@article {pmid39705165,
year = {2024},
author = {Patin, E and Quintana-Murci, L},
title = {Tracing the Evolution of Human Immunity Through Ancient DNA.},
journal = {Annual review of immunology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-immunol-082323-024638},
pmid = {39705165},
issn = {1545-3278},
abstract = {Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.},
}

@article {pmid39703808,
year = {2024},
author = {Veselka, B and Reich, D and Capuzzo, G and Olalde, I and Callan, K and Zalzala, F and Altena, E and Goffette, Q and Ringbauer, H and van der Velde, H and Polet, C and Toussaint, M and Snoeck, C and Cattelain, L},
title = {Assembling Ancestors: the manipulation of Neolithic and Gallo-Roman skeletal remains from Pommerœul, Belgium.},
journal = {Antiquity},
volume = {98},
number = {402},
pages = {1576-1591},
pmid = {39703808},
issn = {0003-598X},
abstract = {The ancient cemetery of Pommerœul, Belgium, was classified as Gallo-Roman in the 1970s', yielding 76 cremation graves and one inhumation. However, subsequent radiocarbon analyses dated the inhumation to the Late Neolithic (4[th]-3[rd] millennium calBC). We report osteoarchaeological analysis indicating that the inhumation was composed of bones from multiple individuals, afterwards buried as "one". Ancient DNA analyses also finds evidence of multiple individuals and revealed another surprise: the cranium is post-Neolithic and genetically related to a pair of siblings from another Belgian Gallo-Roman site. This composite burial may have been created in Late Neolithic times, with Gallo-Romans adding the cranium, or alternatively the burial may have been fully assembled in the Gallo-Roman periods. This exceptional burial documents unexpected burial practices for both prehistoric and Roman times.},
}

@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@article {pmid39698825,
year = {2024},
author = {Shastry, V and Berg, JJ},
title = {Allele ages provide limited information about the strength of negative selection.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae211},
pmid = {39698825},
issn = {1943-2631},
abstract = {For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by re-weighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson Random Field (PRF) method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.},
}

@article {pmid39697594,
year = {2024},
author = {Wang, B and Hao, D and Xu, Y and Zhu, K and Wang, R and Yang, X and Shen, Q and Xu, M and Bai, T and Ma, H and Zheng, J and Wang, X and Zou, X and Zhou, H and Mao, X and Tang, J and Peng, Y and Tao, L and He, H and Chen, H and Guo, J and Ji, Z and Liu, Y and Wen, S and Jin, L and Zhang, Q and Wang, CC},
title = {Population expansion from central plain to northern coastal China inferred from ancient human genomes.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111405},
pmid = {39697594},
issn = {2589-0042},
abstract = {The population history of the northern coastal Chinese is largely unknown due to the lack of ancient human genomes from the Neolithic to historical periods. In this study, we reported 14 newly generated ancient genomes from Linzi, one of China's densely populated and economically prosperous cities from the Zhou to Han Dynasties. The ancient samples in this study were dated to the Warring States period to the Eastern Han Dynasty (∼2,000 BP). We found the samples derived all their ancestry from Late Bronze Age to Iron Age Middle Yellow River farmers rather than local Neolithic populations. They were genetically homogeneous with present-day Han Chinese of Shandong, suggesting 2,000 years of genetic stability. Our results highlight the role of the eastward migration of Yellow River farmers in the Central Plain to northern coastal China in forming the present-day genetic structure of Han Chinese.},
}

