, A and Mathov, Y and Meshorer, E and Yakir, B and Carmel, L}, title = {Reconstructing DNA methylation maps of ancient populations.}, journal = {Nucleic acids research}, volume = {52}, number = {4}, pages = {1602-1612}, pmid = {38261973}, issn = {1362-4962}, support = {2436/22//Israel Science Foundation/ ; 61739//John Templeton Foundation/ ; 1001584586//Israel Ministry of Innovation, Science & Technology/ ; }, mesh = {Humans ; *DNA Methylation/genetics ; *DNA, Ancient ; Genome ; Genomics ; Sequence Analysis, DNA/methods ; Human Genetics ; }, abstract = {Studying premortem DNA methylation from ancient DNA (aDNA) provides a proxy for ancient gene activity patterns, and hence valuable information on evolutionary changes in gene regulation. Due to statistical limitations, current methods to reconstruct aDNA methylation maps are constrained to high-coverage shotgun samples, which comprise a small minority of available ancient samples. Most samples are sequenced using in-situ hybridization capture sequencing which targets a predefined set of genomic positions. Here, we develop methods to reconstruct aDNA methylation maps of samples that were not sequenced using high-coverage shotgun sequencing, by way of pooling together individuals to obtain a DNA methylation map that is characteristic of a population. We show that the resulting DNA methylation maps capture meaningful biological information and allow for the detection of differential methylation across populations. We offer guidelines on how to carry out comparative studies involving ancient populations, and how to control the rate of falsely discovered differentially methylated regions. The ability to reconstruct DNA methylation maps of past populations allows for the development of a whole new frontier in paleoepigenetic research, tracing DNA methylation changes throughout human history, using data from thousands of ancient samples.}, } @article {pmid38257973, year = {2024}, author = {Bennasar-Figueras, A}, title = {The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38257973}, issn = {2076-2607}, abstract = {The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.}, } @article {pmid38247180, year = {2024}, author = {Zhang, M and Wang, CH and Zheng, YX and Jiangzuo, QG and Hou, YM and Cao, P and Dai, QY and Yang, RW and Liu, F and Feng, XT and Mo, LH and Fu, QM}, title = {Ancient DNA unravels species identification from Laosicheng site, Hunan Province, China, and provides insights into maternal genetic history of East Asian leopards.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {226-229}, pmid = {38247180}, issn = {2095-8137}, mesh = {Animals ; China ; *DNA, Ancient ; *Panthera/genetics ; Asia, Eastern ; }, } @article {pmid38238372, year = {2024}, author = {Kırdök, E and Kashuba, N and Damlien, H and Manninen, MA and Nordqvist, B and Kjellström, A and Jakobsson, M and Lindberg, AM and Storå, J and Persson, P and Andersson, B and Aravena, A and Götherström, A}, title = {Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22125}, pmid = {38238372}, issn = {2045-2322}, support = {2019-3-AP3-3729//Mersin University BAP project/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; project no. 2019-00849//The Swedish Research Council/ ; }, mesh = {Animals ; Humans ; Dysbiosis/genetics ; Metagenome ; *Microbiota/genetics ; Oral Health ; *Periodontitis/genetics ; }, abstract = {Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.}, } @article {pmid38233869, year = {2024}, author = {Budaeva, N and Agne, S and Ribeiro, PA and Straube, N and Preick, M and Hofreiter, M}, title = {Wide-spread dispersal in a deep-sea brooding polychaete: the role of natural history collections in assessing the distribution in quill worms (Onuphidae, Annelida).}, journal = {Frontiers in zoology}, volume = {21}, number = {1}, pages = {1}, pmid = {38233869}, issn = {1742-9994}, support = {351649567//Deutsche Forschungsgemeinschaft/ ; 25-17-70184238//Norwegian Biodiversity Information Centre/ ; PRODEEP//FP7 People: Marie-Curie Actions/ ; SFRH/BPD/69232/2010//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {BACKGROUND: Modern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopolitan ranges for many species, which, in many cases, were later found to include cryptic or pseudocryptic lineages with subtle morphological differences. Natural history collections and databases can aid in assessing the geographic ranges of species but depend on correct species identification. Obtaining DNA sequence information from wet-collection museum specimens of marine annelids is often impeded by the use of formaldehyde and/or long-term storage in ethanol resulting in DNA degradation and cross-linking.

RESULTS: The application of ancient DNA extraction methodology in combination with single-stranded DNA library preparation and target gene capture resulted in successful sequencing of a 110-year-old collection specimen of quill worms. Furthermore, a 40-year-old specimen of quill worms was successfully sequenced using a standard extraction protocol for modern samples, PCR and Sanger sequencing. Our study presents the first molecular analysis of Hyalinoecia species including the previously known species Hyalinoecia robusta, H. tubicloa, H. artifex, and H. longibranchiata, and a potentially undescribed species from equatorial western Africa morphologically indistinguishable from H. tubicola. The study also investigates the distribution of these five Hyalinoecia species. Reassessing the distribution of H. robusta reveals a geographical range covering both the Atlantic and the Indian Oceans as indicated by molecular data obtained from recent and historical specimens.

CONCLUSION: Our results represent an example of a very wide geographical distribution of a brooding deep-sea annelid with a complex reproduction strategy and seemingly very limited dispersal capacity of its offspring, and highlights the importance of molecular information from museum specimens for integrative annelid taxonomy and biogeography.}, } @article {pmid38227345, year = {2024}, author = {Grasso, G and Bianciotto, V and Marmeisse, R}, title = {Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14390}, pmid = {38227345}, issn = {1751-7915}, support = {//Alliance Sorbonne Université/ ; ATM 2021//Muséum National d'Histoire Naturelle/ ; Bando Da Vinci 2022//Università Italo Francese/ ; }, mesh = {Humans ; *Microbiota ; DNA ; Microbial Consortia ; }, abstract = {By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non-host-associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre-disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.}, } @article {pmid38216764, year = {2024}, author = {Wong, C}, title = {Ancient DNA reveals first known case of sex-development disorder.}, journal = {Nature}, volume = {625}, number = {7996}, pages = {639}, pmid = {38216764}, issn = {1476-4687}, mesh = {Humans ; *Disorders of Sex Development/genetics/history ; *DNA, Ancient/analysis ; Turner Syndrome/genetics/history ; History, Ancient ; }, } @article {pmid38213708, year = {2023}, author = {Borodko, DD and Zhenilo, SV and Sharko, FS}, title = {Search for differentially methylated regions in ancient and modern genomes.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {27}, number = {7}, pages = {820-828}, doi = {10.18699/VJGB-23-95}, pmid = {38213708}, issn = {2500-0462}, abstract = {Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.}, } @article {pmid38212558, year = {2024}, author = {Anastasiadou, K and Silva, M and Booth, T and Speidel, L and Audsley, T and Barrington, C and Buckberry, J and Fernandes, D and Ford, B and Gibson, M and Gilardet, A and Glocke, I and Keefe, K and Kelly, M and Masters, M and McCabe, J and McIntyre, L and Ponce, P and Rowland, S and Ruiz Ventura, J and Swali, P and Tait, F and Walker, D and Webb, H and Williams, M and Witkin, A and Holst, M and Loe, L and Armit, I and Schulting, R and Skoglund, P}, title = {Detection of chromosomal aneuploidy in ancient genomes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {14}, pmid = {38212558}, issn = {2399-3642}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Male ; Humans ; *Klinefelter Syndrome/diagnosis/genetics ; DNA, Ancient ; Aneuploidy ; *Down Syndrome ; Sex Chromosomes ; }, abstract = {Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes (~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.}, } @article {pmid38207026, year = {2024}, author = {Curry, A}, title = {Ancient DNA ties modern diseases to ancestry.}, journal = {Science (New York, N.Y.)}, volume = {383}, number = {6679}, pages = {138-139}, doi = {10.1126/science.adn9644}, pmid = {38207026}, issn = {1095-9203}, mesh = {Humans ; *DNA, Ancient ; Europe/epidemiology ; Genome, Human ; *Multiple Sclerosis/epidemiology/genetics/history ; }, abstract = {Among Europeans, risk of multiple sclerosis rises with genes from Bronze Age Yamnaya herders.}, } @article {pmid38200339, year = {2024}, author = {Reardon, S}, title = {Ancient DNA reveals origins of multiple sclerosis in Europe.}, journal = {Nature}, volume = {625}, number = {7995}, pages = {431-432}, pmid = {38200339}, issn = {1476-4687}, mesh = {Humans ; Archaeology ; *DNA, Ancient/analysis ; Europe ; *Multiple Sclerosis/genetics/history ; }, } @article {pmid38200296, year = {2024}, author = {Barrie, W and Yang, Y and Irving-Pease, EK and Attfield, KE and Scorrano, G and Jensen, LT and Armen, AP and Dimopoulos, EA and Stern, A and Refoyo-Martinez, A and Pearson, A and Ramsøe, A and Gaunitz, C and Demeter, F and Jørkov, MLS and Møller, SB and Springborg, B and Klassen, L and Hyldgård, IM and Wickmann, N and Vinner, L and Korneliussen, TS and Allentoft, ME and Sikora, M and Kristiansen, K and Rodriguez, S and Nielsen, R and Iversen, AKN and Lawson, DJ and Fugger, L and Willerslev, E}, title = {Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.}, journal = {Nature}, volume = {625}, number = {7994}, pages = {321-328}, pmid = {38200296}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_00036/3/MRC_/Medical Research Council/United Kingdom ; R01 GM138634/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Datasets as Topic ; Diet/ethnology/history ; Europe/ethnology ; *Genetic Predisposition to Disease/history ; Genetics, Medical ; *Genome, Human ; *Grassland ; History, 15th Century ; History, Ancient ; History, Medieval ; Human Migration/history ; Life Style/ethnology/history ; *Multiple Sclerosis/genetics/history/immunology ; Neurodegenerative Diseases/genetics/history/immunology ; Population Density ; }, abstract = {Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated[1]. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age[2], along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.}, } @article {pmid38200208, year = {2024}, author = {Scaggion, C and Marinato, M and Dal Sasso, G and Nodari, L and Saupe, T and Aneli, S and Pagani, L and Scheib, CL and Rigo, M and Artioli, G}, title = {A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1028}, pmid = {38200208}, issn = {2045-2322}, support = {Ph.D. scholarship//Fondazione Cassa di Risparmio di Padova e Rovigo/ ; scholarship//Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali/ ; }, mesh = {Humans ; Spectrophotometry, Infrared ; *Archaeology ; *Burial ; Chromosome Mapping ; DNA, Ancient ; Isotopes ; }, abstract = {Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.}, } @article {pmid38194921, year = {2024}, author = {Bellwood, P}, title = {Archaeogenetics: Tracing ancient migrations from the Yellow River.}, journal = {Current biology : CB}, volume = {34}, number = {1}, pages = {R18-R20}, doi = {10.1016/j.cub.2023.11.024}, pmid = {38194921}, issn = {1879-0445}, mesh = {Humans ; *Rivers ; Asia, Eastern ; China ; *DNA, Ancient ; Language ; }, abstract = {Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans in East Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history.}, } @article {pmid38189170, year = {2024}, author = {Lammers, Y and Taberlet, P and Coissac, E and Elliott, LD and Merkel, MF and Pitelkova, I and , and , and Alsos, IG}, title = {Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13926}, doi = {10.1111/1755-0998.13926}, pmid = {38189170}, issn = {1755-0998}, support = {226134/F50//Norges Forskningsråd/ ; 250963/F20//Norges Forskningsråd/ ; 255415//Norges Forskningsråd/ ; 14-14//Norwegian Biodiversity Information Centre/ ; 70184209//Norwegian Biodiversity Information Centre/ ; 819192//H2020 European Research Council/ ; ANR-10-INBS-09-08//France Génomique/ ; }, mesh = {*DNA, Environmental ; Genetics, Population ; Phylogeography ; DNA, Ancient/analysis ; Multiplex Polymerase Chain Reaction ; Genetic Variation ; }, abstract = {Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.}, } @article {pmid38179684, year = {2024}, author = {Hipp, AL and Lazic, D}, title = {Ancient tree genomes for old questions.}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e17259}, doi = {10.1111/mec.17259}, pmid = {38179684}, issn = {1365-294X}, support = {2129281//Division of Environmental Biology/ ; }, mesh = {*Trees/genetics ; Genomics ; Paleontology ; Wood ; Ecology ; *Quercus/genetics ; }, abstract = {Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.}, } @article {pmid38177452, year = {2024}, author = {Barrie, W and Irving-Pease, EK and Willerslev, E and Iversen, AKN and Fugger, L}, title = {Ancient DNA reveals evolutionary origins of autoimmune diseases.}, journal = {Nature reviews. Immunology}, volume = {24}, number = {2}, pages = {85-86}, pmid = {38177452}, issn = {1474-1741}, mesh = {Humans ; *DNA, Ancient ; Biological Evolution ; Evolution, Molecular ; *Autoimmune Diseases/genetics ; }, } @article {pmid38177408, year = {2024}, author = {Sharko, FS and Boulygina, ES and Tsygankova, SV and Slobodova, NV and Rastorguev, SM and Krasivskaya, AA and Belinsky, AB and Härke, H and Kadieva, AA and Demidenko, SV and Malashev, VY and Shvedchikova, TY and Dobrovolskaya, MV and Reshetova, IK and Korobov, DS and Nedoluzhko, AV}, title = {Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus.}, journal = {European journal of human genetics : EJHG}, volume = {}, number = {}, pages = {}, pmid = {38177408}, issn = {1476-5438}, abstract = {The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.}, } @article {pmid38173222, year = {2024}, author = {Caduff, M and Eckel, R and Leuenberger, C and Wegmann, D}, title = {Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13913}, doi = {10.1111/1755-0998.13913}, pmid = {38173222}, issn = {1755-0998}, support = {310030_200420//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; Bayes Theorem ; *Sex Chromosomes/genetics ; *Genomics ; Genetic Testing ; Karyotype ; }, abstract = {The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.}, } @article {pmid38167834, year = {2024}, author = {Yang, S and Sun, X and Jin, L and Zhang, M}, title = {Inferring language dispersal patterns with velocity field estimation.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {190}, pmid = {38167834}, issn = {2041-1723}, support = {T2122007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32070577//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Cultural Evolution ; Phylogeny ; Language ; Phylogeography ; Agriculture ; }, abstract = {Reconstructing the spatial evolution of languages can deepen our understanding of the demic diffusion and cultural spread. However, the phylogeographic approach that is frequently used to infer language dispersal patterns has limitations, primarily because the phylogenetic tree cannot fully explain the language evolution induced by the horizontal contact among languages, such as borrowing and areal diffusion. Here, we introduce the language velocity field estimation, which does not rely on the phylogenetic tree, to infer language dispersal trajectories and centre. Its effectiveness and robustness are verified through both simulated and empirical validations. Using language velocity field estimation, we infer the dispersal patterns of four agricultural language families and groups, encompassing approximately 700 language samples. Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. Our findings highlight that the agricultural languages dispersed alongside the demic diffusions and cultural spreads during the past 10,000 years. We expect that language velocity field estimation could aid the spatial analysis of language evolution and further branch out into the studies of demographic and cultural dynamics.}, } @article {pmid38150503, year = {2024}, author = {Srigyan, M and Schubert, BW and Bushell, M and Santos, SHD and Figueiró, HV and Sacco, S and Eizirik, E and Shapiro, B}, title = {Mitogenomic analysis of a late Pleistocene jaguar from North America.}, journal = {The Journal of heredity}, volume = {115}, number = {4}, pages = {424-431}, pmid = {38150503}, issn = {1465-7333}, support = {OPP-2131589//NSF/ ; }, mesh = {Animals ; *Panthera/genetics/classification ; *Genome, Mitochondrial ; *Phylogeny ; *Fossils ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; North America ; Georgia ; Evolution, Molecular ; Genetic Variation ; }, abstract = {The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.}, } @article {pmid38150491, year = {2024}, author = {de Flamingh, A and Gnoske, TP and Rivera-Colón, AG and Simeonovski, VA and Kerbis Peterhans, JC and Yamaguchi, N and Witt, KE and Catchen, J and Roca, AL and Malhi, RS}, title = {Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction.}, journal = {The Journal of heredity}, volume = {115}, number = {2}, pages = {155-165}, doi = {10.1093/jhered/esad081}, pmid = {38150491}, issn = {1465-7333}, support = {1645087//National Science Fund/ ; }, mesh = {Animals ; *Lions/genetics ; Genomics ; South Africa ; Genome ; Population Dynamics ; }, abstract = {Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.}, } @article {pmid38132343, year = {2023}, author = {Panitsina, VA and Bodrov, SY and Boulygina, ES and Slobodova, NV and Kosintsev, PA and Abramson, NI}, title = {In Search of the Elusive North: Evolutionary History of the Arctic Fox (Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data.}, journal = {Biology}, volume = {12}, number = {12}, pages = {}, pmid = {38132343}, issn = {2079-7737}, support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 122031100282-2//State research theme/ ; 20-29-01038//Russian Foundation for Basic Research/ ; }, abstract = {Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.}, } @article {pmid38131007, year = {2023}, author = {Lien, A and Legori, LP and Kraft, L and Sackett, PW and Renaud, G}, title = {Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1260486}, pmid = {38131007}, issn = {2673-7647}, abstract = {Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that are sensitive to wrongly merged reads or that rely on quality scores can be significantly impacted by the choice of tool.}, } @article {pmid38123640, year = {2024}, author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Olalde, I and Patterson, N and Reich, D}, title = {Accurate detection of identity-by-descent segments in human ancient DNA.}, journal = {Nature genetics}, volume = {56}, number = {1}, pages = {143-151}, pmid = {38123640}, issn = {1546-1718}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Genotype ; *Genome, Human/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.}, } @article {pmid38118448, year = {2024}, author = {Silva, M and Booth, T and Moore, J and Anastasiadou, K and Walker, D and Gilardet, A and Barrington, C and Kelly, M and Williams, M and Henderson, M and Smith, A and Bowsher, D and Montgomery, J and Skoglund, P}, title = {An individual with Sarmatian-related ancestry in Roman Britain.}, journal = {Current biology : CB}, volume = {34}, number = {1}, pages = {204-212.e6}, doi = {10.1016/j.cub.2023.11.049}, pmid = {38118448}, issn = {1879-0445}, mesh = {Humans ; United Kingdom ; Iran ; *Isotopes ; *Roman World/history ; }, abstract = {In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.[1][,][2][,][3] In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.[4][,][5] Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.}, } @article {pmid38096384, year = {2023}, author = {Fiddaman, SR and Dimopoulos, EA and Lebrasseur, O and du Plessis, L and Vrancken, B and Charlton, S and Haruda, AF and Tabbada, K and Flammer, PG and Dascalu, S and Marković, N and Li, H and Franklin, G and Symmons, R and Baron, H and Daróczi-Szabó, L and Shaymuratova, DN and Askeyev, IV and Putelat, O and Sana, M and Davoudi, H and Fathi, H and Mucheshi, AS and Vahdati, AA and Zhang, L and Foster, A and Sykes, N and Baumberg, GC and Bulatović, J and Askeyev, AO and Askeyev, OV and Mashkour, M and Pybus, OG and Nair, V and Larson, G and Smith, AL and Frantz, LAF}, title = {Ancient chicken remains reveal the origins of virulence in Marek's disease virus.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6676}, pages = {1276-1281}, doi = {10.1126/science.adg2238}, pmid = {38096384}, issn = {1095-9203}, support = {ERC-2019-STG-853272-PALAEOFARM/ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Chickens/virology ; *Herpesvirus 2, Gallid/classification/genetics/pathogenicity ; Lymphoma/virology ; *Marek Disease/history/virology ; Virulence/genetics ; Phylogeny ; }, abstract = {The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.}, } @article {pmid38087919, year = {2023}, author = {Pilowsky, JA and Brown, SC and Llamas, B and van Loenen, AL and Kowalczyk, R and Hofman-Kamińska, E and Manaseryan, NH and Rusu, V and Križnar, M and Rahbek, C and Fordham, DA}, title = {Millennial processes of population decline, range contraction and near extinction of the European bison.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2013}, pages = {20231095}, pmid = {38087919}, issn = {1471-2954}, mesh = {Animals ; Humans ; *Bison/genetics ; Europe ; Fossils ; Human Activities ; Hunting ; }, abstract = {European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.}, } @article {pmid38081999, year = {2024}, author = {Cox, SL and Nicklisch, N and Francken, M and Wahl, J and Meller, H and Haak, W and Alt, KW and Rosenstock, E and Mathieson, I}, title = {Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe.}, journal = {Nature human behaviour}, volume = {8}, number = {2}, pages = {243-255}, pmid = {38081999}, issn = {2397-3374}, support = {Al 287/7-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Al 287/7-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Me 3245/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Me 3245/1-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RO 4148/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BCS2123627//National Science Foundation (NSF)/ ; }, mesh = {Female ; Male ; Humans ; *Genetics, Population ; *Sex Characteristics ; DNA, Mitochondrial ; Europe ; Isotopes ; }, abstract = {The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.}, } @article {pmid38065079, year = {2023}, author = {Olalde, I and Carrión, P and Mikić, I and Rohland, N and Mallick, S and Lazaridis, I and Mah, M and Korać, M and Golubović, S and Petković, S and Miladinović-Radmilović, N and Vulović, D and Alihodžić, T and Ash, A and Baeta, M and Bartík, J and Bedić, Ž and Bilić, M and Bonsall, C and Bunčić, M and Bužanić, D and Carić, M and Čataj, L and Cvetko, M and Drnić, I and Dugonjić, A and Đukić, A and Đukić, K and Farkaš, Z and Jelínek, P and Jovanovic, M and Kaić, I and Kalafatić, H and Krmpotić, M and Krznar, S and Leleković, T and M de Pancorbo, M and Matijević, V and Milošević Zakić, B and Osterholtz, AJ and Paige, JM and Tresić Pavičić, D and Premužić, Z and Rajić Šikanjić, P and Rapan Papeša, A and Paraman, L and Sanader, M and Radovanović, I and Roksandic, M and Šefčáková, A and Stefanović, S and Teschler-Nicola, M and Tončinić, D and Zagorc, B and Callan, K and Candilio, F and Cheronet, O and Fernandes, D and Kearns, A and Lawson, AM and Mandl, K and Wagner, A and Zalzala, F and Zettl, A and Tomanović, Ž and Keckarević, D and Novak, M and Harper, K and McCormick, M and Pinhasi, R and Grbić, M and Lalueza-Fox, C and Reich, D}, title = {A genetic history of the Balkans from Roman frontier to Slavic migrations.}, journal = {Cell}, volume = {186}, number = {25}, pages = {5472-5485.e9}, pmid = {38065079}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Balkan Peninsula ; Europe ; *White People/genetics ; *Human Migration ; }, abstract = {The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1[st] millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.}, } @article {pmid38060128, year = {2024}, author = {Grasso, G and Rotunno, S and Debruyne, R and Bittner, L and Miozzi, L and Marmeisse, R and Bianciotto, V}, title = {Identification of DNA Viruses in Ancient DNA from Herbarium Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {221-234}, pmid = {38060128}, issn = {1940-6029}, mesh = {*DNA, Ancient ; Sequence Analysis, DNA/methods ; Phylogeny ; *DNA Viruses ; Soil ; }, abstract = {Herbaria encompass millions of plant specimens, mostly collected in the nineteenth and twentieth centuries that can represent a key resource for investigating the history and evolution of phytopathogens. In the last years, the application of high-throughput sequencing technologies for the analysis of ancient nucleic acids has revolutionized the study of ancient pathogens including viruses, allowing the reconstruction of historical genomic viral sequences, improving phylogenetic based molecular dating, and providing essential insight into plant virus ecology. In this chapter, we describe a protocol to reconstruct ancient plant and soil viral sequences starting from highly fragmented ancient DNA extracted from herbarium plants and their associated rhizospheric soil. Following Illumina high-throughput sequencing, sequence data are de novo assembled, and DNA viral sequences are selected, according to their similarity with known viruses.}, } @article {pmid38056335, year = {2024}, author = {Peng, K and Liu, X and Cheng, H and Xu, M and Liu, Y and Yang, H and Liu, P and Yang, S}, title = {Characterization of driving factors for the long-term succession of bloom-forming cyanobacterial genera in Lake Erhai, southwest China.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119729}, doi = {10.1016/j.jenvman.2023.119729}, pmid = {38056335}, issn = {1095-8630}, mesh = {China ; *Cyanobacteria ; Eutrophication ; Lakes/microbiology ; *Microcystis/genetics ; Nutrients ; }, abstract = {Cyanobacterial blooms pose a global environmental concern, with various genera contributing to their formation. The harmfulness of cyanobacterial blooms varies depending on the specific genus, yet the factors triggering their formation remain incompletely understood. This study conducted qPCR of sediment DNA in Lake Erhai to reconstruct the historical succession of three common bloom-forming cyanobacterial genera (i.e., Microcystis, Dolichospermum, and Aphanizomenon). The driving factors and their corresponding thresholds were identified, and human activities related to driving factors were evaluated. The results revealed two successions in the past century. The first succession transitioned from Aphanizomenon (1902-1978) to Microcystis and Dolichospermum (1978-1999), driven by TN:TP and TP. The second succession shifted from Microcystis and Dolichospermum (1978-1999) to Microcystis (1999-2010), driven by TP, TN:TP, and temperature. The thresholds of TP and TN:TP for the Microcystis bloom were 0.023 mg/L and 17, respectively. TN:TP was significantly influenced by domestic pollution and crop farming in both successions, while TP was significantly impacted by domestic pollution in the first succession and by pollution from crop and dairy farming in the second succession. These results shed light on the underlying mechanism responsible for the blooms of various cyanobacterial genera and could serve as a valuable reference for effectively preventing and controlling nutrient input in the watershed.}, } @article {pmid38051947, year = {2023}, author = {Wroblewski, TH and Witt, KE and Lee, SB and Malhi, RS and Peede, D and Huerta-Sánchez, E and Villanea, FA and Claw, KG}, title = {Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.}, journal = {Genome biology and evolution}, volume = {15}, number = {12}, pages = {}, pmid = {38051947}, issn = {1759-6653}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; R35 HG011319/HG/NHGRI NIH HHS/United States ; R35HG011319/HG/NHGRI NIH HHS/United States ; 1R35GM128946-01/NH/NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Pharmacogenetics ; Genome, Human ; *Hominidae/genetics ; Biological Evolution ; }, abstract = {Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.}, } @article {pmid38047074, year = {2023}, author = {Xiao, B and Rey-Lglesia, A and Yuan, J and Hu, J and Song, S and Hou, Y and Chen, X and Germonpré, M and Bao, L and Wang, S and Taogetongqimuge, and Valentinovna, LL and Lister, AM and Lai, X and Sheng, G}, title = {Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108406}, pmid = {38047074}, issn = {2589-0042}, abstract = {The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.}, } @article {pmid38047066, year = {2023}, author = {Fewlass, H and Zavala, EI and Fagault, Y and Tuna, T and Bard, E and Hublin, JJ and Hajdinjak, M and Wilczyński, J}, title = {Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108283}, pmid = {38047066}, issn = {2589-0042}, abstract = {Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.}, } @article {pmid38040695, year = {2023}, author = {Fournier, R and Tsangalidou, Z and Reich, D and Palamara, PF}, title = {Haplotype-based inference of recent effective population size in modern and ancient DNA samples.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7945}, pmid = {38040695}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R21 HG010748/HG/NHGRI NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Haplotypes/genetics ; *DNA, Ancient ; Population Density ; *Genomics ; Linkage Disequilibrium ; Genetics, Population ; Polymorphism, Single Nucleotide ; }, abstract = {Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.}, } @article {pmid38030719, year = {2024}, author = {Fortes-Lima, CA and Burgarella, C and Hammarén, R and Eriksson, A and Vicente, M and Jolly, C and Semo, A and Gunnink, H and Pacchiarotti, S and Mundeke, L and Matonda, I and Muluwa, JK and Coutros, P and Nyambe, TS and Cikomola, JC and Coetzee, V and de Castro, M and Ebbesen, P and Delanghe, J and Stoneking, M and Barham, L and Lombard, M and Meyer, A and Steyn, M and Malmström, H and Rocha, J and Soodyall, H and Pakendorf, B and Bostoen, K and Schlebusch, CM}, title = {The genetic legacy of the expansion of Bantu-speaking peoples in Africa.}, journal = {Nature}, volume = {625}, number = {7995}, pages = {540-547}, pmid = {38030719}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Africa, Western ; Datasets as Topic ; Democratic Republic of the Congo ; *DNA, Ancient/analysis ; *Emigration and Immigration/history ; Founder Effect ; Gene Flow/genetics ; Genetic Variation/genetics ; *Genetics, Population ; History, Ancient ; *Language/history ; Linguistics/history ; Zambia ; Geographic Mapping ; }, abstract = {The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent[1-7]. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals[8]. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods[9] and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies[10] and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.}, } @article {pmid38014190, year = {2023}, author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD}, title = {Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014190}, issn = {2692-8205}, support = {R35 GM146886/GM/NIGMS NIH HHS/United States ; }, abstract = {Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P-values of qpAdm models, and f3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f2-statistics, demonstrating the improved demographic inference that could be achieved with advancements in f-statistic estimations.}, } @article {pmid38012935, year = {2023}, author = {Jäger, HY and Atz Zanotelli, D and Maixner, F and Nicklisch, N and Alt, KW and Meller, H and Pap, I and Szikossy, I and Pálfi, G and Zink, AR}, title = {Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102392}, doi = {10.1016/j.tube.2023.102392}, pmid = {38012935}, issn = {1873-281X}, support = {2014-2020_CALL-FESR 2017//European Regional Development Fund/ ; FESR1078//Research and Innovation_Autonomous Province Bolzano-South Tyrol_/ ; NKTIH K 125561//National Research Development and Innovation Office (Hungary)/ ; 57437987//Germany Academic Exchange Service/ ; }, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Tuberculosis/microbiology ; Bone and Bones ; DNA ; DNA, Ancient ; }, abstract = {Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.}, } @article {pmid38012931, year = {2023}, author = {Zink, A and Maixner, F and Jäger, HY and Szikossy, I and Pálfi, G and Pap, I}, title = {Tuberculosis in mummies - New findings, perspectives and limitations.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102371}, doi = {10.1016/j.tube.2023.102371}, pmid = {38012931}, issn = {1873-281X}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Mummies ; DNA, Bacterial/genetics/analysis ; *Tuberculosis/microbiology ; }, abstract = {The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges.}, } @article {pmid38012918, year = {2023}, author = {Kharlamova, N and Ogarkov, O and Berdnikov, I and Berdnikova, N and Galeev, R and Mokrousov, I}, title = {Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102368}, doi = {10.1016/j.tube.2023.102368}, pmid = {38012918}, issn = {1873-281X}, mesh = {Male ; Humans ; Female ; *Mycobacterium tuberculosis/genetics ; Siberia ; Body Remains ; Phylogeny ; Cemeteries ; *Tuberculosis/microbiology ; Genotype ; DNA ; }, abstract = {In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates.}, } @article {pmid38006200, year = {2023}, author = {Houldcroft, CJ and Underdown, S}, title = {Infectious disease in the Pleistocene: Old friends or old foes?.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {513-531}, doi = {10.1002/ajpa.24737}, pmid = {38006200}, issn = {2692-7691}, support = {//Oxford Brookes University/ ; }, mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; }, abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.}, } @article {pmid38002979, year = {2023}, author = {Uricoechea Patiño, D and Collins, A and Romero García, OJ and Santos Vecino, G and Aristizábal Espinosa, P and Bernal Villegas, JE and Benavides Benitez, E and Vergara Muñoz, S and Briceño Balcázar, I}, title = {Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, pmid = {38002979}, issn = {2073-4425}, support = {Convocatoria interna de 2013 (Internal Call of 2013) as per acta 809 de la comisión de asuntos generales, proyecto MED-168-2013.//Universidad de La Sabana/ ; }, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Genetics, Population ; Mitochondria/genetics ; North America ; Human Migration ; }, abstract = {This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.}, } @article {pmid37993617, year = {2023}, author = {Izarraras-Gomez, A and Ortega-Del Vecchyo, D}, title = {Ancient DNA uncovers past migrations in California.}, journal = {Nature}, volume = {624}, number = {7990}, pages = {43-44}, pmid = {37993617}, issn = {1476-4687}, mesh = {*DNA, Ancient ; *Archaeology ; Human Migration ; California ; }, } @article {pmid37992125, year = {2023}, author = {Di Santo, LN and Quilodrán, CS and Currat, M}, title = {Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {37992125}, issn = {1537-1719}, mesh = {Animals ; *Genomics ; Paleontology ; *Neanderthals/genetics ; Genome ; Biological Evolution ; }, abstract = {Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.}, } @article {pmid37971141, year = {2024}, author = {Pečnerová, P and Lord, E and Garcia-Erill, G and Hanghøj, K and Rasmussen, MS and Meisner, J and Liu, X and van der Valk, T and Santander, CG and Quinn, L and Lin, L and Liu, S and Carøe, C and Dalerum, F and Götherström, A and Måsviken, J and Vartanyan, S and Raundrup, K and Al-Chaer, A and Rasmussen, L and Hvilsom, C and Heide-Jørgensen, MP and Sinding, MS and Aastrup, P and Van Coeverden de Groot, PJ and Schmidt, NM and Albrechtsen, A and Dalén, L and Heller, R and Moltke, I and Siegismund, HR}, title = {Population genomics of the muskox' resilience in the near absence of genetic variation.}, journal = {Molecular ecology}, volume = {33}, number = {2}, pages = {e17205}, doi = {10.1111/mec.17205}, pmid = {37971141}, issn = {1365-294X}, support = {CF20-0539//Carlsbergfondet/ ; 8021-00344B//Danmarks Frie Forskningsfond/ ; }, mesh = {Humans ; Animals ; Infant, Newborn ; *Metagenomics ; *Resilience, Psychological ; Biological Evolution ; Genomics ; Ruminants/genetics ; Genetic Variation/genetics ; }, abstract = {Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.}, } @article {pmid37955570, year = {2023}, author = {Harning, DJ and Sacco, S and Anamthawat-Jónsson, K and Ardenghi, N and Thordarson, T and Raberg, JH and Sepúlveda, J and Geirsdóttir, Á and Shapiro, B and Miller, GH}, title = {Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37955570}, issn = {2050-084X}, mesh = {*Betula ; Ecosystem ; Iceland ; Betulaceae ; Biodiversity ; DNA, Ancient ; *Tracheophyta ; }, abstract = {As the Arctic continues to warm, woody shrubs are expected to expand northward. This process, known as 'shrubification,' has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While the future rate of shrubification remains poorly constrained, past records of plant immigration to newly deglaciated landscapes in the Arctic may serve as useful analogs. We provide one new postglacial Holocene sedimentary ancient DNA (sedaDNA) record of vascular plants from Iceland and place a second Iceland postglacial sedaDNA record on an improved geochronology; both show Salicaceae present shortly after deglaciation, whereas Betulaceae first appears more than 1000 y later. We find a similar pattern of delayed Betulaceae colonization in eight previously published postglacial sedaDNA records from across the glaciated circum North Atlantic. In nearly all cases, we find that Salicaceae colonizes earlier than Betulaceae and that Betulaceae colonization is increasingly delayed for locations farther from glacial-age woody plant refugia. These trends in Salicaceae and Betulaceae colonization are consistent with the plant families' environmental tolerances, species diversity, reproductive strategies, seed sizes, and soil preferences. As these reconstructions capture the efficiency of postglacial vascular plant migration during a past period of high-latitude warming, a similarly slow response of some woody shrubs to current warming in glaciated regions, and possibly non-glaciated tundra, may delay Arctic shrubification and future changes in the structure of tundra ecosystems and temperature amplification.}, } @article {pmid37955431, year = {2024}, author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA}, title = {Large variance in inbreeding within the Iberian wolf population.}, journal = {The Journal of heredity}, volume = {115}, number = {4}, pages = {349-359}, pmid = {37955431}, issn = {1465-7333}, support = {P18-FR-5099//Junta de Andalucía/ ; PCI2022-135098-2//WOLFNESS Biodiversa+ project/ ; FPU17/02584//Spanish Ministry of Universities/ ; //Asociación Apadrina La Ciencia-Ford Spain/ ; //Ford Motor Company Fund/ ; BES-2017-082260//Spanish Ministry of Economy, Industry, and Competitiveness/ ; }, mesh = {*Wolves/genetics ; Animals ; *Inbreeding ; *Genetics, Population ; Spain ; *Genetic Variation ; Gene Flow ; }, abstract = {The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.}, } @article {pmid37955259, year = {2023}, author = {}, title = {Neolithic Community Revealed Using Ancient DNA Data.}, journal = {American journal of medical genetics. Part A}, volume = {191}, number = {12}, pages = {2797-2798}, doi = {10.1002/ajmg.a.62840}, pmid = {37955259}, issn = {1552-4833}, mesh = {Humans ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Haplotypes ; Europe ; }, } @article {pmid37953960, year = {2023}, author = {Coia, V and Paladin, A and Zingale, S and Wurst, C and Croze, M and Maixner, F and Zink, A}, title = {Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108215}, pmid = {37953960}, issn = {2589-0042}, abstract = {In South Tyrol (Eastern Italian Alps), during Late Antiquity-Early Middle Ages, archeological records indicate cultural hybridization among alpine groups and peoples of various origin. Using paleogenomics, we reconstructed the ancestry of 20 individuals (4[th]-7[th] cent. AD) from a cemetery to analyze whether they had heterogeneous or homogeneous ancestry and to study their social organization. The results revealed a primary genetic ancestry from southern Europe and additional ancestries from south-western, western, and northern Europe, suggesting that cultural hybridization was accompanied by complex genetic admixture. Kinship analyses found no genetic relatedness between the only two individuals buried with grave goods. Instead, a father-son pair was discovered in one multiple grave, together with unrelated individuals and one possible non-local female. These genetic findings indicate the presence of a high social status familia, which is supported by the cultural materials and the proximity of the grave to the most sacred area of the church.}, } @article {pmid37949985, year = {2023}, author = {Callaway, E}, title = {How to keep wildcats wild: ancient DNA offers fresh insights.}, journal = {Nature}, volume = {623}, number = {7987}, pages = {463-465}, pmid = {37949985}, issn = {1476-4687}, mesh = {Animals ; *Animals, Wild/genetics ; *Conservation of Natural Resources/methods ; *DNA, Ancient/analysis ; Scotland ; *Tigers/genetics ; Animals, Domestic/genetics ; *Endangered Species ; }, } @article {pmid37935117, year = {2023}, author = {Jamieson, A and Carmagnini, A and Howard-McCombe, J and Doherty, S and Hirons, A and Dimopoulos, E and Lin, AT and Allen, R and Anderson-Whymark, H and Barnett, R and Batey, C and Beglane, F and Bowden, W and Bratten, J and De Cupere, B and Drew, E and Foley, NM and Fowler, T and Fox, A and Geigl, EM and Gotfredsen, AB and Grange, T and Griffiths, D and Groß, D and Haruda, A and Hjermind, J and Knapp, Z and Lebrasseur, O and Librado, P and Lyons, LA and Mainland, I and McDonnell, C and Muñoz-Fuentes, V and Nowak, C and O'Connor, T and Peters, J and Russo, IM and Ryan, H and Sheridan, A and Sinding, MS and Skoglund, P and Swali, P and Symmons, R and Thomas, G and Trolle Jensen, TZ and Kitchener, AC and Senn, H and Lawson, D and Driscoll, C and Murphy, WJ and Beaumont, M and Ottoni, C and Sykes, N and Larson, G and Frantz, L}, title = {Limited historical admixture between European wildcats and domestic cats.}, journal = {Current biology : CB}, volume = {33}, number = {21}, pages = {4751-4760.e14}, doi = {10.1016/j.cub.2023.08.031}, pmid = {37935117}, issn = {1879-0445}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Cats/genetics ; Animals ; Cattle ; Bees ; Sheep ; Swine ; *Hybridization, Genetic ; Chickens ; *Felis/genetics ; Europe ; Gene Flow ; }, abstract = {Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.}, } @article {pmid37935112, year = {2023}, author = {Schurr, TG and Shengelia, R and Shamoon-Pour, M and Chitanava, D and Laliashvili, S and Laliashvili, I and Kibret, R and Kume-Kangkolo, Y and Akhvlediani, I and Bitadze, L and Mathieson, I and Yardumian, A}, title = {Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).}, journal = {Genome biology and evolution}, volume = {15}, number = {11}, pages = {}, pmid = {37935112}, issn = {1759-6653}, support = {BCS-1824826//National Science Foundation/ ; //University of Pennsylvania Museum of Archaeology and Anthropology/ ; //University of Pennsylvania Faculty Research Funds/ ; //Paul Carpenter Scholars Program/ ; //Bryn Athyn College Summer Research Funds/ ; }, mesh = {Humans ; Male ; Female ; *Genetics, Population ; Georgia (Republic) ; *Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Europe ; Haplotypes ; Genetic Variation ; }, abstract = {To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.}, } @article {pmid37928683, year = {2023}, author = {Roche, K and Dalle, F and Capelli, N and Borne, R and Jouffroy-Bapicot, I and Valot, B and Grenouillet, F and Le Bailly, M}, title = {From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1249884}, pmid = {37928683}, issn = {1664-302X}, abstract = {Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.}, } @article {pmid37927550, year = {2023}, author = {Childebayeva, A and Zavala, EI}, title = {Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108066}, pmid = {37927550}, issn = {2589-0042}, abstract = {Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.}, } @article {pmid37926832, year = {2023}, author = {Duitama González, C and Vicedomini, R and Lemane, T and Rascovan, N and Richard, H and Chikhi, R}, title = {decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {243}, pmid = {37926832}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Metagenome ; *Metagenomics/methods ; }, abstract = {BACKGROUND: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.

