@article {pmid40272380,
year = {2025},
author = {Boucher, RD and Godfrey, LV and Fehren-Schmitz, L and Koch, PL},
title = {Examination of Fe and Cu Isotope Variation in Great Apes Using an Optimized Protocol.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {39},
number = {14},
pages = {e10051},
doi = {10.1002/rcm.10051},
pmid = {40272380},
issn = {1097-0231},
support = {//Leakey Foundation/ ; 2216033//National Science Foundation/ ; },
mesh = {Animals ; Female ; Pan troglodytes ; Male ; *Copper/analysis ; *Iron Isotopes/analysis ; Pan paniscus ; Bone and Bones/chemistry ; Mass Spectrometry/methods ; },
abstract = {RATIONALE: Iron deficiency plagues reproductive-aged women across the world, and blood loss during menstruation is proposed as the driving force. To assess if other factors related to reproduction influence Fe and Cu isotope variation in females, we measured Fe and Cu isotope compositions in the bones of chimpanzees and bonobos.

METHODS: To do this, we optimize the protocol for isolating Fe and Cu (and Zn) from phosphate-rich skeletal materials for further analysis via MC-ICP-MS. Then, we address possible Fe and Cu variation sources in non-menstruating apes (n = 26, of which the sex of 10 was obtained by DNA analysis).

RESULTS: The optimized method reduced acid volume by ~14%, and sample preparation time by ~37.5%. We did not find significant sex differences in δ[56]Fe values (Δ[56]Fef-m = 0.13‰) or δ[65]Cu values (Δ[65]Cuf-m = 0.33‰).

CONCLUSION: Given the similar Δ[56]Fef-m values between non-menstruating apes and humans, reproductive investment, instead of menstruation alone, is a key factor that drives Fe deficiency in reproductive-aged women and is important to consider with proxies of iron status. Our optimized protocol provides an effective method for exploring iron status in other mammalian species.},
}

Animals
Female
Pan troglodytes
Male
*Copper/analysis
*Iron Isotopes/analysis
Pan paniscus
Bone and Bones/chemistry
Mass Spectrometry/methods

@article {pmid40272075,
year = {2025},
author = {Wooldridge, TB and Wang, MS and Saremi, NF and Kapp, JD and Moon, KL and Heintzman, PD and Dumbacher, JP and Alagona, PS and Long, B and Shapiro, B},
title = {Genomic data from the extinct California brown bear suggests a source population for reintroduction to California.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esaf018},
pmid = {40272075},
issn = {1465-7333},
abstract = {California brown bears, also known as California grizzlies or golden bears, are an extinct group that once thrived in North America's western coastal habitats. Despite being common in the region as recently as the early 19th century, intense poisoning, trapping, and hunting led to their extinction by 1924. Today, California is emerging as a candidate for brown bear reintroduction as a component of larger ecosystem restoration efforts. Questions remain, however, about whether living brown bears are suitable proxies for the bears that once inhabited California. While recent work suggests that brown bears from California were similar in size and overall diet to brown bears living today in continental North America, the a) extent to which California bears were genetically differentiated from other populations, and b) what this means for proposed reintroductions, remain outstanding questions. We generated genomes from two of the last living California brown bears and compared them to genomes from living brown bears. Genomic estimates of divergence time combined with radiocarbon dating points towards brown bears arriving recently to California, having diverged within the last 10,000 years from a common ancestor with brown bears found today in Yellowstone National Park, Wyoming. This timeline, the overall genetic similarity between the California and Yellowstone populations, and the strong pattern of isolation-by-distance we observe all suggest that no closer living relatives are likely to be found. If genetic background is to be a consideration for reintroduction efforts in California, brown bears from Yellowstone might serve as a source population.},
}

@article {pmid40269306,
year = {2025},
author = {Callaway, E},
title = {Ancient DNA reveals Phoenicians' surprising genetic ancestry.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40269306},
issn = {1476-4687},
}

@article {pmid40269169,
year = {2025},
author = {Ringbauer, H and Salman-Minkov, A and Regev, D and Olalde, I and Peled, T and Sineo, L and Falsone, G and van Dommelen, P and Mittnik, A and Lazaridis, I and Pettener, D and Bofill, M and Mezquida, A and Costa, B and Jiménez, H and Smith, P and Vai, S and Modi, A and Shaus, A and Callan, K and Curtis, E and Kearns, A and Lawson, AM and Mah, M and Micco, A and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Márquez-Grant, N and Sáez Romero, AM and Lavado Florido, ML and Jiménez-Arenas, JM and Toro Moyano, IJ and Viguera, E and Padilla, JS and Chamizo, SL and Marques-Bonet, T and Lizano, E and Riaza, AR and Olivieri, F and Toti, P and Giuliana, V and Barash, A and Carmel, L and Boaretto, E and Faerman, M and Lucci, M and La Pastina, F and Nava, A and Genchi, F and Del Vais, C and Lauria, G and Meli, F and Sconzo, P and Catalano, G and Cilli, E and Fariselli, AC and Fontani, F and Luiselli, D and Culleton, BJ and Mallick, S and Rohland, N and Nigro, L and Coppa, A and Caramelli, D and Pinhasi, R and Lalueza-Fox, C and Gronau, I and Reich, D},
title = {Punic people were genetically diverse with almost no Levantine ancestors.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40269169},
issn = {1476-4687},
abstract = {The maritime Phoenician civilization from the Levant transformed the entire Mediterranean during the first millennium BCE[1-3]. However, the extent of human movement between the Levantine Phoenician homeland and Phoenician-Punic settlements in the central and western Mediterranean has been unclear in the absence of comprehensive ancient DNA studies. Here, we generated genome-wide data for 210 individuals, including 196 from 14 sites traditionally identified as Phoenician and Punic in the Levant, North Africa, Iberia, Sicily, Sardinia and Ibiza, and an early Iron Age individual from Algeria. Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries BCE, despite abundant archaeological evidence of cultural, historical, linguistic and religious links[4]. Instead, these inheritors of Levantine Phoenician culture derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean. Much of the remaining ancestry originated from North Africa, reflecting the growing influence of Carthage[5]. However, this was a minority contributor of ancestry in all of the sampled sites, including in Carthage itself. Different Punic sites across the central and western Mediterranean show similar patterns of high genetic diversity. We also detect genetic relationships across the Mediterranean, reflecting shared demographic processes that shaped the Punic world.},
}

@article {pmid40269167,
year = {2025},
author = {Feng, C and Chen, B and Hofer, J and Shi, Y and Jiang, M and Song, B and Cheng, H and Lu, L and Wang, L and Howard, A and Bendahmane, A and Fouchal, A and Moreau, C and Sawada, C and LeSignor, C and Zhang, C and Vikeli, E and Tsanakas, G and Zhao, H and Cheema, J and Barclay, JE and Hou, J and Sayers, L and Wingen, L and Vigouroux, M and Vickers, M and Ambrose, M and Dalmais, M and Higuera-Poveda, P and Li, P and Yuan, Q and Spanner, R and Horler, R and Wouters, R and Chundakkad, S and Wu, T and Zhao, X and Li, X and Sun, Y and Huang, Z and Wu, Z and Deng, XW and Steuernagel, B and Domoney, C and Ellis, N and Chayut, N and Cheng, S},
title = {Genomic and genetic insights into Mendel's pea genes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40269167},
issn = {1476-4687},
abstract = {Mendel[1] studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes[2-7], including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the 'semi-leafless' form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.},
}

@article {pmid40236176,
year = {2025},
author = {Xu, J and Zavala, EI and Moorjani, P},
title = {sedimix : A workflow for the analysis of hominin nuclear DNA sequences from sediments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.28.640818},
pmid = {40236176},
issn = {2692-8205},
abstract = {SUMMARY: Sediment DNA--the ability to extract DNA from archaeological sediments-- is an exciting new frontier in ancient DNA research, offering the potential to study individuals at a given archaeological site without destructive sampling. In recent years, several studies have demonstrated the promise of this approach by recovering hominin DNA from prehistoric sediments, including those dating back to the Middle or Late Pleistocene. However, a lack of open-source workflows for analysis of hominin sediment DNA samples poses a challenge for data processing and reproducibility of findings across studies. Here we introduce a snakemake workflow, sedimix , for processing genomic sequences from archaeological sediment DNA samples to identify hominin sequences and generate relevant summary statistics to assess the reliability of the pipeline. By performing simulations and comparing to published studies, we show that sedimix has high sensitivity and precision. sedimix offers a reliable and adaptable framework to aid in the analysis of sediment DNA datasets and improve reproducibility across studies.

sedimix is available as an open-source software with the associated code and user manual available at https://github.com/jierui-cell/sedimix Contact: Jierui Xu (jierui.xu@berkeley.edu) Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40129172,
year = {2025},
author = {De Cahsan, B and Sandoval Velasco, M and Westbury, MV and Duchêne, DA and Strander Sinding, MH and Morales, HE and Kalthoff, DC and Barnes, I and Brace, S and Portela Miguez, R and Roca, AL and Greenwood, AD and Johnson, RN and Lott, MJ and Gilbert, MTP},
title = {Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala.},
journal = {Molecular biology and evolution},
volume = {42},
number = {4},
pages = {},
doi = {10.1093/molbev/msaf057},
pmid = {40129172},
issn = {1537-1719},
abstract = {Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.},
}

@article {pmid40217095,
year = {2025},
author = {Barnes, I},
title = {A tour de force of ancient DNA analysis.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40217095},
issn = {1471-0064},
}

@article {pmid40216956,
year = {2025},
author = {},
title = {Mystery of medieval manuscripts revealed by ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40216956},
issn = {1476-4687},
}

@article {pmid40214271,
year = {2025},
author = {Gersak, ZM and Zupanic-Pajnic, I and Podovsovnik, E and Salapura, V},
title = {Computed tomography differentiation of compact and cancellous bone tissue in short and sesamoid bones.},
journal = {Radiology and oncology},
volume = {},
number = {},
pages = {},
pmid = {40214271},
issn = {1581-3207},
abstract = {BACKGROUND: Selecting the most suitable skeletal remains for genetic analysis is challenging due to the variable DNA yield across different bone types and within individual bones. Compact bone typically preserves DNA longer, whereas cancellous bones, such as those in the hands and feet, often contain higher DNA quantities. This study aimed to incorporate dual-source computed tomography (DSCT), a technique frequently utilized for assessing bone density in living subjects, into targeted DNA sampling for dry, skeletonized remains by mapping compact and cancellous regions within six small skeletal elements.

MATERIALS AND METHODS: A total of 137 bones were analysed using an imaging protocol specifically adapted to highlight the skeletal structure of small bones. This tailored protocol involved meticulous calibration of imaging parameters. Anatomical landmarks for six distinct elements were identified, and regions of interest were selected for bone density measurement in Hounsfield units (HU).

RESULTS: Among 461 assessed regions, 312 (68%) were classified as compact bone, and 149 (32%) as cancellous bone. Given the abnormal distribution of data, statistical differences were evaluated using 95% confidence intervals, with significance indicated by non-overlapping intervals. The analysis revealed statistically significant differences between compact and cancellous bone, as well as within each type across different bones.

CONCLUSIONS: DSCT proved effective in mapping the internal structure of six small skeletal elements in dry, skeletonized remains, underscoring significant intra-bone variability in density. The findings illustrate DSCT's substantial potential for enhancing DNA sampling in forensic and paleogenetic studies, setting the stage for future research advancements.},
}

@article {pmid40206852,
year = {2025},
author = {Lévêque, É and Teasdale, MD and Fiddyment, S and Bro-Jørgensen, MH and Spindler, L and Macleod, R and Bougard, F and Tange Olsen, M and Collins, M},
title = {Hiding in plain sight: the biomolecular identification of pinniped use in medieval manuscripts.},
journal = {Royal Society open science},
volume = {12},
number = {4},
pages = {241090},
pmid = {40206852},
issn = {2054-5703},
abstract = {The survival of medieval manuscripts in their original bindings remains a rare occurrence. Taking advantage of the diversity of bindings in Cistercian libraries such as Clairvaux and its daughter abbeys during the twelfth and thirteenth centuries, this study focuses on the biocodicological analysis of medieval manuscript bindings, with particular emphasis on the use of sealskins. Using innovative methods such as electrostatic zooarchaeology by mass spectrometry (eZooMS) and ancient DNA (aDNA) analysis, this research identifies the animal species and origin of the leather used in these bindings as predominantly pinniped (seal) species. In particular, the collagen-based eZooMS technique facilitated the classification of seven chemises into the pinniped clade, although species identification remained elusive, except in one additional case where a bearded seal (Erignathus barbatus) was definitively identified. aDNA analysis was instrumental in verifying the origin of the sealskins, with four samples identified as harbour seals and a single sample as a harp seal and sourced to (contemporary) populations in Scandinavia, Scotland and Iceland or Greenland. This geographical inference supports the notion of a robust medieval trade network that went well beyond local sourcing, linking the Cistercians to wider economic circuits that included fur trade with the Norse. The study, therefore, highlights the use of an unexpected skin (seal) from an unexpected source (the northwestern Atlantic). The widespread use of sealskins in Cistercian libraries such as Clairvaux and its daughter abbeys during the twelfth and thirteenth centuries hints at broader trade networks that brought, for example, walrus ivory from the far north into continental Europe. This integration of the biological sciences into the study of historical manuscripts not only provides a clearer picture of the material culture of medieval Europe, but also illustrates the extensive trade networks that Cistercian monasteries were part of, challenging previous assumptions about local resource use in manuscript production.},
}