@article {pmid39697469,
year = {2024},
author = {Owsley, DW and Bruwelheide, KS and Harney, É and Mallick, S and Rohland, N and Olalde, I and Barca, KG and Ramsey, AJ and Hull-Walski, DA and Kelso, WM and May, JE and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Simon, VE and Givens, DM and Lavin, MD and Reich, DE},
title = {Historical and Archaeogenomic Identification of High-Status Englishmen at Jamestown, Virginia.},
journal = {Antiquity},
volume = {98},
number = {400},
pages = {1040-1054},
pmid = {39697469},
issn = {0003-598X},
abstract = {Ancient DNA (aDNA) data are reported for two human skeletons buried within the chancel of the 1608-1616 church at the North American colonial settlement of Jamestown, Virginia. The men are suspected kinsmen of the colony's first Governor, Thomas West, 3[rd] Baron De La Warr based on archaeological, osteological, and documentary evidence. Genomic analyses of these men, Sir Ferdinando Wenman and Captain William West, identify a shared mitochondrial haplogroup, H10e, inferring maternal relatedness. In this unusual case, aDNA prompted further historical research that led to the discovery of illegitimacy, an aspect of identity omitted, likely intentionally, from genealogical records.},
}

@article {pmid39694065,
year = {2024},
author = {Barquera, R and Sitter, TL and Kirkpatrick, CL and Ramirez, DA and Kocher, A and Spyrou, MA and Couoh, LR and Talavera-González, JA and Castro, M and von Hunnius, T and Guevara, EK and Hamilton, WD and Roberts, P and Scott, E and Fabra, M and Da Peña, GV and Pacheco, A and Rodriguez, M and Aspillaga, E and Tiliakou, A and Nelson, EA and Giffin, KL and Bianco, RA and Rohrlach, AB and de Los Ángeles García Martínez, M and Ballesteros Solís, FA and Sajantila, A and Saunders, SR and Nores, R and Herbig, A and Krause, J and Bos, KI},
title = {Ancient genomes reveal a deep history of treponemal disease in the Americas.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-024-08515-5},
pmid = {39694065},
issn = {1476-4687},
abstract = {Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most famously, syphilis[1]. Debates on both a common origin for these pathogens and the history of syphilis itself has weighed evidence for the "Columbian hypothesis"[2], which argues for an American origin, against that for the "pre-Columbian hypothesis"[3], which argues for presence of the disease in Eurasia in the Medieval period and possibly earlier. While molecular data has provided a genetic basis for distinction of the typed subspecies[4], deep evolution of the complex has remained unresolved due to limitations in the conclusions that can be drawn from the sparse paleogenomic data currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the T. pallidum pallidum (syphilis), T. pallidum pertenue (yaws) and T. pallidum endemicum (bejel) lineages. Our data indicate unexplored diversity and an emergence of T. pallidum that post-dates human occupation in the Americas. Together these results support an American origin for all T. pallidum characterized at the genomic level, both modern and ancient.},
}

@article {pmid39689706,
year = {2024},
author = {Donegan, MA and Kahn, AK and Becker, N and Castillo Siri, A and Campos, PE and Boyer, K and Colwell, A and Briand, M and Almeida, RPP and Rieux, A},
title = {Century-old herbarium specimen provides insights into Pierce's disease of grapevines emergence in the Americas.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.11.029},
pmid = {39689706},
issn = {1879-0445},
abstract = {Fossils and other preserved specimens are integral for informing timing and evolutionary history in every biological system. By isolating a plant pathogen genome from herbarium-preserved diseased grapevine material from 1906 (Herb_1906), we were able to answer questions about an enigmatic system. The emergence of Pierce's disease (PD) of grapevine has shaped viticultural production in North America; yet, there are uncertainties about the geographic origin of the pathogen (Xylella fastidiosa subsp. fastidiosa, Xff) and the timing and route of its introduction. We produced a high-quality, de novo genome assembly of this historical plant pathogen and confirmed degradation patterns unique to ancient DNA. Due to the inclusion of the Herb_1906 sample, we were able to generate a significant temporal signal in the genomic data. This allowed us to build a time-calibrated phylogeny, where we estimate the introduction of Xff into the US between 1734 and 1741 CE, an earlier time frame than previously inferred. In a large collection of >300 Xff genomes, the Herb_1906 sample was genetically most similar to a small population from Northern California but not basal to the entire Xff California clade. Based on phylogenetic placement and a phylogeographic reconstruction, our data support a single introduction of Xff into the Southeastern US from Central America, with multiple subsequent introductions into California.},
}