RESULTS: We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.

CONCLUSIONS: decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.}, } @article {pmid37923262, year = {2024}, author = {Fracasso, I and Zaccone, C and Oskolkov, N and Da Ros, L and Dinella, A and Belelli Marchesini, L and Buzzini, P and Sannino, C and Turchetti, B and Cesco, S and Le Roux, G and Tonon, G and Vernesi, C and Mimmo, T and Ventura, M and Borruso, L}, title = {Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168159}, doi = {10.1016/j.scitotenv.2023.168159}, pmid = {37923262}, issn = {1879-1026}, mesh = {Humans ; *Soil ; *DNA, Ancient ; Ecosystem ; Bacteria/genetics ; Metagenome ; Fungi/genetics ; }, abstract = {Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.}, } @article {pmid37909055, year = {2023}, author = {Seeber, PA and Palmer, Z and Schmidt, A and Chagas, A and Kitagawa, K and Marinova-Wolff, E and Tafelmaier, Y and Epp, LS}, title = {The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation.}, journal = {Biology letters}, volume = {19}, number = {11}, pages = {20230343}, pmid = {37909055}, issn = {1744-957X}, mesh = {Animals ; Phylogeny ; *Hyaenidae/genetics ; *Genome, Mitochondrial ; DNA ; Perissodactyla/genetics/metabolism ; Fossils ; }, abstract = {The woolly rhinoceros (Coelodonta antiquitatis) is an iconic species of the Eurasian Pleistocene megafauna, which was abundant in Eurasia in the Pleistocene until its demise beginning approximately 10 000 years ago. Despite the early recovery of several specimens from well-known European archaeological sites, including its type specimen (Blumenbach 1799), no genomes of European populations were available so far, and all available genomic data originated exclusively from Siberian populations. Using coprolites of cave hyenas (Crocuta crocuta spelea) recovered from Middle Palaeolithic layers of two caves in Germany (Bockstein-Loch and Hohlenstein-Stadel), we isolated and enriched predator and prey DNA to assemble the first European woolly rhinoceros mitogenomes, in addition to cave hyena mitogenomes. Both coprolite samples produced copious sequences assigned to C. crocuta (27% and 59% mitogenome coverage, respectively) and woolly rhinoceros (Coelodonta antiquitatis; 27% and 81% coverage, respectively). The sequences suggested considerable DNA degradation, which may limit the conclusions to be drawn; however, the mitogenomes of European woolly rhinoceros are genetically distinct from the Siberian woolly rhinoceros, and analyses of the more complete mitogenome suggest a split of the populations potentially coinciding with the earliest fossil records of woolly rhinoceros in Europe.}, } @article {pmid37908771, year = {2023}, author = {Zhur, KV and Sharko, FS and Sedov, VV and Dobrovolskaya, MV and Volkov, VG and Maksimov, NG and Seslavine, AN and Makarov, NA and Prokhortchouk, EB}, title = {The Rurikids: The First Experience of Reconstructing the Genetic Portrait of the Ruling Family of Medieval Rus' Based on Paleogenomic Data.}, journal = {Acta naturae}, volume = {15}, number = {3}, pages = {50-65}, pmid = {37908771}, issn = {2075-8251}, abstract = {The Rurikids were the reigning house of Rus', its principalities and, ultimately the Tsardom of Russia, for seven centuries: from the IX to the end of the XVI century. According to the Primary Chronicle (the Tale of Bygone Years), the main chronicle of Rus', the Rurik dynasty was founded by the Varangian prince Rurik, invited to reign in Novgorod in 862, but still there is no direct genetic evidence of the origin of the early Rurikids. This research, for the first time, provides a genome-wide paleogenetic analysis of bone remains belonging to one of the Rurikids, Prince Dmitry Alexandrovich (?-1294), the son of the Grand Prince of Vladimir Alexander Yaroslavich Nevsky (1221-1263). It has been established that his Y chromosome belongs to the N1a haplogroup. Most of the modern Rurikids, according to their genealogies, belonging to the N1a haplogroup, have the most similar variants of Y chromosomes to each other, as well as to the Y chromosome of Prince Dmitry Alexandrovich. Genome-wide data of the medieval and modern Rurikids unequivocally indicates that they belong to the N1a haplogroup of the Y chromosome, starting at least from the XI century (since the time of Prince Yaroslav the Wise). All the other alleged Rurikids, both ancient and modern, being carriers of other haplogroups (R1a, I2a), possess high heterogeneity of the sequence of Y chromosomes, meaning that we cannot confirm their common ancestry. The most probable ancestors of Prince Dmitry Alexandrovich in the male line were the men who left the burial ground Bolshoy Oleny Island on the coast of the Kola Peninsula about 3,600 years ago. The reconstruction of the genome of Prince Dmitry Alexandrovich indicates the contribution of three ancestral components to his origin: (1) the early medieval population of the east of Scandinavia from the island of Oland, (2) representatives of the steppe nomadic peoples of the Eurasian steppes of the Iron Age or the early medieval population of central Europe (steppe nomads from the territory of Hungary), and (3) the ancient East-Eurasian component. Reliable statistics were also obtained when the Scandinavians were replaced with the Medieval Russian Slavic populations of the XI century. Thus, for the first time, we have shown the complex nature of interethnic interactions in the formation of the nobility of medieval Rus' on the example of the ancient Rurikid.}, } @article {pmid37907573, year = {2023}, author = {Zedda, N and Meheux, K and Blöcher, J and Diekmann, Y and Gorelik, AV and Kalle, M and Klein, K and Titze, AL and Winkelbach, L and Naish, E and Brou, L and Valotteau, F and Le Brun-Ricalens, F and Burger, J and Brami, M}, title = {Biological and substitute parents in Beaker period adult-child graves.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18765}, pmid = {37907573}, issn = {2045-2322}, mesh = {Humans ; Adult ; Female ; *Archaeology ; *Burial/methods ; Europe ; Parents ; Adult Children ; }, abstract = {Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.}, } @article {pmid37905072, year = {2023}, author = {Cheng, X and Steinrücken, M}, title = {diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37905072}, issn = {2692-8205}, support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; }, abstract = {SUMMARY: Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA (aDNA) sequences and data from evolve-and-resequence (E&R) experiments are generated at a rapid pace. Such data presents unprecedented opportunities to elucidate the dynamics of adaptative genetic variation. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications. Here, we present diplo-locus, an open-source Python package that provides functionality to simulate and perform inference from time-series under the Wright-Fisher diffusion with general diploid selection. The package includes Python modules as well as command-line tools.