@article {pmid40203146,
year = {2025},
author = {Anaïs, A and Yaxal, PG and Amélie, C and Philippe, C and Nicolás, R},
title = {An ancient Epstein-Barr virus genome recovered from a museum penis gourd from Papua.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf189},
pmid = {40203146},
issn = {1537-6613},
abstract = {Ancient DNA provides a unique opportunity to study the history and spread of infectious diseases. Here, we analyzed 21 samples from a collection of 20th-century penis gourds (koteka) from Papua New Guinea housed at the Musée du quai Branly - Jacques Chirac in Paris. Despite the presence of environmental species, we identified human-associated bacteria and, notably, an Epstein-Barr Virus (EBV) genome at high coverage. Phylogenetic analysis placed this strain within a Papua New Guinea-Indonesian cluster. These findings highlight museum collections as valuable reservoirs of genetic data, offering historical insights into the evolution and spread of human pathogens.},
}

@article {pmid40202701,
year = {2025},
author = {More, KD and Lebrasseur, O and Garrido, JL and Seguin-Orlando, A and Discamps, E and Estrada, O and Tonasso-Calvière, L and Chauvey, L and Tressières, G and Schiavinato, S and Gibert, M and Padula, H and Chiavazza, H and Fernández, PM and Guardia, NM and Borges, C and Bertani, S and Contreras-Mancilla, J and Allccarima-Crisóstomo, D and Fhon, M and Barrey, E and Charliquart, L and Robbe, E and de Noblet, T and Zhumatayev, R and Shakenov, S and Vila, E and Berthon, R and Mashkour, M and Khazaeli, R and Nikgoftar, A and Vahdati, AA and Kosintsev, P and Houle, JL and Bayarsaikhan, J and Wilczynski, J and Moskal-Del Hoyo, M and Nowak, M and Taylor, W and Bălășescu, A and Dobrescu, R and Benecke, N and Arbuckle, B and Steadman, S and McMahon, G and Šikanjić, PR and Buric, M and Vukičević, TT and Alvarez, N and Castel, JC and Boudadi-Maligne, M and Star, B and Post-Melbye, JR and Rødsrud, CL and Stanton, DWG and Charlton, S and Mullin, VE and Daly, KG and Burgos, NS and Pablos, A and Dalen, L and Bradley, DG and Frantz, L and Larson, G and Orlando, L},
title = {Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14112},
doi = {10.1111/1755-0998.14112},
pmid = {40202701},
issn = {1755-0998},
support = {101032990-PALEOQINOA//H2020 Marie Skłodowska-Curie Actions/ ; 101062645-ZEPHYRUS//H2020 Marie Skłodowska-Curie Actions/ ; 895107-ARAUCANA//H2020 Marie Skłodowska-Curie Actions/ ; 897931-PALEOS//H2020 Marie Skłodowska-Curie Actions/ ; CoproDNA//CNRS Zone Atelier PYGAR/ ; ANR-17-CE27-0004//Agence Nationale de la Recherche (ANR)/ ; //Knut and Alice Wallenberg Foundation/ ; 101071707//European Research Council (ERC)/ ; 101117101//European Research Council (ERC)/ ; 681605//European Research Council (ERC)/ ; 949330//European Research Council (ERC)/ ; 101054984//European Research Council (ERC)/ ; MCIN/AEI/10.13039/501100011033//Fondo Social Europeo and Agencia Estatal de Investigación/ ; RYC2020-029656-I//Fondo Social Europeo and Agencia Estatal de Investigación/ ; CENIEH//Centro Nacional de Investigación sobre la Evolución Humana/ ; SciLifeLab//Science for Life Laboratory/ ; 2021-00625//Swedish Research Council/ ; CAGT//Université de Toulouse/ ; SBPLY/24/180801/000019//Junta de Comunidades de Castilla la Mancha/ ; AnimalFarmIRP//Centre National de la Recherche Scientifique/ ; },
abstract = {In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.},
}

@article {pmid40199243,
year = {2025},
author = {Mathieson, I},
title = {Iain Mathieson.},
journal = {Current biology : CB},
volume = {35},
number = {7},
pages = {R240-R241},
doi = {10.1016/j.cub.2025.03.005},
pmid = {40199243},
issn = {1879-0445},
mesh = {Humans ; *Biological Evolution ; *DNA, Ancient/analysis ; History, 21st Century ; History, 20th Century ; },
abstract = {Interview with Iain Mathieson, who studies ancient DNA and its relevance to recent human evolution at the University of Pennsylvania.},
}

Humans
*Biological Evolution
*DNA, Ancient/analysis
History, 21st Century
History, 20th Century

@article {pmid40196638,
year = {2025},
author = {Olalde, I and Altena, E and Bourgeois, Q and Fokkens, H and Amkreutz, L and Deguilloux, MF and Fichera, A and Flas, D and Gandini, F and Kegler, JF and Kootker, LM and Leijnse, K and Kooijmans, LL and Lauwerier, R and Miller, R and Molthof, H and Noiret, P and Raemaekers, DCM and Rivollat, M and Smits, L and Stewart, JR and Ten Anscher, T and Toussaint, M and Callan, K and Cheronet, O and Frost, T and Iliev, L and Mah, M and Micco, A and Oppenheimer, J and Patterson, I and Qiu, L and Soos, G and Workman, JN and Edwards, CJ and Lazaridis, I and Mallick, S and Patterson, N and Rohland, N and Richards, MB and Pinhasi, R and Haak, W and Pala, M and Reich, D},
title = {Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.24.644985},
pmid = {40196638},
issn = {2692-8205},
abstract = {The first phase of the ancient DNA revolution painted a broad-brush picture of European Holocene prehistory, whereby 6500-4000 BCE, farmers descending from western Anatolians mixed with local hunter-gatherers resulting in 70-100% ancestry turnover, then 3000-2500 BCE people associated with the Corded Ware complex spread steppe ancestry into north-central Europe. We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry (∼50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a characteristic early Corded Ware Y-chromosome. The limited influx may reflect the unique ecology of the region's river-dominated landscapes, which were not amenable to wholesale adoption of the early Neolithic type of farming introduced by Linearbandkeramik, making it possible for previously established groups to thrive, and creating a persistent but permeable boundary that allowed transfer of ideas and low-level gene flow. This changed with the formation-through-mixture of Bell Beaker using populations ∼2500 BCE by fusion of local Rhine-Meuse people (9-17%) and Corded Ware associated migrants of both sexes. Their expansion from the Rhine-Meuse region then had a disruptive impact across a much wider part of northwest Europe, including Britain where its arrival was the main source of a 90-100% replacement of local Neolithic peoples.},
}

@article {pmid40196503,
year = {2025},
author = {Tabin, D and Patterson, N and Mah, M and Reich, D},
title = {Addendum to Ancient DNA data from Mengzi Ren, a Late Pleistocene individual from Southeast Asia, cannot be reliably used in population genetic analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.24.645126},
pmid = {40196503},
issn = {2692-8205},
abstract = {In addition to the issues pointed out in Tabin et al [1] , the MZR data from Zhang et. al 2022 [2] are suggestive of high levels of contamination from a source similar to modern Han Chinese, the majority population in the country where MZR was sequenced. In fact, MZR can be modeled entirely as Han-related ancestry and noise. These results raise further concerns about the veracity of the MZR data and thus the paper's historical conclusions.},
}

@article {pmid40189540,
year = {2025},
author = {Li, H and Wang, B and Yang, X and Yang, X and He, H and Wang, R and Wang, CC},
title = {Ancient genomes shed light on the genetic history of the Iron Age to historical central Xinjiang, northwest China.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {93},
pmid = {40189540},
issn = {1741-7007},
mesh = {China ; Humans ; *DNA, Ancient/analysis ; *Genome, Human ; *Genetics, Population ; History, Ancient ; Human Migration ; },
abstract = {BACKGROUND: The genetic profile of the population in Xinjiang, northwest China, has been shaped by interregional movement and admixture since the Bronze Age. However, the detailed and intraregional population history of Xinjiang, especially central Xinjiang, has been unsolved due to uneven sample distribution.

RESULTS: Here, we reported the ancient genomes from 8 individuals between the Iron Age and the historical period in central Xinjiang. We observed an east-west admixed ancestry profile and a degree of genetic continuity between the Iron Age and historical central Xinjiang individuals. Furthermore, these central Xinjiang individuals harboured ancestry related to ancient farmers of the Yellow River. We also identified a temporal change of the Yellow River farmers-related ancestry in central Xinjiang, showing an increase the Yelllow River affinity from Iron Age to Historical Era.

CONCLUSIONS: The finding indicated that the genetic structure of the central Xinjiang population since the Iron Age could have resulted from immigration from northern China, which was attributed to geopolitical factors. Hence, our results indicated that the geopolitical change with the deepening of Central Plains' management has influenced the genetic profile of central Xinjiang.},
}

China
Humans
*DNA, Ancient/analysis
*Genome, Human
*Genetics, Population
History, Ancient
Human Migration

@article {pmid40179167,
year = {2025},
author = {Curry, A},
title = {Ancient DNA illuminates 'green Sahara' dwellers.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {18},
doi = {10.1126/science.adx9095},
pmid = {40179167},
issn = {1095-9203},
mesh = {*DNA, Ancient/analysis ; Humans ; History, Ancient ; },
abstract = {Skeletons from an ancient, lush interlude offer genetic peek at a lost population.},
}

*DNA, Ancient/analysis
Humans
History, Ancient

@article {pmid40175742,
year = {2025},
author = {Prendergast, M},
title = {Rare ancient DNA from Sahara opens a window on the region's verdant past.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175742},
issn = {1476-4687},
}

@article {pmid40175549,
year = {2025},
author = {Salem, N and van de Loosdrecht, MS and Sümer, AP and Vai, S and Hübner, A and Peter, B and Bianco, RA and Lari, M and Modi, A and Al-Faloos, MFM and Turjman, M and Bouzouggar, A and Tafuri, MA and Manzi, G and Rotunno, R and Prüfer, K and Ringbauer, H and Caramelli, D and di Lernia, S and Krause, J},
title = {Ancient DNA from the Green Sahara reveals ancestral North African lineage.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175549},
issn = {1476-4687},
abstract = {Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch[1]. DNA rarely preserves well in this region, limiting knowledge of the Sahara's genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals' ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco[2], associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.},
}

@article {pmid40174641,
year = {2025},
author = {He, T and Zhang, X and Zhang, X},
title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.057},
pmid = {40174641},
issn = {2090-1224},
abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.

OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.

METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.

RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.

CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.},
}

@article {pmid40167159,
year = {2025},
author = {Qiu, Y and Liu, L and Huang, M and Ruan, D and Ding, R and Zhang, Z and Zheng, E and Wang, S and Deng, S and Meng, X and Cheng, X and Shi, J and Yang, Y and Zhou, F and Huang, S and Yang, H and Li, Z and Cai, G and Wu, Z and Yang, J},
title = {Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2416573},
doi = {10.1002/advs.202416573},
pmid = {40167159},
issn = {2198-3844},
support = {2023YFD1300201//National Key Research and Development Program of China/ ; 2022B0202090002//key Technologies R&D Program of Guangdong Province/ ; 2024A1515010967//Natural Science Foundation of Guangdong Province/ ; 2019BT02N630//Local Innovative and Research Teams Project of Guangdong Province/ ; SL2023A04J00485//Young Scholars "Qihang" Program/ ; },
abstract = {Human mediated intra-continental exchange of genetic material among domesticated organisms has never been restricted to a single direction. The introduction of pig breeds between China and Europe aims to enhance economically important traits in local populations. However, the reciprocal introgression pattern, specifically the role of introgressed genes and structural variations (SVs), remains underexplored. A global collection of whole-genome resequencing data is utilized from 418 pigs to generate comprehensive dataset, including single-nucleotide polymorphisms (SNPs) as well as SVs. The analysis reveals incomplete linkage disequilibrium between SVs and adjacent SNPs, highlighting the limitations of conventional SNP-based analyses in capturing the genetic effects of SVs. By examining both population-level SNPs and SVs, bidirectional introgression between Chinese and European pig populations is characterized. It is identified 3558 bidirectional introgressed genomic segments and 30 SVs, with haplotypes at BMP2, which are associated with improved body size. The origin and allele frequency trajectory of the BMP2 segment are further validated using ancient genomes, suggesting that the body size-enhancing haplotype likely originated from ancient European populations and has since maintained a relatively high allele frequency. Overall, the results highlight the significant role of bidirectional introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.},
}