@article {pmid39677618,
year = {2024},
author = {Yediay, FE and Kroonen, G and Sabatini, S and Frei, KM and Frank, AB and Pinotti, T and Wigman, A and Thorsø, R and Vimala, T and McColl, H and Moutafi, I and Altinkaya, I and Ramsøe, A and Gaunitz, C and Renaud, G and Mederos Martin, A and Demeter, F and Scorrano, G and Canci, A and Fischer, P and Duyar, I and Serhal, C and Varzari, A and Türkteki, M and O'Shea, J and Rahmstorf, L and Polat, G and Atamtürk, D and Vinner, L and Omura, S and Matsumura, K and Cao, J and Valeur Seersholm, F and Morillo Leon, JM and Voutsaki, S and Orgeolet, R and Burke, B and Herrmann, NP and Recchia, G and Corazza, S and Borgna, E and Cipolloni Sampò, M and Trucco, F and Pajuelo Pando, A and Schjellerup Jørkov, ML and Courtaud, P and Peake, R and Gibaja Bao, JF and Parditka, G and Stenderup, J and Sjögren, KG and Staring, J and Olsen, L and Deyneko, IV and Pálfi, G and López Aldana, PM and Burns, B and Paja, L and Mühlenbock, C and Cavazzuti, C and Cazzella, A and Lagia, A and Lambrinoudakis, V and Kolonas, L and Rambach, J and Sava, E and Agulnikov, S and Castañeda Fernández, V and Broné, M and Peña Romo, V and Molina González, F and Cámara Serrano, JA and Jiménez Brobeil, S and Nájera Molino, T and Rodríguez Ariza, MO and Galán Saulnier, C and González Martín, A and Cauwe, N and Mordant, C and Roscio, M and Staniaszek, L and Tafuri, MA and Yıldırım, T and Salzani, L and Sand Korneliussen, T and Moreno-Mayar, JV and Allentoft, ME and Sikora, M and Nielsen, R and Kristiansen, K and Willerslev, E},
title = {Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.02.626332},
pmid = {39677618},
issn = {2692-8205},
abstract = {The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious [1-5] . It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age [6,7] . However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages [8,9] . To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic [10,11] and Graeco-Armenian [1,12,13] hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.},
}

@article {pmid39674265,
year = {2024},
author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B},
title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39674265},
issn = {1477-4054},
support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; },
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; },
abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Sequence Analysis, DNA/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome
Workflow
DNA Contamination

@article {pmid39672950,
year = {2024},
author = {Tournebize, R and Chikhi, L},
title = {Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39672950},
issn = {2397-334X},
support = {ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events-such as ancient bottlenecks or admixture-is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.},
}

@article {pmid39666807,
year = {2024},
author = {Curry, A},
title = {Study reveals kinship among first modern humans in Europe.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6727},
pages = {1207},
doi = {10.1126/science.adv2424},
pmid = {39666807},
issn = {1095-9203},
mesh = {Humans ; *DNA, Ancient/analysis ; Europe ; Human Migration/history ; Pedigree ; History, Ancient ; Family ; },
abstract = {Ancient DNA links people across hundreds of kilometers.},
}

Humans
*DNA, Ancient/analysis
Europe
Human Migration/history
Pedigree
History, Ancient
Family

@article {pmid39660047,
year = {2024},
author = {Klapper, M and Stallforth, P},
title = {Accessing microbial natural products of the past.},
journal = {microLife},
volume = {5},
number = {},
pages = {uqae023},
pmid = {39660047},
issn = {2633-6693},
abstract = {Microbial natural products-low molecular weight compounds biosynthesized by microorganisms-form the foundation of important modern therapeutics, including antibiotics, immunomodulators, and anti-cancer agents. This perspective discusses and contrasts two emerging approaches for uncovering natural products of the past. On the one hand, ancestral sequence reconstruction allows recreating biosynthetic pathways that date back hundreds of millions of years. On the other hand, sequencing and de novo assembly of ancient DNA reveals the biosynthetic potential of ancient microbial communities up to 100 000 years. Together, these approaches unveil an otherwise hidden reservoir of functional and structural molecular diversity. They also offer new opportunities to study the biological function and evolution of these molecules within an archaeological context.},
}