AVAILABILITY: Python package and command-line tool avilable at: https://github.com/steinrue/diplo_locus or https://pypi.org/project/diplo-locus/.}, } @article {pmid37904954, year = {2023}, author = {Poyraz, L and Colbran, LL and Mathieson, I}, title = {Predicting functional consequences of recent natural selection in Britain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37904954}, issn = {2692-8205}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; }, abstract = {Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.}, } @article {pmid37900966, year = {2023}, author = {Papa, V and Galassi, FM and Varotto, E and Gori, A and Vaccarezza, M}, title = {The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review.}, journal = {Pathogens & immunity}, volume = {8}, number = {1}, pages = {93-116}, pmid = {37900966}, issn = {2469-2964}, abstract = {Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.}, } @article {pmid37895202, year = {2023}, author = {Uricoechea Patiño, D and Collins, A and García, OJR and Santos Vecino, G and Cuenca, JVR and Bernal, JE and Benavides Benítez, E and Vergara Muñoz, S and Briceño Balcázar, I}, title = {High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895202}, issn = {2073-4425}, mesh = {Humans ; Colombia ; *DNA, Mitochondrial/genetics/analysis ; *Genetic Variation/genetics ; Haplotypes/genetics ; Indians, South American ; Genetics, Population ; }, abstract = {The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.}, } @article {pmid37894136, year = {2023}, author = {Pusadkar, V and Azad, RK}, title = {Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894136}, issn = {2076-2607}, abstract = {Taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. Although a number of methods for metagenome profiling have been developed, most of them have been assessed on modern metagenomes or simulated metagenomes mimicking modern metagenomes. Further, a comparative assessment of metagenome profilers on simulated metagenomes representing a spectrum of degradation depth, from the extremity of ancient (most degraded) to current or modern (not degraded) metagenomes, has not yet been performed. To understand the strengths and weaknesses of different metagenome profilers, we performed their comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes. All classes of profilers, namely, DNA-to-DNA, DNA-to-protein, and DNA-to-marker comparison-based profilers were evaluated on metagenomes with varying levels of damage simulating deamination, fragmentation, and contamination. Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. Further, the DNA-to-DNA (e.g., Kraken2, Bracken) and DNA-to-marker (e.g., MetaPhlAn4) based profiling approaches showed complementary strengths, which can be leveraged to elevate the state-of-the-art of ancient metagenome profiling.}, } @article {pmid37884848, year = {2023}, author = {}, title = {Ancient DNA reveals traces of elusive first humans in Europe.}, journal = {Nature}, volume = {623}, number = {7985}, pages = {11}, pmid = {37884848}, issn = {1476-4687}, mesh = {Animals ; Humans ; *DNA, Ancient ; *Hominidae ; Europe ; }, } @article {pmid37876815, year = {2023}, author = {Duitama González, C and Rangavittal, S and Vicedomini, R and Chikhi, R and Richard, H}, title = {aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108057}, pmid = {37876815}, issn = {2589-0042}, abstract = {Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.}, } @article {pmid37873879, year = {2023}, author = {Kim, AS and Kreiner, JM and Hernández, F and Bock, DG and Hodgins, KA and Rieseberg, LH}, title = {Temporal collections to study invasion biology.}, journal = {Molecular ecology}, volume = {32}, number = {24}, pages = {6729-6742}, doi = {10.1111/mec.17176}, pmid = {37873879}, issn = {1365-294X}, mesh = {*DNA/genetics ; *Museums ; Biology ; }, abstract = {Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.}, } @article {pmid37872569, year = {2023}, author = {Pochon, Z and Bergfeldt, N and Kırdök, E and Vicente, M and Naidoo, T and van der Valk, T and Altınışık, NE and Krzewińska, M and Dalén, L and Götherström, A and Mirabello, C and Unneberg, P and Oskolkov, N}, title = {aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {242}, pmid = {37872569}, issn = {1474-760X}, mesh = {Workflow ; *Metagenome ; *Metagenomics ; Archaeology ; DNA, Ancient ; }, abstract = {Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.}, } @article {pmid37852263, year = {2023}, author = {Tao, L and Yuan, H and Zhu, K and Liu, X and Guo, J and Min, R and He, H and Cao, D and Yang, X and Zhou, Z and Wang, R and Zhao, D and Ma, H and Chen, J and Zhao, J and Li, Y and He, Y and Suo, D and Zhang, R and Li, S and Li, L and Yang, F and Li, H and Zhang, L and Jin, L and Wang, CC}, title = {Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China.}, journal = {Current biology : CB}, volume = {33}, number = {22}, pages = {4995-5002.e7}, doi = {10.1016/j.cub.2023.09.055}, pmid = {37852263}, issn = {1879-0445}, mesh = {Humans ; *Millets/genetics ; *Rivers ; Agriculture ; Genome ; Farms ; DNA, Ancient ; Human Migration ; }, abstract = {The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.[1][,][2] However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.}, } @article {pmid37844237, year = {2023}, author = {Lucquin, A and Robson, HK and Oras, E and Lundy, J and Moretti, G and González Carretero, L and Dekker, J and Demirci, Ö and Dolbunova, E and McLaughlin, TR and Piezonka, H and Talbot, HM and Adamczak, K and Czekaj-Zastawny, A and Groß, D and Gumiński, W and Hartz, S and Kabaciński, J and Koivisto, S and Linge, TE and Meyer, AK and Mökkönen, T and Philippsen, B and Piličiauskas, G and Visocka, V and Kriiska, A and Raemaekers, D and Meadows, J and Heron, C and Craig, OE}, title = {The impact of farming on prehistoric culinary practices throughout Northern Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {43}, pages = {e2310138120}, pmid = {37844237}, issn = {1091-6490}, mesh = {Animals ; Humans ; *Archaeology ; *Agriculture ; Europe ; Farms ; Farmers ; }, abstract = {To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.}, } @article {pmid37836192, year = {2023}, author = {Papalini, S and Di Vittori, V and Pieri, A and Allegrezza, M and Frascarelli, G and Nanni, L and Bitocchi, E and Bellucci, E and Gioia, T and Pereira, LG and Susek, K and Tenaillon, M and Neumann, K and Papa, R}, title = {Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, pmid = {37836192}, issn = {2223-7747}, support = {862862//European Union's Horizon 2020 research and innovation programme/ ; 20177RL4KL//Italian Government (MIUR)/ ; }, abstract = {Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.}, } @article {pmid37830773, year = {2023}, author = {Muschick, M and Jemmi, E and Lengacher, N and Hänsch, S and Wales, N and Kishe, MA and Mwaiko, S and Dieleman, J and Lever, MA and Salzburger, W and Verschuren, D and Seehausen, O}, title = {Ancient DNA is preserved in fish fossils from tropical lake sediments.}, journal = {Molecular ecology}, volume = {32}, number = {22}, pages = {5913-5931}, doi = {10.1111/mec.17159}, pmid = {37830773}, issn = {1365-294X}, support = {CRSII5_183566//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 324249//FP7 Ideas: European Research Council/ ; //Strategy pool of the Faculty of Natural Sciences of the University of Bern/ ; 11-97251-000-INP//MacArthur Foundation/ ; }, mesh = {Animals ; *Lakes ; Phylogeny ; Fossils ; DNA, Ancient ; *Cichlids/genetics ; }, abstract = {Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.}, } @article {pmid37829208, year = {2022}, author = {Atağ, G and Vural, KB and Kaptan, D and Özkan, M and Koptekin, D and Sağlıcan, E and Doğramacı, S and Köz, M and Yılmaz, A and Söylev, A and Togan, İ and Somel, M and Özer, F}, title = {MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes.}, journal = {Open research Europe}, volume = {2}, number = {}, pages = {100}, pmid = {37829208}, issn = {2732-5121}, abstract = {A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.}, } @article {pmid37828091, year = {2023}, author = {Breglia, F and Bouby, L and Wales, N and Ivorra, S and Fiorentino, G}, title = {Disentangling the origins of viticulture in the western Mediterranean.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {17284}, pmid = {37828091}, issn = {2045-2322}, mesh = {Italy ; *Domestication ; *Vitis/genetics ; Archaeology ; Radiometric Dating ; }, abstract = {We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.}, } @article {pmid37821799, year = {2023}, author = {Reeves, IM and Totterdell, JA and Betty, EL and Donnelly, DM and George, A and Holmes, S and Moller, L and Stockin, KA and Wellard, R and White, C and Foote, AD}, title = {Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers.}, journal = {The Journal of heredity}, volume = {114}, number = {6}, pages = {598-611}, pmid = {37821799}, issn = {1465-7333}, support = {ERC-COG-101045346/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Whale, Killer/genetics ; Australia ; Whales/genetics ; Base Sequence ; New Zealand ; }, abstract = {Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom," washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.}, } @article {pmid37819893, year = {2023}, author = {Reynoso-García, J and Santiago-Rodriguez, TM and Narganes-Storde, Y and Cano, RJ and Toranzos, GA}, title = {Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292077}, pmid = {37819893}, issn = {1932-6203}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Puerto Rico ; *Diet ; Ethnicity ; Fungi ; }, abstract = {Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.}, } @article {pmid37819677, year = {2024}, author = {Marchi, N and Kapopoulou, A and Excoffier, L}, title = {Demogenomic inference from spatially and temporally heterogeneous samples.}, journal = {Molecular ecology resources}, volume = {24}, number = {1}, pages = {e13877}, doi = {10.1111/1755-0998.13877}, pmid = {37819677}, issn = {1755-0998}, support = {310030_188883/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Humans ; *Genetics, Population ; *Genome ; Genomics ; DNA, Ancient ; Models, Genetic ; }, abstract = {Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.}, } @article {pmid37819040, year = {2023}, author = {Quiroz-Morales, SE and Muriel-Millán, LF and Ponce-Soto, GY and González-Valdez, A and Castillo-Juárez, I and Servín-González, L and Soberón-Chávez, G}, title = {Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {10}, pages = {}, pmid = {37819040}, issn = {1465-2080}, mesh = {Animals ; Mice ; *Quorum Sensing/genetics ; Pseudomonas aeruginosa/metabolism ; *Solanum lycopersicum ; Rhizosphere ; Signal Transduction/genetics ; Virulence Factors/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.}, } @article {pmid37810237, year = {2023}, author = {Gînguță, A and Kovács, B and Schütz, O and Tihanyi, B and Nyerki, E and Maár, K and Maróti, Z and Varga, GIB and Băcueț-Crișan, D and Keresztes, T and Török, T and Neparáczki, E}, title = {Genetic identification of members of the prominent Báthory aristocratic family.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107911}, pmid = {37810237}, issn = {2589-0042}, abstract = {The Báthory family was one of the most powerful noble families in the medieval Hungarian Kingdom. Their influence peaked during the Ottoman occupation of Hungary, when the only partially autonomous region of the country was Transylvania, under Turkish protectorate. Several members of the family became Princes of Transylvania, and one of them, István Báthory, was also the elected King of Poland. We hereby present the first genetic data about this extinct family. Archaeological excavations in Pericei, a settlement now part of Romania, revealed the former family chapel of the Báthory family. Through this work, two Báthory family members were successfully identified among the 13 skeletons found at the site. The presence of Y chromosome haplogroup R-S498 fits the historical account describing the family's German (Swabian) origins. Their genomic composition also indicates a family of Germanic origin that intermixed with medieval Hungarians.}, } @article {pmid37810206, year = {2023}, author = {Menéndez, LP and Barbieri, C and López Cruz, IG and Schmelzle, T and Breidenstein, A and Barquera, R and Borzi, G and Schuenemann, VJ and Sánchez-Villagra, MR}, title = {On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis.}, journal = {Swiss journal of palaeontology}, volume = {142}, number = {1}, pages = {26}, pmid = {37810206}, issn = {1664-2384}, abstract = {The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.}, } @article {pmid37809321, year = {2023}, author = {Dillon, EM and Dunne, EM and Womack, TM and Kouvari, M and Larina, E and Claytor, JR and Ivkić, A and Juhn, M and Carmona, PSM and Robson, SV and Saha, A and Villafaña, JA and Zill, ME}, title = {Challenges and directions in analytical paleobiology.}, journal = {Paleobiology}, volume = {49}, number = {3}, pages = {377-393}, pmid = {37809321}, issn = {0094-8373}, support = {P 31592/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.}, } @article {pmid37808674, year = {2023}, author = {Tretmanis, JM and Jay, F and Avila-Árcos, MC and Huerta-Sanchez, E}, title = {Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37808674}, issn = {2692-8205}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, abstract = {Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.}, } @article {pmid37797036, year = {2023}, author = {Dalén, L and Heintzman, PD and Kapp, JD and Shapiro, B}, title = {Deep-time paleogenomics and the limits of DNA survival.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {48-53}, pmid = {37797036}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; 101054984/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; DNA/genetics ; *DNA, Ancient ; *Genomics/methods ; Paleontology ; *Biological Evolution ; Animals ; }, abstract = {Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.}, } @article {pmid37797028, year = {2023}, author = {Burbano, HA and Gutaker, RM}, title = {Ancient DNA genomics and the renaissance of herbaria.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {59-63}, doi = {10.1126/science.adi1180}, pmid = {37797028}, issn = {1095-9203}, mesh = {*DNA, Ancient ; Genomics ; *Plants/genetics ; *Collections as Topic ; Conservation of Natural Resources ; Biological Evolution ; Adaptation, Biological/genetics ; Phenotype ; }, abstract = {Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.}, } @article {pmid37797024, year = {2023}, author = {Ávila-Arcos, MC and Raghavan, M and Schlebusch, C}, title = {Going local with ancient DNA: A review of human histories from regional perspectives.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {53-58}, doi = {10.1126/science.adh8140}, pmid = {37797024}, issn = {1095-9203}, support = {R35 GM143094/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Africa ; Americas ; Asia ; *DNA, Ancient ; Oceania ; *Demography/history ; *Social Structure ; *Health/history ; }, abstract = {Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.}, } @article {pmid37797011, year = {2023}, author = {Curry, A}, title = {Family ties.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {24-27}, doi = {10.1126/science.adl1577}, pmid = {37797011}, issn = {1095-9203}, abstract = {Giant family trees based on ancient DNA from thousands of people are revealing prehistoric politics and social structure.}, } @article {pmid37767965, year = {2023}, author = {Grathwol, F and Roos, C and Zinner, D and Hume, B and Porcier, SM and Berthet, D and Cuisin, J and Merker, S and Ottoni, C and Van Neer, W and Dominy, NJ and Kopp, GH}, title = {Adulis and the transshipment of baboons during classical antiquity.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37767965}, issn = {2050-084X}, mesh = {Humans ; Animals ; *Papio ; Phylogeny ; Africa ; Egypt ; Geography ; }, abstract = {Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers-Agatharchides of Cnidus, Pliny the Elder, Strabo-noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud ('Valley of the Monkeys'), Egypt. Dated to ca. 800-540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five centuries. Previously, Dominy et al. (2020) used stable isotope analysis to show that two New Kingdom specimens of Papio hamadryas originate from the Horn of Africa. Here, we report the complete mitochondrial genomes from a mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of P. hamadryas in Eritrea, Ethiopia, and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, corroborates Greco-Roman historiographies by pointing toward present-day Eritrea, and by extension Adulis, as a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history.}, } @article {pmid37752842, year = {2023}, author = {Ruiz-Puerta, EJ and Keighley, X and Desjardins, SPA and Gotfredsen, AB and Pan, SE and Star, B and Boessenkool, S and Barrett, JH and McCarthy, ML and Andersen, LW and Born, EW and Howse, LR and Szpak, P and Pálsson, S and Malmquist, HJ and Rufolo, S and Jordan, PD and Olsen, MT}, title = {Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2007}, pages = {20231349}, pmid = {37752842}, issn = {1471-2954}, abstract = {Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.}, } @article {pmid37752477, year = {2023}, author = {Kroes, R and Winkel, Y and Breeuwer, JAJ and van Loon, EE and Loader, SP and Maclaine, JS and Verdonschot, PFM and van der Geest, HG}, title = {Phylogenetic analysis of museum specimens of houting Coregonus oxyrinchus shows the need for a revision of its extinct status.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {57}, pmid = {37752477}, issn = {2730-7182}, mesh = {Animals ; Phylogeny ; *Museums ; *Salmonidae/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {According to the IUCN Red List the anadromous houting Coregonus oxyrinchus is categorized as 'extinct'. However, this extinct status might be incorrect because taxonomic difference between C. oxyrinchus and the closely related C. lavaretus is based on a disputable morphological comparison. Also, phylogenetic studies on mtDNA only focused on recent obtained coregonids. We are the first to perform a mtDNA analysis on both historic and recent specimens, including the syntype specimen which was used for species description by Linnaeus originally. Two primer pairs for mitochondrial CytB and ND3 were used to extract sequences for phylogenetic analysis. Sequences from 14 out of 21 C. oxyrinchus museum specimens were successfully obtained and compared with sequences from recent obtained C. lavaretus. The sequences were combined with GenBank data from a previous phylogenetic study on houting to create a phylogenetic tree and two minimum spanning haplotype networks. Results show that C. oxyrinchus and C. lavaretus form a clade with limited genetic variation. Low bootstrap values also show weak support for geographical patterns in distribution of mitochondrial haplotypes. Statistical analysis of the haplotype networks also shows that historic and recent specimens are similar species. Our results suggest that C. oxyrinchus is a junior synonym of C. lavaretus. A definitive taxonomic revision could not be made because only CytB sequencing was successful for the syntype specimen. We discuss taxonomic consequences and the species-specific focus in nature conservation. We propose a shift in nature conservation to a more functional approach based on traits rather than species.}, } @article {pmid37749660, year = {2023}, author = {Wegner, CE and Stahl, R and Velsko, I and Hübner, A and Fagernäs, Z and Warinner, C and Lehmann, R and Ritschel, T and Totsche, KU and Küsel, K}, title = {A glimpse of the paleome in endolithic microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {210}, pmid = {37749660}, issn = {2049-2618}, mesh = {*Genomics ; Paleontology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {BACKGROUND: The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS: By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 10[5] cells × g[-1] rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS: Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.}, } @article {pmid37738339, year = {2023}, author = {Oliveira, S and Fehn, AM and Amorim, B and Stoneking, M and Rocha, J}, title = {Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.}, journal = {Science advances}, volume = {9}, number = {38}, pages = {eadh3822}, pmid = {37738339}, issn = {2375-2548}, mesh = {Humans ; *Black People/genetics ; *DNA, Ancient ; Namibia ; }, abstract = {Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.}, } @article {pmid37719142, year = {2023}, author = {Wang, K and Prüfer, K and Krause-Kyora, B and Childebayeva, A and Schuenemann, VJ and Coia, V and Maixner, F and Zink, A and Schiffels, S and Krause, J}, title = {High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry.}, journal = {Cell genomics}, volume = {3}, number = {9}, pages = {100377}, pmid = {37719142}, issn = {2666-979X}, abstract = {The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.}, } @article {pmid37717498, year = {2023}, author = {Díaz-Navarro, S and Haber Uriarte, M and García-González, R}, title = {Holes in the Head. Double cranial surgery on an individual from the Chalcolithic burial site of Camino del Molino (SE Spain).}, journal = {International journal of paleopathology}, volume = {43}, number = {}, pages = {22-30}, doi = {10.1016/j.ijpp.2023.09.003}, pmid = {37717498}, issn = {1879-9825}, mesh = {Adult ; Humans ; Female ; Spain ; *Skull/pathology ; *Trephining ; Burial/methods ; Europe ; }, abstract = {OBJECTIVE: This article analyses new prehistoric evidence of trepanation from a collective burial site in the south-eastern Iberian Peninsula.

MATERIALS: The trepanned individual was documented in the Chalcolithic burial site of Camino del Molino, where 1348 individuals (30.7 % non-adults and 69.3 % adults) were deposited in two contiguous funerary phases, making it a reference site for the knowledge of Recent Prehistoric populations.

METHODS: The individual has been sexed using traditional anthropological methods and ancient DNA. C14 dating has also been obtained. The lesion has been analysed macroscopically and microscopically using SEM.

RESULTS: The skull under study belonged to an adult female deposited in the second burial phase (2566-2239 years cal BCE). It exhibits in the anterior region of the right temporal fossa two contiguous and partially overlapping holes that correspond to two trepanations performed using the scraping technique.

CONCLUSIONS: It is a double cranial trepanation with signs of bone remodelling suggesting survival from surgery. No pathological signs were identified potentially associated with the intervention.

SIGNIFICANCE: This is the second case of surgical interventions in the geographical area of study and one of the few evidences of this practice in women during prehistoric times.

LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed.

Further intensive review of skull collection is advised to learn more about these surgical interventions in Copper Age and to go deeper into the causes that motivated their execution.}, } @article {pmid37712846, year = {2023}, author = {Davidson, R and Williams, MP and Roca-Rada, X and Kassadjikova, K and Tobler, R and Fehren-Schmitz, L and Llamas, B}, title = {Allelic bias when performing in-solution enrichment of ancient human DNA.}, journal = {Molecular ecology resources}, volume = {23}, number = {8}, pages = {1823-1840}, doi = {10.1111/1755-0998.13869}, pmid = {37712846}, issn = {1755-0998}, support = {DE190101069//Australian Research Council/ ; FT170100448//Australian Research Council/ ; 1515138//National Science Foundation/ ; }, abstract = {In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.}, } @article {pmid37701515, year = {2022}, author = {Jaramillo-Valverde, L and Vásquez-Domínguez, A and Levano, KS and Castrejon-Cabanillas, R and Novoa-Bellota, P and Machacuay-Romero, M and Garcia-de-la-Guarda, R and Cano, RJ and Shady Solis, R and Guio, H}, title = {A mobile lab for ancient DNA extraction in Perug.}, journal = {Bioinformation}, volume = {18}, number = {12}, pages = {1114-1118}, pmid = {37701515}, issn = {0973-2063}, abstract = {We report the use of a mobile laboratory set up to extract ancient DNA (aDNA) from 34 human coprolites (fossilized faeces) samples. Our approach enabled the rapid genetic characterization of 5,000 years old archeological samples. It is useful for the on-site screening of museums and freshly excavated samples for DNA. This approach is accessible to other investigators as the mobile laboratory was set up using commercially available instruments.}, } @article {pmid37699853, year = {2023}, author = {Chocholova, E and Roudnicky, P and Potesil, D and Fialova, D and Krystofova, K and Drozdova, E and Zdrahal, Z}, title = {Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.}, journal = {Journal of proteome research}, volume = {22}, number = {10}, pages = {3311-3319}, pmid = {37699853}, issn = {1535-3907}, abstract = {Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.}, } @article {pmid37683613, year = {2023}, author = {Sandoval-Velasco, M and Jagadeesan, A and Ramos-Madrigal, J and Ávila-Arcos, MC and Fortes-Lima, CA and Watson, J and Johannesdóttir, E and Cruz-Dávalos, DI and Gopalakrishnan, S and Moreno-Mayar, JV and Niemann, J and Renaud, G and Robson Brown, KA and Bennett, H and Pearson, A and Helgason, A and Gilbert, MTP and Schroeder, H}, title = {The ancestry and geographical origins of St Helena's liberated Africans.}, journal = {American journal of human genetics}, volume = {110}, number = {9}, pages = {1590-1599}, pmid = {37683613}, issn = {1537-6605}, mesh = {Humans ; Female ; Male ; *African People ; DNA, Ancient ; Black People/genetics ; *Enslaved Persons ; Genotype ; }, abstract = {The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.}, } @article {pmid37673908, year = {2023}, author = {Hodgins, HP and Chen, P and Lobb, B and Wei, X and Tremblay, BJM and Mansfield, MJ and Lee, VCY and Lee, PG and Coffin, J and Duggan, AT and Dolphin, AE and Renaud, G and Dong, M and Doxey, AC}, title = {Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5475}, pmid = {37673908}, issn = {2041-1723}, support = {R01 NS080833/NS/NINDS NIH HHS/United States ; R01 NS117626/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *DNA, Ancient ; Neurotoxins ; *Tetanus ; Phylogeny ; Clostridium ; Chile ; Mammals ; }, abstract = {The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.}, } @article {pmid37666338, year = {2023}, author = {Han, W and Zhang, E and Sun, W and Lin, Q and Meng, X and Ni, Z and Ning, D and Shen, J}, title = {Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166715}, doi = {10.1016/j.scitotenv.2023.166715}, pmid = {37666338}, issn = {1879-1026}, mesh = {Humans ; *Ecosystem ; Tibet ; *Lakes ; Anthropogenic Effects ; Eutrophication ; China ; }, abstract = {Lakes on the Qinghai-Tibet Plateau (QTP) have been subject to multiple environmental pressures from rapid climate change and intensified human activity in recent decades. However, their ecological effects on the lake ecosystem remain largely unclear due to the lack of long-term monitoring data. This study presented the environmental and ecological changes of the lake Yamzhog Yumco (Southern QTP) over the past three decades based on multi-proxy analysis (geochemistry and sedaDNA) on a high-time resolution sediment core. The result showed that the lake exhibited a continuous eutrophication process from 2004 CE, which has accelerated since 2014 CE. The nutrient enrichment was mainly attributed to anthropogenic emissions from the catchment. The sedimentary ancient DNA (sedaDNA) metabarcoding data registered a sensitive response of aquatic communities to the additional nutrient supply. Eukaryotic algae and aquatic invertebrate communities exhibited similar temporal dynamics, characterized by the increase in eutrophic taxa and the decrease in oligotrophic taxa. Change points analysis suggested that lake ecosystems underwent a slight ecological shift in 2003 CE and an abrupt shift in 2012 CE driven by nutrient enrichment. Quantitative analysis revealed that nutrients and human activity accounted for 27.9 % and 21.7 % of the temporal variation in aquatic communities, whereas climate change only explained 6.9 % of the total variation. From a paleolimnological view, our study supported that regional human activity could distinctly alter the nutrient level and aquatic community structure of lake ecosystems in the QTP. Considering that anthropogenic disturbance will continuously increase, it is crucial to strengthen the field monitoring of the lakes on the plateau and make effective management measures to avoid irreversible ecological consequences.}, } @article {pmid37652999, year = {2023}, author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ}, title = {Ancient DNA reveals genetic admixture in China during tiger evolution.}, journal = {Nature ecology & evolution}, volume = {7}, number = {11}, pages = {1914-1929}, pmid = {37652999}, issn = {2397-334X}, support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; }, mesh = {Animals ; *Tigers/genetics ; DNA, Ancient ; Phylogeny ; Russia ; China ; }, abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.}, } @article {pmid37652634, year = {2023}, author = {Beltrame, MO and Moviglia, GS and De Tommaso, D and Quintana, S}, title = {Gastrointestinal parasites of domestic sheep from Patagonia throughout historical times: A paleoparasitological approach.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {44}, number = {}, pages = {100915}, doi = {10.1016/j.vprsr.2023.100915}, pmid = {37652634}, issn = {2405-9390}, mesh = {Animals ; Sheep ; *Parasites ; Sheep, Domestic ; *Intestinal Diseases, Parasitic/veterinary ; *Fascioliasis/veterinary ; Argentina/epidemiology ; *Eimeria ; *Nematodirus ; *Sheep Diseases ; }, abstract = {Sheep husbandry in Patagonia, Argentina, started at the beginning of the 20th century from European settlers. Sanitary management is minimal, which has serious implications for the sheep health. Sheep can be infested by diverse parasites, with well over 150 species of internal and external parasites reported worldwide. Gastrointestinal parasitism is one of the most common and important infections in sheep concerning the health status, and is the cause of significant morbidity and mortality, which generates considerable production losses. The present work is the first paleoparasitological study of sheep coprolites from Patagonia throughout historical times. Fifty-seven coprolites from the 'Cueva Peligro' archaeological site (Patagonia, Argentina) were analyzed using the Lutz spontaneous sedimentation technique and the modified Faust flotation technique. Ancient DNA (aDNA) study was carried out in order to identify the zoological origin of coprolites. The results obtained from Cytb analysis confirmed the identity of the host as Ovis aries (domestic sheep). A total of 39 coprolites examined were positive for parasites by at least one of the studied methods. Thirty eight samples were positive by spontaneous sedimentation and 10 samples were positive by the modified Faust technique. The parasitic fauna found was Trichuris sp. (Trichinellida: Trichuridae), Nematodirus sp., Nematodirus spathiger (Strongylida, Trichostrongyloidea), two unidentified Strongylida-type egg morphotypes, Fasciola hepatica (Trematoda: Digenea) and coccidia oocysts of Eimeria spp. (Apicomplexa: Eimeriidae). The modified Faust technique provided satisfactory results in terms of sensitivity for the detection of Eimeria spp. The use of this methodology as a routine procedure enables the processing of ancient samples, in order to increase recoveries. These results show the importance of integrating different diagnostic approaches in order to optimize parasitic findings. The recorded parasite diversity appears to have not changed over the last 120 years. The study displayed the presence of different parasitic species which suggests potential exposure to parasitic diseases through the historical times, both for sheep and for other domestic and wild mammals from Patagonia. Also, suggests the presence of fasciolosis, a zoonotic disease that implies a potential risk for Patagonian populations in the past.}, } @article {pmid37644833, year = {2023}, author = {Aoki, K and Takahata, N and Oota, H and Wakano, JY and Feldman, MW}, title = {Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2005}, pages = {20231262}, pmid = {37644833}, issn = {1471-2954}, mesh = {Humans ; *Archaeology ; Asia, Eastern ; *Communicable Diseases ; DNA, Ancient ; East Asian People ; }, abstract = {An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.}, } @article {pmid37633281, year = {2023}, author = {Vyas, DN and Koncz, I and Modi, A and Mende, BG and Tian, Y and Francalacci, P and Lari, M and Vai, S and Straub, P and Gallina, Z and Szeniczey, T and Hajdu, T and Pejrani Baricco, L and Giostra, C and Radzevičiūtė, R and Hofmanová, Z and Évinger, S and Bernert, Z and Pohl, W and Caramelli, D and Vida, T and Geary, PJ and Veeramah, KR}, title = {Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia.}, journal = {Current biology : CB}, volume = {33}, number = {18}, pages = {3951-3961.e11}, doi = {10.1016/j.cub.2023.07.063}, pmid = {37633281}, issn = {1879-0445}, mesh = {Humans ; Female ; *Archaeology ; *Cemeteries/history ; Culture ; Base Sequence ; Europe ; }, abstract = {As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.[1][,][2] To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5[th] century cemeteries[3][,][4][,][5] at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site[6] and analyzed them alongside data from over 550 penecontemporaneous individuals.[7][,][8][,][9][,][10][,][11][,][12][,][13][,][14][,][15][,][16][,][17][,][18][,][19] The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial customs and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artifacts and genetic ancestry among 5[th] century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.}, } @article {pmid37631973, year = {2023}, author = {Burk, RD and Mirabello, L and DeSalle, R}, title = {Distinguishing Genetic Drift from Selection in Papillomavirus Evolution.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37631973}, issn = {1999-4915}, support = {P30 CA013330/CA/NCI NIH HHS/United States ; U01 CA238592/CA/NCI NIH HHS/United States ; U01 CA078527/CA/NCI NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeny ; *Papillomaviridae/genetics ; *Alphapapillomavirus ; Genetic Drift ; Codon Usage ; }, abstract = {Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.}, } @article {pmid37628575, year = {2023}, author = {Kusliy, MA and Yurlova, AA and Neumestova, AI and Vorobieva, NV and Gutorova, NV and Molodtseva, AS and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Semibratov, VP and Iderkhangai, TO and Kovalev, AA and Erdenebaatar, D and Graphodatsky, AS and Tishkin, AA}, title = {Genetic History of the Altai Breed Horses: From Ancient Times to Modernity.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628575}, issn = {2073-4425}, mesh = {Animals ; Horses/genetics ; Phylogeny ; *Hybridization, Genetic ; *DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes/genetics ; }, abstract = {This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.}, } @article {pmid37611212, year = {2023}, author = {van Waaij, J and Li, S and Garcia-Erill, G and Albrechtsen, A and Wiuf, C}, title = {Evaluation of population structure inferred by principal component analysis or the admixture model.}, journal = {Genetics}, volume = {225}, number = {2}, pages = {}, doi = {10.1093/genetics/iyad157}, pmid = {37611212}, issn = {1943-2631}, support = {8021-00360B//Independent Research Fund Denmark/ ; //China Scholarship Council/ ; }, abstract = {Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome-wide human data, we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.}, } @article {pmid37608001, year = {2023}, author = {Arbøll, TP and Rasmussen, SL and de Jonge, N and Hansen, AH and Pertoldi, C and Nielsen, JL}, title = {Revealing the secrets of a 2900-year-old clay brick, discovering a time capsule of ancient DNA.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13092}, pmid = {37608001}, issn = {2045-2322}, mesh = {*Clay/chemistry ; *Construction Materials/history ; *DNA, Ancient/analysis/isolation & purification ; History, Ancient ; Iraq ; Museums ; *Plants/classification/genetics ; Time Factors ; Archaeology/methods ; }, abstract = {The recent development of techniques to sequence ancient DNA has provided valuable insights into the civilisations that came before us. However, the full potential of these methods has yet to be realised. We extracted ancient DNA from a recently exposed fracture surface of a clay brick deriving from the palace of king Ashurnasirpal II (883-859 BCE) in Nimrud, Iraq. We detected 34 unique taxonomic groups of plants. With this research we have made the pioneering discovery that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2900-year-old clay brick. We encourage future research into this subject, as the scientific prospects for this approach are substantial, potentially leading to a deeper understanding of ancient and lost civilisations.}, } @article {pmid37604894, year = {2023}, author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L}, title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13635}, pmid = {37604894}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; }, abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.}, } @article {pmid37589132, year = {2023}, author = {Essel, E}, title = {Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel.}, journal = {BioTechniques}, volume = {75}, number = {2}, pages = {42-46}, doi = {10.2144/btn-2023-0067}, pmid = {37589132}, issn = {1940-9818}, mesh = {Humans ; Female ; *DNA, Ancient ; *Anthropology ; Body Remains ; Sequence Analysis, DNA ; Universities ; }, abstract = {Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow.}, } @article {pmid37584528, year = {2023}, author = {Kambouris, ME and Patrinos, GP and Velegraki, A and Manoussopoulos, Y}, title = {Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {681-693}, doi = {10.2217/fmb-2023-0031}, pmid = {37584528}, issn = {1746-0921}, mesh = {Humans ; *Paleopathology/methods ; *Fellowships and Scholarships ; Pandemics ; }, abstract = {The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.}, } @article {pmid37582830, year = {2023}, author = {Serrano, JG and Ordóñez, AC and Santana, J and Sánchez-Cañadillas, E and Arnay, M and Rodríguez-Rodríguez, A and Morales, J and Velasco-Vázquez, J and Alberto-Barroso, V and Delgado-Darias, T and de Mercadal, MCC and Hernández, JC and Moreno-Benítez, MA and Pais, J and Ringbauer, H and Sikora, M and McColl, H and Pino-Yanes, M and Ferrer, MH and Bustamante, CD and Fregel, R}, title = {The genomic history of the indigenous people of the Canary Islands.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4641}, pmid = {37582830}, issn = {2041-1723}, mesh = {Humans ; Spain ; *Genetic Drift ; Africa, Northern ; *Genomics ; Indigenous Peoples ; Islands ; Genetic Variation ; Genetics, Population ; }, abstract = {The indigenous population of the Canary Islands, which colonized the archipelago around the 3[rd] century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3[rd]-16[rd] centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.}, } @article {pmid37580949, year = {2024}, author = {Bretschneider, A and Mazanec, J and Wittmeier, P and Flux, AL and Schmidt, D and Hummel, S}, title = {X-chromosomal STRs in aDNA kinship analysis.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {81}, number = {2}, pages = {131-138}, doi = {10.1127/anthranz/2023/1714}, pmid = {37580949}, issn = {0003-5548}, mesh = {Humans ; *DNA, Ancient ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; Germany ; Body Remains ; Microsatellite Repeats/genetics ; Chromosomes, Human, Y/genetics ; }, abstract = {The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.}, } @article {pmid37567955, year = {2023}, author = {Kim, J and Rosenberg, NA}, title = {Record-matching of STR profiles with fragmentary genomic SNP data.}, journal = {European journal of human genetics : EJHG}, volume = {31}, number = {11}, pages = {1283-1290}, pmid = {37567955}, issn = {1476-5438}, support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA Fingerprinting/methods ; Microsatellite Repeats ; Genotype ; Genomics ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.}, } @article {pmid37562011, year = {2023}, author = {Gerber, D and Szeifert, B and Székely, O and Egyed, B and Gyuris, B and Giblin, JI and Horváth, A and Köhler, K and Kulcsár, G and Kustár, Á and Major, I and Molnár, M and Palcsu, L and Szeverényi, V and Fábián, S and Mende, BG and Bondár, M and Ari, E and Kiss, V and Szécsényi-Nagy, A}, title = {Interdisciplinary Analyses of Bronze Age Communities from Western Hungary Reveal Complex Population Histories.}, journal = {Molecular biology and evolution}, volume = {40}, number = {9}, pages = {}, pmid = {37562011}, issn = {1537-1719}, mesh = {Humans ; History, Ancient ; Hungary ; *Human Migration ; *Genome, Human ; Europe ; DNA, Ancient ; }, abstract = {In this study, we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archeological cultures (3,530-1,620 cal Bce). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted Pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture-associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture-related population and one from a previously unrecognized source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted Pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analyzing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.}, } @article {pmid37561011, year = {2023}, author = {Sánchez-Barreiro, F and De Cahsan, B and Westbury, MV and Sun, X and Margaryan, A and Fontsere, C and Bruford, MW and Russo, IM and Kalthoff, DC and Sicheritz-Pontén, T and Petersen, B and Dalén, L and Zhang, G and Marquès-Bonet, T and Gilbert, MTP and Moodley, Y}, title = {Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.}, journal = {Molecular biology and evolution}, volume = {40}, number = {9}, pages = {}, pmid = {37561011}, issn = {1537-1719}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; 681396/ERC_/European Research Council/International ; }, mesh = {Animals ; Africa, Eastern ; Africa South of the Sahara ; *Biological Evolution ; *Perissodactyla/genetics ; Endangered Species ; }, abstract = {The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.}, } @article {pmid37559969, year = {2023}, author = {Ozga, AT and Ottoni, C}, title = {Dental calculus as a proxy for animal microbiomes.}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {653-654}, number = {}, pages = {47-52}, pmid = {37559969}, issn = {1040-6182}, abstract = {The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.}, } @article {pmid37548135, year = {2023}, author = {Arencibia, V and Muñoz, M and Crespo, CM and Russo, MG and Vera, P and Lia, VV and García Guraieb, S and Goñi, RA and Avena, S and Puebla, A and Dejean, CB}, title = {Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24822}, pmid = {37548135}, issn = {2692-7691}, support = {PICT 2014-3012//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Fundación Científica Felipe Fiorellino/ ; //Fundación de Historia Natural Félix Azara/ ; UBACyT 20020150200233BA//Universidad de Buenos Aires/ ; UBACyT 20020170200363BA//Universidad de Buenos Aires/ ; //CONICET/ ; }, abstract = {OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia.

MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network.

RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established.

DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.}, } @article {pmid37541241, year = {2023}, author = {Harney, É and Sirak, K and Sedig, J and Micheletti, S and Curry, R and Ancona Esselmann, S and Reich, D}, title = {Ethical considerations when co-analyzing ancient DNA and data from private genetic databases.}, journal = {American journal of human genetics}, volume = {110}, number = {9}, pages = {1447-1453}, pmid = {37541241}, issn = {1537-6605}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Reproducibility of Results ; *Communication ; DNA/genetics ; Databases, Genetic ; }, abstract = {Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.}, } @article {pmid37537290, year = {2023}, author = {Callaway, E}, title = {Ancient DNA reveals the living descendants of enslaved people through 23andMe.}, journal = {Nature}, volume = {620}, number = {7973}, pages = {251-252}, pmid = {37537290}, issn = {1476-4687}, mesh = {Humans ; *Black People/genetics/history ; *DNA, Ancient/analysis ; *Enslaved Persons/history ; *Genetic Testing ; *Genetics, Population ; Genome, Human ; *Genomics ; History, 18th Century ; History, 19th Century ; Mass Screening ; }, } @article {pmid37535713, year = {2023}, author = {Jackson, FLC}, title = {Community-initiated genomics.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6657}, pages = {482-483}, doi = {10.1126/science.adj2380}, pmid = {37535713}, issn = {1095-9203}, mesh = {Humans ; *Black or African American/genetics ; *DNA, Ancient ; Metagenomics ; *Enslavement/history ; }, abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.}, } @article {pmid37531864, year = {2023}, author = {Klever, AM and Alexander, KA and Almeida, D and Anderson, MZ and Ball, RL and Beamer, G and Boggiatto, P and Buikstra, JE and Chandler, B and Claeys, TA and Concha, AE and Converse, PJ and Derbyshire, KM and Dobos, KM and Dupnik, KM and Endsley, JJ and Endsley, MA and Fennelly, K and Franco-Paredes, C and Hagge, DA and Hall-Stoodley, L and Hayes, D and Hirschfeld, K and Hofman, CA and Honda, JR and Hull, NM and Kramnik, I and Lacourciere, K and Lahiri, R and Lamont, EA and Larsen, MH and Lemaire, T and Lesellier, S and Lee, NR and Lowry, CA and Mahfooz, NS and McMichael, TM and Merling, MR and Miller, MA and Nagajyothi, JF and Nelson, E and Nuermberger, EL and Pena, MT and Perea, C and Podell, BK and Pyle, CJ and Quinn, FD and Rajaram, MVS and Mejia, OR and Rothoff, M and Sago, SA and Salvador, LCM and Simonson, AW and Spencer, JS and Sreevatsan, S and Subbian, S and Sunstrum, J and Tobin, DM and Vijayan, KKV and Wright, CTO and Robinson, RT}, title = {The Many Hosts of Mycobacteria 9 (MHM9): A conference report.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {142}, number = {}, pages = {102377}, pmid = {37531864}, issn = {1873-281X}, support = {R01 AI176943/AI/NIAID NIH HHS/United States ; R01 AI166304/AI/NIAID NIH HHS/United States ; R01 AI127715/AI/NIAID NIH HHS/United States ; R01 AI130236/AI/NIAID NIH HHS/United States ; K23 AI131913/AI/NIAID NIH HHS/United States ; R13 AI169929/AI/NIAID NIH HHS/United States ; R01 AI150765/AI/NIAID NIH HHS/United States ; R01 HL126066/HL/NHLBI NIH HHS/United States ; R01 AI125517/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Humans ; Nontuberculous Mycobacteria ; *Mycobacterium tuberculosis ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Tuberculosis, Bovine ; *Coinfection ; }, abstract = {The Many Hosts of Mycobacteria (MHM) meeting series brings together basic scientists, clinicians and veterinarians to promote robust discussion and dissemination of recent advances in our knowledge of numerous mycobacterial diseases, including human and bovine tuberculosis (TB), nontuberculous mycobacteria (NTM) infection, Hansen's disease (leprosy), Buruli ulcer and Johne's disease. The 9th MHM conference (MHM9) was held in July 2022 at The Ohio State University (OSU) and centered around the theme of "Confounders of Mycobacterial Disease." Confounders can and often do drive the transmission of mycobacterial diseases, as well as impact surveillance and treatment outcomes. Various confounders were presented and discussed at MHM9 including those that originate from the host (comorbidities and coinfections) as well as those arising from the environment (e.g., zoonotic exposures), economic inequality (e.g. healthcare disparities), stigma (a confounder of leprosy and TB for millennia), and historical neglect (a confounder in Native American Nations). This conference report summarizes select talks given at MHM9 highlighting recent research advances, as well as talks regarding the historic and ongoing impact of TB and other infectious diseases on Native American Nations, including those in Southwestern Alaska where the regional TB incidence rate is among the highest in the Western hemisphere.}, } @article {pmid37529780, year = {2023}, author = {Zhao, C and Han, B and Yi, G and Jin, S and Zhang, Z and Li, S}, title = {Editorial: Epigenomics implication for economic traits in domestic animals.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1252640}, doi = {10.3389/fgene.2023.1252640}, pmid = {37529780}, issn = {1664-8021}, } @article {pmid37528780, year = {2023}, author = {Fesenko, DO and Aramova, OY and Vdovchenkov, EV and Ivanovsky, ID and Fesenko, OE and Polyakov, SA and Faleeva, TG and Filippova, MA and Florinskaya, VS and Kornienko, IV}, title = {[DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia].}, journal = {Molekuliarnaia biologiia}, volume = {57}, number = {4}, pages = {597-608}, pmid = {37528780}, issn = {0026-8984}, mesh = {Humans ; *Eye Color ; DNA/genetics ; Burial ; Russia ; *Blood Group Antigens ; }, abstract = {Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate.}, } @article {pmid37528222, year = {2023}, author = {Delsol, N and Stucky, BJ and Oswald, JA and Cobb, CR and Emery, KF and Guralnick, R}, title = {Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12444}, pmid = {37528222}, issn = {2045-2322}, mesh = {Humans ; Animals ; Cattle/genetics ; *DNA, Ancient ; Phylogeny ; Americas ; Europe ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Haplotypes ; }, abstract = {Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.}, } @article {pmid37525572, year = {2023}, author = {Tamburrini, C and Dahinten, SL and Saihueque, RRR and Ávila-Arcos, MC and Parolin, ML}, title = {Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia.}, journal = {American journal of biological anthropology}, volume = {182}, number = {2}, pages = {161-176}, doi = {10.1002/ajpa.24821}, pmid = {37525572}, issn = {2692-7691}, mesh = {Humans ; *Genomics ; Argentina ; }, abstract = {Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.}, } @article {pmid37510218, year = {2023}, author = {Zhang, N and Shao, X and Guo, Y and Zhang, X and Zhou, Y and Yuan, J and Tang, Z and Hu, S and Minyaev, SS and Cai, D}, title = {Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China.}, journal = {Genes}, volume = {14}, number = {7}, pages = {}, pmid = {37510218}, issn = {2073-4425}, mesh = {Animals ; Cattle/genetics ; *Genome, Mitochondrial ; Phylogeny ; Genetic Variation ; DNA, Ancient ; DNA, Mitochondrial/genetics ; China ; }, abstract = {Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle.}, } @article {pmid37503227, year = {2024}, author = {Simon, A and Coop, G}, title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37503227}, issn = {2692-8205}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; }, abstract = {Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.}, } @article {pmid37499002, year = {2023}, author = {Heggarty, P and Anderson, C and Scarborough, M and King, B and Bouckaert, R and Jocz, L and Kümmel, MJ and Jügel, T and Irslinger, B and Pooth, R and Liljegren, H and Strand, RF and Haig, G and Macák, M and Kim, RI and Anonby, E and Pronk, T and Belyaev, O and Dewey-Findell, TK and Boutilier, M and Freiberg, C and Tegethoff, R and Serangeli, M and Liosis, N and Stroński, K and Schulte, K and Gupta, GK and Haak, W and Krause, J and Atkinson, QD and Greenhill, SJ and Kühnert, D and Gray, RD}, title = {Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6656}, pages = {eabg0818}, doi = {10.1126/science.abg0818}, pmid = {37499002}, issn = {1095-9203}, mesh = {Bayes Theorem ; Europe ; Farms ; *Language/history ; Phylogeny ; }, abstract = {The origins of the Indo-European language family are hotly disputed. Bayesian phylogenetic analyses of core vocabulary have produced conflicting results, with some supporting a farming expansion out of Anatolia ~9000 years before present (yr B.P.), while others support a spread with horse-based pastoralism out of the Pontic-Caspian Steppe ~6000 yr B.P. Here we present an extensive database of Indo-European core vocabulary that eliminates past inconsistencies in cognate coding. Ancestry-enabled phylogenetic analysis of this dataset indicates that few ancient languages are direct ancestors of modern clades and produces a root age of ~8120 yr B.P. for the family. Although this date is not consistent with the Steppe hypothesis, it does not rule out an initial homeland south of the Caucasus, with a subsequent branch northward onto the steppe and then across Europe. We reconcile this hybrid hypothesis with recently published ancient DNA evidence from the steppe and the northern Fertile Crescent.}, } @article {pmid37495791, year = {2023}, author = {Callaway, E}, title = {Seven generations of a prehistoric family mapped with ancient DNA.}, journal = {Nature}, volume = {620}, number = {7972}, pages = {19}, pmid = {37495791}, issn = {1476-4687}, mesh = {History, Ancient ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Human Migration ; }, } @article {pmid37495780, year = {2023}, author = {}, title = {Family trees of a Neolithic community uncovered by ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37495780}, issn = {1476-4687}, } @article {pmid37495691, year = {2023}, author = {Rivollat, M and Rohrlach, AB and Ringbauer, H and Childebayeva, A and Mendisco, F and Barquera, R and Szolek, A and Le Roy, M and Colleran, H and Tuke, J and Aron, F and Pemonge, MH and Späth, E and Télouk, P and Rey, L and Goude, G and Balter, V and Krause, J and Rottier, S and Deguilloux, MF and Haak, W}, title = {Extensive pedigrees reveal the social organization of a Neolithic community.}, journal = {Nature}, volume = {620}, number = {7974}, pages = {600-606}, pmid = {37495691}, issn = {1476-4687}, mesh = {Adult ; Child ; Female ; Humans ; Male ; Agriculture/history ; *Anthropology, Cultural ; Burial/history ; Fathers/history ; Fertility ; France ; History, Ancient ; Mortality/history ; *Pedigree ; Siblings ; Social Support/history ; Strontium Isotopes/analysis ; *Social Environment ; Mothers/history ; }, abstract = {Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations[1-4]. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality[5]. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.}, } @article {pmid37494435, year = {2023}, author = {Salazar, L and Burger, R and Forst, J and Barquera, R and Nesbitt, J and Calero, J and Washburn, E and Verano, J and Zhu, K and Sop, K and Kassadjikova, K and Ibarra Asencios, B and Davidson, R and Bradley, B and Krause, J and Fehren-Schmitz, L}, title = {Insights into the genetic histories and lifeways of Machu Picchu's occupants.}, journal = {Science advances}, volume = {9}, number = {30}, pages = {eadg3377}, doi = {10.1126/sciadv.adg3377}, pmid = {37494435}, issn = {2375-2548}, abstract = {Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.}, } @article {pmid37491505, year = {2023}, author = {Barsch, E and Kowarik, K and Rodler, K and Hörweg, C and Reschreiter, H and Sattmann, H and Walochnik, J}, title = {First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12055}, pmid = {37491505}, issn = {2045-2322}, mesh = {Animals ; Humans ; Ascaris lumbricoides/genetics ; Austria ; Ascaris/genetics ; *Ascariasis ; *Nematode Infections ; Trichuris/genetics ; Feces/parasitology ; Soil ; }, abstract = {Palaeoparasitological studies can provide valuable information on the emergence, distribution, and elimination of parasites during a particular time in the past. In the prehistoric salt mines of Hallstatt, located in the Austrian Alps, human faeces have been conserved in salt. The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. Altogether, 35 coprolites from the Hallstatt salt mines, dating back to the Bronze Age mining phase (1158-1063 BCE) and the Iron Age mining phase (750-662 BCE), respectively, were analysed by microscopy and molecular methods. In 91% of the coprolite samples, eggs of soil-transmitted helminths (STH), namely of Trichuris and/or Ascaris were detected by light microscopy. The Ascaris eggs were exceptionally well preserved. For further analysis, DNA was extracted from the palaeofaecal samples and species-specific primers targeting different genes were designed. While amplification of Trichuris DNA remained unsuccessful, sequence data of A. lumbricoides species complex were successfully obtained from 16 coprolites from three different genes, the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), the mitochondrial cytochrome B gene (cytB) and the mitochondrial NADH dehydrogenase subunit 1 gene (nadh1). Importantly, these included two Ascaris sequences from a coprolite from the Bronze Age, which to the best of our knowledge are the first molecular data of this genus from this period.}, } @article {pmid37488251, year = {2023}, author = {Fontani, F and Boano, R and Cinti, A and Demarchi, B and Sandron, S and Rampelli, S and Candela, M and Traversari, M and Latorre, A and Iacovera, R and Abondio, P and Sarno, S and Mackie, M and Collins, M and Radini, A and Milani, C and Petrella, E and Giampalma, E and Minelli, A and Larocca, F and Cilli, E and Luiselli, D}, title = {Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant'Angelo (Calabria, Italy).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11978}, pmid = {37488251}, issn = {2045-2322}, mesh = {Humans ; *Burial ; *Archaeology ; Body Remains ; Bone Matrix ; Italy ; }, abstract = {The Neolithic burial of Grotta di Pietra Sant'Angelo (CS) represents a unique archaeological finding for the prehistory of Southern Italy. The unusual placement of the inhumation at a rather high altitude and far from inhabited areas, the lack of funerary equipment and the prone deposition of the body find limited similarities in coeval Italian sites. These elements have prompted wider questions on mortuary customs during the prehistory of Southern Italy. This atypical case requires an interdisciplinary approach aimed to build an integrated bioarchaeological profile of the individual. The paleopathological investigation of the skeletal remains revealed the presence of numerous markers that could be associated with craft activities, suggesting possible interpretations of the individual's lifestyle. CT analyses, carried out on the maxillary bones, showed the presence of a peculiar type of dental wear, but also a good density of the bone matrix. Biomolecular and micromorphological analyses of dental calculus highlight the presence of a rich Neolithic-like oral microbiome, the composition of which is consistent with the presence pathologies. Finally, paleogenomic data obtained from the individual were compared with ancient and modern Mediterranean populations, including unpublished high-resolution genome-wide data for 20 modern inhabitants of the nearby village of San Lorenzo Bellizzi, which provided interesting insights into the biodemographic landscape of the Neolithic in Southern Italy.}, } @article {pmid37485357, year = {2023}, author = {Ginja, C and Guimarães, S and da Fonseca, RR and Rasteiro, R and Rodríguez-Varela, R and Simões, LG and Sarmento, C and Belarte, MC and Kallala, N and Torres, JR and Sanmartí, J and Arruda, AM and Detry, C and Davis, S and Matos, J and Götherström, A and Pires, AE and Valenzuela-Lamas, S}, title = {Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.}, journal = {iScience}, volume = {26}, number = {7}, pages = {107196}, pmid = {37485357}, issn = {2589-0042}, abstract = {The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.}, } @article {pmid37474518, year = {2023}, author = {Campos, PE and Pruvost, O and Boyer, K and Chiroleu, F and Cao, TT and Gaudeul, M and Baider, C and Utteridge, TMA and Becker, N and Rieux, A and Gagnevin, L}, title = {Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4306}, pmid = {37474518}, issn = {2041-1723}, mesh = {Humans ; Phylogeny ; *Xanthomonas/genetics ; Genomics ; *Citrus/microbiology ; Plant Diseases/microbiology ; }, abstract = {Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).}, } @article {pmid37465192, year = {2023}, author = {Malyarchuk, BA}, title = {The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {27}, number = {4}, pages = {373-382}, doi = {10.18699/VJGB-23-45}, pmid = {37465192}, issn = {2500-0462}, abstract = {The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.}, } @article {pmid37463880, year = {2023}, author = {Louis, M and Korlević, P and Nykänen, M and Archer, F and Berrow, S and Brownlow, A and Lorenzen, ED and O'Brien, J and Post, K and Racimo, F and Rogan, E and Rosel, PE and Sinding, MS and van der Es, H and Wales, N and Fontaine, MC and Gaggiotti, OE and Foote, AD}, title = {Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4020}, pmid = {37463880}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Genetics, Population ; Genomics ; Paleontology ; *Bottle-Nosed Dolphin/genetics ; Ecosystem ; }, abstract = {Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.}, } @article {pmid37463752, year = {2023}, author = {Mármol-Sánchez, E and Fromm, B and Oskolkov, N and Pochon, Z and Kalogeropoulos, P and Eriksson, E and Biryukova, I and Sekar, V and Ersmark, E and Andersson, B and Dalén, L and Friedländer, MR}, title = {Historical RNA expression profiles from the extinct Tasmanian tiger.}, journal = {Genome research}, volume = {33}, number = {8}, pages = {1299-1316}, pmid = {37463752}, issn = {1549-5469}, mesh = {Animals ; *Genomics/methods ; Phylogeny ; Extinction, Biological ; Paleontology ; *Marsupialia/genetics ; RNA/genetics ; }, abstract = {Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.}, } @article {pmid37463654, year = {2023}, author = {Lin, H and Hu, J and Baleka, S and Yuan, J and Chen, X and Xiao, B and Song, S and Du, Z and Lai, X and Hofreiter, M and Sheng, G}, title = {A genetic glimpse of the Chinese straight-tusked elephants.}, journal = {Biology letters}, volume = {19}, number = {7}, pages = {20230078}, pmid = {37463654}, issn = {1744-957X}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Elephants/genetics ; Fossils ; Phylogeny ; Phylogeography ; }, abstract = {Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.}, } @article {pmid37452091, year = {2023}, author = {Yang, C and Zhou, Y and Song, Y and Wu, D and Zeng, Y and Nie, L and Liu, P and Zhang, S and Chen, G and Xu, J and Zhou, H and Zhou, L and Qian, X and Liu, C and Tan, S and Zhou, C and Dai, W and Xu, M and Qi, Y and Wang, X and Guo, L and Fan, G and Wang, A and Deng, Y and Zhang, Y and Jin, J and He, Y and Guo, C and Guo, G and Zhou, Q and Xu, X and Yang, H and Wang, J and Xu, S and Mao, Y and Jin, X and Ruan, J and Zhang, G}, title = {The complete and fully-phased diploid genome of a male Han Chinese.}, journal = {Cell research}, volume = {33}, number = {10}, pages = {745-761}, pmid = {37452091}, issn = {1748-7838}, mesh = {Humans ; Male ; Asian People/genetics ; *Diploidy ; *East Asian People/ethnology/genetics ; *Genome, Human/genetics ; Genomics ; *Telomere/genetics ; }, abstract = {Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.}, } @article {pmid37450551, year = {2023}, author = {Pryor, Y and Lindo, J}, title = {Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives.}, journal = {Evolutionary anthropology}, volume = {32}, number = {4}, pages = {195-205}, doi = {10.1002/evan.21993}, pmid = {37450551}, issn = {1520-6505}, support = {1926075//Division of Behavioral and Cognitive Sciences/ ; 1945046//Division of Behavioral and Cognitive Sciences/ ; //Ford Foundation Predoctoral Fellowship/ ; 21602//National Science Foundation Graduate Research Fellowship/ ; }, mesh = {Animals ; Humans ; *Skin Pigmentation ; Biological Evolution ; *Hominidae ; Genomics ; }, abstract = {The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.}, } @article {pmid37438988, year = {2023}, author = {Lewis, DA and Simpson, R and Hermes, A and Brown, A and Llamas, B}, title = {More than dirt: Sedimentary ancient DNA and Indigenous Australia.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13835}, pmid = {37438988}, issn = {1755-0998}, support = {2011277//National Health and Medical Research Council/ ; 1137563//National Health and Medical Research Council/ ; }, abstract = {The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.}, } @article {pmid37438447, year = {2023}, author = {Tran, HL and Mai, HP and Le Thi, D and Thi, ND and Le Tung, L and Thanh, TP and Manh, HT and Mau, HN and Chu, HH and Hoang, H}, title = {The first maternal genetic study of hunter-gatherers from Vietnam.}, journal = {Molecular genetics and genomics : MGG}, volume = {298}, number = {5}, pages = {1225-1235}, pmid = {37438447}, issn = {1617-4623}, support = {DL0000.08/20-23//Vietnam Academy of Science and Technology/ ; }, mesh = {Humans ; Vietnam ; *Archaeology ; *DNA, Ancient/analysis ; Genome, Human ; }, abstract = {The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.}, } @article {pmid37433640, year = {2023}, author = {Weissensteiner, MH and Cremona, MA and Guiblet, WM and Stoler, N and Harris, RS and Cechova, M and Eckert, KA and Chiaromonte, F and Huang, YF and Makova, KD}, title = {Accurate sequencing of DNA motifs able to form alternative (non-B) structures.}, journal = {Genome research}, volume = {33}, number = {6}, pages = {907-922}, pmid = {37433640}, issn = {1549-5469}, support = {R01 GM136684/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Nucleotide Motifs ; *DNA, Z-Form ; Sequence Analysis, DNA ; DNA/genetics ; Base Composition ; High-Throughput Nucleotide Sequencing ; *Nanopores ; }, abstract = {Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.}, } @article {pmid37431939, year = {2023}, author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S}, title = {Diversity in matrilineages among the Jomon individuals of Japan.}, journal = {Annals of human biology}, volume = {50}, number = {1}, pages = {324-331}, doi = {10.1080/03014460.2023.2224060}, pmid = {37431939}, issn = {1464-5033}, mesh = {Humans ; Japan ; *Body Remains ; *Archaeology ; High-Throughput Nucleotide Sequencing ; Knowledge ; }, abstract = {BACKGROUND: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited.