@article {pmid40163762,
year = {2025},
author = {Martin, N and Thibeault, A and Varadzinová, L and Usai, D and Ambrose, SH and Antoine, D and Brukner Havelková, P and Honegger, M and Irish, JD and Jesse, F and Maréchal, L and Osypińska, M and Osypiński, P and Santos, F and Vanderesse, N and Varadzin, L and Whiting, RJ and Zanolli, C and Velemínský, P and Crevecoeur, I},
title = {Enamel-dentine junction morphology reveals population replacement and mobility in the late prehistoric Middle Nile Valley.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {15},
pages = {e2419122122},
doi = {10.1073/pnas.2419122122},
pmid = {40163762},
issn = {1091-6490},
support = {IRP ABASC//Centre National de la Recherche Scientifique (CNRS)/ ; project NeoNile//French governement - University of Bordeaux IdEx "Investments for the Future" program / GPR "Human Past"/ ; ANR-14-CE31//Agence Nationale de la Recherche (ANR)/ ; 23-06488S//Grantová Agentura České Republiky (GAČR)/ ; Cooperatio program//Filozofická Fakulta, Univerzita Karlova v Praze (Faculty of Arts, Charles University)/ ; DKRVO 2024-2028/7.I.a 7.I.b National Museum 00023272//Ministerstvo Kultury (Ministry of Culture)/ ; UMO-2020/37/B/HS3/00519//Narodowe Centrum Nauki (NCN)/ ; },
mesh = {Humans ; *Dental Enamel ; History, Ancient ; *Dentin ; Population Dynamics/history ; Fossils ; Sudan ; Human Migration/history ; X-Ray Microtomography ; },
abstract = {Transitions from foraging to food-production represent a worldwide turning point in recent human history. In the Middle Nile Valley this cultural shift occurred between the sixth and beginning of the fifth millennium BCE. Significant craniodental morphological differences remain inadequately tested by biometric analyses of ancestry and may reflect population origins or diet change between the last hunter-fisher-gatherers (Mesolithic) and first food-producers (Neolithic). Moreover, with no ancient DNA data for this region and very few morphological studies including large samples of Mesolithic individuals, the late prehistoric population history of the Nile Valley remains unclear. Here, we present enamel-dentine junction (EDJ) morphological analyses (based on X-ray microtomography) and biological affinities for 88 individuals spanning 14,000 y from Sudan and southern Egypt. Significant EDJ morphological differences between the last foragers and first food-producers suggest major biological discontinuity at the Neolithic transition. Nevertheless, the persistence of the earlier forager population in the Sudanese Eastern Sahara indicates settlement and population replacement mainly along the Nile. We also present biological evidence of interaction and mobility between these contemporaneous populations during the middle Holocene in the region. It supports the phylogenetic value of EDJ morphology for investigating population affinities at a microevolutionary scale. These results yield insights into the deep population history of the Nile Valley. They provide firm evidence for population replacement and migration toward the region at the onset of the Neolithic transition, attesting that these key changes were not solely triggered by cultural diffusion and diet change.},
}

Humans
*Dental Enamel
History, Ancient
*Dentin
Population Dynamics/history
Fossils
Sudan
Human Migration/history
X-Ray Microtomography

@article {pmid40148574,
year = {2025},
author = {Raghavan, M},
title = {The genesis of paleogenetics.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40148574},
issn = {1471-0064},
}

@article {pmid40141254,
year = {2025},
author = {Rayner, T and Mundy, JEA and Bilham, LJ and Moreau, C and Lawson, DM and Domoney, C and Wang, TL},
title = {A Suite of Pea (Pisum sativum L.) Near-Isolines: Genetic Resources and Molecular Tools to Breed for Seed Carbohydrate and Protein Quality in Legumes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
pmid = {40141254},
issn = {1422-0067},
support = {BB/J004561/1, BBS/E/J/000PR9799, BB/H009787/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; LK09126, IF0147, CH0103, CH0111//Department for Environment Food and Rural Affairs/ ; },
mesh = {*Pisum sativum/genetics/metabolism ; *Seeds/genetics/metabolism ; Mutation ; Phenotype ; Plant Proteins/genetics/metabolism ; Plant Breeding/methods ; Starch/metabolism ; },
abstract = {In recent years there has been a resurgent interest in plant products as substitutes for animal-derived food products, in which legumes, including peas, feature highly. Here, we report on a set of Pisum sativum L. (pea) near-isolines, comprising 24 unique mutants at five loci, where the impact of the mutations on the corresponding enzymes of the starch pathway confers a wrinkled-seeded phenotype. Together with a set of round-seeded mutants impacted at a sixth locus, all 27 mutants show variation for starch composition and protein content. The mutations have been mapped onto three-dimensional protein models to examine potential effects on the corresponding enzyme structures and their activities, and to guide targeted mutagenesis. The mutant lines represent a unique suite of alleles for rapid introduction into elite pea varieties to create new materials for the food and feed markets and industrial applications.},
}

*Pisum sativum/genetics/metabolism
*Seeds/genetics/metabolism
Mutation
Phenotype
Plant Proteins/genetics/metabolism
Plant Breeding/methods
Starch/metabolism

@article {pmid40132550,
year = {2025},
author = {Tabin, D and Patterson, N and Mah, M and Reich, D},
title = {Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia.},
journal = {Current biology : CB},
volume = {35},
number = {6},
pages = {R212-R213},
doi = {10.1016/j.cub.2024.10.012},
pmid = {40132550},
issn = {1879-0445},
mesh = {*DNA, Ancient/analysis ; Asia, Southeastern ; Humans ; Fossils ; Female ; Sequence Analysis, DNA ; Animals ; Genetics, Population ; Caves ; },
abstract = {In a 2022 Current Biology paper, Zhang et al.[1] reported DNA sequences from an approximately 14-thousand-year-old female skeleton from Red Deer Cave referred to as 'Mengzi Ren' (MZR). MZR's data are the first DNA sequences reported from pre-Holocene Southeast Asia, revealing genetic affinities dissimilar to all previously published ancient DNA data. Here, we show extremely high error rates, an abnormal error distribution and evidence of contamination by modern human sequences in the published DNA sequences of MZR. Even ignoring these issues, we fail to replicate key population genetic findings of Zhang et al.[1], namely that Native Americans are equally related to MZR and ancient Northeast Asians. These results raise concerns regarding the paper's conclusions about population history, such as the claim that there was "an express northward expansion of AMHs starting in southern East Asia through the coastal line of China … eventually crossing the Bering Strait and reaching the Americas," and also about the general usability of the published sequences.},
}

*DNA, Ancient/analysis
Asia, Southeastern
Humans
Fossils
Female
Sequence Analysis, DNA
Animals
Genetics, Population
Caves

@article {pmid40106345,
year = {2025},
author = {Günther, T and Chisausky, J and Galindo-Pellicena, ÁM and Iriarte, E and Cortes Gardyn, O and Eusebi, PG and García-González, R and Ureña, I and Moreno-García, M and Alday, A and Rojo, M and Pérez, A and Tejedor Rodríguez, C and García Martínez de Lagrán, I and Arsuaga, JL and Carretero, JM and Götherström, A and Smith, C and Valdiosera, C},
title = {The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40106345},
issn = {2050-084X},
support = {2017-05267//Vetenskapsrådet/ ; RYC2018-025223-I//Ramón y Cajal/ ; BGS220-461AA-69201//Beatriz Galindo Fellowship/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovación y Universidades/ ; A way of making Europe//European Regional Development Fund/ ; },
mesh = {Animals ; Cattle/genetics ; *Hybridization, Genetic ; *Gene Flow ; Spain ; Female ; Genomics/methods ; Male ; History, Ancient ; Genome ; Archaeology ; },
abstract = {Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.},
}

Animals
Cattle/genetics
*Hybridization, Genetic
*Gene Flow
Spain
Female
Genomics/methods
Male
History, Ancient
Genome
Archaeology

@article {pmid40090872,
year = {2025},
author = {Rhodes, C and Price, R and Willetts, C and Swall, J and Combs, LG and Seashols-Williams, S},
title = {Improved DNA recovery and STR profile development from weathered Bos taurus bones using demineralized bone slices.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70023},
pmid = {40090872},
issn = {1556-4029},
support = {//Forensic Sciences Foundation/ ; 15PNIJ-23-GG-01944-RESS//National Institute of Justice/ ; },
abstract = {Current processing techniques for harvesting DNA from osseous elements are destructive, and success rates vary widely. When skeletal elements are homogenized into a fine powder, endogenous DNA may be subjected to fragmentation, and the likelihood of introducing co-purified inhibitory substances to the sample increases. While a limited number of articles in the relevant literature have challenged the status quo of pulverization, powdering hard tissue samples before DNA isolation continues to be standard practice in the forensic and ancient DNA communities. In this work, we have developed and optimized an alternative front-end processing method for demineralizing and slicing cortical bone using aged and weathered bovine skeletal samples as a model for degraded human bone. Additionally, this study evaluated the enzymatic digestion of demineralized bone slices using collagenase I as a powder-free alternative for cell isolation. The efficacy of pulverization, demineralized slices, and collagenase-digested demineralized slices was assessed via DNA quantitation and STR profile data. The combined treatment incorporating collagenase digestion of demineralized slices did not improve the recovery of endogenous DNA yields or STR profile development; however, profiles developed from demineralized slices retained a significantly greater percentage of expected alleles and higher peak heights than samples processed with conventional powdering and organic chemistry extraction. By eliminating pulverization of bone and employing modified silica-based extraction chemistry, the susceptibility to inhibitory and competitive effects from native and foreign components often found in degraded skeletal remains can be minimized when utilizing total demineralization of small fragments with subsequent slicing before lysis.},
}

@article {pmid40078674,
year = {2023},
author = {Odenbaugh, J},
title = {Philosophy and ethics of de-extinction.},
journal = {Cambridge prisms. Extinction},
volume = {1},
number = {},
pages = {e7},
pmid = {40078674},
issn = {2755-0958},
abstract = {In this essay, we explore the philosophical and ethical issues concerning de-extinction. First, we will characterize what de-extinction is. This requires clarification of the process of extinction. Second, we consider whether de-extinction is even possible. There are a variety of arguments involving the nature of species that purport to show that once they have disappeared they cannot be resurrected. Third, we examine whether de-extinction is morally permissible. There are arguments that suggest we are obligated to do it based on restorative justice and biodiversity conservation. There are other arguments that conclude we are not permitted to do so based on considerations of animal welfare, hubris and the allocation of conservation resources.},
}

@article {pmid40075538,
year = {2025},
author = {Borba, VH and Gurjão, L and Martin, C and Dufour, B and Le Bailly, M and Iñiguez, AM},
title = {Capillariid diversity in archaeological material from the New and the Old World: clustering and artificial intelligence approaches.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {104},
pmid = {40075538},
issn = {1756-3305},
support = {23038000059/2015-61//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; 33387UA, 88887.508110/2020-00, 465 88887.694725/2022-00//COFECUB/ ; 315634/2021-9//National Council for Scientific and Technological Development (CNPq)/ ; E-26/201.069/2021, E-461 26/210.131/2023//Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro (FAPERJ)/ ; },
mesh = {Animals ; *Archaeology ; *Artificial Intelligence ; Brazil ; Europe ; Humans ; Nematoda/classification/isolation & purification ; Biodiversity ; Cluster Analysis ; History, Ancient ; Feces/parasitology ; },
abstract = {BACKGROUND: Capillariid nematode eggs have been reported in archaeological material in both the New and the Old World, mainly in Europe and South America. They have been found in various types of samples, as coprolites, sediments from latrines, pits, or burial. Modern parasitological records show that around 300 species of capillariids have been described in all vertebrate taxa, including humans, making it a very diversified group. The main proposal of this work is to characterize and identify capillariid eggs found in archaeological sites from Europe and Brazil.

METHODS: A total of 39 samples of archeological sites from Europe, deposited in the paleoparasitological collection of the University Marie & Louis Pasteur, Besançon, France was analyzed. In addition, 80 coprolites from the pre-Colombian archaeological site Gruta do Gentio II, Brazil, deposited in the Paleogenetic Laboratory at Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, were evaluated. Samples were treated according to the protocols of each laboratory and then analyzed under light microscopy. Capillariid eggs were classified according to length, width, plugs, and eggshell sizes, and statistical analysis of the morphometric dataset was performed. Using a reference dataset of specimens provided by both Institutional Collections, three approaches to species identification were applied: discriminant analysis, hierarchical clustering, and artificial intelligence/machine learning.

RESULTS: A total of 10 samples from Europe and 4 from Brazil were positive for capillariid eggs, showing 13 different morphotypes. As European samples were mainly collected from latrines and pits, parasite-host information was absent, and consequently, species identification was impaired. In contrast, the availability of host information rendered the identification of capillariid species for the Brazilian coprolites. The new methodology indicates capillariid species identified on various samples, resulting in the presence of Capillaria exigua (Dujardin, 1845) in feline coprolite, Baruscapillaria resecta (Dujardin, 1845) in opossum, and Aonchotheca bovis (Schnyder, 1906) in bovid, in the Brazilian site, while in European sites, Capillaria venusta (Freitas e Mendonça, 1958), Aonchotheca myoxinitelae (Diesing, 1851), Eucoleus madjerdae (Bernard, 1964), and Baruscapillaria spiculata (Freitas, 1933) were found.