@article {pmid39658639,
year = {2024},
author = {Bergström, A and Fellows Yates, JA and Warinner, C},
title = {Ancient DNA data hold insights into past organisms and ecosystems - handle them with more care.},
journal = {Nature},
volume = {636},
number = {8042},
pages = {296-298},
pmid = {39658639},
issn = {1476-4687},
}

@article {pmid39658338,
year = {2024},
author = {Simeone, CA and McNulty, MT and Gupta, Y and Genovese, G and Sampson, MG and Sanna-Cherchi, S and Friedman, DJ and Pollak, MR},
title = {The APOL1 p.N264K variant is co-inherited with the G2 kidney disease risk variant through a proximity recombination event.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae290},
pmid = {39658338},
issn = {2160-1836},
abstract = {Black Americans are three to four times more likely to develop nondiabetic kidney disease than other populations. Exclusively found in people of recent African (AFR) ancestry, risk variants in Apolipoprotein L1 (APOL1) termed G1 and G2 contribute significantly to this increased susceptibility. Our group and others showed that a missense variant in APOL1, rs73885316 (p.N264K, "M1"), is remarkably protective against APOL1 kidney disease when co-inherited with the G2 risk allele. Since the distance between the M1 and G2 variants is only 367 base pairs, we initially suspected that two independent mutation events occurred to create non-risk M1-G0 and M1-G2 haplotypes. Here, we examined APOL1 haplotypes in individuals of AFR ancestry from the 1000 Genomes Project, the Nephrotic Syndrome Study Network (NEPTUNE), and an ancient individual from the Allen Ancient Genome Diversity Project to determine how the M1-G2 haplotype arose. We demonstrate that M1 most likely first appeared on a non-risk G0 haplotype, and that a subsequent recombination event bypassed strong recombination hotspots flanking APOL1 and occurred between p.N388Y389del on a G2 haplotype and M1 on a G0 haplotype to create the M1-G2 haplotype. Observing a recombination event within a small region between clinically relevant loci emphasizes the importance of studying the entire haplotype repertoire of a disease gene and the impact of haplotype backgrounds in disease susceptibility.},
}

@article {pmid39638089,
year = {2024},
author = {Wang, L and Wang, Y and Sun, B and Zhang, D and Liang, G and Ma, P and Zhang, H and Li, C and Hu, X and Zhang, Q and Cui, Y},
title = {Ancient DNA reveals genetic exchange in the Hehuang Valley in the context of demic diffusion during the Han Dynasty.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.11.013},
pmid = {39638089},
issn = {1673-8527},
}

@article {pmid39637852,
year = {2024},
author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N},
title = {The genomic origin of early maize in eastern North America.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.11.003},
pmid = {39637852},
issn = {1097-4172},
abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.},
}

@article {pmid39635427,
year = {2022},
author = {Tiesler, V and Sedig, J and Nakatsuka, N and Mallick, S and Lazaridis, I and Bernardos, R and Broomandkhoshacht, N and Oppenheimer, J and Lawson, AM and Stewardson, K and Rohland, N and Kennett, DJ and Price, TD and Reich, D},
title = {Life and death in early colonial Campeche: new insights from ancient DNA.},
journal = {Antiquity},
volume = {96},
number = {388},
pages = {937-954},
pmid = {39635427},
issn = {0003-598X},
}

@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.},
}

*Gadus morhua/genetics
*DNA, Ancient/analysis
Norway
Animals
History, Medieval
Carbon Isotopes/analysis
Fisheries
Nitrogen Isotopes/analysis
Archaeology
History, 17th Century

@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.},
}

*Models, Genetic
Polymorphism, Single Nucleotide
Hybridization, Genetic
Animals
Phylogeny
Genetic Introgression
Alleles

@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 {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.},
}

Humans
Bone and Bones
*DNA, Ancient/analysis
*Human Migration/history
India
*South Asian People/history