AIM: We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.

SUBJECTS AND METHODS: For human remains dated to 8200-8600 cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing.

RESULTS: We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period.

CONCLUSION: The genetic diversity within the population was not found to be low even in the Initial Jomon period.}, } @article {pmid37423869, year = {2023}, author = {Bailey, E}, title = {Ancient DNA reveals an early adoption of horse culture by Native Americans.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {11}, pages = {808-809}, doi = {10.1016/j.tig.2023.06.010}, pmid = {37423869}, issn = {0168-9525}, mesh = {Animals ; Humans ; *American Indian or Alaska Native ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Horses/genetics ; }, abstract = {Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.}, } @article {pmid37422275, year = {2023}, author = {Ibrahim, J and Rechav, K and Boaretto, E and Weiner, S}, title = {Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation.}, journal = {Journal of structural biology}, volume = {215}, number = {3}, pages = {107998}, doi = {10.1016/j.jsb.2023.107998}, pmid = {37422275}, issn = {1095-8657}, mesh = {Animals ; Swine ; *DNA, Ancient ; *Odonata ; Petrous Bone ; Collagen ; Minerals ; }, abstract = {We report on the 3D ultrastructure of the mineralized petrous bone of mature pig using focused ion beam - scanning electron microscopy (FIB-SEM). We divide the petrous bone into two zones based on the degree of mineralization; one zone close to the otic chamber has higher mineral density than the second zone further away from the otic chamber. The hypermineralization of the petrous bone results in the collagen D-banding being poorly revealed in the lower mineral density zone (LMD), and absent in the high mineral density zone (HMD). We therefore could not use D-banding to decipher the 3D structure of the collagen assembly. Instead we exploited the anisotropy option in the Dragonfly image processing software to visualize the less mineralized collagen fibrils and/or nanopores that surround the more mineralized zones known as tesselles. This approach therefore indirectly tracks the orientations of the collagen fibrils in the matrix itself. We show that the HMD bone has a structure similar to that of woven bone, and the LMD is composed of lamellar bone with a plywood-like structural motif. This agrees with the fact that the bone close to the otic chamber is fetal bone and is not remodeled. The lamellar structure of the bone further away from the otic chamber is consistent with modeling/remodeling. The absence of the less mineralized collagen fibrils and nanopores resulting from the confluence of the mineral tesselles may contribute to shielding DNA during diagenesis. We show that anisotropy evaluation of the less mineralized collagen fibrils could be a useful tool to analyze bone ultrastructures and in particular the directionality of collagen fibril bundles that make up the bone matrix.}, } @article {pmid37395407, year = {2023}, author = {Brázda, V and Dobrovolná, M and Bohálová, N and Mergny, JL}, title = {G-quadruplexes in the evolution of hepatitis B virus.}, journal = {Nucleic acids research}, volume = {51}, number = {14}, pages = {7198-7204}, pmid = {37395407}, issn = {1362-4962}, mesh = {Humans ; *G-Quadruplexes ; Genome, Human ; Genomics ; *Hepatitis B virus/genetics ; Paleontology ; Biological Evolution ; }, abstract = {Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.}, } @article {pmid37387654, year = {2023}, author = {Kerner, G and Quintana-Murci, L}, title = {[Paleogenomics and the evolution of the human immune system over the last ten millennia].}, journal = {Medecine sciences : M/S}, volume = {39}, number = {6-7}, pages = {496-499}, doi = {10.1051/medsci/2023070}, pmid = {37387654}, issn = {1958-5381}, mesh = {Humans ; *Genomics ; *Paleontology ; }, } @article {pmid37380840, year = {2023}, author = {Lewis, D}, title = {Ancient-DNA researcher fired for 'serious misconduct' lands new role.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-023-02147-x}, pmid = {37380840}, issn = {1476-4687}, } @article {pmid37372418, year = {2023}, author = {Bonfigli, A and Cesare, P and Volpe, AR and Colafarina, S and Forgione, A and Aloisi, M and Zarivi, O and Poma, AMG}, title = {Estimation of DNA Degradation in Archaeological Human Remains.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372418}, issn = {2073-4425}, mesh = {Humans ; *DNA, Ancient ; Italy ; *Body Remains ; Bone and Bones ; DNA, Mitochondrial/genetics ; }, abstract = {The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.}, } @article {pmid37372367, year = {2023}, author = {Song, S and Xiao, B and Hu, J and Lin, H and Du, Z and Xiang, K and Pan, D and Hou, X and Yuan, J and Lai, X and Sheng, G}, title = {Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372367}, issn = {2073-4425}, mesh = {Humans ; Animals ; Phylogeny ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Ruminants ; Asia ; }, abstract = {As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.}, } @article {pmid37339987, year = {2023}, author = {Sousa da Mota, B and Rubinacci, S and Cruz Dávalos, DI and G Amorim, CE and Sikora, M and Johannsen, NN and Szmyt, MH and Włodarczak, P and Szczepanek, A and Przybyła, MM and Schroeder, H and Allentoft, ME and Willerslev, E and Malaspinas, AS and Delaneau, O}, title = {Imputation of ancient human genomes.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3660}, pmid = {37339987}, issn = {2041-1723}, support = {R35 GM142939/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Genotyping Techniques/methods ; *Genome, Human/genetics ; DNA, Ancient ; Genotype ; Genome-Wide Association Study/methods ; Polymorphism, Single Nucleotide ; }, abstract = {Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.}, } @article {pmid37337956, year = {2023}, author = {Doan, K and Schnitzler, A and Preston, F and Griggo, C and Lang, G and Belhaoues, F and Blaise, E and Crégut-Bonnoure, E and Frère, S and Foucras, S and Gardeisen, A and Laurent, A and Müller, W and Picavet, R and Puissant, S and Yvinec, JH and Pilot, M}, title = {Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.}, journal = {Molecular ecology}, volume = {32}, number = {16}, pages = {4627-4647}, doi = {10.1111/mec.17054}, pmid = {37337956}, issn = {1365-294X}, mesh = {Dogs ; Animals ; *Wolves/genetics ; Phylogeny ; Biological Evolution ; Phylogeography ; France ; Haplotypes/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.}, } @article {pmid37330109, year = {2024}, author = {Yang, L and Zhang, X and Hu, Y and Zhu, P and Li, H and Peng, Z and Xiang, H and Zhou, X and Zhao, X}, title = {Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {1}, pages = {87-95}, doi = {10.1016/j.jgg.2023.06.002}, pmid = {37330109}, issn = {1673-8527}, mesh = {Sheep/genetics ; Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Asia, Eastern ; China ; }, abstract = {Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.}, } @article {pmid37323114, year = {2023}, author = {Russo, MG and Arencibia, V and Emery, M and Bettera Marcat, G and Seldes, V and Mercolli, P and Soria, S and Maldonado, L and Kamenetzky, L and Avena, S and Dejean, C and Stone, AC}, title = {Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina.}, journal = {American journal of biological anthropology}, volume = {181}, number = {4}, pages = {597-610}, doi = {10.1002/ajpa.24795}, pmid = {37323114}, issn = {2692-7691}, mesh = {Humans ; Argentina ; *Genome, Mitochondrial/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; South America ; }, abstract = {OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina).

MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset.

RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya.

DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.}, } @article {pmid37317074, year = {2023}, author = {Sant'Anna, TB and Araujo, NM}, title = {Hepatitis B Virus Genotype D: An Overview of Molecular Epidemiology, Evolutionary History, and Clinical Characteristics.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317074}, issn = {2076-2607}, support = {E-26/210.450/2019//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {The hepatitis B virus (HBV) genotype D (HBV/D) is the most extensively distributed genotype worldwide with distinct molecular and epidemiological features. This report provides an up-to-date review on the history of HBV/D subgenotyping and misclassifications, along with large-scale analysis of over 1000 HBV/D complete genome sequences, with the aim of gaining a thorough understanding of the global prevalence and geographic distribution of HBV/D subgenotypes. We have additionally explored recent paleogenomic findings, which facilitated the detection of HBV/D genomes dating back to the late Iron Age and provided new perspectives on the origins of modern HBV/D strains. Finally, reports on distinct disease outcomes and responses to antiviral therapy among HBV/D subgenotypes are discussed, further highlighting the complexity of this genotype and the importance of HBV subgenotyping in the management and treatment of hepatitis B.}, } @article {pmid37313847, year = {2023}, author = {Legendre, L and Rode, J and Germon, I and Pavie, M and Quiviger, C and Policarpo, M and Leclercq, J and Père, S and Fumey, J and Hyacinthe, C and Ornelas-García, P and Espinasa, L and Rétaux, S and Casane, D}, title = {Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining.}, journal = {Zoological research}, volume = {44}, number = {4}, pages = {701-711}, pmid = {37313847}, issn = {2095-8137}, mesh = {Animals ; Biological Evolution ; *Caves ; Population Density ; *Fishes/genetics ; }, abstract = {The sizes of Astyanax mexicanus blind cavefish populations of North-East Mexico are demographic parameters of great importance for investigating a variety of ecological, evolutionary, and conservation issues. However, few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but their feasibility and interpretation of results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals (three days and three years) can give insights into cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachón cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachón cave since the last census in 1971 raises serious conservation issues.}, } @article {pmid37311857, year = {2023}, author = {de Sousa, AA and Beaudet, A and Calvey, T and Bardo, A and Benoit, J and Charvet, CJ and Dehay, C and Gómez-Robles, A and Gunz, P and Heuer, K and van den Heuvel, MP and Hurst, S and Lauters, P and Reed, D and Salagnon, M and Sherwood, CC and Ströckens, F and Tawane, M and Todorov, OS and Toro, R and Wei, Y}, title = {From fossils to mind.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {636}, pmid = {37311857}, issn = {2399-3642}, support = {P20 GM103653/GM/NIGMS NIH HHS/United States ; R01 AG067419/AG/NIA NIH HHS/United States ; R01 HG011641/HG/NHGRI NIH HHS/United States ; R24 NS092988/NS/NINDS NIH HHS/United States ; }, mesh = {*Fossils ; Phylogeny ; *Brain ; Archaeology ; Artifacts ; }, abstract = {Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.}, } @article {pmid37291482, year = {2023}, author = {Chen, N and Nedoluzhko, A}, title = {Ancient DNA: the past for the future.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {309}, pmid = {37291482}, issn = {1471-2164}, mesh = {Animals ; *DNA, Ancient ; Sequence Analysis, DNA/methods ; *Plants/genetics ; Laboratories ; }, abstract = {The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.}, } @article {pmid37286670, year = {2023}, author = {Humphrey, L and Bouzouggar, A}, title = {Ancient DNA reveals how farming spread into northwest Africa.}, journal = {Nature}, volume = {618}, number = {7965}, pages = {460-461}, pmid = {37286670}, issn = {1476-4687}, mesh = {History, Ancient ; *DNA, Ancient ; Africa ; *Anthropology ; Agriculture ; Archaeology ; }, } @article {pmid37284851, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M}, title = {Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology.}, journal = {International journal of legal medicine}, volume = {137}, number = {5}, pages = {1629-1638}, pmid = {37284851}, issn = {1437-1596}, support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {Male ; Humans ; Adult ; Middle Aged ; Child ; *Eye Color/genetics ; *Hair Color/genetics ; Powders ; DNA/genetics ; Bone and Bones ; Polymorphism, Single Nucleotide ; }, abstract = {Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.}, } @article {pmid37269363, year = {2023}, author = {Garcia-Heras, J}, title = {The 2022 Nobel Prize in Physiology or Medicine.}, journal = {Journal of the Association of Genetic Technologists}, volume = {49}, number = {2}, pages = {56-67}, pmid = {37269363}, issn = {1523-7834}, abstract = {The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.}, } @article {pmid37268008, year = {2023}, author = {Guzmán-Solís, AA and Navarro, MA and Ávila-Arcos, MC and Blanco-Melo, D}, title = {A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History.}, journal = {Annual review of virology}, volume = {10}, number = {1}, pages = {49-75}, doi = {10.1146/annurev-virology-111821-123859}, pmid = {37268008}, issn = {2327-0578}, mesh = {Humans ; Genomics ; *Virus Diseases/genetics ; *Viruses/genetics ; Disease Outbreaks ; Genome, Viral ; }, abstract = {Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.}, } @article {pmid37265549, year = {2022}, author = {Elalouf, JM and Palacio, P and Bon, C and Berthonaud, V and Maksud, F and Stafford, TW and Hitte, C}, title = {The genome and diet of a 35,000-year-old Canis lupus specimen from the Paleolithic painted cave, Chauvet-Pont d'Arc, France.}, journal = {Ecology and evolution}, volume = {12}, number = {8}, pages = {e9238}, pmid = {37265549}, issn = {2045-7758}, abstract = {The Chauvet-Pont-d'Arc Cave (Ardèche, France) contains some of the oldest Paleolithic paintings recorded to date, as well as thousands of bones of the extinct cave bear, and some remains and footprints of other animals. As part of the interdisciplinary research project devoted to this reference cave site, we analyzed a coprolite collected within the deep cave. AMS radiocarbon dating of bone fragments from the coprolite yielded an age of 30,450 ± 550 RC yr. BP (AAR-19656; 36,150-34,000 cal BP), similar to ages assigned to Paleolithic artwork and cave bear remains from the same cave sector. Using high-throughput shotgun DNA sequencing, we demonstrated a high abundance of canid DNA and lesser amounts of DNA from the extinct cave bear. We interpret the sample as feces from a canid that had consumed cave bear tissue. The high amount of canid DNA allowed us to reconstruct a complete canid mitochondrial genome sequence (average coverage: 83×) belonging to a deeply divergent clade of extinct mitochondrial wolf lineages that are most closely related to coeval (~35 ka) Belgian wolves. Analysis of the nuclear genome yielded a similar coverage for the X chromosome (2.4×) and the autosomes (range: 2.3-3.2×), indicating that the Chauvet canid was a female. Comparing the relationship of the nuclear genome of this specimen with that of a variety of canids, we found it more closely related to gray wolves' genomes than to other wild canid or dog genomes, especially wolf genomes from Europe and the Middle East. We conclude that the coprolite is feces from an animal within an extinct wolf lineage. The consumption of cave bear by this wolf likely explains its intrusion into the dark cave sectors and sheds new light on the paleoecology of a major cave site.}, } @article {pmid37259901, year = {2023}, author = {Signore, AV and Morrison, PR and Brauner, CJ and Fago, A and Weber, RE and Campbell, KL}, title = {Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller's sea cows.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37259901}, issn = {2050-084X}, mesh = {Animals ; *Dugong ; Mammals ; Hemoglobins/genetics ; Climate ; Oxygen ; }, abstract = {The extinct Steller's sea cow (Hydrodamalis gigas; †1768) was a whale-sized marine mammal that manifested profound morphological specializations to exploit the harsh coastal climate of the North Pacific. Yet despite first-hand accounts of their biology, little is known regarding the physiological adjustments underlying their evolution to this environment. Here, the adult-expressed hemoglobin (Hb; α2β/δ2) of this sirenian is shown to harbor a fixed amino acid replacement at an otherwise invariant position (β/δ82Lys→Asn) that alters multiple aspects of Hb function. First, our functional characterization of recombinant sirenian Hb proteins demonstrates that the Hb-O2 affinity of this sub-Arctic species was less affected by temperature than those of living (sub)tropical sea cows. This phenotype presumably safeguarded O2 delivery to cool peripheral tissues and largely arises from a reduced intrinsic temperature sensitivity of the H. gigas protein. Additional experiments on H. gigas β/δ82Asn→Lys mutant Hb further reveal this exchange renders Steller's sea cow Hb unresponsive to the potent intraerythrocytic allosteric effector 2,3-diphosphoglycerate, a radical modification that is the first documented example of this phenotype among mammals. Notably, β/δ82Lys→Asn moreover underlies the secondary evolution of a reduced blood-O2 affinity phenotype that would have promoted heightened tissue and maternal/fetal O2 delivery. This conclusion is bolstered by analyses of two Steller's sea cow prenatal Hb proteins (Hb Gower I; ζ2ε2 and HbF; α2γ2) that suggest an exclusive embryonic stage expression pattern, and reveal uncommon replacements in H. gigas HbF (γ38Thr→Ile and γ101Glu→Asp) that increased Hb-O2 affinity relative to dugong HbF. Finally, the β/δ82Lys→Asn replacement of the adult/fetal protein is shown to increase protein solubility, which may have elevated red blood cell Hb content within both the adult and fetal circulations and contributed to meeting the elevated metabolic (thermoregulatory) requirements and fetal growth rates associated with this species cold adaptation.}, } @article {pmid37252429, year = {2023}, author = {Furtwängler, A and Baumann, C and Majander, K and Wilkin, S and Tomoum, N and Rühli, F and Jaeggi, AV and Eppenberger, P and Bender, N and Schuenemann, VJ}, title = {The Mummy Explorer-a self-regulated open-access online teaching tool.}, journal = {Evolution, medicine, and public health}, volume = {11}, number = {1}, pages = {129-138}, pmid = {37252429}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: Virtual teaching tools have gained increasing importance in recent years. In particular, the COVID-19 pandemic has reinforced the need for media-based and self-regulated tools. What is missing are tools that allow us to interlink highly interdisciplinary fields such as evolutionary medicine and, at the same time, allow us to adapt content to different lectures.

METHODOLOGY: We designed an interactive online teaching tool, namely, the Mummy Explorer, using open-access software (Google Web Designer), and we provided a freely downloadable template. We tested the tool on students and lecturers of evolutionary medicine using questionnaires and improved the tool according to their feedback.

RESULTS: The tool has a modular design and provides an overview of a virtual mummy excavation, including the subfields of palaeopathology, paleoradiology, cultural and ethnographic context, provenance studies, paleogenetics, and physiological analyses. The template allows lecturers to generate their own versions of the tool for any topic of interest by simply changing the text and pictures. Tests undertaken with students of evolutionary medicine showed that the tool was helpful during their studies. Lecturers commented that they appreciated having a similar tool in other fields.

CONCLUSIONS AND IMPLICATIONS: Mummy Explorer fills a gap in the virtual teaching landscape of highly interdisciplinary fields such as evolutionary medicine. It will be offered for free download and can be adapted to any educational topic. Translations into German and possibly other languages are in progress.}, } @article {pmid37250315, year = {2023}, author = {Clavel, P and Louis, L and Sarkissian, C and Thèves, C and Gillet, C and Chauvey, L and Tressières, G and Schiavinato, S and Calvière-Tonasso, L and Telmon, N and Clavel, B and Jonvel, R and Tzortzis, S and Bouniol, L and Fémolant, JM and Klunk, J and Poinar, H and Signoli, M and Costedoat, C and Spyrou, MA and Seguin-Orlando, A and Orlando, L}, title = {Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106787}, pmid = {37250315}, issn = {2589-0042}, abstract = {Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17[th] and 18[th] centuries Common Era.}, } @article {pmid37239398, year = {2023}, author = {Buss, DL and Atmore, LM and Zicos, MH and Goodall-Copestake, WP and Brace, S and Archer, FI and Baker, CS and Barnes, I and Carroll, EL and Hart, T and Kitchener, AC and Sabin, R and Sremba, AL and Weir, CR and Jackson, JA}, title = {Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239398}, issn = {2073-4425}, mesh = {Animals ; *Fin Whale/genetics ; Whales/genetics ; Population Density ; Antarctic Regions ; }, abstract = {Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.}, } @article {pmid37239354, year = {2023}, author = {Thomas, JT and Cavagnino, C and Kjelland, K and Anderson, E and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Amory, C and Spatola, B and Moran, K and Parson, W and Marshall, C}, title = {Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239354}, issn = {2073-4425}, mesh = {Humans ; *DNA Fingerprinting/methods ; *Microsatellite Repeats/genetics ; Bone and Bones ; DNA, Mitochondrial/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.}, } @article {pmid37237270, year = {2023}, author = {Nedoluzhko, A}, title = {Sea of opportunities: marine genomics in an era of global environmental change.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {286}, pmid = {37237270}, issn = {1471-2164}, mesh = {Oceans and Seas ; *Aquatic Organisms/genetics ; *Ecosystem ; Genomics ; Seawater ; }, abstract = {Overexploitation of natural resources and pollution of seas, acidification of the ocean, and rising temperatures all contribute to the destruction of marine habitats and, in 2015, the protection of the ocean became one of the UN Sustainable Development Goals (SDG 14: Life Below Water). This collection aims to highlight the molecular genetic changes currently happening in marine organisms.}, } @article {pmid37224187, year = {2023}, author = {Gibbon, VE and Feris, L and Gretzinger, J and Smith, K and Hall, S and Penn, N and Mutsvangwa, TEM and Heale, M and Finaughty, DA and Karanja, YW and Esterhuyse, J and Kotze, D and Barnes, N and Gunston, G and May, J and Krause, J and Wilkinson, CM and Schiffels, S and Februarie, D and Alves, S and Sealy, JC}, title = {Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0284785}, pmid = {37224187}, issn = {1932-6203}, mesh = {Humans ; South Africa ; *Anthropology ; *Archaeology ; Cemeteries ; DNA, Ancient ; }, abstract = {We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.}, } @article {pmid37220274, year = {2023}, author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A}, title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2213061120}, pmid = {37220274}, issn = {1091-6490}, mesh = {Humans ; Animals ; Africa ; *Neanderthals ; Acclimatization ; Arabia ; Selection, Genetic ; }, abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.}, } @article {pmid37216609, year = {2023}, author = {Ciecierski, L and Stolarek, I and Figlerowicz, M}, title = {Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W269-W273}, pmid = {37216609}, issn = {1362-4962}, mesh = {Humans ; *Genomics/methods ; Software ; Human Genetics ; DNA, Ancient ; Databases, Genetic ; }, abstract = {Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.}, } @article {pmid37215481, year = {2023}, author = {Mármol-Sánchez, E and Heidemann, PL and Gredal, H and Cirera, S}, title = {MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1144084}, pmid = {37215481}, issn = {2297-1769}, abstract = {INTRODUCTION: Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment.

METHODS: By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group.

RESULTS: Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO.

DISCUSSION: Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.}, } @article {pmid37212188, year = {2023}, author = {Bunce, M}, title = {It is time for ancient DNA to sweat the small stuff.}, journal = {Molecular ecology}, volume = {32}, number = {11}, pages = {2689-2691}, doi = {10.1111/mec.16970}, pmid = {37212188}, issn = {1365-294X}, mesh = {Animals ; *DNA, Ancient ; Sweat ; DNA/genetics ; Biological Evolution ; Birds/genetics ; *Mammoths/genetics ; Fossils ; Phylogeny ; }, abstract = {When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs - despite the pervasive idea of 'dino DNA' from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected 'small stuff' - lizards, frogs, and other herpetofauna. But here's the rub - extracting DNA from the bones of this 'small stuff' is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.}, } @article {pmid37208611, year = {2023}, author = {Sharko, F and Rbbani, G and Siriyappagouder, P and Raeymaekers, JAM and Galindo-Villegas, J and Nedoluzhko, A and Fernandes, JMO}, title = {CircPrime: a web-based platform for design of specific circular RNA primers.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {205}, pmid = {37208611}, issn = {1471-2105}, support = {683210/ERC_/European Research Council/International ; }, mesh = {*RNA, Circular/genetics ; *RNA/genetics ; Sequence Analysis, RNA/methods ; Polymerase Chain Reaction ; Computational Biology/methods ; Internet ; }, abstract = {BACKGROUND: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication.

RESULTS: Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods.