CONCLUSIONS: The study provides new results by applying innovative methodologies for parasite identification and gaining insights into the past host (human or animal)/parasite relationships.},
}

Animals
*Archaeology
*Artificial Intelligence
Brazil
Europe
Humans
Nematoda/classification/isolation & purification
Biodiversity
Cluster Analysis
History, Ancient
Feces/parasitology

@article {pmid40075199,
year = {2025},
author = {Callaway, E},
title = {Ancient DNA shows Stone Age Europeans voyaged by sea to Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40075199},
issn = {1476-4687},
}

@article {pmid40074896,
year = {2025},
author = {Lipson, M and Ringbauer, H and Lucarini, G and Aouadi, N and Aoudia, L and Belhouchet, L and Cheronet, O and Dahmani, AR and Genchi, F and La Pastina, F and Lucci, M and de Lumley, H and Mansouri, N and Nava, A and Touj, F and Mallick, S and Rohland, N and Coppa, A and Pinhasi, R and Reich, D},
title = {High continuity of forager ancestry in the Neolithic period of the eastern Maghreb.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40074896},
issn = {1476-4687},
abstract = {Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food-producing economies[1-6]. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco)[1-3]. Here we present genome-wide data for nine individuals from the Later Stone Age through the Neolithic period from Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (around 15,000-7,600 years before present (BP)), showing that this 'Maghrebi' ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to around 8,000 years BP, harboured ancestry from European hunter-gatherers, probably reflecting movement in the Early Holocene across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry, together with smaller contributions from European farmers (by around 7,000 years BP) and Levantine groups (by around 6,800 years BP), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.},
}

@article {pmid40059317,
year = {2025},
author = {Yang, Q and Sun, Y and Duan, S and Nie, S and Liu, C and Deng, H and Wang, M and He, G},
title = {High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf022},
pmid = {40059317},
issn = {2210-3244},
abstract = {Large-scale international and regional human genomic and pangenomic resources derived from population-scale biobanks and ancient DNA sequences have provided significant insights into human evolution and the genetic determinants of complex diseases and traits. Despite these advances, challenges persist in optimizing the integration of phasing tools, merging haplotype reference panels (HRPs), developing imputation algorithms, and fully exploiting the diverse applications of post-imputation data. This review comprehensively summarizes the advancements, applications, limitations, and future directions of HRPs in human genomics research. Recent progress in the reconstruction of HRPs, based on over 830,000 human whole-genome sequences, has been synthesized, highlighting the broad spectrum of human genetic diversity captured. Additionally, we recapitulate advancements in fifty-six HRPs for global and regional populations. The evaluation of imputation accuracy indicated that Beagle and GLIMPSE are the most effective tools for phasing and imputing data from genotyping arrays and low-coverage sequencing, respectively. A critical strategy for selecting an appropriate HRP involves matching the population background of target groups with HRP reference populations and considering multi-ancestry or homogeneous genetic structures. The necessity of a single, integrative, high-quality HRP that captures haplotype structures and genetic diversity across various genetic variation types from globally representative populations is emphasized to support both modern and ancient genomic research and advance human precision medicine.},
}

@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}

@article {pmid40052289,
year = {2025},
author = {Berg, AA and Askew, M and Seersholm, FV and Verry, AJF and Hoelzel, AR and Welch, A and Greig, K and Walter, R and Knapp, M and Barlow, A and Paijmans, JLA and Waters, JM and Bunce, M and McDonald, K and O'Connor, S and Hall, B and Koch, PL and Baroni, C and Salvatore, MC and Faulkner, P and Ho, SYW and Rawlence, NJ and de Bruyn, M},
title = {Postglacial Recolonization of the Southern Ocean by Elephant Seals Occurred From Multiple Glacial Refugia.},
journal = {Global change biology},
volume = {31},
number = {3},
pages = {e70101},
doi = {10.1111/gcb.70101},
pmid = {40052289},
issn = {1365-2486},
support = {//Office of Polar Programs, U.S. National Science Foundation./ ; FT200100464//Australian Research Council Future Fellowship/ ; },
mesh = {*Seals, Earless/physiology ; Animals ; *Refugium ; *Climate Change ; Australia ; Antarctic Regions ; New Zealand ; Fossils ; Phylogeny ; Oceans and Seas ; },
abstract = {The Southern Ocean is warming more rapidly than other parts of our planet. How this region's endemic biodiversity will respond to such changes can be illuminated by studying past events through genetic analyses of time-series data sets, including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analyzed ancient seal samples from Australia (Tasmania), New Zealand and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures over surprisingly short evolutionary timeframes for such a large, long-lived mammal.},
}

*Seals, Earless/physiology
Animals
*Refugium
*Climate Change
Australia
Antarctic Regions
New Zealand
Fossils
Phylogeny
Oceans and Seas

@article {pmid40045199,
year = {2025},
author = {Nedoluzhko, A and Vergasova, E and Sharko, F and Agapitova, N and Kharitonov, D and Sukhanova, X and Pushkina, O and Pankova, S and Slobodova, N and Boulygina, E and Plotnikov, N and Kim, A and Uchaneva, E and Pogodina, N and Ilinskaya, A and Rakitko, A and Chugunov, K and Ilinsky, V},
title = {Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the "Valley of the Kings", Tuva.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {220},
pmid = {40045199},
issn = {1471-2164},
mesh = {Humans ; *DNA, Ancient/analysis ; *Archaeology ; Russia ; DNA, Mitochondrial/genetics ; Transients and Migrants/history ; History, Ancient ; },
abstract = {BACKGROUND: In the I[st] millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style and economy can be traced to the eastern part of this steppe "corridor", primarily to the territory of the present-day Republic of Tuva in Russia. Here, in the Turan-Uyuk Basin, also known as the "Valley of the Kings", some of the earliest known Scythian-type archaeological sites called Arzhan-1, Arzhan-2, Chinge-Tey I, Tunnug 1 were studied. Each of them is a large-scale funerary commemorative complex with burials of tribal nomadic leaders, surrounded by graves of supposed members of their families or associates. All these people belonged to the societies which are associated with the earliest nomadic cultures in Asia. Representatives of similar cultures will later be known and described as the Scythians/the Saka in Assyrian, Achaemenid, and Greek sources. Arzhan 2 and Chinge-Tey I elite level sites as well as ordinary pastoralist burials of the early-Scythian period in Tuva are attributed to the Aldy-Bel archaeological culture of the Early Iron Age (8th- 6th century BC). Taking the first step to shed light on the genetic origin of Aldy-Bel elites, we carried out a comparative genome-wide analysis of an elite level person buried in grave 9 at Chinge-Tey I (7th- 6th centuries BC) and two published earlier genomes of individuals, whose burials (graves 14 and 22) accompanied the 'royal couple' (grave 5) at Arzhan-2. This study aims also at checking a hypothesis of genetic kinship between human individuals buried in the large-scale burial complexes of the "Valley of the Kings" and brings up the issue of possible dynastic connections of local elites, buried under different kurgans of the valley.

RESULTS: First, ancient DNA analysis of an elite nomadic warrior from Chinge-Tey I has been carried out, thus a third wide-genome dataset for Aldy-Bel culture- one of the earliest nomadic cultures in Asia, is presented in this study. Second, we undertook a comparative analysis of genome-wide data of three mentioned Aldy-Bel culture representatives and individuals of the other Bronze and Early Iron Age population groups of Asia to estimate their possible genetic connections. Then, kinship analysis was undertaken for these three Aldy-Bel culture individuals. Finally, mitochondrial and Y-chromosome haplogroups of Chinge-Tey princely person were compared to those of other Aldy-Bel culture representatives and to individuals of subsequent Scythian-type Uyuk-Sagly culture in Tuva.

CONCLUSION: (1) Generating the third wide-genome of the enabled us to undertake its comparison with two other genomes of Aldy-Bel culture representatives (Arzhan-2, graves 14 and 22) and with other Bronze and Early Iron Age population groups in Asia to trace the origin and genetic connection of Aldy-Bel population, representing one of the earliest Scythian-type nomadic group. (2) The results obtained show that the princely individual from Chinge-Tey I and two 'king's associates' from Arzhan-2 were genetically close to nomads of simultaneous Tasmola culture in Eastern and Central Kazakhstan and pastoralists buried in the Early Iron Age cemeteries of present-day Xinjiang (first of all, Abusanteer archaeological site). Aldy-Bel culture representatives appeared also close to individuals of the Middle Bronze Age Okunevo culture in the Minusinsk Basin. Besides, Aldy-Bel pastoralists turned out genetically close to nomads of the subsequent Uyuk-Sagly culture in Mongolia (5th - 3rd centuries BC). (3) Ancient DNA kinship analyses, undertaken for three Aldy-Bel culture individuals pointed out to the absence of their tribe kinship. (4) On the other hand, Chinge-Tey warrior's mitochondrial haplogroup G was previously described in two (graves 14 and 5) individuals from Arzhan-2, including a female individual from the "royal" tomb 5. This result provided a possibility of maternal kinship among this so called 'queen' from Arzhan-2 and the princely person from Chinge-Tey I. This possibility supported a hypothesis of their family ties suggested on archaeological materials. Y-chromosome haplogroup Q1b1, revealed for the princely person, was widely distributed among local people of Aldy-Bel and subsequent Uyuk-Sagly cultures.},
}

Humans
*DNA, Ancient/analysis
*Archaeology
Russia
DNA, Mitochondrial/genetics
Transients and Migrants/history
History, Ancient

@article {pmid40040400,
year = {2025},
author = {Moosa, T and Ewuoso, C},
title = {Ancient DNA research may be conducted in the absence of consent from descendant communities.},
journal = {Indian journal of medical ethics},
volume = {X},
number = {1},
pages = {16-23},
doi = {10.20529/IJME.2024.081},
pmid = {40040400},
issn = {0975-5691},
mesh = {Humans ; *Informed Consent/ethics/standards ; *DNA, Ancient/analysis ; Genetic Research/ethics ; Ethics, Research ; Africa ; Morals ; Archaeology/ethics ; },
abstract = {BACKGROUND: Ancient deoxyribonucleic acid (aDNA) research studies the genomes of human ancestors. Since the archaeological remains that carry this aDNA are often those of the non-living ancestors of living humans, one less explored question is whether aDNA research ought to be permissible in the absence of informed consent of descendant communities. We interrogate this question.

METHOD: To address this question, this paper is a primarily conceptual paper that draws on moral norms arising from pre-existing - albeit competing - formulations of harmony in African moral philosophy. This methodological approach is not uncommon and has been accepted as a valid research method.

RESULT: The paper's methodological approach yields the conclusion that it is ethically permissible to conduct aDNA research on human archaeological remains in the absence of informed consent from descendant communities or individuals. Although we justify the ethical permissibility of conducting research without consent, we also emphasise the importance of consultation with descendant communities - where they are known - and the researchers' responsibility to share benefits with them before, during, and after aDNA research.

CONCLUSION: The sort of aDNA research that this paper considers permissible is that which is likely to enhance harmonious relationships in relevant ways. aDNA research is advancing rapidly and in proportion to technological advances. To ensure that aDNA research in a more technologically advanced world is undertaken in ethically permissible ways, global research guidelines would be required. Future studies can focus on articulating such guidelines.},
}

Humans
*Informed Consent/ethics/standards
*DNA, Ancient/analysis
Genetic Research/ethics
Ethics, Research
Africa
Morals
Archaeology/ethics

@article {pmid40027244,
year = {2025},
author = {David, O and Vidal, M and Gorczyńska, A and Penaud, A and Pailler, Y and Nicolas, C and Debruyne, R and Martin, N and Goor, M and Garcia-Ladieu, P and Goubert, E and Stéphan, P and Ollivier, M and Barloy-Hubler, F},
title = {New coastal records in northern Brittany (Plouescat, NW France): Sedimentological, palynological and paleogenomic data over the last 7.3 ka BP.},
journal = {Data in brief},
volume = {59},
number = {},
pages = {111361},
pmid = {40027244},
issn = {2352-3409},
abstract = {The multidisciplinary approach conducted on the coastal cores ANE-C3 and PADMé (48°38'54.5114"N; 4°10'21.3848"W; Kerallé watershed, NW Brittany, NW France) revealed paleoenvironmental trajectories under both relative sea level rise and anthropogenic dynamics during Middle to Late Holocene, in the research paper: "From a coastal plain to an anthropized fluvial valley (NW Brittany, France): 7.3 kyr of paleoenvironmental evolution from sedimentological, palynological and paleogenomic perspectives" [1]. This additional article presents all the ANE-C3 and PADMé cores dataset discussed in [1] including sedimentological (XRF, grain size), palynological (pollen assemblages) and paleogenomic (plant and mammal sedimentary ancient DNA or sedaDNA) data. For the sedimentological data, the documents included here comprise high-resolution photographs and normalization of XRF-counts. A special emphasis was placed on characterising the modern pollinic signal in different sub-environments (i.e., salt marsh, coastal meadow, field) of the studied area. This was done to identify anthropogenic pollen indicators specific to this coastal zone, and, ultimately to detect more precisely the pollinic signature of human disturbances in the fossil record. Finally, this paper provides additional information on the methodologies developed, with a particular emphasis on sedaDNA analysis.},
}

@article {pmid40022192,
year = {2025},
author = {da Silva, NA and Özer, O and Haller-Caskie, M and Chen, YR and Kolbe, D and Schade-Lindig, S and Wahl, J and Berszin, C and Francken, M and Görner, I and Schierhold, K and Pechtl, J and Grupe, G and Rinne, C and Müller, J and Lenz, TL and Nebel, A and Krause-Kyora, B},
title = {Admixture as a source for HLA variation in Neolithic European farming communities.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {43},
pmid = {40022192},
issn = {1474-760X},
support = {290391021 (CRC 1266 project)//Deutsche Forschungsgemeinschaft/ ; 390870439 (Clusters of Excellence ROOTS - EXC 2150)//Deutsche Forschungsgemeinschaft/ ; 437857095//Deutsche Forschungsgemeinschaft/ ; 400993799 (RTG 2501)//Deutsche Forschungsgemeinschaft/ ; 390884018 (Precision Medicine in Chronic Inflammation - EXC 2167)//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Haplotypes ; Male ; Gene Frequency ; HLA Antigens/genetics ; Female ; Farmers ; Agriculture ; Germany ; Genetic Variation ; Human Migration ; Genetics, Population ; Chromosomes, Human, Y/genetics ; },
abstract = {BACKGROUND: The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied.