@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.},
}

*DNA, Ancient/analysis
*Selection, Genetic
Humans
Europe
*Genetic Drift
*Gene Frequency
Haplotypes/genetics
Animals
Lactase/genetics
Genetics, Population/methods
Evolution, Molecular
Genotype

@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},
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 {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.},
}

Italy
Humans
*Radiometric Dating
Fossils
Male
Body Remains/chemistry
Femur/chemistry/metabolism

@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.},
}

*Biofilms/growth & development
*Fresh Water/microbiology/virology
*Calcium Carbonate/metabolism/chemistry
Geologic Sediments/microbiology/virology
Viruses/genetics/metabolism
Principal Component Analysis
Metagenomics/methods

@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.},
}

*Ursidae/genetics
Animals
Scandinavian and Nordic Countries
*Genome, Mitochondrial
*Haplotypes
*Genetic Variation
*Phylogeny
Female
DNA, Mitochondrial/genetics
Genetics, Population

@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.},
}

Animals
*Sheep, Domestic/genetics
*Domestication
Sheep/genetics
Genome
DNA, Ancient/analysis
Europe

@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.},
}

*G-Quadruplexes
Animals
Humans
Transcription Factors/metabolism/genetics
DNA/metabolism/genetics
RNA, Untranslated/genetics/metabolism
DNA Repair
Caenorhabditis elegans/genetics/metabolism

@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.},
}

Animals
*Phylogeny
*Genome, Mitochondrial
Endangered Species
Rodentia/genetics/classification

@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.},
}

Humans
*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome
Geography
Microbiota/genetics

@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.},
}

*Ursidae/genetics
Animals
Arctic Regions
*Alleles
*Genome
Adaptation, Physiological/genetics
Evolution, Molecular
Selection, Genetic

@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.},
}

Humans
United Kingdom
*Human Migration
*Rural Population
History, Ancient
DNA, Ancient/analysis
Genetics, Population

@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.},
}

*Metagenomics/methods
Humans
*Metadata
High-Throughput Nucleotide Sequencing/methods
Software
Metagenome
Computational Biology/methods
DNA, Ancient/analysis

@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.},
}

Animals
*Genome
*Eagles/genetics
Female
DNA Transposable Elements/genetics
Phylogeny
Evolution, Molecular
Retroelements/genetics
Genomics/methods

@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.},
}

*DNA, Ancient/analysis
France
Humans
*Burial/history
*Archaeology
Male
Bayes Theorem
Female
History, Ancient

@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.},
}

*DNA, Ancient/analysis
*Geologic Sediments
Humans
Animals
Archaeology/methods
Fossils
High-Throughput Nucleotide Sequencing/methods
Hominidae/genetics
Europe
Africa

@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.},
}

Humans
*Archaeology
*Roman World/history
Italy
History, Medieval
Human Migration/history
History, Ancient

@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.},
}

Humans
History, 20th Century
History, 21st Century
*Interleukin-17/metabolism
Autoimmunity

@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.},
}

Humans
*Fossils
Europe
*Phenotype
*Tooth/anatomy & histology
*Population Dynamics
Bayes Theorem
Archaeology

@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.},
}

Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Antimicrobial Peptides/pharmacology
Machine Learning
Drug Resistance, Bacterial
Proteomics/methods

@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.},
}

Animals
*Beluga Whale/genetics
Northwest Territories
Female
Male
Hunting
Nitrogen Isotopes/analysis
Carbon Isotopes/analysis
DNA, Mitochondrial/genetics
Inuit

@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 = {},
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.},
}

*Selection, Genetic
Humans
*DNA, Ancient/analysis
*Models, Genetic
*Gene Frequency
Likelihood Functions
Markov Chains
Algorithms
Evolution, Molecular
Alleles
Computer Simulation

@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.},
}

Animals
Biological Evolution
*Birds/genetics
DNA, Ancient/analysis
*Fossils
*Genome
*Genomics/ethics
New Zealand
Sequence Analysis, DNA