CONCLUSIONS: User-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).}, } @article {pmid37207647, year = {2023}, author = {Fleskes, RE and Owsley, DW and Bruwelheide, KS and Barca, KG and Griffith, DR and Cabana, GS and Schurr, TG}, title = {Historical genomes elucidate European settlement and the African diaspora in Delaware.}, journal = {Current biology : CB}, volume = {33}, number = {11}, pages = {2350-2358.e7}, doi = {10.1016/j.cub.2023.04.069}, pmid = {37207647}, issn = {1879-0445}, mesh = {Adult ; Child ; Humans ; *Black People/genetics ; Delaware ; DNA, Mitochondrial/genetics ; Genetics, Population ; Haplotypes ; *Human Migration ; White ; Black or African American ; }, abstract = {The 17[th]-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.[1] The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.[2] European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.[3][,][4] To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.[5] Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17[th] and early 18[th] century North America.}, } @article {pmid37187366, year = {2023}, author = {Wilke, T and Kehlmaier, C and Stelbrink, B and Albrecht, C and Bouchet, P}, title = {Historical DNA solves century-old mystery on sessility in freshwater gastropods.}, journal = {Molecular phylogenetics and evolution}, volume = {185}, number = {}, pages = {107813}, doi = {10.1016/j.ympev.2023.107813}, pmid = {37187366}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Fresh Water ; *Rivers ; DNA/genetics ; Snails/genetics ; }, abstract = {Extinction rates are increasing unabatedly but resources available for conservation action are limited. Therefore, some conservationists are pushing for ecology- and evolution-based conservation choices, prioritizing taxa with phylogenetic and trait-based originality. Extinction of original taxa may result in a disproportionate loss of evolutionary innovations and potentially prevent transformative changes in living systems. Here, we generated historical DNA data from an almost 120-year-old syntype of the enigmatic sessile snail Helicostoa sinensis from the Three Gorges region of the Yangtze River (PR China), using a next-generation sequencing protocol developed for ancient DNA. In a broader phylogenetic context, we assessed the phylogenetic and trait-based originality of this enigmatic taxon to solve the century-old puzzle of sessility in freshwater gastropods. Our multi-locus data confirm the phylogenetic and trait-based originality of H. sinensis. It is an ultra-rare, subfamily-level taxon (Helicostoinae stat. nov.) within the family Bithyniidae, which exhibits the evolutionary innovation of sessility. While we conservatively classify H. sinensis as "Critically Endangered", there is mounting evidence of the biological annihilation of this endemic species. Although rapidly rising extinction rates in invertebrates are increasingly recognized, the potential loss of originality in these "little things that run the world" has received little attention. We therefore call for comprehensive surveys of originality in invertebrates, particularly from extreme environments such as rapids of large rivers, as a basis for urgently needed ecology- and evolution-based conservation decisions.}, } @article {pmid37167404, year = {2023}, author = {Llamas, B and Roca-Rada, X}, title = {Paleogenomic study of the Mexican past.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6645}, pages = {578-579}, doi = {10.1126/science.adh7902}, pmid = {37167404}, issn = {1095-9203}, mesh = {Humans ; *DNA, Ancient ; Mexico ; *North American People/genetics/history ; Anthropology ; Genomics ; Demography ; }, abstract = {Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.}, } @article {pmid37163039, year = {2023}, author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM}, title = {Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37163039}, issn = {2692-8205}, abstract = {Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G12ancient, on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.}, } @article {pmid37157914, year = {2023}, author = {Whitehouse, LS and Schrider, DR}, title = {Timesweeper: accurately identifying selective sweeps using population genomic time series.}, journal = {Genetics}, volume = {224}, number = {3}, pages = {}, pmid = {37157914}, issn = {1943-2631}, support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R35 GM138286/GM/NIGMS NIH HHS/United States ; R35GM138286/GF/NIH HHS/United States ; }, mesh = {*Metagenomics ; Time Factors ; *Genetics, Population ; Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations, only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper analyzes population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional convolutional neural network on said simulations, and inferring which polymorphisms in this serialized data set were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.}, } @article {pmid37153511, year = {2023}, author = {Sharko, FS and Zhur, KV and Trifonov, VA and Prokhortchouk, EB}, title = {Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.}, journal = {Acta naturae}, volume = {15}, number = {1}, pages = {87-96}, pmid = {37153511}, issn = {2075-8251}, abstract = {Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.}, } @article {pmid37141673, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Zupanc, T and Podovšovnik, E}, title = {A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples.}, journal = {Forensic science international. Genetics}, volume = {65}, number = {}, pages = {102882}, doi = {10.1016/j.fsigen.2023.102882}, pmid = {37141673}, issn = {1878-0326}, mesh = {Humans ; Aged ; Powders ; Edetic Acid ; *DNA Fingerprinting/methods ; *Microsatellite Repeats ; DNA ; }, abstract = {An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.}, } @article {pmid37141315, year = {2023}, author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P}, title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6645}, pages = {619-624}, doi = {10.1126/science.adf5300}, pmid = {37141315}, issn = {1095-9203}, mesh = {Animals ; Humans ; *Biological Products/metabolism ; *Genome, Bacterial ; *Hominidae/genetics ; Metagenome ; *Neanderthals/genetics ; *Furans/metabolism ; DNA, Ancient ; }, abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.}, } @article {pmid37138779, year = {2023}, author = {Aqil, A and Gill, S and Gokcumen, O and Malhi, RS and Reese, EA and Smith, JL and Heaton, TT and Lindqvist, C}, title = {A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106581}, pmid = {37138779}, issn = {2589-0042}, abstract = {Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.}, } @article {pmid37137206, year = {2023}, author = {Zupanič Pajnič, I and Geršak, ŽM and Leskovar, T and Črešnar, M}, title = {Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site.}, journal = {Forensic science international. Genetics}, volume = {65}, number = {}, pages = {102886}, doi = {10.1016/j.fsigen.2023.102886}, pmid = {37137206}, issn = {1878-0326}, mesh = {Female ; Child ; Humans ; Male ; Middle Aged ; Powders ; *DNA Fingerprinting ; *DNA/genetics ; Bone and Bones ; Microsatellite Repeats ; Chromosomes, Human, Y ; Indigenous Peoples ; Haplotypes ; }, abstract = {The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.}, } @article {pmid37127762, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M}, title = {Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology.}, journal = {International journal of legal medicine}, volume = {137}, number = {4}, pages = {1007-1015}, pmid = {37127762}, issn = {1437-1596}, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; DNA ; Skeleton ; Probability ; Sequence Analysis, DNA ; }, abstract = {In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10[7] (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.}, } @article {pmid37117261, year = {2023}, author = {Ferrando-Bernal, M}, title = {Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6968}, pmid = {37117261}, issn = {2045-2322}, mesh = {Humans ; Skull ; DNA, Ancient ; Paleopathology ; *Anemia/complications ; *Hyperostosis/genetics ; *Bone Diseases, Metabolic/complications ; }, abstract = {Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.}, } @article {pmid37114314, year = {2022}, author = {Benítez-Burraco, A and Torres-Ruiz, R and Gelabert, P and Lalueza-Fox, C and Rodríguez-Perales, S and García-Bellido, P}, title = {Human-specific changes in two functional enhancers of FOXP2.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {68}, number = {11}, pages = {16-19}, doi = {10.14715/cmb/2022.68.11.3}, pmid = {37114314}, issn = {1165-158X}, mesh = {Humans ; *Forkhead Transcription Factors/genetics/metabolism ; }, abstract = {FOXP2 is a gene involved in language development and function. Neanderthals and humans share the same coding region of the gene, although the formers are thought to have exhibited less sophisticated language abilities. In this paper, we report on several human-specific changes in two functional enhancers of FOXP2. Two of these variants are located within the binding sites for the transcription factors POLR2A and SMARCC1, respectively. Interestingly, SMARCC1 is involved in brain development and vitamin D metabolism. We hypothesize that the human specific change in this position might have resulted in a different regulation pattern of FOXP2 expression in our species compared to extinct hominins, with a potential impact on our language abilities.}, } @article {pmid37101579, year = {2023}, author = {Kowal, E and Weyrich, LS and Argüelles, JM and Bader, AC and Colwell, C and Cortez, AD and Davis, JL and Figueiro, G and Fox, K and Malhi, RS and Matisoo-Smith, E and Nayak, A and Nelson, EA and Nicholas, G and Nieves-Colón, MA and Russell, L and Ulm, S and Vergara-Silva, F and Villanea, FA and Wagner, JK and Yracheta, JM and Tsosie, KS}, title = {Community partnerships are fundamental to ethical ancient DNA research.}, journal = {HGG advances}, volume = {4}, number = {2}, pages = {100161}, pmid = {37101579}, issn = {2666-2477}, mesh = {Humans ; *DNA, Ancient ; *Ethics, Research ; Family ; Population Groups ; Research Personnel ; *Human Genetics/ethics ; Guidelines as Topic ; Stakeholder Participation ; Community-Institutional Relations ; }, abstract = {The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.}, } @article {pmid37096383, year = {2023}, author = {da Silva Coelho, FA and Gill, S and Tomlin, CM and Papavassiliou, M and Farley, SD and Cook, JA and Sonsthagen, SA and Sage, GK and Heaton, TH and Talbot, SL and Lindqvist, C}, title = {Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.}, journal = {Molecular ecology}, volume = {32}, number = {13}, pages = {3641-3656}, doi = {10.1111/mec.16960}, pmid = {37096383}, issn = {1365-294X}, mesh = {Animals ; *Ursidae/genetics ; Alaska ; Refugium ; *Genome, Mitochondrial ; North America ; }, abstract = {During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.}, } @article {pmid37072186, year = {2023}, author = {Fernandes, DM and Sirak, KA and Cheronet, O and Novak, M and Brück, F and Zelger, E and Llanos-Lizcano, A and Wagner, A and Zettl, A and Mandl, K and Duffet Carlson, KS and Oberreiter, V and Özdoğan, KT and Sawyer, S and La Pastina, F and Borgia, E and Coppa, A and Dobeš, M and Velemínský, P and Reich, D and Bell, LS and Pinhasi, R}, title = {Density separation of petrous bone powders for optimized ancient DNA yields.}, journal = {Genome research}, volume = {33}, number = {4}, pages = {622-631}, pmid = {37072186}, issn = {1549-5469}, mesh = {Humans ; *DNA, Ancient ; *Petrous Bone ; Powders ; Plastics ; DNA/genetics ; }, abstract = {Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm[3], in 0.05 increments). We found that the 2.30 to 2.35 g/cm[3] and 2.35 to 2.40 g/cm[3] intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm[3] intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm[3] yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.}, } @article {pmid37071008, year = {2023}, author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L}, title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0437422}, pmid = {37071008}, issn = {2165-0497}, mesh = {Animals ; Humans ; Sicily ; *Bacteria ; *Biodiversity ; Anti-Bacterial Agents ; Soil/chemistry ; }, abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.}, } @article {pmid37070964, year = {2023}, author = {Vallebueno-Estrada, M and Hernández-Robles, GG and González-Orozco, E and Lopez-Valdivia, I and Rosales Tham, T and Vásquez Sánchez, V and Swarts, K and Dillehay, TD and Vielle-Calzada, JP and Montiel, R}, title = {Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37070964}, issn = {2050-084X}, mesh = {Peru ; *Domestication ; *Zea mays/genetics ; South America ; Mexico ; }, abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700-5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.}, } @article {pmid37065506, year = {2023}, author = {Gancz, AS and Weyrich, LS}, title = {Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {109}, pmid = {37065506}, issn = {2046-1402}, mesh = {Humans ; *Noncommunicable Diseases/epidemiology ; *Microbiota/genetics ; *Diabetes Mellitus/epidemiology ; Diet ; Prevalence ; }, abstract = {Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.}, } @article {pmid37068234, year = {2023}, author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M}, title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2213563120}, pmid = {37068234}, issn = {1091-6490}, mesh = {History, Ancient ; *Vitis/genetics ; *Wine ; DNA, Ancient ; Archaeology ; Israel ; }, abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.}, } @article {pmid37066305, year = {2023}, author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D}, title = {The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066305}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.}, } @article {pmid37059363, year = {2023}, author = {Kattner, AA}, title = {When it doesn't run in the blood(vessels) - events involved in vascular disorders.}, journal = {Biomedical journal}, volume = {46}, number = {2}, pages = {100591}, pmid = {37059363}, issn = {2320-2890}, mesh = {Infant, Newborn ; Humans ; Male ; Child ; Follow-Up Studies ; *COVID-19 ; Vesicular Transport Proteins ; }, abstract = {In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.}, } @article {pmid37057308, year = {2023}, author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R}, title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.}, journal = {Environmental microbiology reports}, volume = {15}, number = {5}, pages = {383-391}, pmid = {37057308}, issn = {1758-2229}, mesh = {Animals ; Humans ; Latvia ; *Microbiota/genetics ; DNA ; Burial ; }, abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.}, } @article {pmid37052272, year = {2023}, author = {Bader, AC and Carbaugh, AE and Davis, JL and Krupa, KL and Malhi, RS}, title = {Biological samples taken from Native American Ancestors are human remains under NAGPRA.}, journal = {American journal of biological anthropology}, volume = {181}, number = {4}, pages = {527-534}, doi = {10.1002/ajpa.24726}, pmid = {37052272}, issn = {2692-7691}, mesh = {Humans ; *American Indian or Alaska Native ; *Indians, North American ; United States ; *Human Body ; Funeral Rites ; *Culture ; *Human Rights/legislation & jurisprudence ; }, abstract = {In the United States, the Native American Graves Protection and Repatriation Act (NAGPRA) provides a specific framework for the disposition of Native American Ancestral remains within its purview. However, samples such as a bone fragment, tooth, or other biological tissue taken from the remains of these Ancestors have been treated by institutions and researchers as independent of the individual from whom they were removed and used in destructive research such as paleogenomic and other archaeometric analyses without consultation, consent, and collaboration from Native American communities; are not cared for in keeping with the current best practices for Indigenous Ancestors; and are not likely to be repatriated to their communities. Here, we demonstrate that any biological samples removed from Ancestors who are covered under NAGPRA must also be handled according to the stipulations defined for "human remains" within the legislation. As such, we are not proposing a change to existing legislation, but rather best practices, specific to the context of the United States and NAGPRA, relating to the use of and care for biological samples taken from Native American Ancestors.}, } @article {pmid37044651, year = {2023}, author = {Scarsbrook, L and Walton, K and Rawlence, NJ and Hitchmough, RA}, title = {Revision of the New Zealand gecko genus Hoplodactylus, with the description of a new species.}, journal = {Zootaxa}, volume = {5228}, number = {3}, pages = {267-291}, doi = {10.11646/zootaxa.5228.3.3}, pmid = {37044651}, issn = {1175-5334}, mesh = {Animals ; New Zealand ; *Lizards ; }, abstract = {The New Zealand endemic gecko genus Hoplodactylus is revised. Two species are recognized: Hoplodactylus duvaucelii (Duméril & Bibron, 1836) from the North Island and some near-shore islands, and H. tohu n. sp., which was formerly widespread throughout the South Island but is presently restricted to some islands in the Cook Strait region. H. delcourti (Bauer & Russell, 1986) is retained in Hoplodactylus sensu lato in the interest of taxonomic stability, pending further research, but is probably neither congeneric nor from New Zealand.}, } @article {pmid37043523, year = {2023}, author = {Rümpler, F and Tessari, C and Gramzow, L and Gafert, C and Blohs, M and Theißen, G}, title = {The Origin of Floral Quartet Formation-Ancient Exon Duplications Shaped the Evolution of MIKC-type MADS-domain Transcription Factor Interactions.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37043523}, issn = {1537-1719}, mesh = {*Transcription Factors/metabolism ; Phylogeny ; *MADS Domain Proteins/genetics ; Genes, Plant ; Exons ; Plant Proteins/genetics ; Gene Expression Regulation, Plant ; }, abstract = {During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute "floral quartets" or related "floral quartet-like complexes" (FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerization of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerization and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that FQC formation likely originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus, generating the tetramerization interface found in extant MIKCC-type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other K-domain exons occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerization between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.}, } @article {pmid37040705, year = {2023}, author = {Wegmann, D and Eckel, R}, title = {Human evolution: When admixture met selection.}, journal = {Current biology : CB}, volume = {33}, number = {7}, pages = {R259-R261}, doi = {10.1016/j.cub.2023.02.077}, pmid = {37040705}, issn = {1879-0445}, mesh = {Humans ; *DNA, Ancient ; *Biological Evolution ; }, abstract = {Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.}, } @article {pmid37002784, year = {2023}, author = {Honap, TP and Monroe, CR and Johnson, SJ and Jacobson, DK and Abin, CA and Austin, RM and Sandberg, P and Levine, M and Sankaranarayanan, K and Lewis, CM}, title = {Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {542-556}, doi = {10.1002/ajpa.24735}, pmid = {37002784}, issn = {2692-7691}, support = {NSF BCS-2045308//National Science Foundation/ ; }, mesh = {Humans ; *American Indian or Alaska Native ; Calculi/genetics ; Chloroflexi/genetics ; DNA, Bacterial/analysis ; *Metagenome/genetics ; Periodontitis/microbiology ; Treponema denticola/genetics ; *Mouth/microbiology ; }, abstract = {OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.}, } @article {pmid37002389, year = {2023}, author = {Callaway, E}, title = {Ancient DNA illuminates Swahili culture's origins.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37002389}, issn = {1476-4687}, } @article {pmid36996223, year = {2023}, author = {Curry, A}, title = {'Persian princes' helped found early African trade power.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6639}, pages = {1284-1285}, doi = {10.1126/science.adi0093}, pmid = {36996223}, issn = {1095-9203}, abstract = {Ancient DNA reflects foreign influx to Swahili coast, but its culture is largely local.}, } @article {pmid36994803, year = {2023}, author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F}, title = {Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis.}, journal = {Molecular ecology resources}, volume = {23}, number = {6}, pages = {1226-1240}, doi = {10.1111/1755-0998.13790}, pmid = {36994803}, issn = {1755-0998}, mesh = {Horses/genetics ; Animals ; *DNA, Ancient ; *Epistasis, Genetic ; DNA/genetics ; Biological Evolution ; Algorithms ; }, abstract = {Innovations in ancient DNA (aDNA) preparation and sequencing technologies have exponentially increased the quality and quantity of aDNA data extracted from ancient biological materials. The additional temporal component from the incoming aDNA data can provide improved power to address fundamental evolutionary questions like characterizing selection processes that shape the phenotypes and genotypes of contemporary populations or species. However, utilizing aDNA to study past selection processes still involves considerable hurdles like how to eliminate the confounding factor of genetic interactions in the inference of selection. To address this issue, we extend the approach of He et al., 2023 to infer temporally variable selection from the aDNA data in the form of genotype likelihoods with the flexibility of modelling linkage and epistasis in this work. Our posterior computation is carried out by a robust adaptive version of the particle marginal Metropolis-Hastings algorithm with a coerced acceptance rate. Our extension inherits the desirable features of He et al., 2023 such as modelling sample uncertainty resulting from the damage and fragmentation of aDNA molecules and reconstructing underlying gamete frequency trajectories of the population. We evaluate its performance through extensive simulations and show its utility with an application to the aDNA data from pigmentation loci in horses.}, } @article {pmid36993413, year = {2023}, author = {Barton, AR and Santander, CG and Skoglund, P and Moltke, I and Reich, D and Mathieson, I}, title = {Insufficient evidence for natural selection associated with the Black Death.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993413}, issn = {2692-8205}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, abstract = {Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2, for which they estimate a selection coefficient of 0.39-several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis, we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.}, } @article {pmid36991187, year = {2023}, author = {Brielle, ES and Fleisher, J and Wynne-Jones, S and Sirak, K and Broomandkhoshbacht, N and Callan, K and Curtis, E and Iliev, L and Lawson, AM and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Zalzala, F and Ayodo, G and Gidna, AO and Kabiru, A and Kwekason, A and Mabulla, AZP and Manthi, FK and Ndiema, E and Ogola, C and Sawchuk, E and Al-Gazali, L and Ali, BR and Ben-Salem, S and Letellier, T and Pierron, D and Radimilahy, C and Rakotoarisoa, JA and Raaum, RL and Culleton, BJ and Mallick, S and Rohland, N and Patterson, N and Mwenje, MA and Ahmed, KB and Mohamed, MM and Williams, SR and Monge, J and Kusimba, S and Prendergast, ME and Reich, D and Kusimba, CM}, title = {Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.}, journal = {Nature}, volume = {615}, number = {7954}, pages = {866-873}, pmid = {36991187}, issn = {1476-4687}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Female ; Humans ; Male ; *Genetics, Population ; *African People/genetics ; *Asian/genetics ; History, Medieval ; Indian Ocean ; Tanzania ; Kenya ; Mozambique ; Comoros ; History, 15th Century ; History, 16th Century ; History, 17th Century ; India/ethnology ; Persia/ethnology ; Arabia/ethnology ; DNA, Ancient/analysis ; }, abstract = {The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people[1,2]. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast[3]. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia[4]. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.}, } @article {pmid36980999, year = {2023}, author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D}, title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980999}, issn = {2073-4425}, mesh = {Animals ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Rare Diseases/genetics ; *Hominidae/genetics ; Genome, Human ; DNA ; }, abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.}, } @article {pmid36980972, year = {2023}, author = {Sharko, F and Slobodova, N and Boulygina, E and Cheprasov, M and Gladysheva-Azgari, M and Tsygankova, S and Rastorguev, S and Novgorodov, G and Boeskorov, G and Grigorieva, L and Hwang, WS and Tikhonov, A and Nedoluzhko, A}, title = {Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980972}, issn = {2073-4425}, mesh = {Animals ; Female ; Cattle ; *Hares/genetics ; Phylogeny ; DNA, Ancient ; *Lagomorpha/genetics ; Asia ; }, abstract = {Paleoclimatic changes during the Pleistocene-Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller's sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene-Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the "young" specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.}, } @article {pmid36968599, year = {2023}, author = {Yu, HX and Ao, C and Wang, XP and Zhang, XP and Sun, J and Li, H and Liu, KJ and Wei, LH}, title = {The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1139722}, pmid = {36968599}, issn = {1664-8021}, abstract = {Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis. Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch. Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China. Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.}, } @article {pmid36967935, year = {2023}, author = {Sen, A and Andersen, LW and Kjeldsen, KU and Michel, LN and Hong, WL and Choquet, M and Rasmussen, TL}, title = {The phylogeography and ecology of Oligobrachia frenulate species suggest a generalist chemosynthesis-based fauna in the arctic.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14232}, pmid = {36967935}, issn = {2405-8440}, abstract = {We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments). Due to its similarity with O. webbi, the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known.}, } @article {pmid36966434, year = {2023}, author = {Hixson, KK and Fajardo, DA and Devitt, NP and Sena, JA and Costa, MA and Meng, Q and Boschiero, C and Zhao, PX and Baack, EJ and Paurus, VL and Davin, LB and Lewis, NG and Bell, CJ}, title = {Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {6}, pages = {}, pmid = {36966434}, issn = {2160-1836}, mesh = {*Alnus/metabolism ; Diploidy ; Plant Breeding ; Symbiosis ; Trees ; }, abstract = {Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.}, } @article {pmid36964154, year = {2023}, author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U}, title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1650}, pmid = {36964154}, issn = {2041-1723}, mesh = {*Ecosystem ; *DNA, Ancient ; Ice Cover ; Climate ; Geologic Sediments ; Arctic Regions ; Oceans and Seas ; }, abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.}, } @article {pmid36963383, year = {2023}, author = {Davy, T and Ju, D and Mathieson, I and Skoglund, P}, title = {Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers.}, journal = {Current biology : CB}, volume = {33}, number = {7}, pages = {1365-1371.e3}, pmid = {36963383}, issn = {1879-0445}, support = {852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; R35 GM133708/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {Humans ; *Farmers ; Europe ; *DNA ; Alleles ; Selection, Genetic ; }, abstract = {Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.[1][,][2][,][3][,][4] Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10[-56]). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.}, } @article {pmid36958333, year = {2023}, author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J}, title = {Genomic analyses of hair from Ludwig van Beethoven.}, journal = {Current biology : CB}, volume = {33}, number = {8}, pages = {1431-1447.e22}, doi = {10.1016/j.cub.2023.02.041}, pmid = {36958333}, issn = {1879-0445}, mesh = {Male ; Humans ; Genetic Predisposition to Disease ; *Famous Persons ; *Deafness ; Genomics ; *Music ; Hair ; }, abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.}, } @article {pmid36951219, year = {2023}, author = {Kolbe, D and da Silva, NA and Dose, J and Torres, GG and Caliebe, A and Krause-Kyora, B and Nebel, A}, title = {Current allele distribution of the human longevity gene APOE in Europe can mainly be explained by ancient admixture.}, journal = {Aging cell}, volume = {22}, number = {5}, pages = {e13819}, pmid = {36951219}, issn = {1474-9726}, mesh = {Humans ; Infant, Newborn ; Alleles ; Gene Frequency/genetics ; *Longevity/genetics ; *Apolipoproteins E/genetics ; Europe ; }, abstract = {Variation in apolipoprotein E (APOE) has been shown to have the strongest genetic effect on human longevity. The aim of this study was to unravel the evolutionary history of the three major APOE alleles in Europe by analysing ancient samples up to 12,000 years old. We detected significant allele frequency shifts between populations and over time. Our analyses indicated that selection led to large frequency differences between the earliest European populations (i.e., hunter-gatherers vs. first farmers), possibly due to changes in diet/lifestyle. In contrast, the allele distributions in populations from ~4000 BCE onward can mainly be explained by admixture, suggesting that it also played an important role in shaping current APOE variation. In any case, the resulting allele frequencies strongly influence the predisposition for longevity today, likely as a consequence of past adaptations and demographic processes.}, } @article {pmid36945531, year = {2023}, author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Patterson, N and Reich, D}, title = {ancIBD - Screening for identity by descent segments in human ancient DNA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36945531}, issn = {2692-8205}, abstract = {Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.}, } @article {pmid36933795, year = {2023}, author = {Zhang, G and Cui, C and Wangdue, S and Lu, H and Chen, H and Xi, L and He, W and Yuan, H and Tsring, T and Chen, Z and Yang, F and Tsering, T and Li, S and Tashi, N and Yang, T and Tong, Y and Wu, X and Li, L and He, Y and Cao, P and Dai, Q and Liu, F and Feng, X and Wang, T and Yang, R and Ping, W and Zhang, M and Gao, X and Liu, Y and Wang, W and Fu, Q}, title = {Maternal genetic history of ancient Tibetans over the past 4000 years.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {50}, number = {10}, pages = {765-775}, doi = {10.1016/j.jgg.2023.03.007}, pmid = {36933795}, issn = {1673-8527}, mesh = {Tibet ; Humans ; *Phylogeny ; *Haplotypes/genetics ; Female ; Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; History, Ancient ; Asian People/genetics ; Genetics, Population ; Maternal Inheritance/genetics ; East Asian People ; }, abstract = {The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.}, } @article {pmid36930997, year = {2023}, author = {Schats, R}, title = {Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward.}, journal = {International journal of paleopathology}, volume = {41}, number = {}, pages = {32-42}, doi = {10.1016/j.ijpp.2023.03.002}, pmid = {36930997}, issn = {1879-9825}, mesh = {Humans ; *Archaeology ; *Malaria/diagnosis/epidemiology ; Forecasting ; Prevalence ; }, abstract = {OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.

MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.

METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.

RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.

CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.

SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.

LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.

More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.}, } @article {pmid36930529, year = {2023}, author = {de-Dios, T and Scheib, CL and Houldcroft, CJ}, title = {An Adagio for Viruses, Played Out on Ancient DNA.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36930529}, issn = {1759-6653}, mesh = {Humans ; *Genomics/methods ; DNA, Ancient ; Paleontology ; DNA ; *Viruses/genetics ; }, abstract = {Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.}, } @article {pmid36922577, year = {2023}, author = {Kerner, G and Choin, J and Quintana-Murci, L}, title = {Ancient DNA as a tool for medical research.}, journal = {Nature medicine}, volume = {29}, number = {5}, pages = {1048-1051}, pmid = {36922577}, issn = {1546-170X}, mesh = {*DNA, Ancient ; Fossils ; *Biomedical Research ; Sequence Analysis, DNA ; }, } @article {pmid36919783, year = {2023}, author = {Motti, JMB and Pauro, M and Scabuzzo, C and García, A and Aldazábal, V and Vecchi, R and Bayón, C and Pastor, N and Demarchi, DA and Bravi, CM and Reich, D and Cabana, GS and Nores, R}, title = {Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.}, journal = {American journal of biological anthropology}, volume = {181}, number = {2}, pages = {216-230}, doi = {10.1002/ajpa.24727}, pmid = {36919783}, issn = {2692-7691}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Humans ; Argentina ; Phylogeny ; *Genome, Mitochondrial/genetics ; Bayes Theorem ; South America ; }, abstract = {OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.

MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.

RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.}, } @article {pmid36919199, year = {2023}, author = {Bellec, A and Sow, MD and Pont, C and Civan, P and Mardoc, E and Duchemin, W and Armisen, D and Huneau, C and Thévenin, J and Vernoud, V and Depège-Fargeix, N and Maunas, L and Escale, B and Dubreucq, B and Rogowsky, P and Bergès, H and Salse, J}, title = {Tracing 100 million years of grass genome evolutionary plasticity.}, journal = {The Plant journal : for cell and molecular biology}, volume = {114}, number = {6}, pages = {1243-1266}, doi = {10.1111/tpj.16185}, pmid = {36919199}, issn = {1365-313X}, support = {0001455 project SyntenyViewer//Institut Carnot Plant2Pro/ ; 'Pack Ambition Recherche Project' TransBlé//ISITE CAP2025/ ; #23000816//Région Auvergne-Rhône-Alpes/ ; }, mesh = {*Poaceae/genetics ; *Genome, Plant/genetics ; Phylogeny ; Evolution, Molecular ; Edible Grain/genetics ; Polyploidy ; Gene Duplication ; }, abstract = {Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.}, } @article {pmid36918761, year = {2023}, author = {Marsh, WA and Brace, S and Barnes, I}, title = {Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {111}, pmid = {36918761}, issn = {1471-2164}, mesh = {Humans ; *DNA, Ancient/analysis ; *Software ; Genotype ; Genome ; }, abstract = {BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material.

RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors).

CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.}, } @article {pmid36906188, year = {2023}, author = {Rbbani, G and Nedoluzhko, A and Siriyappagouder, P and Sharko, F and Galindo-Villegas, J and Raeymaekers, JAM and Joshi, R and Fernandes, JMO}, title = {The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia.}, journal = {Genomics}, volume = {115}, number = {3}, pages = {110598}, pmid = {36906188}, issn = {1089-8646}, support = {683210/ERC_/European Research Council/International ; }, mesh = {Animals ; RNA, Circular/genetics ; *Cichlids/genetics ; *MicroRNAs/metabolism ; RNA, Messenger/metabolism ; Muscles/metabolism ; Gene Regulatory Networks ; }, abstract = {Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.}, } @article {pmid36869137, year = {2023}, author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M}, title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {240}, pmid = {36869137}, issn = {2399-3642}, support = {NGS-371R-18//National Geographic Society/ ; }, mesh = {Humans ; Child ; *Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient ; }, abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.}, } @article {pmid36862777, year = {2023}, author = {Curry, A}, title = {Ancient DNA upends European prehistory.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6635}, pages = {865-866}, doi = {10.1126/science.adh3912}, pmid = {36862777}, issn = {1095-9203}, mesh = {*Cultural Diversity ; *DNA, Ancient ; Europe ; Humans ; }, abstract = {Genes reveal striking diversity within similar ice age cultures.}, } @article {pmid36855115, year = {2023}, author = {Nyerki, E and Kalmár, T and Schütz, O and Lima, RM and Neparáczki, E and Török, T and Maróti, Z}, title = {correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {38}, pmid = {36855115}, issn = {1474-760X}, mesh = {Humans ; *Genome, Human ; *Forensic Medicine ; Whole Genome Sequencing ; }, abstract = {Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.}, } @article {pmid39017120, year = {2023}, author = {Leonard, D}, title = {Quick Hits: A linguistic puzzle, ancient DNA, the origins of bipedalism, and much more in this month's Quick Hits.}, journal = {Scientific American}, volume = {328}, number = {3}, pages = {13}, doi = {10.1038/scientificamerican0323-13}, pmid = {39017120}, issn = {0036-8733}, } @article {pmid36853456, year = {2023}, author = {Ayling, C}, title = {TA Cloning Approaches to Cloning DNA with Damaged Ends DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2633}, number = {}, pages = {55-64}, pmid = {36853456}, issn = {1940-6029}, mesh = {*DNA/genetics ; *DNA, Ancient ; DNA Damage ; Sonication ; Cloning, Molecular ; }, abstract = {DNA ends can become damaged for various reasons making them unsuitable for TA cloning techniques, the easiest and most common of the DNA cloning technologies. Examples of end-damaged DNA include ancient DNA and those produced by laboratory methods such as sonication. In this chapter, we discuss how to deal with end-damaged DNA prior to cloning with either the popular pGEM[®]-T Easy Vector Systems Kit and TOPO™ TA Cloning™ Kits.}, } @article {pmid36853452, year = {2023}, author = {Mikić, A and Alomari, A and Gowers, DM}, title = {Classical Recombinant DNA Cloning.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2633}, number = {}, pages = {1-24}, pmid = {36853452}, issn = {1940-6029}, mesh = {*DNA, Recombinant ; *Escherichia coli/genetics ; Cloning, Molecular ; Polymerase Chain Reaction ; Genetic Vectors/genetics ; DNA Ligase ATP ; }, abstract = {Traditional molecular cloning involves a series of linked experimental steps performed with the overall goal of isolating ("cloning") a specific DNA sequence-often a gene. The main purpose of cloning is to study either that DNA sequence or the RNA or protein product it encodes. Building on key enzymatic discoveries in the late 1960s, gene cloning was pioneered in the early 1970s. Since then, DNA cloning and manipulation have been used in every area of biological and biomedical research, from molecular genetics, structural biology, and developmental biology to neurobiology, ancient DNA studies, and immunology. It is a versatile technique that can be applied to a variety of starting DNA types and lengths, including cDNAs, genes, gene fragments, chromosomal regions, or shorter fragments such as PCR products and functional control regions such as enhancers or promoters. The starting DNA can originate from any cell, tissue, or organism. In this chapter we will cover traditional ("classic") molecular cloning strategy. This comprises six linked stages in which (1) PCR is used to amplify a DNA region of interest that is then (2) digested with restriction enzymes, alongside a selected vector, to produce complementary ends crucial for the two molecules to be (3) ligated by an ATP-dependent DNA ligase, creating a recombinant DNA molecule. The recombinant DNA is then (4) introduced into competent bacterial cells by transformation and (5) grown on a selective agar media, followed by (6) colony-PCR for screening purposes. We provide a worked example to demonstrate the cloning of an average-size gene (in this case the 2 kb DNA ligase A gene) from E. coli into a common plasmid expression vector. We have included six color figures and two tables to depict the key stages of a classical molecular cloning protocol. If you are cloning a segment of DNA or a gene, remember that each DNA cloning experiment is unique in terms of sequence, length, and experimental purpose. However, the principles of traditional cloning covered in this chapter are the same for any DNA sequence; we have included a detailed notes section, so you should easily be able to transfer them to your own work. Some of the following chapters in this volume will cover other, more recently developed, cloning protocols.}, } @article {pmid36847465, year = {2022}, author = {Hublin, JJ and Changeux, JP}, title = {Paleoanthropology of cognition: an overview on Hominins brain evolution.}, journal = {Comptes rendus biologies}, volume = {345}, number = {2}, pages = {57-75}, doi = {10.5802/crbiol.92}, pmid = {36847465}, issn = {1768-3238}, mesh = {Humans ; Animals ; *Hominidae ; Biological Evolution ; Brain ; Cognition/physiology ; Neurons ; Fossils ; }, abstract = {Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.}, } @article {pmid36847121, year = {2023}, author = {Salse, J}, title = {Translational research from models to crops: comparative genomics for plant breeding.}, journal = {Comptes rendus biologies}, volume = {345}, number = {4}, pages = {111-128}, doi = {10.5802/crbiol.103}, pmid = {36847121}, issn = {1768-3238}, mesh = {*Plant Breeding/methods ; *Translational Research, Biomedical ; Genomics/methods ; Crops, Agricultural/genetics ; Genotype ; Genome, Plant/genetics ; }, abstract = {The concept of translational research, which originated in the medical field in the 1980s, consists in improving the efficient transfer of research results obtained in a species (which can be considered as a model or pivot) to all the species for which these results are of interest for its improvement in Agriculture. In this context, comparative genomics is an important tool for translational research, effectively identifying genes controlling common functions between species. Editing and phenotyping tools must thus allow the functional validation of the gene conserved within the species for which the knowledge has been extrapolated, that is to say transferred, and the identification of the best alleles and associated genotypes for exploitation in current breeding programs.}, } @article {pmid36845441, year = {2023}, author = {Boeckx, C}, title = {What made us "hunter-gatherers of words".}, journal = {Frontiers in neuroscience}, volume = {17}, number = {}, pages = {1080861}, pmid = {36845441}, issn = {1662-4548}, abstract = {This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.}, } @article {pmid36841239, year = {2023}, author = {Eaton, K and Sidhu, RK and Klunk, J and Gamble, JA and Boldsen, JL and Carmichael, AG and Varlık, N and Duchene, S and Featherstone, L and Grimes, V and Golding, GB and DeWitte, SN and Holmes, EC and Poinar, HN}, title = {Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.}, journal = {Current biology : CB}, volume = {33}, number = {6}, pages = {1147-1152.e5}, doi = {10.1016/j.cub.2023.01.064}, pmid = {36841239}, issn = {1879-0445}, mesh = {Humans ; *Yersinia pestis/genetics ; *Plague/epidemiology/microbiology ; Phylogeny ; Genome, Bacterial ; Denmark ; }, abstract = {The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.[1][,][2] A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.[3] Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.[4][,][5] To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.}, } @article {pmid36833406, year = {2023}, author = {Dalal, V and Pasupuleti, N and Chaubey, G and Rai, N and Shinde, V}, title = {Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833406}, issn = {2073-4425}, mesh = {Humans ; *DNA, Ancient ; *Evolution, Molecular ; *Human Migration ; }, abstract = {Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.}, } @article {pmid36833230, year = {2023}, author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833230}, issn = {2073-4425}, mesh = {Animals ; Humans ; *Parasites ; *Parasitic Diseases/parasitology ; Paleopathology/methods ; Diet ; Life Style ; }, abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.}, } @article {pmid36824241, year = {2023}, author = {D Farhud, D}, title = {The 2022 Nobel Prize in Medicine for Paleogenomics Discovery the Genomes of Extinct Hominins and Human Evolution.}, journal = {Iranian journal of public health}, volume = {52}, number = {1}, pages = {i-iii}, pmid = {36824241}, issn = {2251-6093}, } @article {pmid36822963, year = {2023}, author = {Lalueza-Fox, C}, title = {Across the North Sea and beyond.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {4}, pages = {240-241}, doi = {10.1016/j.tig.2023.01.006}, pmid = {36822963}, issn = {0168-9525}, mesh = {North Sea ; Humans ; Human Genetics ; *Genetics, Population ; Human Migration ; }, abstract = {Increasing numbers of ancient genomes from the Viking period retrieved across the North Sea regions are revealing a complex layer of genetic ancestries and a past cosmopolitanism that was triggered by different mobility patterns.}, } @article {pmid36819665, year = {2023}, author = {Kerner, G and Neehus, AL and Philippot, Q and Bohlen, J and Rinchai, D and Kerrouche, N and Puel, A and Zhang, SY and Boisson-Dupuis, S and Abel, L and Casanova, JL and Patin, E and Laval, G and Quintana-Murci, L}, title = {Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe.}, journal = {Cell genomics}, volume = {3}, number = {2}, pages = {100248}, pmid = {36819665}, issn = {2666-979X}, abstract = {Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.}, } @article {pmid36812666, year = {2023}, author = {Bľandová, G and Patlevičová, A and Palkovičová, J and Pavlíková, Š and Beňuš, R and Repiská, V and Baldovič, M}, title = {Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia.}, journal = {International journal of paleopathology}, volume = {41}, number = {}, pages = {1-7}, doi = {10.1016/j.ijpp.2023.02.001}, pmid = {36812666}, issn = {1879-9825}, mesh = {Humans ; Pilot Projects ; Slovakia ; *Lactose Intolerance/genetics ; *Anemia ; Cemeteries ; }, abstract = {OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains.

MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Devín (11th-12th century AD) and Cífer-Pác (8th-9th century AD).

METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917 + 326 C>T (rs4988235) associated with lactose intolerance.

RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917 + 326 C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion.

SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance.

LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out.

Genetic research based on larger sample sizes and in more diverse geographical regions.}, } @article {pmid36812179, year = {2023}, author = {Kalisher, R and Cradic, MS and Adams, MJ and Martin, MAS and Finkelstein, I}, title = {Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281020}, pmid = {36812179}, issn = {1932-6203}, mesh = {Male ; Young Adult ; Humans ; History, Ancient ; Israel ; *Trephining ; Siblings ; DNA, Ancient ; *Communicable Diseases ; }, abstract = {Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death.}, } @article {pmid36796758, year = {2023}, author = {Min-Shan Ko, A}, title = {The 2022 nobel prize in physiology or medicine awarded for the decoding of the complete ancient human genome.}, journal = {Biomedical journal}, volume = {46}, number = {2}, pages = {100584}, pmid = {36796758}, issn = {2320-2890}, mesh = {Male ; Humans ; *Nobel Prize ; DNA, Ancient ; Genome, Human/genetics ; *Medicine ; Germany ; }, abstract = {Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.}, } @article {pmid36790695, year = {2022}, author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ}, title = {Metagenomic analysis of Ancient Egyptian canopic jars.}, journal = {American journal of biological anthropology}, volume = {179}, number = {2}, pages = {307-313}, pmid = {36790695}, issn = {2692-7691}, mesh = {Humans ; Egypt ; *DNA, Ancient ; *Mummies/pathology ; Lung ; Base Sequence ; }, abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.

OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.

METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).

RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.

DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.}, } @article {pmid36790664, year = {2022}, author = {Vigeant, J and Ribot, I and Hélie, JF}, title = {Investigating individual migration life histories: An isotopic case study from 17th to 18th century Nouvelle France.}, journal = {American journal of biological anthropology}, volume = {177}, number = {2}, pages = {232-248}, doi = {10.1002/ajpa.24455}, pmid = {36790664}, issn = {2692-7691}, mesh = {Child ; Humans ; Male ; Adult ; *Diet/history ; Oxygen Isotopes/analysis ; *Cemeteries/history ; Europe ; France ; }, abstract = {OBJECTIVES: This isotopic study explores the mobility patterns of a growing urban population from Notre Dame's Catholic cemetery (1691-1796), located in Montreal (Canada). The site offers a unique opportunity to investigate early colonial settlement in Nouvelle France through individual life patterns.

MATERIALS AND METHODS: Stable oxygen isotopic compositions (δ[18]O) were measured on the enamel of 32 individuals from the Notre Dame collection. Premolars and third molars were selected, as they reflected the δ[18]O of the drinking water during childhood (2.5-5.5 years) and pre-adulthood (9.5-15.5 years). Firstly, premolars from three children (4-8 years of age) allowed us to provide a mean δ[18]O for the water consumed locally (22.7 ±  1.0 ‰ vs. VSMOW). Then, our δ[18]O were compared with published data from various geographical regions in North America (Eastern Canada and the United States) and Europe (France and the British Isles) to highlight mobility patterns of each individual.

RESULTS: Forty-eight percent of our sample (14 out of 29 individuals) did not reflect any long-distance mobility, as all their δ[18]O reflected Montreal's variation during their lifetime. The remaining (15 out of 29 individuals) experienced mobility within (n = 8) and outside (n = 7) North America and at different phases of their life (five at pre-adulthood, six at adulthood and four during both phases). Their migration patterns were analyzed according to age, sex, diet and possible ancestry in order to propose some "biographies."

DISCUSSION: This study highlights high population diversity in early colonial Montreal. Historians wrote that the city was growing, not only with the arrival of Europeans (e.g., young male workers, sailors), but also other groups (e.g., Indigenous people, slaves from North America). Additional analyses (e.g., ancient DNA) will be needed to explore further this phenomenon.}, } @article {pmid36790637, year = {2023}, author = {Balentine, CM and Alfonso-Durruty, M and Reynolds, AW and Vilar, M and Morello, F and Román, MS and Springs, LC and Smith, RWA and Archer, SM and Mata-Míguez, J and Wing, N and Bolnick, DA}, title = {Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.}, journal = {American journal of biological anthropology}, volume = {180}, number = {1}, pages = {144-161}, doi = {10.1002/ajpa.24638}, pmid = {36790637}, issn = {2692-7691}, mesh = {Humans ; Chile ; *Mitochondria/genetics ; *Archaeology ; Y Chromosome ; DNA, Ancient ; DNA, Mitochondrial/genetics ; }, abstract = {OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.

METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.

RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.

DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.}, } @article {pmid36787794, year = {2023}, author = {Baca, M and Popović, D and Agadzhanyan, AK and Baca, K and Conard, NJ and Fewlass, H and Filek, T and Golubiński, M and Horáček, I and Knul, MV and Krajcarz, M and Krokhaleva, M and Lebreton, L and Lemanik, A and Maul, LC and Nagel, D and Noiret, P and Primault, J and Rekovets, L and Rhodes, SE and Royer, A and Serdyuk, NV and Soressi, M and Stewart, JR and Strukova, T and Talamo, S and Wilczyński, J and Nadachowski, A}, title = {Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1993}, pages = {20222238}, pmid = {36787794}, issn = {1471-2954}, mesh = {Animals ; *DNA, Ancient ; *Arvicolinae/genetics ; Bayes Theorem ; Phylogeny ; Population Dynamics ; DNA, Mitochondrial/genetics ; Genetic Variation ; }, abstract = {The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.}, } @article {pmid36787792, year = {2022}, author = {Broccard, N and Silva, NM and Currat, M}, title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.}, journal = {American journal of biological anthropology}, volume = {177}, number = {1}, pages = {134-146}, pmid = {36787792}, issn = {2692-7691}, mesh = {*Mitochondria/genetics ; Europe ; *DNA, Mitochondrial/genetics ; Emigration and Immigration ; Biological Evolution ; DNA, Ancient ; }, abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.

MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.

RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.

DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.}, } @article {pmid36778139, year = {2022}, author = {Fregel, R}, title = {The origin of the Carpathian Avar elites revealed.}, journal = {Cell genomics}, volume = {2}, number = {6}, pages = {100143}, pmid = {36778139}, issn = {2666-979X}, abstract = {In the sixth century, the Avar elites established themselves in the Carpathian Basin as evidenced today by the astounding archaeological sites with exquisite grave goods made of silver and gold. Recently reported in Cell, Gnecchi-Ruscone et al.[1] obtained paleogenomic evidence from Avar sites in Hungary, placing the Avar elites' origin in Mongolia and confirming their own historical claims.}, } @article {pmid36776693, year = {2023}, author = {Hagymási, K}, title = {The Nobel prize in physiology and medicine - 2022.}, journal = {Structural chemistry}, volume = {34}, number = {2}, pages = {733-736}, pmid = {36776693}, issn = {1040-0400}, abstract = {The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.}, } @article {pmid36762361, year = {2022}, author = {Riedel, A}, title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.}, journal = {ZooKeys}, volume = {1124}, number = {}, pages = {109-130}, pmid = {36762361}, issn = {1313-2989}, abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka & Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo & Riedel is chosen to prevail over T.tounaensis Narakusumo & Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.}, } @article {pmid36760997, year = {2023}, author = {Chang, X and Pamjav, H and Zhabagin, M and Wen, S}, title = {Editorial: The genetic history of human populations along the ancient silk road.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1130104}, pmid = {36760997}, issn = {1664-8021}, } @article {pmid36748324, year = {2024}, author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L}, title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e16859}, pmid = {36748324}, issn = {1365-294X}, support = {339728/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; }, mesh = {Humans ; *Wood ; *Quercus/genetics ; Ecosystem ; Forests ; Trees/genetics ; }, abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.}, } @article {pmid36747166, year = {2023}, author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F}, title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {9}, pmid = {36747166}, issn = {1741-7007}, mesh = {Humans ; Female ; Aged ; Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/epidemiology/microbiology ; Switzerland ; *Syphilis ; Virulence ; }, abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.}, } @article {pmid36721228, year = {2023}, author = {He, G and Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M}, title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.}, journal = {Human genomics}, volume = {17}, number = {1}, pages = {3}, pmid = {36721228}, issn = {1479-7364}, mesh = {Humans ; Haplotypes/genetics ; Alleles ; China ; *Asian People/genetics ; *Adaptation, Biological ; }, abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.}, } @article {pmid36714834, year = {2022}, author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C}, title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.}, journal = {PNAS nexus}, volume = {1}, number = {4}, pages = {pgac148}, pmid = {36714834}, issn = {2752-6542}, support = {MR/T022302/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.}, } @article {pmid36712342, year = {2022}, author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG}, title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac209}, pmid = {36712342}, issn = {2752-6542}, abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.}, } @article {pmid36691623, year = {2023}, author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC}, title = {Genetic and functional odorant receptor variation in the Homo lineage.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105908}, pmid = {36691623}, issn = {2589-0042}, abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.}, } @article {pmid36672975, year = {2023}, author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K}, title = {Methodological Changes in the Field of Paleogenetics.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672975}, issn = {2073-4425}, mesh = {Sequence Analysis, DNA/methods ; *DNA, Ancient/analysis ; *High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.}, } @article {pmid36672874, year = {2023}, author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A}, title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672874}, issn = {2073-4425}, mesh = {Humans ; Romania ; *Genetics, Population ; Phylogeny ; *Genome, Mitochondrial/genetics ; Chromosomes, Human, Y/genetics ; }, abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.}, } @article {pmid36672816, year = {2022}, author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA}, title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672816}, issn = {2073-4425}, mesh = {Humans ; Animals ; *Wolves/genetics ; Genetics, Population ; Population Growth ; Europe ; Genetic Variation/genetics ; }, abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.}, } @article {pmid36669262, year = {2023}, author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J}, title = {Kinship analysis of skeletal remains from the Middle Ages.}, journal = {Forensic science international. Genetics}, volume = {63}, number = {}, pages = {102829}, doi = {10.1016/j.fsigen.2023.102829}, pmid = {36669262}, issn = {1878-0326}, mesh = {Humans ; Male ; *Body Remains ; Chromosomes, Human, Y ; *DNA Fingerprinting/methods ; Family ; Genetic Markers ; Haplotypes ; Microsatellite Repeats ; History, Medieval ; }, abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.}, } @article {pmid36661852, year = {2023}, author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F}, title = {Estimating Temporally Variable Selection Intensity from Ancient DNA Data.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36661852}, issn = {1537-1719}, mesh = {Animals ; Horses/genetics ; *DNA, Ancient ; Bayes Theorem ; Gene Frequency ; *DNA/genetics ; Time Factors ; Models, Genetic ; }, abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage, and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat coloration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.}, } @article {pmid36661298, year = {2023}, author = {Henriksen, RA and Zhao, L and Korneliussen, TS}, title = {NGSNGS: next-generation simulator for next-generation sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36661298}, issn = {1367-4811}, support = {R302-2018-2155//Lundbeck Foundation Centre for Disease Evolution/ ; //Carlsberg Foundation in 2019/ ; }, mesh = {*Software ; *Genome ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; DNA, Ancient ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data have become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here, we present a multithreaded next-generation simulator for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform-specific characteristics based on nucleotide quality score profiles as well as including a post-mortem damage model which is relevant for simulating ancient DNA. The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.

The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36656838, year = {2023}, author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE}, title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.}, journal = {PLoS genetics}, volume = {19}, number = {1}, pages = {e1010551}, pmid = {36656838}, issn = {1553-7404}, mesh = {Animals ; *Chickens/genetics ; Gene Flow ; *Genome/genetics ; Genotype ; Phylogeny ; *Genetics, Population ; }, abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.}, } @article {pmid36653523, year = {2023}, author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S}, title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {72}, pmid = {36653523}, issn = {2399-3642}, mesh = {Humans ; *DNA, Ancient ; Lakes/microbiology ; Anthropogenic Effects ; *Cyanobacteria/genetics ; Ecology ; }, abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.}, } @article {pmid36650598, year = {2023}, author = {Popli, D and Peyrégne, S and Peter, BM}, title = {KIN: a method to infer relatedness from low-coverage ancient DNA.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {10}, pmid = {36650598}, issn = {1474-760X}, mesh = {Humans ; *DNA, Ancient ; *Inbreeding ; }, abstract = {Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.}, } @article {pmid36649412, year = {2023}, author = {Wang, X and Skourtanioti, E and Benz, M and Gresky, J and Ilgner, J and Lucas, M and Morsch, M and Peters, J and Pöllath, N and Ringbauer, H and le Roux, P and Schultz, M and Krause, J and Roberts, P and Stockhammer, PW}, title = {Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2210611120}, pmid = {36649412}, issn = {1091-6490}, mesh = {Animals ; Humans ; History, Ancient ; Turkey ; Jordan ; *Domestication ; *Carbon ; Archaeology ; DNA ; }, abstract = {Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ([87]Sr/[86]Sr), carbon, and oxygen (δ[18]O and δ[13]Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. [87]Sr/[86]Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.}, } @article {pmid36649410, year = {2023}, author = {Lewis, CM and Akinyi, MY and DeWitte, SN and Stone, AC}, title = {Ancient pathogens provide a window into health and well-being.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2209476119}, pmid = {36649410}, issn = {1091-6490}, mesh = {Humans ; History, Ancient ; *Communicable Diseases ; Genome ; DNA, Ancient ; }, abstract = {This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.}, } @article {pmid36646948, year = {2023}, author = {Skourtanioti, E and Ringbauer, H and Gnecchi Ruscone, GA and Bianco, RA and Burri, M and Freund, C and Furtwängler, A and Gomes Martins, NF and Knolle, F and Neumann, GU and Tiliakou, A and Agelarakis, A and Andreadaki-Vlazaki, M and Betancourt, P and Hallager, BP and Jones, OA and Kakavogianni, O and Kanta, A and Karkanas, P and Kataki, E and Kissas, K and Koehl, R and Kvapil, L and Maran, J and McGeorge, PJP and Papadimitriou, A and Papathanasiou, A and Papazoglou-Manioudaki, L and Paschalidis, K and Polychronakou-Sgouritsa, N and Preve, S and Prevedorou, EA and Price, G and Protopapadaki, E and Schmidt-Schultz, T and Schultz, M and Shelton, K and Wiener, MH and Krause, J and Jeong, C and Stockhammer, PW}, title = {Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.}, journal = {Nature ecology & evolution}, volume = {7}, number = {2}, pages = {290-303}, pmid = {36646948}, issn = {2397-334X}, mesh = {Humans ; *DNA, Ancient ; *Human Migration/history ; Europe ; Greece ; Genome ; }, abstract = {The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.}, } @article {pmid36641836, year = {2023}, author = {Barrenechea Angeles, I and Romero-Martínez, ML and Cavaliere, M and Varrella, S and Francescangeli, F and Piredda, R and Mazzocchi, MG and Montresor, M and Schirone, A and Delbono, I and Margiotta, F and Corinaldesi, C and Chiavarini, S and Montereali, MR and Rimauro, J and Parrella, L and Musco, L and Dell'Anno, A and Tangherlini, M and Pawlowski, J and Frontalini, F}, title = {Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107738}, doi = {10.1016/j.envint.2023.107738}, pmid = {36641836}, issn = {1873-6750}, mesh = {Humans ; Animals ; *Ecosystem ; *Biodiversity ; Biota ; Europe ; Human Activities ; Geologic Sediments ; }, abstract = {The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.}, } @article {pmid36638796, year = {2023}, author = {Wang, K and Yu, H and Radzevičiūtė, R and Kiryushin, YF and Tishkin, AA and Frolov, YV and Stepanova, NF and Kiryushin, KY and Kungurov, AL and Shnaider, SV and Tur, SS and Tiunov, MP and Zubova, AV and Pevzner, M and Karimov, T and Buzhilova, A and Slon, V and Jeong, C and Krause, J and Posth, C}, title = {Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia.}, journal = {Current biology : CB}, volume = {33}, number = {3}, pages = {423-433.e5}, doi = {10.1016/j.cub.2022.11.062}, pmid = {36638796}, issn = {1879-0445}, mesh = {Humans ; History, Ancient ; Infant, Newborn ; *Gene Pool ; *Genome, Human ; Asia ; Russia ; Siberia ; Human Migration ; Genetics, Population ; }, abstract = {The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.}, } @article {pmid36637197, year = {2023}, author = {Neuenschwander, S and Cruz Dávalos, DI and Anchieri, L and Sousa da Mota, B and Bozzi, D and Rubinacci, S and Delaneau, O and Rasmussen, S and Malaspinas, AS}, title = {Mapache: a flexible pipeline to map ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637197}, issn = {1367-4811}, support = {PCEGP3_181251//SNSF/ ; //Novo Nordisk Foundation/ ; }, mesh = {*Software ; *DNA, Ancient ; Genome ; Workflow ; }, abstract = {SUMMARY: We introduce mapache, a flexible, robust and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large datasets-such as reference panels and multiple extracts and libraries per sample - to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.

Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36630487, year = {2023}, author = {Kehlmaier, C and Graciá, E and Ali, JR and Campbell, PD and Chapman, SD and Deepak, V and Ihlow, F and Jalil, NE and Pierre-Huyet, L and Samonds, KE and Vences, M and Fritz, U}, title = {Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar.}, journal = {Science advances}, volume = {9}, number = {2}, pages = {eabq2574}, pmid = {36630487}, issn = {2375-2548}, abstract = {Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.}, } @article {pmid36625884, year = {2023}, author = {Xu, Y and Wang, N and Gao, S and Li, C and Ma, P and Yang, S and Jiang, H and Shi, S and Wu, Y and Zhang, Q and Cui, Y}, title = {Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches.}, journal = {International journal of legal medicine}, volume = {137}, number = {2}, pages = {319-327}, pmid = {36625884}, issn = {1437-1596}, support = {20210508040RQ//Jilin Scientific and Technological Development Program/ ; 20200201138JC//Jilin Scientific and Technological Development Program/ ; 715069-FINDER-ERC-2016-STG//H2020 European Research Council/ ; }, mesh = {Humans ; *DNA, Ancient ; Reproducibility of Results ; *DNA ; Mass Spectrometry ; Bone and Bones ; DNA Fingerprinting/methods ; }, abstract = {Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.}, } @article {pmid36625391, year = {2023}, author = {Straiton, J}, title = {Ancient DNA sequencing: telling the tale of human history and evolution.}, journal = {BioTechniques}, volume = {74}, number = {1}, pages = {5-7}, doi = {10.2144/btn-2022-0121}, pmid = {36625391}, issn = {1940-9818}, mesh = {Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; Base Sequence ; }, abstract = {Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].}, } @article {pmid36623185, year = {2023}, author = {Fleskes, RE and Cabana, GS and Gilmore, JK and Juarez, C and Karcher, E and Oubré, L and Mishoe, G and Ofunniyin, AA and Schurr, TG}, title = {Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {3}, pages = {e2201620120}, pmid = {36623185}, issn = {1091-6490}, support = {P2C HD044964/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Male ; *Black People/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Genomics ; Haplotypes/genetics ; South Carolina/ethnology ; Black or African American ; }, abstract = {In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.}, } @article {pmid36620416, year = {2023}, author = {Alfieri, JM and Johnson, T and Linderholm, A and Blackmon, H and Athrey, GN}, title = {Genomic investigation refutes record of most diverged avian hybrid.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9689}, pmid = {36620416}, issn = {2045-7758}, support = {R35 GM138098/GM/NIGMS NIH HHS/United States ; }, abstract = {The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.}, } @article {pmid36610858, year = {2023}, author = {Miao, B and Liu, Y and Yang, R and Feng, X and Liu, F and Cao, P and Dai, Q and Ping, W and Liu, Y and Fu, Q}, title = {Assessment of contaminants associated with gold-standard ancient DNA protocols.}, journal = {Science bulletin}, volume = {68}, number = {1}, pages = {5-9}, doi = {10.1016/j.scib.2022.12.027}, pmid = {36610858}, issn = {2095-9281}, mesh = {*DNA, Ancient ; Sequence Analysis, DNA/methods ; *Fossils ; }, } @article {pmid36593352, year = {2023}, author = {Montag, A}, title = {[The history of skin color is the history of mankind!].}, journal = {Dermatologie (Heidelberg, Germany)}, volume = {74}, number = {2}, pages = {75-79}, pmid = {36593352}, issn = {2731-7013}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Skin Pigmentation/genetics ; *Neanderthals ; Africa, Eastern ; Hair Color/genetics ; }, abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.}, } @article {pmid36582485, year = {2022}, author = {Zhu, K and Du, P and Li, J and Zhang, J and Hu, X and Meng, H and Chen, L and Zhou, B and Yang, X and Xiong, J and Allen, E and Ren, X and Ding, Y and Xu, Y and Chang, X and Yu, Y and Han, S and Dong, G and Wang, CC and Wen, S}, title = {Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105636}, pmid = {36582485}, issn = {2589-0042}, abstract = {A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.}, } @article {pmid36581666, year = {2022}, author = {Changmai, P and Pinhasi, R and Pietrusewsky, M and Stark, MT and Ikehara-Quebral, RM and Reich, D and Flegontov, P}, title = {Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22507}, pmid = {36581666}, issn = {2045-2322}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Genetics, Population ; *DNA, Ancient ; Cambodia ; South Asian People ; Asian People ; }, abstract = {Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.}, } @article {pmid36576953, year = {2022}, author = {Nägele, K and Rivollat, M and Yu, H and Wang, K}, title = {Ancient genomic research - From broad strokes to nuanced reconstructions of the past.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {193-230}, doi = {10.4436/JASS.10017}, pmid = {36576953}, issn = {2037-0644}, mesh = {Humans ; History, Ancient ; *Genomics ; *Archaeology ; DNA, Ancient ; }, abstract = {Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past.}, } @article {pmid36565457, year = {2022}, author = {Vallini, L and Pagani, L}, title = {The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {231-241}, doi = {10.4436/JASS.10013}, pmid = {36565457}, issn = {2037-0644}, mesh = {Humans ; Africa ; Italy ; *Population Dynamics ; }, abstract = {The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years.}, } @article {pmid36553640, year = {2022}, author = {Taufik, L and Teixeira, JC and Llamas, B and Sudoyo, H and Tobler, R and Purnomo, GA}, title = {Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.}, journal = {Genes}, volume = {13}, number = {12}, pages = {}, pmid = {36553640}, issn = {2073-4425}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Human Migration ; New Guinea ; Australia ; Phylogeography ; *Coleoptera ; }, abstract = {Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.}, } @article {pmid36547255, year = {2022}, author = {van der Kuyl, AC}, title = {Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {3}, number = {4}, pages = {443-464}, pmid = {36547255}, issn = {2673-3986}, abstract = {Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.}, } @article {pmid36537881, year = {2022}, author = {Muktupavela, RA and Petr, M and Ségurel, L and Korneliussen, T and Novembre, J and Racimo, F}, title = {Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36537881}, issn = {2050-084X}, support = {R01 GM132383/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Alleles ; Gene Frequency ; *Selection, Genetic ; }, abstract = {Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.}, } @article {pmid36531224, year = {2022}, author = {Xiang, H and Wang, Z and Yang, L and Zhang, X and Zhao, X}, title = {Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1000123}, pmid = {36531224}, issn = {1664-8021}, abstract = {Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10[-3] ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.}, } @article {pmid36525814, year = {2023}, author = {Bardan, F and Higgins, D and Austin, JJ}, title = {A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.}, journal = {Forensic science international. Genetics}, volume = {63}, number = {}, pages = {102822}, doi = {10.1016/j.fsigen.2022.102822}, pmid = {36525814}, issn = {1878-0326}, mesh = {Female ; Humans ; Male ; *Chromosomes, Human, Y/genetics ; *DNA Fingerprinting/methods ; DNA, Mitochondrial/genetics ; *Eye Color/genetics ; *Forensic Genetics/methods ; Hair ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; }, abstract = {Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.}, } @article {pmid36525576, year = {2023}, author = {de Flamingh, A and Rivera-Colón, AG and Gnoske, TP and Kerbis Peterhans, JC and Catchen, J and Malhi, RS and Roca, AL}, title = {Numt Parser: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera.}, journal = {The Journal of heredity}, volume = {114}, number = {2}, pages = {120-130}, doi = {10.1093/jhered/esac065}, pmid = {36525576}, issn = {1465-7333}, mesh = {Animals ; Pseudogenes ; *Genome, Mitochondrial ; *Panthera/genetics ; Phylogeny ; Reproducibility of Results ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; }, abstract = {Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from 2 ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to 2 other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.}, } @article {pmid36520391, year = {2023}, author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T}, title = {Analysis of Ancient Microbial DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {103-131}, pmid = {36520391}, issn = {1940-6029}, mesh = {Animals ; Humans ; DNA, Ancient ; Body Remains ; *Hominidae/genetics ; DNA/genetics ; Genome, Microbial ; *Neanderthals/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.}, } @article {pmid36518622, year = {2022}, author = {Anderson, LA}, title = {Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.}, journal = {Ecology and evolution}, volume = {12}, number = {12}, pages = {e9518}, pmid = {36518622}, issn = {2045-7758}, abstract = {Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.}, } @article {pmid36517229, year = {2022}, author = {Rohland, N and Mallick, S and Mah, M and Maier, R and Patterson, N and Reich, D}, title = {Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2068-2078}, pmid = {36517229}, issn = {1549-5469}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA ; *Polymorphism, Single Nucleotide ; DNA/genetics ; Gene Library ; }, abstract = {The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.}, } @article {pmid36516232, year = {2022}, author = {Söylev, A and Çokoglu, SS and Koptekin, D and Alkan, C and Somel, M}, title = {CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.}, journal = {PLoS computational biology}, volume = {18}, number = {12}, pages = {e1010788}, pmid = {36516232}, issn = {1553-7358}, mesh = {Humans ; *DNA Copy Number Variations/genetics ; Genotype ; *Genomics/methods ; Genome, Human/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.}, } @article {pmid36514938, year = {2023}, author = {Rannamäe, E and Saarma, U and Kantanen, J and Bläuer, A}, title = {Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.}, journal = {Animal genetics}, volume = {54}, number = {2}, pages = {177-188}, doi = {10.1111/age.13281}, pmid = {36514938}, issn = {1365-2052}, support = {SA286499//Academy of Finland/ ; PRG29//Eesti Teadusagentuur/ ; PRG1209//Eesti Teadusagentuur/ ; }, mesh = {Animals ; *Goats/genetics ; Estonia ; Finland ; *Genetic Variation ; Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; }, abstract = {Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.}, } @article {pmid36513080, year = {2023}, author = {Peltola, S and Majander, K and Makarov, N and Dobrovolskaya, M and Nordqvist, K and Salmela, E and Onkamo, P}, title = {Genetic admixture and language shift in the medieval Volga-Oka interfluve.}, journal = {Current biology : CB}, volume = {33}, number = {1}, pages = {174-182.e10}, doi = {10.1016/j.cub.2022.11.036}, pmid = {36513080}, issn = {1879-0445}, mesh = {Humans ; *White People ; Russia ; Language ; *Multilingualism ; }, abstract = {The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.[1][,][2][,][3] A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9[th] century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.[4][,][5][,][6] In the 10[th]-11[th] centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.[3] This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.}, } @article {pmid36510283, year = {2022}, author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B}, title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {250}, pmid = {36510283}, issn = {1474-760X}, support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; }, mesh = {Middle Aged ; Humans ; Phylogeny ; *Coinfection ; Mycobacterium leprae/genetics ; *Leprosy/epidemiology/history/microbiology ; DNA, Ancient ; }, abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.

RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.

CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.}, } @article {pmid36494546, year = {2022}, author = {Forshaw, R}, title = {Dental calculus - oral health, forensic studies and archaeology: a review.}, journal = {British dental journal}, volume = {233}, number = {11}, pages = {961-967}, pmid = {36494546}, issn = {1476-5373}, mesh = {Humans ; Dental Calculus ; Oral Health ; Archaeology ; *Dental Plaque ; *Microbiota ; }, abstract = {Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.}, } @article {pmid36493775, year = {2023}, author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M}, title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.}, journal = {Current biology : CB}, volume = {33}, number = {1}, pages = {41-57.e15}, pmid = {36493775}, issn = {1879-0445}, mesh = {Humans ; Male ; History, Ancient ; *Racial Groups ; Iran ; *Genome, Human ; Gene Flow ; Human Migration ; Genetics, Population ; }, abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.}, } @article {pmid36493597, year = {2023}, author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J}, title = {Reassessment of the human mandible from Banyoles (Girona, Spain).}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103291}, doi = {10.1016/j.jhevol.2022.103291}, pmid = {36493597}, issn = {1095-8606}, mesh = {Animals ; Humans ; Spain ; Proteomics ; *Hominidae/anatomy & histology ; Mandible/anatomy & histology ; *Neanderthals/anatomy & histology ; Fossils ; Biological Evolution ; }, abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.}, } @article {pmid36481947, year = {2022}, author = {Bundell, S}, title = {Record-breaking ancient DNA found in frozen soil.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-04398-6}, pmid = {36481947}, issn = {1476-4687}, } @article {pmid36481704, year = {2023}, author = {Zhang, J and Shi, K and Paerl, HW and Rühland, KM and Yuan, Y and Wang, R and Chen, J and Ge, M and Zheng, L and Zhang, Z and Qin, B and Liu, J and Smol, JP}, title = {Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change.}, journal = {Water research}, volume = {229}, number = {}, pages = {119435}, doi = {10.1016/j.watres.2022.119435}, pmid = {36481704}, issn = {1879-2448}, mesh = {Humans ; *DNA, Ancient ; Ecosystem ; Climate Change ; Eutrophication ; *Cyanobacteria/genetics ; Lakes/microbiology ; China ; }, abstract = {Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.}, } @article {pmid36472532, year = {2022}, author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K}, title = {Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36472532}, issn = {1537-1719}, mesh = {Animals ; Gorilla gorilla ; Phylogeny ; Dental Calculus ; *Hominidae ; *Microbiota/genetics ; }, abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.}, } @article {pmid36465121, year = {2022}, author = {Ma, X and Xu, S}, title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105614}, pmid = {36465121}, issn = {2589-0042}, abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.}, } @article {pmid36463384, year = {2022}, author = {Wang, K and Bleasdale, M and Le Moyne, C and Freund, C and Krause, J and Boivin, N and Schiffels, S}, title = {4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20939}, pmid = {36463384}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient ; Africa, Eastern ; *Hair ; Sudan ; Body Remains ; }, abstract = {Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.}, } @article {pmid36455558, year = {2022}, author = {Waldman, S and Backenroth, D and Harney, É and Flohr, S and Neff, NC and Buckley, GM and Fridman, H and Akbari, A and Rohland, N and Mallick, S and Olalde, I and Cooper, L and Lomes, A and Lipson, J and Cano Nistal, J and Yu, J and Barzilai, N and Peter, I and Atzmon, G and Ostrer, H and Lencz, T and Maruvka, YE and Lämmerhirt, M and Beider, A and Rutgers, LV and Renson, V and Prufer, KM and Schiffels, S and Ringbauer, H and Sczech, K and Carmi, S and Reich, D}, title = {Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14[th] century.}, journal = {Cell}, volume = {185}, number = {25}, pages = {4703-4716.e16}, pmid = {36455558}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Jews/genetics ; *White People ; Genetics, Population ; Genome, Human ; }, abstract = {We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14[th] century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14[th] century and highlight late medieval genetic heterogeneity no longer present in modern AJ.}, } @article {pmid36450657, year = {2023}, author = {Oh, CS and Kim, MJ and Kim, YS and Min, S and Oh, KT and Lee, SD and Shin, DH}, title = {Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.}, journal = {Anatomy & cell biology}, volume = {56}, number = {1}, pages = {54-60}, pmid = {36450657}, issn = {2093-3665}, abstract = {Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.}, } @article {pmid36437963, year = {2022}, author = {Charlier, P and Bourdin, V and Augias, A and Brun, L and Kenmogne, JB and Josue, E}, title = {Are museums the future of evolutionary medicine?.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1043702}, pmid = {36437963}, issn = {1664-8021}, } @article {pmid36437603, year = {2023}, author = {Jeunen, GJ and Dowle, E and Edgecombe, J and von Ammon, U and Gemmell, NJ and Cross, H}, title = {crabs-A software program to generate curated reference databases for metabarcoding sequencing data.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {725-738}, doi = {10.1111/1755-0998.13741}, pmid = {36437603}, issn = {1755-0998}, support = {CAWX1904//Ministry of Business, Innovation and Employment/ ; MFP-21-UOO-087//Royal Society Te Apārangi/ ; }, mesh = {Animals ; *Brachyura ; Reproducibility of Results ; DNA Barcoding, Taxonomic/methods ; Software ; Eukaryota ; }, abstract = {The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data have been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present crabs (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. crabs includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness and taxonomic resolution. crabs is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. crabs can be installed via docker and is available for download as a conda package and via GitHub (https://github.com/gjeunen/reference_database_creator).}, } @article {pmid36426357, year = {2022}, author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G}, title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {987655}, pmid = {36426357}, issn = {1664-3224}, mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; }, abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.}, } @article {pmid36414613, year = {2022}, author = {Quagliariello, A and Modi, A and Innocenti, G and Zaro, V and Conati Barbaro, C and Ronchitelli, A and Boschin, F and Cavazzuti, C and Dellù, E and Radina, F and Sperduti, A and Bondioli, L and Ricci, S and Lognoli, M and Belcastro, MG and Mariotti, V and Caramelli, D and Mariotti Lippi, M and Cristiani, E and Martino, ME and Muntoni, IM and Lari, M}, title = {Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6927}, pmid = {36414613}, issn = {2041-1723}, mesh = {Humans ; *Agriculture ; *Microbiota ; Diet ; Farmers ; Italy ; }, abstract = {The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.}, } @article {pmid36405775, year = {2022}, author = {Arzelier, A and Rivollat, M and De Belvalet, H and Pemonge, MH and Binder, D and Convertini, F and Duday, H and Gandelin, M and Guilaine, J and Haak, W and Deguilloux, MF and Pruvost, M}, title = {Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities.}, journal = {iScience}, volume = {25}, number = {11}, pages = {105387}, pmid = {36405775}, issn = {2589-0042}, abstract = {Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.}, } @article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, } @article {pmid36399972, year = {2023}, author = {Pilli, E and Morelli, S and Poggiali, B and Alladio, E}, title = {Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology.}, journal = {Forensic science international. Genetics}, volume = {62}, number = {}, pages = {102806}, doi = {10.1016/j.fsigen.2022.102806}, pmid = {36399972}, issn = {1878-0326}, mesh = {Humans ; DNA/genetics ; *Forensic Genetics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Least-Squares Analysis ; Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; *Population Groups/genetics ; }, abstract = {As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.}, } @article {pmid36399550, year = {2022}, author = {Sugiyama, N and Sugiyama, S and Cagnato, C and France, CAM and Iriki, A and Hughes, KS and Singleton, RR and Thornton, E and Hofman, CA}, title = {Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {47}, pages = {e2212431119}, pmid = {36399550}, issn = {1091-6490}, mesh = {Humans ; Animals ; *Diplomacy ; Ceremonial Behavior ; DNA, Ancient ; *Atelinae ; Mexico ; }, abstract = {A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human-primate interaction include age at capture and transport (before ∼3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey's sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state's eventual ascent to prominence.}, } @article {pmid36377787, year = {2023}, author = {Ausmees, K and Nettelblad, C}, title = {Achieving improved accuracy for imputation of ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36377787}, issn = {1367-4811}, support = {2017-00453//Formas/ ; }, mesh = {Animals ; Dogs ; Humans ; *DNA, Ancient ; Genotype ; Haplotypes ; *Software ; Ethnicity ; }, abstract = {MOTIVATION: Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.

RESULTS: We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.

The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser.

SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.}, } @article {pmid36375244, year = {2022}, author = {Harvati, K and Reyes-Centeno, H}, title = {Evolution of Homo in the Middle and Late Pleistocene.}, journal = {Journal of human evolution}, volume = {173}, number = {}, pages = {103279}, pmid = {36375244}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; }, abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.}, } @article {pmid36373266, year = {2022}, author = {Gaughran, SJ and vonHoldt, B}, title = {Pleistocene parades of carnivores into North America.}, journal = {Molecular ecology}, volume = {31}, number = {24}, pages = {6387-6389}, doi = {10.1111/mec.16783}, pmid = {36373266}, issn = {1365-294X}, mesh = {Animals ; Humans ; *Carnivora/genetics ; Phylogeography ; *Ursidae/genetics ; Biological Evolution ; *Lions ; North America ; Phylogeny ; }, abstract = {The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.}, } @article {pmid36371979, year = {2022}, author = {Howarth, A and Drummond, B and Wasef, S and Matheson, CD}, title = {An assessment of DNA extraction methods from blood-stained soil in forensic science.}, journal = {Forensic science international}, volume = {341}, number = {}, pages = {111502}, doi = {10.1016/j.forsciint.2022.111502}, pmid = {36371979}, issn = {1872-6283}, mesh = {Humans ; *Soil ; Polymerase Chain Reaction/methods ; DNA/analysis ; Chloroform/analysis ; Povidone ; Endopeptidase K ; *Blood Stains ; Silicon Dioxide ; }, abstract = {In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.}, } @article {pmid36360198, year = {2022}, author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A}, title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360198}, issn = {2073-4425}, mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.}, } @article {pmid36348137, year = {2023}, author = {Kimsis, J and Petersone-Gordina, E and Poksane, A and Vilcāne, A and Moore, J and Gerhards, G and Ranka, R}, title = {Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study.}, journal = {Forensic science, medicine, and pathology}, volume = {19}, number = {1}, pages = {8-15}, pmid = {36348137}, issn = {1556-2891}, support = {lzp-2018/1-0395.//Latvijas Zinātnes Padome/ ; }, mesh = {Humans ; Pilot Projects ; Latvia ; *Burial ; *DNA, Mitochondrial/genetics ; Cemeteries/history ; }, abstract = {Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.}, } @article {pmid36344562, year = {2022}, author = {Miszkiewicz, JJ and Buckley, HR and Feldman, M and Kiko, L and Carlhoff, S and Naegele, K and Bertolini, E and Guimarães, NRD and Walker, MM and Powell, A and Posth, C and Kinaston, RL}, title = {Female bone physiology resilience in a past Polynesian Outlier community.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18857}, pmid = {36344562}, issn = {2045-2322}, support = {DE190100068//Australian Research Council/ ; ERC758967//European Research Council Starting Grant 'Waves'/ ; }, mesh = {Male ; Humans ; Female ; *Haversian System ; *Femur ; Bone and Bones ; Bone Remodeling ; Melanesia ; }, abstract = {Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region.}, } @article {pmid36329382, year = {2022}, author = {Lord, E and Marangoni, A and Baca, M and Popović, D and Goropashnaya, AV and Stewart, JR and Knul, MV and Noiret, P and Germonpré, M and Jimenez, EL and Abramson, NI and Vartanyan, S and Prost, S and Smirnov, NG and Kuzmina, EA and Olsen, RA and Fedorov, VB and Dalén, L}, title = {Population dynamics and demographic history of Eurasian collared lemmings.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {126}, pmid = {36329382}, issn = {2730-7182}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; P20 GM130443/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Ecosystem ; *Arvicolinae ; Population Dynamics ; Arctic Regions ; DNA, Ancient ; }, abstract = {BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.

RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.

CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.}, } @article {pmid36322514, year = {2022}, author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J}, title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1986}, pages = {20221078}, pmid = {36322514}, issn = {1471-2954}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; }, abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.}, } @article {pmid36322483, year = {2022}, author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV}, title = {Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36322483}, issn = {1537-1719}, mesh = {Animals ; Humans ; *Antelopes/genetics ; Biological Evolution ; Phylogeny ; Genome ; *Mustelidae/genetics ; }, abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.}, } @article {pmid36316157, year = {2022}, author = {Mathieson, I and Terhorst, J}, title = {Direct detection of natural selection in Bronze Age Britain.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2057-2067}, pmid = {36316157}, issn = {1549-5469}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; United Kingdom ; *Selection, Genetic ; Skin Pigmentation ; Genome, Human ; }, abstract = {We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.}, } @article {pmid36300941, year = {2022}, author = {Nino Barreat, JG and Katzourakis, A}, title = {Evolutionary Analysis of Placental Orthologues Reveals Two Ancient DNA Virus Integrations.}, journal = {Journal of virology}, volume = {96}, number = {22}, pages = {e0093322}, pmid = {36300941}, issn = {1098-5514}, mesh = {Animals ; Female ; Humans ; Pregnancy ; *DNA, Ancient ; Eutheria ; *Evolution, Molecular ; Genome, Human ; *Mammals/genetics/virology ; Marsupialia ; Phylogeny ; Virus Integration ; *DNA Viruses/genetics ; }, abstract = {The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.}, } @article {pmid36292743, year = {2022}, author = {Nedoluzhko, A and Orlova, SY and Kurnosov, DS and Orlov, AM and Galindo-Villegas, J and Rastorguev, SM}, title = {Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii).}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292743}, issn = {2073-4425}, mesh = {Animals ; *Adaptation, Physiological/genetics ; Pacific Ocean ; *Lakes ; Genomics ; }, abstract = {Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as "genomic islands of divergence". Moreover, the Tajima's D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait-osmoregulation.}, } @article {pmid36292570, year = {2022}, author = {Hou, X and Zhao, J and Zhang, H and Preick, M and Hu, J and Xiao, B and Wang, L and Deng, M and Liu, S and Chang, F and Sheng, G and Lai, X and Hofreiter, M and Yuan, J}, title = {Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292570}, issn = {2073-4425}, mesh = {Animals ; *Bison/genetics ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Fossils ; Biological Evolution ; }, abstract = {Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.}, } @article {pmid36289417, year = {2022}, author = {Thompson, B and Bundell, S}, title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03460-7}, pmid = {36289417}, issn = {1476-4687}, } @article {pmid36282902, year = {2022}, author = {Atmore, LM and Martínez-García, L and Makowiecki, D and André, C and Lõugas, L and Barrett, JH and Star, B}, title = {Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {45}, pages = {e2208703119}, pmid = {36282902}, issn = {1091-6490}, mesh = {Animals ; Humans ; *Fisheries ; *DNA, Ancient ; Conservation of Natural Resources ; Population Dynamics ; Fishes/genetics ; Genomics ; Baltic States ; }, abstract = {The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.}, } @article {pmid36282813, year = {2022}, author = {Ibrahim, J and Brumfeld, V and Addadi, Y and Rubin, S and Weiner, S and Boaretto, E}, title = {The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0269348}, pmid = {36282813}, issn = {1932-6203}, mesh = {Humans ; Swine ; Animals ; *Osteocytes/pathology ; *DNA, Ancient ; Petrous Bone/diagnostic imaging ; Bone and Bones ; DNA/genetics ; }, abstract = {The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.}, } @article {pmid36277234, year = {2022}, author = {Cessford, C and Neil, B}, title = {The people of the Cambridge Austin friars.}, journal = {Archaeological journal}, volume = {179}, number = {2}, pages = {383-444}, pmid = {36277234}, issn = {2373-2288}, support = {200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The Austin friars in Cambridge was an important religious institution between the late thirteenth and mid-sixteenth centuries. Excavations have revealed well-dated and contextualised burials associated with the friary, as well as a range of material culture. The burials have been subject to a wide range of analyses including osteology, palaeopathology, stable isotopes, ancient DNA and geometric morphometrics. Significantly the distinction between clothed and shrouded burials allows members of the Augustinian order and the laity to be identified. This represents the best-understood published group of burials from an Austin friars in the British Isles and emphasises the importance of nuanced interpretation, as burial at friaries was a structured and multi-local phenomenon. These burials and other material can be interpreted in terms of both mendicant ideals and anti-fraternal criticisms.}, } @article {pmid36276948, year = {2022}, author = {Xu, B and Yang, G and Jiao, B and Zhu, H}, title = {Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {944933}, pmid = {36276948}, issn = {1664-8021}, abstract = {Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs' potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.}, } @article {pmid36261712, year = {2022}, author = {Enard, D}, title = {Ancient DNA reveals rapid natural selection during the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {237-238}, pmid = {36261712}, issn = {1476-4687}, mesh = {Humans ; *DNA, Ancient ; *Plague ; Selection, Genetic ; Evolution, Molecular ; }, } @article {pmid36261521, year = {2022}, author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB}, title = {Evolution of immune genes is associated with the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {312-319}, pmid = {36261521}, issn = {1476-4687}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Aminope