RESULTS: We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500-4800 years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations.

CONCLUSIONS: Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.},
}

Humans
*Haplotypes
Male
Gene Frequency
HLA Antigens/genetics
Female
Farmers
Agriculture
Germany
Genetic Variation
Human Migration
Genetics, Population
Chromosomes, Human, Y/genetics

@article {pmid40006948,
year = {2025},
author = {Antoneli, F and Peter, CM and Briones, MRS},
title = {Statistical Distributions of Genome Assemblies Reveal Random Effects in Ancient Viral DNA Reconstructions.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
pmid = {40006948},
issn = {1999-4915},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, Brazil)/ ; 311154/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brazil)/ ; },
mesh = {*DNA, Ancient/analysis ; *Genome, Viral ; *DNA, Viral/genetics ; Humans ; Animals ; Neanderthals/genetics/virology ; Sequence Analysis, DNA/methods ; Signal-To-Noise Ratio ; Viruses/genetics/classification/isolation & purification ; },
abstract = {Ancient human viruses have been detected in ancient DNA (aDNA) samples of both Anatomically Modern Humans and Neanderthals. Reconstructing genomes from aDNA using reference mapping presents numerous problems due to the unique nature of ancient samples, their degraded state, smaller read sizes and the limitations of current methodologies. The spurious alignments of reads to reference sequences (mapping) are a main source of false positives in aDNA assemblies and the assessment of signal-to-noise ratios is essential to differentiate bona fide reconstructions from random, noisy assemblies. Here, we analyzed the statistical distributions of viral genome assemblies, ancient and modern, and their respective random "mock" controls used to evaluate the signal-to-noise ratio. We tested if differences between real and random assemblies could be detected from their statistical distributions. Our analysis shows that the coverage distributions of (1) real viral aDNA assemblies of adenovirus (ADV), herpesvirus (HSV) and papillomavirus (HPV) do not follow power laws nor log-normal laws, (2) (ADV) and control aDNA assemblies are well approximated by log-normal laws, (3) negative control parvovirus B19 (real and random) follow a power law with infinite variance and (4) the mapDamage negative control with non-ancient DNA (modern ADV) and the mapDamage positive control (human mtDNA) are well approximated by the negative binomial distribution, consistent with the Lander-Waterman model. Our results show that the tails of the distributions of aDNA and their controls reveal the weight of random effects and can differentiate spurious assemblies, or false positives, from bona fide assemblies.},
}

*DNA, Ancient/analysis
*Genome, Viral
*DNA, Viral/genetics
Humans
Animals
Neanderthals/genetics/virology
Sequence Analysis, DNA/methods
Signal-To-Noise Ratio
Viruses/genetics/classification/isolation & purification

@article {pmid39993190,
year = {2025},
author = {Gnecchi-Ruscone, GA and Rácz, Z and Liccardo, S and Lee, J and Huang, Y and Traverso, L and Radzevičiūtė, R and Hajnal, Z and Szécsényi-Nagy, A and Gyuris, B and Mateovics-László, O and Bernert, Z and Szeniczey, T and Hajdu, T and Mészáros, B and Bálint, M and Mende, BG and Miller, B and Samashev, Z and Childebayeva, A and Djansugurova, L and Geary, P and Ringbauer, H and Vida, T and Jeong, C and Pohl, W and Krause, J and Hofmanová, Z},
title = {Ancient genomes reveal trans-Eurasian connections between the European Huns and the Xiongnu Empire.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {9},
pages = {e2418485122},
doi = {10.1073/pnas.2418485122},
pmid = {39993190},
issn = {1091-6490},
mesh = {Humans ; Europe ; *Genome, Human ; *Archaeology ; History, Ancient ; *DNA, Ancient/analysis ; Human Migration/history ; },
abstract = {The Huns appeared in Europe in the 370s, establishing an Empire that reshaped West Eurasian history. Yet until today their origins remain a matter of extensive debate. Traditional theories link them to the Xiongnu, the founders of the first nomadic empire of the Mongolian steppe. The Xiongnu empire dissolved, however, ~300 y before the Huns appeared in Europe, and there is little archaeological and historical evidence of Huns in the steppe during this time gap. Furthermore, despite the rich 5th to 6th centuries current era (CE) archaeological record of the Carpathian Basin, the cultural elements of connections with the steppe are limited to few findings and even fewer solitary eastern-type burials. In this study, we coanalyze archaeological evidence with 35 newly sequenced and published genomic data for a total of 370 individuals-from 5th to 6th century CE contexts in the Carpathian Basin including 10 Hun-period eastern-type burials, 2nd to 5th century sites across Central Asia and 2nd c. before current era (BCE) to 1st c. CE Xiongnu period sites across the Mongolian steppe. We find no evidence for the presence of a large eastern/steppe descent community among the Hun- and post-Hun-period Carpathian Basin population. We also observe a high genetic diversity among the eastern-type burials that recapitulates the variability observed across the Eurasian Steppe. This suggests a mixed origin of the incoming steppe conquerors. Nevertheless, long-shared genomic tracts provide compelling evidence of genetic lineages directly connecting some individuals of the highest Xiongnu-period elite with 5th to 6th century CE Carpathian Basin individuals, showing that some European Huns descended from them.},
}

Humans
Europe
*Genome, Human
*Archaeology
History, Ancient
*DNA, Ancient/analysis
Human Migration/history

@article {pmid39987348,
year = {2025},
author = {Qiao, X and Shi, J and Xu, H and Liu, K and Pu, Y and Xue, X and Zheng, W and Guo, Y and Ma, H and Wang, CC and Bitsue, HK and Xu, X and Wang, S and Zhao, J and Guo, X and Hou, X and Wang, X and Peng, L and Qiu, Z and Su, B and Tang, W and He, Y and Guo, J and Yang, Z},
title = {Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {291},
pmid = {39987348},
issn = {2399-3642},
support = {32370664//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32070579//National Natural Science Foundation of China (National Science Foundation of China)/ ; 222300420067//Natural Science Foundation of Henan Province (Henan Province Natural Science Foundation)/ ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Asian People/genetics ; *Genetic Variation ; Diet ; China/epidemiology ; Whole Genome Sequencing ; Adaptation, Physiological/genetics ; Genome, Human ; Asia, Eastern ; Male ; East Asian People ; Fatty Acid Desaturases ; },
abstract = {The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obtained 22.65 million SNPs, 4.26 million INDELs and 41,959 SVs. We found the CPHC has a higher level of genetic diversity and the glycolipid metabolic genes show strong selection signals, e.g. LONP2, FADS2, FGF21 and SLC19A2. Ancient DNA analyses suggest that the domestication of crops, which drove the emergence of the candidate mutations. Notably, East Asian-specific SVs, e.g., DEL_21699 (LINC01749) and DEL_38406 (FAM102A) may be associated with the high prevalence of esophageal squamous carcinoma and primary angle-closure glaucoma. Our results provide an important genetic resource and show that dietary adaptations play an important role in phenotypic evolution in East Asian populations.},
}

Humans
*Polymorphism, Single Nucleotide
*Asian People/genetics
*Genetic Variation
Diet
China/epidemiology
Whole Genome Sequencing
Adaptation, Physiological/genetics
Genome, Human
Asia, Eastern
Male
East Asian People
Fatty Acid Desaturases

@article {pmid39980208,
year = {2025},
author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K},
title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14086},
doi = {10.1111/1755-0998.14086},
pmid = {39980208},
issn = {1755-0998},
support = {856488//H2020 European Research Council/ ; },
abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.},
}

@article {pmid39979344,
year = {2025},
author = {Plascencia, AG and Jakobsson, M and Sánchez-Quinto, F},
title = {Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6161},
pmid = {39979344},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient/analysis ; Europe ; *Gene Frequency ; *Histocompatibility Testing/methods ; HLA Antigens/genetics ; Alleles ; Evolution, Molecular ; Genome, Human ; },
abstract = {Computational HLA typing has surged as a cost-effective strategy to uncover questions regarding the evolution of the HLA system, enabling immunogenic characterization from ancient DNA (aDNA) data. Nevertheless, it remains to be seen whether these methods are suitable for analyzing aDNA generated without target-enrichment. To investigate this, we evaluated the performance of five HLA typing tools using present-day data with simulated profiles typical of aDNA, as well as from high-coverage aDNA genomes downsampled at different read depths. We found that characterization of Class I genes at the first field resolution is feasible at read depths as low as 2x, where it retains an accuracy of ≈ 80%. Next, we used this insight to characterize HLA evolution in Europe from 154 ancient genomes by detecting allele frequency changes throughout distinct prehistoric European populations. We observed important shifts in alleles associated with infectious and autoimmune diseases, most of which are found by contrasting the HLA landscape of Neolithic Farmers to that of present-day. Interestingly, several of these observations are in line with findings that have been previously reported by target-enrichment-based studies. Our results highlight the feasibility of applying HLA typing on shotgun aDNA data to examine the evolution of this loci during important transitions.},
}

Humans
*DNA, Ancient/analysis
Europe
*Gene Frequency
*Histocompatibility Testing/methods
HLA Antigens/genetics
Alleles
Evolution, Molecular
Genome, Human

@article {pmid39975133,
year = {2025},
author = {Smith, SP and Smith, OS and Mostafavi, H and Peng, D and Berg, JJ and Edge, MD and Harpak, A},
title = {A Litmus Test for Confounding in Polygenic Scores.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.01.635985},
pmid = {39975133},
issn = {2692-8205},
abstract = {Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on their phenotype. However, because PGSs are constructed from population-level associations, they are influenced by factors other than direct genetic effects, including stratification, assortative mating, and dynastic effects ("SAD effects"). Our interpretation and application of PGSs may hinge on the relative impact of SAD effects, since they may often be environmentally or culturally mediated. We developed a method that estimates the proportion of variance in a PGS (in a given sample) that is driven by direct effects, SAD effects, and their covariance. We leverage a comparison of a PGS of interest based on a standard GWAS with a PGS based on a sibling GWAS-which is largely immune to SAD effects-to quantify the relative contribution of each type of effect to variance in the PGS of interest. Our method, Partitioning Genetic Scores Using Siblings (PGSUS, pron. "Pegasus"), breaks down variance components further by axes of genetic ancestry, allowing for a nuanced interpretation of SAD effects. In particular, PGSUS can detect stratification along major axes of ancestry as well as SAD variance that is "isotropic" with respect to axes of ancestry. Applying PGSUS, we found evidence of stratification in PGSs constructed using large meta-analyses of height and educational attainment as well as in a range of PGSs constructed using the UK Biobank. In some instances, a given PGS appears to be stratified along a major axis of ancestry in one prediction sample but not in another (for example, in comparisons of prediction in samples from different countries, or in ancient DNA vs. contemporary samples). Finally, we show that different approaches for adjustment for population structure in GWASs have distinct advantages with respect to mitigation of ancestry-axis-specific and isotropic SAD variance in PGS. Our study illustrates how family-based designs can be combined with standard population-based designs to guide the interpretation and application of genomic predictors.},
}

@article {pmid39967865,
year = {2025},
author = {Oras, E and de Groot, J and Björkstén, U},
title = {The "biomolecular humanities"? New challenges and perspectives.},
journal = {iScience},
volume = {28},
number = {2},
pages = {111679},
pmid = {39967865},
issn = {2589-0042},
abstract = {Biomolecular humanities is a developing transdisciplinary research area in which we see natural sciences and humanities increasingly integrated and conceived of as data production and scientific discovery entities on an equal basis. This umbrella term allows us to think generatively about how humanities and natural sciences are providing study material, methodologies, theoretical conceptualizations, analytical results, and synergetic interpretations together, for and about each other.},
}

@article {pmid39962096,
year = {2025},
author = {Parker, LD and West, CF and Tatum, KH and Etnier, M and Bethke, B and Reedy, K and Shellikoff, N and Hofman, CA},
title = {Polar bears and expanding sea ice in the Mid Holocene Aleutian Islands, Alaska.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5767},
pmid = {39962096},
issn = {2045-2322},
support = {2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; },
mesh = {Animals ; *Ursidae ; Alaska ; *Ice Cover ; Climate Change ; Archaeology ; Islands ; Humans ; },
abstract = {The archaeological record offers the opportunity to infer the effects of regional climatic shifts on species distributions and human-animal interactions. In Alaska's temperate Aleutian Islands, the archaeological record suggests that the Neoglacial climate phase (ca. 4700 - 2500 rcyr BP) was significantly colder and the region likely supported sea ice and ice-dependent animals. Previous analyses have identified polar bear (Ursus maritimus) remains in archaeological sites in Unalaska Bay, which have been used to infer bear range expansion and significant climate changes during this period. However, morphological similarities between polar and brown (Ursus arctos) bears make it difficult to distinguish between the two species, and the presence of bear material in Unalaska Bay could be the result of long-distance travel or trade rather than local harvest. Here, we applied zooarchaeological methods to address potential morphological and size differences, to age the bears, and to interpret human use of the bears. Our results suggest that the small assemblage is likely composed of both brown and polar bear remains, but that morphological analyses alone are insufficient to definitively reconstruct bear distributions in this context. Bear age profiles and butchery patterns suggest that the animals were harvested locally and the extension of sea ice in the Neoglacial phase likely facilitated their presence around Unalaska Island. Future analyses that use ancient DNA, collagen fingerprinting, and stable isotopes to determine the species, sex, number of individuals, and relationships to modern populations will be necessary to illuminate regional bear population dynamics in the Neoglacial.},
}

Animals
*Ursidae
Alaska
*Ice Cover
Climate Change
Archaeology
Islands
Humans

@article {pmid39953642,
year = {2025},
author = {Abood, S and Oota, H},
title = {Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations.},
journal = {Journal of physiological anthropology},
volume = {44},
number = {1},
pages = {5},
pmid = {39953642},
issn = {1880-6805},
mesh = {Humans ; *Human Migration ; Animals ; *Adaptation, Physiological/genetics ; Genome, Human/genetics ; Neanderthals/genetics ; Anthropology, Physical ; Biological Evolution ; },
abstract = {Humans have long pondered their genesis. The answer to the great question of where Homo sapiens come from has evolved in conjunction with biotechnologies that have allowed us to more brightly illuminate our distant past. The "Multiregional Evolution" model was once the hegemonic theory of Homo sapiens origins, but in the last 30 years, it has been supplanted by the "Out of Africa" model. Here, we review the major findings that have resulted in this paradigmatic shift. These include hominin brain expansion, classical insight from the mitochondrial genome (mtDNA) regarding the timing of the divergence point between Africans and non-Africans, and next-generation sequencing (NGS) of the Neanderthal and Denisovan genomes. These findings largely bolstered the "Out of Africa" model, although they also revealed a small degree of introgression of the Neanderthal and Denisovan genomes into those of non-African Homo sapiens. We also review paleogenomic studies for which migration route, north or south, early migrants to East Eurasia most likely traversed. Whichever route was taken, the migrants moved to higher latitudes, which necessitated adaptation for lower light conditions, colder clines, and pro-adipogenic mechanisms to counteract food scarcity. Further genetic and epigenetic investigations of these physiological adaptations constitute an integral aspect of the story of human origins and human migration to East Asia.},
}

Humans
*Human Migration
Animals
*Adaptation, Physiological/genetics
Genome, Human/genetics
Neanderthals/genetics
Anthropology, Physical
Biological Evolution

@article {pmid39934375,
year = {2025},
author = {Wang, R and Liu, W and Wu, Y and Ma, H and Lv, J and He, H and Qiu, L and Chen, H and Zhao, Y and Sun, B and Wang, CC},
title = {East and West admixture in eastern China of Tang Dynasty inferred from ancient human genomes.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {219},
pmid = {39934375},
issn = {2399-3642},
mesh = {Humans ; China ; *Genome, Human ; *DNA, Ancient/analysis ; *Polymorphism, Single Nucleotide ; DNA, Mitochondrial/genetics ; Haplotypes ; Asian People/genetics ; Genetics, Population ; Male ; Chromosomes, Human, Y/genetics ; History, Ancient ; Human Migration/history ; },
abstract = {The ancestry composition and Sinicisation process of the descendants of the immigrants of Hu people living in ancient China are largely unknown due to the lack of genetic evidence. Tang Dynasty people in Fudamen cemetery () excavated from Shandong province in eastern China are believed to be related to the descendants of Hu people, as some of the individuals with the surnames An (). The genetic origin of the Fudamen population requires genetic clarification using ancient DNA data. Here we successfully obtain genome-wide SNP data for 17 Tang dynasty individuals from Fudamen cemetery. Based on autosomal data, although all Fudamen individuals show high levels of middle reaches of Yellow River-related ancestry as previously published historical period Shandong populations, 2 Fudamen individuals require ~5% Western Eurasian/Central Asian-related ancestry to describe their ancestry composition best. To the best of our knowledge, it is the first evidence of such ancestry in Shandong, the eastern part of today's China. Moreover, the admixture pattern is also reflected by the presence of both west and east Eurasian-specific mtDNA and Y chromosomal haplogroups in Fudamen people. The estimated admixture time is also consistent with periods when Sogdians and other non-Han populations were active in ancient China. These genomic findings suggest that intermarriage with Han Chinese involved the Sinicization process of the Hu people.},
}

Humans
China
*Genome, Human
*DNA, Ancient/analysis
*Polymorphism, Single Nucleotide
DNA, Mitochondrial/genetics
Haplotypes
Asian People/genetics
Genetics, Population
Male
Chromosomes, Human, Y/genetics
History, Ancient
Human Migration/history

@article {pmid39919708,
year = {2025},
author = {Fortes-Lima, CA and Diallo, MY and Janoušek, V and Černý, V and Schlebusch, CM},
title = {Population history and admixture of the Fulani people from the Sahel.},
journal = {American journal of human genetics},
volume = {112},
number = {2},
pages = {261-275},
doi = {10.1016/j.ajhg.2024.12.015},
pmid = {39919708},
issn = {1537-6605},
mesh = {Humans ; *Genetics, Population ; *Black People/genetics ; Africa South of the Sahara ; Genome, Human ; Ethnicity/genetics ; Genetic Variation ; Central African People ; East African People ; West African People ; },
abstract = {The Fulani people, one of the most important pastoralist groups in sub-Saharan Africa, are still largely underrepresented in population genomic research. They speak a Niger-Congo language called Fulfulde or Pulaar and live in scattered locations across the Sahel/Savannah belt, from the Atlantic Ocean to Lake Chad. According to historical records, their ancestors spread from Futa Toro in the Middle Senegal Valley to Futa-Jallon in Guinea and then eastward into the Sahel belt over the past 1,500 years. However, the earlier history of this traditionally pastoral population has not been well studied. To uncover the genetic structure and ancestry of this widespread population, we gathered genome-wide genotype data from 460 individuals across 18 local Fulani populations, along with comparative data from both modern and ancient worldwide populations. This represents a comprehensive geographically wide-scaled genome-wide study of the Fulani. We revealed a genetic component closely associated with all local Fulani populations, suggesting a shared ancestral component possibly linked to the beginning of African pastoralism in the Green Sahara. Comparison to ancient DNA results also identified the presence of an ancient Iberomaurusian-associated component across all Fulani groups, providing additional insights into their deep genetic history. Additionally, our genetic data indicate a later Fulani expansion from the western to the eastern Sahel, characterized by a clinal pattern and admixture with several other African populations north of the equator.},
}

Humans
*Genetics, Population
*Black People/genetics
Africa South of the Sahara
Genome, Human
Ethnicity/genetics
Genetic Variation
Central African People
East African People
West African People

@article {pmid39920258,
year = {2025},
author = {Eriksen, EF and Andrews, AJ and Nielsen, SV and Persson, P and Malca, E and Onar, V and Aniceti, V and Piquès, G and Piattoni, F and Fontani, F and Wiech, M and Ferter, K and Kersten, O and Ferrari, G and Cariani, A and Tinti, F and Cilli, E and Atmore, LM and Star, B},
title = {Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA.},
journal = {Heredity},
volume = {},
number = {},
pages = {},
pmid = {39920258},
issn = {1365-2540},
support = {813383//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 951649//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; NA20OAR4320472//United States Department of Commerce | NOAA | National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA Fisheries)/ ; },
abstract = {Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.},
}

@article {pmid39912442,
year = {2025},
author = {Gilardet, A and Lord, E and García, GO and Xenikoudakis, G and Douka, K and Wooller, MJ and Rowe, T and Martin, MD and Le Moullec, M and Anisimov, M and Heintzman, PD and Dalén, L},
title = {A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14077},
doi = {10.1111/1755-0998.14077},
pmid = {39912442},
issn = {1755-0998},
support = {325589//Norges Forskningsråd/ ; 2021-00625//Vetenskapsrådet/ ; KAW 2021.0048//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0033//Knut och Alice Wallenbergs Stiftelse/ ; 715069 (FINDER)/ERC_/European Research Council/International ; PrimiGenomes 101054984/ERC_/European Research Council/International ; OPP 2310505//Office of Polar Programs/ ; },
abstract = {Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.},
}

@article {pmid39910300,
year = {2025},
author = {Lazaridis, I and Patterson, N and Anthony, D and Vyazov, L and Fournier, R and Ringbauer, H and Olalde, I and Khokhlov, AA and Kitov, EP and Shishlina, NI and Ailincăi, SC and Agapov, DS and Agapov, SA and Batieva, E and Bauyrzhan, B and Bereczki, Z and Buzhilova, A and Changmai, P and Chizhevsky, AA and Ciobanu, I and Constantinescu, M and Csányi, M and Dani, J and Dashkovskiy, PK and Évinger, S and Faifert, A and Flegontov, P and Frînculeasa, A and Frînculeasa, MN and Hajdu, T and Higham, T and Jarosz, P and Jelínek, P and Khartanovich, VI and Kirginekov, EN and Kiss, V and Kitova, A and Kiyashko, AV and Koledin, J and Korolev, A and Kosintsev, P and Kulcsár, G and Kuznetsov, P and Magomedov, R and Mamedov, AM and Melis, E and Moiseyev, V and Molnár, E and Monge, J and Negrea, O and Nikolaeva, NA and Novak, M and Ochir-Goryaeva, M and Pálfi, G and Popovici, S and Rykun, MP and Savenkova, TM and Semibratov, VP and Seregin, NN and Šefčáková, A and Mussayeva, RS and Shingiray, I and Shirokov, VN and Simalcsik, A and Sirak, K and Solodovnikov, KN and Tárnoki, J and Tishkin, AA and Trifonov, V and Vasilyev, S and Akbari, A and Brielle, ES and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Flegontova, O and Iliev, L and Kearns, A and Keating, D and Lawson, AM and Mah, M and Micco, A and Michel, M and Oppenheimer, J and Qiu, L and Workman, JN and Zalzala, F and Szécsényi-Nagy, A and Palamara, PF and Mallick, S and Rohland, N and Pinhasi, R and Reich, D},
title = {The genetic origin of the Indo-Europeans.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39910300},
issn = {1476-4687},
abstract = {The Yamnaya archaeological complex appeared around 3300 BC across the steppes north of the Black and Caspian Seas, and by 3000 BC it reached its maximal extent, ranging from Hungary in the west to Kazakhstan in the east. To localize Yamnaya origins among the preceding Eneolithic people, we assembled ancient DNA from 435 individuals, demonstrating three genetic clines. A Caucasus-lower Volga (CLV) cline suffused with Caucasus hunter-gatherer[1] ancestry extended between a Caucasus Neolithic southern end and a northern end at Berezhnovka along the lower Volga river. Bidirectional gene flow created intermediate populations, such as the north Caucasus Maikop people, and those at Remontnoye on the steppe. The Volga cline was formed as CLV people mixed with upriver populations of Eastern hunter-gatherer[2] ancestry, creating hypervariable groups, including one at Khvalynsk. The Dnipro cline was formed when CLV people moved west, mixing with people with Ukraine Neolithic hunter-gatherer ancestry[3] along the Dnipro and Don rivers to establish Serednii Stih groups, from whom Yamnaya ancestors formed around 4000 BC and grew rapidly after 3750-3350 BC. The CLV people contributed around four-fifths of the ancestry of the Yamnaya and, entering Anatolia, probably from the east, at least one-tenth of the ancestry of Bronze Age central Anatolians, who spoke Hittite[4,5]. We therefore propose that the final unity of the speakers of 'proto-Indo-Anatolian', the language ancestral to both Anatolian and Indo-European people, occurred in CLV people some time between 4400 BC and 4000 BC.},
}

@article {pmid39910371,
year = {2025},
author = {Callaway, E},
title = {How one language family took over the world: ancient DNA traces its spread.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39910371},
issn = {1476-4687},
}

@article {pmid39902286,
year = {2024},
author = {Gurjão, L and Brito, L and Dias, O and Neto, J and Iñiguez, AM},
title = {Integrating paleoparasitological, paleogenetic, and archaeological data to understand the paleoecological scenario of pre-Columbian archaeological site Gruta do Gentio II, Brazil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1505059},
pmid = {39902286},
issn = {1664-302X},
abstract = {Paleoparasitology and paleogenetics is the study parasites in ancient remains from latrines, mummified individuals, and coprolites, that is fossilized or desiccated feces. Paleoparasitological studies in Brazil began with analyses of coprolites from the Gruta do Gentio II (GGII) archaeological site, the oldest site related to the Una ceramist tradition (12,000 to 410 BP), Brazil. The GGII archaeological site contained numerous human burials, lithics, and cultural artifacts such as basketry, ceremonial ornaments, and unique pottery of the Una tradition. Coprolites of GGII were submitted to paleoparasitological, and paleogenetic analyses for parasite identification and coprolite origin. In addition, the archaeological characterization of the GGII site was integrated into paleo analyses for proposing a paleoecological scenario. Five taxa of parasites, including Ancylostomidae, Echinostoma sp., Spirometra sp., and Trichostrongylus sp., and three different morphotypes of Capillariidae were recognized in multiple coprolites that were distributed heterogeneously in several stratigraphical layers. The origin of coprolites was genetically defined as five species of mammals, humans, felines as Panthera onca and Leopardus pardalis, and marsupials as Didelphis albiventris and Philander opossum. This is the first study in Brazil that identified both, parasites and species of animals in Pleistocene/Holocene producers of coprolites with geographical and temporal information. The integration of paleoparasitology, paleogenetics, and archaeology is essential to propose paleoecological scenarios from the past of Brazil.},
}

@article {pmid39895972,
year = {2024},
author = {Benítez-Burraco, A},
title = {How (and why) languages became more complex as we evolved more prosocial: the human self-domestication view.},
journal = {Frontiers in psychology},
volume = {15},
number = {},
pages = {1499994},
pmid = {39895972},
issn = {1664-1078},
abstract = {This paper aims to re-examine the problem of the emergence of present-day languages from the specific perspective of the self-domestication account of human evolution. According to this view, our species went through an evolutionary process that parallels the changes experienced by domesticated mammals. Relying on evidence of diverse kind (from paleogenetic to clinical), the paper argues that our self-domestication might have potentiated the cognitive and behavioral features of the human phenotype with an impact on language acquisition and use. Specifically, it might have facilitated the creation of the cultural niche that favors the complexification of languages via a cultural mechanism. The paper further proposes a model of language complexification in the past under the effects of human self-domestication, including the complexification of the structural aspects of language (grammar, prosody, and semantics) and the potentiation of its functional properties (pragmatics). The paper concludes with some suggestions for any future research aimed to test and improve this view.},
}

@article {pmid39881595,
year = {2025},
author = {Piffer, D},
title = {Directional Selection and Evolution of Polygenic Traits in Eastern Eurasia: Insights from Ancient DNA.},
journal = {Twin research and human genetics : the official journal of the International Society for Twin Studies},
volume = {},
number = {},
pages = {1-20},
doi = {10.1017/thg.2024.49},
pmid = {39881595},
issn = {1832-4274},
abstract = {This study explores directional selection on physical and psychosocial phenotypes in Eastern Eurasian populations, utilizing a dataset of 1245 ancient genomes. By analyzing polygenic scores (PGS) for traits including height, educational attainment (EA), IQ, autism, schizophrenia, and others, we observed significant temporal trends spanning the Holocene era. The results suggest positive selection for cognitive-related traits such as IQ, EA and autism spectrum disorder (ASD), alongside negative selection for anxiety and depression. The results for height were mixed and showed nonlinear relationships with Years Before Present (BP). These trends were partially mediated by genetic components linked to distinct ancestral populations. Regression models incorporating admixture, geography, and temporal variables were used to account for biases in population composition over time. Latitude showed a positive effect on ASD PGS, EA and height, while it had a negative effect on skin pigmentation scores. Additionally, latitude exhibited significant nonlinear effects on multiple phenotypes. The observed patterns highlight the influence of climate-mediated selection pressures on trait evolution. Spline regression revealed that several polygenic scores had nonlinear relationships with years BP. The findings provide evidence for complex evolutionary dynamics, with distinct selective pressures shaping phenotypic diversity across different timescales and environments.},
}

@article {pmid39875364,
year = {2025},
author = {Liu, Y and Lisovski, S and Courtin, J and Stoof-Leichsenring, KR and Herzschuh, U},
title = {Plant interactions associated with a directional shift in the richness range size relationship during the Glacial-Holocene transition in the Arctic.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1128},
pmid = {39875364},
issn = {2041-1723},
support = {202106620011//China Scholarship Council (CSC)/ ; },
mesh = {Arctic Regions ; Siberia ; *Biodiversity ; Alaska ; *Lakes ; *Plants ; Tundra ; Ecosystem ; Geologic Sediments ; Ice Cover ; },
abstract = {A nearly ubiquitous negative relationship between taxonomic richness and mean range-size (average area of taxa) is observed across space. However, the complexity of the mechanism limits its applicability for conservation or range prediction. We explore whether the relationship holds over time, and whether plant speciation, environmental heterogeneity, or plant interactions are major factors of the relationship within northeast Siberia and Alaska. By analysing sedimentary ancient DNA from seven lakes, we reconstruct plant richness, biotic environmental heterogeneity, and mean range-size over the last 30,000 years. We find positive richness to range-size relationships during the glacial period, shifting to negative during the interglacial period. Our results indicate neither speciation nor environmental heterogeneity is the principal driver. Network analyses show more positive interactions during the glacial period, which may contribute to positive richness to range-size relationships. Conversely, in the interglacial environment, negative interactions may result in negative relationships. Our findings suggest potential susceptibility to invasion but conservation advantages in far northern tundra given their positive interactions.},
}

Arctic Regions
Siberia
*Biodiversity
Alaska
*Lakes
*Plants
Tundra
Ecosystem
Geologic Sediments
Ice Cover

@article {pmid39868711,
year = {2024},
author = {Ollivier, M},
title = {[Thousands of years of human-dog relationship].},
journal = {Biologie aujourd'hui},
volume = {218},
number = {3-4},
pages = {115-127},
doi = {10.1051/jbio/2024011},
pmid = {39868711},
issn = {2105-0686},
mesh = {Humans ; Animals ; Dogs ; *Biological Evolution ; Europe ; },
abstract = {During recent years, much progress has been made in understanding the origin and evolution of the dog. Thanks to the collaboration between zooarchaeology, genomics and paleogenetics, researchers were able to hypothesize scenarios regarding the origins of the canine lineages present in Europe at the end of the Pleistocene and the beginning of the Holocene. Research has also shown a correlation between human and canine migration across time and space, highlighting a strong relationship between man and his best friend. This proximity between the two species is also illustrated by the adaptation of this species to anthropogenic selective pressures, particularly in parallel with cultural transitions. Although the history of this species still requires much exploration to be fully understood, these results provide new theoretical bases for understanding the interplay between humans and dogs.},
}

Humans
Animals
Dogs
*Biological Evolution
Europe

@article {pmid39868174,
year = {2025},
author = {Malomane, DK and Williams, MP and Huber, CD and Mangul, S and Abedalthagafi, M and Chiang, CWK},
title = {Patterns of population structure and genetic variation within the Saudi Arabian population.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.10.632500},
pmid = {39868174},
issn = {2692-8205},
abstract = {The Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, we investigated how the population history and cultural practices such as endogamy have shaped the genetic variation of the Saudi Arabians. We genotyped 3,352 individuals and identified twelve genetic sub-clusters that corresponded to the geographical distribution of different tribal regions, differentiated by distinct components of ancestry based on comparisons to modern and ancient DNA references. These sub-clusters also showed variation across ranges of the genome covered in runs of homozygosity, as well as differences in population size changes over time. Using 25,488,981 variants found in whole genome sequencing data (WGS) from 302 individuals, we found that the Saudi tend to show proportionally more deleterious alleles than neutral alleles when compared to Africans/African Americans from gnomAD (e.g. a 13% increase of deleterious alleles annotated by AlphaMissense between 0.5 -5% frequency in Saudi, compared to 7% decrease of the benign alleles; P < 0.001). Saudi sub-clusters with greater inbreeding and lower effective population sizes showed greater enrichment of deleterious alleles as well. Additionally, we found that approximately 10% of the variants discovered in our WGS data are not observed in gnomAD; these variants are also enriched with deleterious annotations. To accelerate studying the population-enriched deleterious alleles and their health consequences in this population, we made available the allele frequency estimates of 25,488,981 variants discovered in our samples. Taken together, our results suggest that Saudi's population history impacts its pattern of genetic variation with potential consequences to the population health. It further highlights the need to sequence diverse and unique populations so to provide a foundation on which to interpret medical-and pharmaco-genomic findings from these populations.},
}

@article {pmid39858625,
year = {2025},
author = {Jeromelj, T and Leskovar, T and Zupanič Pajnič, I},
title = {The Impact of Storage Conditions on DNA Preservation in Human Skeletal Remains: A Comparison of Freshly Excavated Samples and Those Stored for 12 Years in a Museum Depot.},
journal = {Genes},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/genes16010078},
pmid = {39858625},
issn = {2073-4425},
support = {J3-3080//The Slovenian Research and Innovation Agency/ ; },
mesh = {Humans ; *Specimen Handling/methods ; *Museums ; *DNA, Ancient/analysis ; Body Remains ; Bone and Bones/chemistry ; Humidity ; Archaeology/methods ; Preservation, Biological/methods ; Temperature ; },
abstract = {Background: As the field of ancient DNA research continues to evolve and produce significant discoveries, it is important to address the crucial limitations it still faces. Under conducive conditions, DNA can persist for thousands of years within human skeletal remains, but, as excavation occurs, the environment abruptly changes, often leading to the loss of DNA and valuable genetic information. Proper storage procedures are needed to mediate DNA degradation and maintain sample integrity. This study aimed to investigate the impact of long-term storage under unregulated temperatures and humidity conditions on DNA preservation in human skeletal remains. Methods: To achieve this, archaeological petrous bones were used for DNA recovery. The DNA yield and degree of DNA degradation were compared for samples originating from historically and geographically equivalent archaeological sites, which differed in times of excavation and, consequently, in storage durations and conditions. DNA yield and the degree of DNA degradation were determined using real time PCR. Results: A significant reduction in the DNA yield and a borderline significant increase in the degree of DNA degradation were detected for samples stored at unregulated conditions for approximately 12 years. Conclusions: Our results show the imperative need for adhering to scientific recommendations regarding the optimal temperature and humidity in the long-term storage of human skeletal material.},
}

Humans
*Specimen Handling/methods
*Museums
*DNA, Ancient/analysis
Body Remains
Bone and Bones/chemistry
Humidity
Archaeology/methods
Preservation, Biological/methods
Temperature

@article {pmid39858570,
year = {2024},
author = {Haarkötter, C and Roca-Rada, X and Saiz, M and Vinueza-Espinosa, DC and Gálvez, X and Medina-Lozano, MI and Díaz-Ruiz, D and Álvarez, JC and Llamas, B and Lorente, JA and Austin, J},
title = {Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones.},
journal = {Genes},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/genes16010023},
pmid = {39858570},
issn = {2073-4425},
support = {FPU 20/01967 and EST 23/0110//Ministerio de Universidades (Spain)/ ; PTDC/HAR-ARQ/6273/2020//FCT - Foundation for Science and Technology/ ; },
mesh = {Humans ; *Bone and Bones/chemistry ; *DNA Fingerprinting/methods ; *Forensic Genetics/methods ; *DNA, Ancient/analysis ; Microsatellite Repeats/genetics ; Nucleic Acid Hybridization/methods ; Genome, Human ; Body Remains ; },
abstract = {UNLABELLED: In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains.

BACKGROUND/OBJECTIVES: This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis.

METHODS: Six highly degraded human bones from the Spanish Civil War (1936-1939) were quantified with Quantifiler[™] Trio and amplified with GlobalFiler[™]. Independently, partially UDG-treated double-stranded DNA libraries were generated and shotgun sequenced to screen for endogenous human DNA content. Subsequently, libraries were enriched with the Twist Bioscience "Twist Ancient DNA" reagent enrichment kit, which had not been previously tested for forensic purposes.

RESULTS: The results show that the samples behave similarly with both approaches (well-preserved samples yield good results). However, capture enrichment provides some new relevant insights, suggesting that its implementation in current NGS forensic platforms could be beneficial.

CONCLUSIONS: Shotgun results show that the analyzed samples exhibit the same characteristics as ancient DNA samples in terms of DNA fragmentation and molecular damage, which may enhance the value of this approach when authenticating the endogenous DNA of forensic samples.},
}

Humans
*Bone and Bones/chemistry
*DNA Fingerprinting/methods
*Forensic Genetics/methods
*DNA, Ancient/analysis
Microsatellite Repeats/genetics
Nucleic Acid Hybridization/methods
Genome, Human
Body Remains

@article {pmid39856224,
year = {2025},
author = {Heinrich, F and Simianer, H and Bölling, J and Röckelein, H and Roos, C and Reimer, C and Schmitt, AO},
title = {Genomic analysis of three medieval parchments from German monasteries.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3156},
pmid = {39856224},
issn = {2045-2322},
mesh = {Animals ; Cattle/genetics ; Germany ; *DNA, Ancient/analysis ; History, Medieval ; *DNA, Mitochondrial/genetics ; *Polymorphism, Single Nucleotide ; *Haplotypes ; *Genomics/methods ; Phylogeny ; },
abstract = {In the last two decades there has been growing interest in the analysis of ancient DNA obtained from the parchment used in historic documents. The genetic insight that this data provides makes collections of historic documents an invaluable source for studying the development and spread of historical livestock populations. Additionally, the biological data may provide new information for the historical analysis that could be used to determine the provenance as well as the authenticity of these documents. In this study, we extracted DNA from three medieval parchments that were written in German monasteries in the twelfth century. The source animal of the parchments could be identified as cattle and we compared their genome sequences with those of modern populations that are part of the 1000 Bull Genomes Project. The three animals were found to carry mtDNA haplogroup T3 and show a closer genetic relationship to other historic animals than to modern breeds. We further identified 39 haplotypes and 132 SNPs variants, which are rare (< 0.1) or even non-existent in modern breeds. Finally, the genetic distances between the parchment samples show a putative association with the dates when the documents were written, indicating the usefulness of genetic analysis for provenance research.},
}

Animals
Cattle/genetics
Germany
*DNA, Ancient/analysis
History, Medieval
*DNA, Mitochondrial/genetics
*Polymorphism, Single Nucleotide
*Haplotypes
*Genomics/methods
Phylogeny

@article {pmid39854269,
year = {2025},
author = {Huang, Y and Carmi, S and Ringbauer, H},
title = {Estimating effective population size trajectories from time-series identity-by-descent segments.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae212},
pmid = {39854269},
issn = {1943-2631},
support = {//Max Planck Society/ ; },
abstract = {Long, identical haplotypes shared between pairs of individuals, known as identity-by-descent (IBD) segments, result from recently shared co-ancestry. Various methods have been developed to utilize IBD sharing for demographic inference in contemporary DNA data. Recent methodological advances have extended the screening for IBD segments to ancient DNA (aDNA) data, making demographic inference based on IBD also possible for aDNA. However, aDNA data typically have varying sampling times, but most demographic inference methods for modern data assume that sampling is contemporaneous. Here, we present Ttne (Time-Transect Ne), which models time-transect sampling to infer recent effective population size trajectories. Using simulations, we show that utilizing IBD sharing in time series increased resolution to infer recent fluctuations in effective population sizes compared with methods that only use contemporaneous samples. To account for IBD detection errors common in empirical analyses, we implemented an approach to estimate and model IBD detection errors. Finally, we applied Ttne to two aDNA time transects: individuals associated with the Copper Age Corded Ware Culture and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records.},
}

@article {pmid39850751,
year = {2025},
author = {Shen, W and Kruse, S and Liu, S and Stoof-Leichsenring, K and Kühn, I and Li, W and Cao, X and Zhang, ZR and Zeng, CX and Yang, JB and Li, DZ and Herzschuh, U},
title = {Post-Glacial Vegetation Trajectories on the Eastern Tibetan Plateau Reflect Millennial-Scale Migration Lags in Complex Mountain Terrain Based on Sedimentary Ancient DNA and Dynamic Dispersal Modeling.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70862},
pmid = {39850751},
issn = {2045-7758},
abstract = {Mountains with complex terrain and steep environmental gradients are biodiversity hotspots such as the eastern Tibetan Plateau (TP). However, it is generally assumed that mountain terrain plays a secondary role in plant species assembly on a millennial time-scale compared to climate change. Here, we investigate plant richness and community changes during the last 18,000 years at two sites: Lake Naleng and Lake Ximen on the eastern TP with similar elevation and climatic conditions but contrasting terrain. We applied plant DNA metabarcoding to lake sediments leveraging a new regional reference database for taxa identification. Furthermore, we developed a simplified species dispersal model named SMARC. This was used to simulate species migration along river valleys in response to past climate change at the taxonomic resolution of the sedimentary ancient DNA (sedaDNA) approach. Statistical analyses, including ordination-based ecological trajectory analysis, yielded a significant match between sedaDNA and simulated results at single taxon and community levels including certain site-specific differences. Steep terrain downstream of Lake Naleng enhances connectivity to glacial lowland refugia during postglacial warming. In contrast, gentle terrain over long distances implies weak connectivity to the lowland and thus resulted in a strong migration lag at Lake Ximen. Likewise, terrain differences among our sites defined the different connectivity to alpine refugia during late-Holocene cooling. Our consistent proxy- and model-based results, for the first time, indicate that dispersal related migration lags in complex mountain terrain lead to uneven vegetation trajectories at sites with similar climatic conditions mainly because of differences in connectivity to refugia. Ultimately our results indicate that connectivity to refugia is a first-order factor for species migration in addition to elevation-related climatic conditions shaping the postglacial vegetation trajectory in mountainous terrain. This has hitherto largely been ignored when forecasting mountain vegetation responses to climate change and related risk assessment.},
}

@article {pmid39848961,
year = {2025},
author = {Mazières, S and Condemi, S and El Nemer, W and Chiaroni, J},
title = {Rapid change in red cell blood group systems after the main Out of Africa of Homo sapiens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1597},
pmid = {39848961},
issn = {2045-2322},
support = {ANR-20-CE03-0002//Agence Nationale de la Recherche/ ; },
mesh = {Humans ; Animals ; *Blood Group Antigens/genetics ; *Neanderthals/genetics ; *Genetic Variation ; Haplotypes ; Phylogeny ; Erythrocytes ; Alleles ; Africa ; },
abstract = {Despite the advances in paleogenomics, red cell blood group systems in ancient human populations remain scarcely known. Pioneer attempts showed that Neandertal and Denisova, two archaic hominid populations inhabiting Eurasia, expressed blood groups currently found in sub-Saharans and a rare "rhesus", part of which is found in Oceanians. Herein we fully pictured the blood group genetic diversity of 22 Homo sapiens and 14 Neandertals from Eurasia living between 120,000 and 20,000 years before present (yBP). From the ABO, Rh, Kell, Duffy, Kidd, MNS, Diego, H, secretor and Indian systems, we noted that the blood group allele diversity in the Neandertals remained unchanged since 120,000 yBP, while H. sapiens conquered Eurasia with blood group alleles presently exclusive to non-African populations, suggesting they may have differentiated right after the Out of Africa, between 70,000 and 45,000 yBP. Notably, Ust'Ishim possessed unknown alleles that may illustrate the lost genetic heritage of the early Eurasians. Lastly, Neandertals shared a unique Rh haplotype from which we updated the current RHD phylogeny. The contribution of this study is twofold. It enlightens the expansion patterns of H sapiens and recalls the anthropological effectiveness of genetic polymorphisms currently being surveyed for transfusion safety and pregnancy monitoring.},
}

Humans
Animals
*Blood Group Antigens/genetics
*Neanderthals/genetics
*Genetic Variation
Haplotypes
Phylogeny
Erythrocytes
Alleles
Africa

@article {pmid39835499,
year = {2025},
author = {Fleskes, RE and Gilmore, JK and Oubré, LS and Ofunniyin, AA and Cabana, GS and Schurr, TG},
title = {Immersive Videography of Ancient DNA Extraction for Community Engagement and Educational Initiatives by the Anson Street African Burial Ground Project.},
journal = {American journal of biological anthropology},
volume = {186},
number = {1},
pages = {e25055},
pmid = {39835499},
issn = {2692-7691},
support = {//College of Charleston/ ; //The City of Charleston/ ; NGS-52378R-18//National Geographic Society/ ; NGS-54324E-18//National Geographic Society/ ; },
mesh = {Humans ; *DNA, Ancient/analysis ; Video Recording ; Burial ; Community Participation/methods ; Archaeology/methods ; Africa ; },
abstract = {OBJECTIVE: Community engagement is an increasingly important component of ancient DNA (aDNA) research, especially when it involves archeological individuals connected to contemporary descendants or other invested communities. However, effectively explaining methods to non-specialist audiences can be challenging due to the intricacies of aDNA laboratory work. To overcome this challenge, the Anson Street African Burial Ground (ASABG) Project employed a GoPro camera to visually document the process of aDNA extraction for use in community engagement and education events.

METHODS: A GoPro Hero 6 camera enclosed in a decontaminated underwater case was used to film multiple rounds of aDNA extractions from first- and third-person perspectives. The raw footage was edited into long (13-minute) and short (5-minute) format videos to summarize the steps of aDNA extraction for different educational aims.

RESULTS: The videos were used at community engagement events, as well as in classrooms and other educational venues for students of different age groups. General feedback from the community was solicited at the events. We found that the use of videographic methods increased the transparency and accessibility of the aDNA research conducted by the ASABG Project team.

DISCUSSION: Providing a visual guide to the often destructive nature of aDNA testing served as an important step in the continuing practice of informed (dynamic) consent with the descendant community. Future initiatives could expand these visualization efforts by illustrating other steps in the aDNA testing process, such as library preparation or sequencing, or incorporating approaches such as live streaming to foster trust and expand public science literacy.},
}

Humans
*DNA, Ancient/analysis
Video Recording
Burial
Community Participation/methods
Archaeology/methods
Africa

@article {pmid39824823,
year = {2025},
author = {Gelabert, P and Oberreiter, V and Straus, LG and Morales, MRG and Sawyer, S and Marín-Arroyo, AB and Geiling, JM and Exler, F and Brueck, F and Franz, S and Cano, FT and Szedlacsek, S and Zelger, E and Hämmerle, M and Zagorc, B and Llanos-Lizcano, A and Cheronet, O and Tejero, JM and Rattei, T and Kraemer, SM and Pinhasi, R},
title = {Author Correction: A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {779},
doi = {10.1038/s41467-025-56198-x},
pmid = {39824823},
issn = {2041-1723},
}

@article {pmid39823473,
year = {2025},
author = {Bettisworth, B and Psonis, N and Poulakakis, N and Pavlidis, P and Stamatakis, A},
title = {Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf006},
pmid = {39823473},
issn = {1537-1719},
abstract = {A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database. As a consequence, these tools may not be able to accurately place such reads in a phylogenetic context. Phylogenetic placement is a technique where a read is placed onto a specific branch of a phylogenetic reference tree, which allows for a substantially finer resolution when identifying reads. Prior applications of phylogenetic placement has deployed only on data from extant sources. Therefore, it is unclear how the aDNA damage affects phylogenetic placement's applicability to aDNA data. To investigate how aDNA damage affects placement accuracy, we re-implemented a statistical model of aDNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to seven empirical datasets with four leading tools: APPLES, EPA-NG, pplacer, and RAPPAS. We explore the aDNA damage parameter space via a grid search in order to identify the aDNA damage factors that exhibit the largest impact on placement accuracy. We find that the frequency of DNA backbone nicks (and consequently read length) has the, by far, largest impact on aDNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.},
}

@article {pmid39814885,
year = {2025},
author = {Wang, K and Tobias, B and Pany-Kucera, D and Berner, M and Eggers, S and Gnecchi-Ruscone, GA and Zlámalová, D and Gretzinger, J and Ingrová, P and Rohrlach, AB and Tuke, J and Traverso, L and Klostermann, P and Koger, R and Friedrich, R and Wiltschke-Schrotta, K and Kirchengast, S and Liccardo, S and Wabnitz, S and Vida, T and Geary, PJ and Daim, F and Pohl, W and Krause, J and Hofmanová, Z},
title = {Ancient DNA reveals reproductive barrier despite shared Avar-period culture.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39814885},
issn = {1476-4687},
abstract = {After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry[1,2]. We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter[1,2]. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture[3,4]. We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.},
}

@article {pmid39809323,
year = {2025},
author = {Boast, AP and Wood, JR and Cooper, J and Bolstridge, N and Perry, GLW and Wilmshurst, JM},
title = {DNA and spores from coprolites reveal that colourful truffle-like fungi endemic to New Zealand were consumed by extinct moa (Dinornithiformes).},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240440},
pmid = {39809323},
issn = {1744-957X},
support = {//University of Auckland/ ; //Linnean Society of NSW/ ; //Ornithological Society of New Zealand/ ; //Royal Society Te Apārangi/ ; //New Zealand Ministry of Business, Innovation and Employment's Science and Innovation Group/ ; },
mesh = {Animals ; New Zealand ; *Spores, Fungal ; DNA, Fungal/genetics ; Extinction, Biological ; Feces/microbiology ; Ascomycota/genetics/physiology ; },
abstract = {Mycovores (animals that consume fungi) are important for fungal spore dispersal, including ectomycorrhizal (ECM) fungi symbiotic with forest-forming trees. As such, fungi and their symbionts may be impacted by mycovore extinction. New Zealand (NZ) has a diversity of unusual, colourful, endemic sequestrate (truffle-like) fungi, most of which are ECM. As NZ lacks native land mammals (except bats), and sequestrate fungi are typically drab and mammal-dispersed, NZ's sequestrate fungi are hypothesized to be adapted for bird dispersal. However, there is little direct evidence for this hypothesis, as 41% of NZ's native land bird species became extinct since initial human settlement in the thirteenth century. Here, we report ancient DNA and spores from the inside of two coprolites of NZ's extinct, endemic upland moa (Megalapteryx didinus) that reveal consumption and likely dispersal of ECM fungi, including at least one colourful sequestrate species. Contemporary data from NZ show that birds rarely consume fungi and that the introduced mammals preferentially consume exotic fungi. NZ's endemic sequestrate fungi could therefore be dispersal limited compared with fungi that co-evolved with mammalian dispersers. NZ's fungal communities may thus be undergoing a gradual species turnover following avian mycovore extinction and the establishment of mammalian mycovores, potentially affecting forest resilience and facilitating invasion by exotic tree taxa.},
}

Animals
New Zealand
*Spores, Fungal
DNA, Fungal/genetics
Extinction, Biological
Feces/microbiology
Ascomycota/genetics/physiology

@article {pmid39803566,
year = {2025},
author = {Szécsényi-Nagy, A and Virag, C and Jakab, K and Rohland, N and Ringbauer, H and Anders, A and Raczky, P and Hajdu, T and Kiss, K and Szeniczey, T and Évinger, S and Keszi, T and Virág, ZM and Cheronet, O and Mallick, S and Akbari, A and Pinhasi, R and Reich, D and Siklósi, Z},
title = {Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.02.631136},
pmid = {39803566},
issn = {2692-8205},
abstract = {We present a comprehensive genetic investigation of Late Neolithic (LN) and Early Copper Age (ECA) populations living in the Carpathian Basin, leveraging whole genome data from 125 previously unreported individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 cal BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals we analyzed from a large community cemetery was genetically diverse, another site was more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. These results document radically different kinship systems in contemporaneous ECA communities using similar material culture and living only about 100 km apart.},
}

@article {pmid39794407,
year = {2025},
author = {Weber, GW and Šimková, PG and Fernandes, DM and Cheronet, O and Úry, E and Wilfing, H and Matiasek, K and Llano-Lizcano, A and Gelabert, P and Trinks, I and Douka, K and Ladstätter, S and Higham, T and Steskal, M and Pinhasi, R},
title = {The cranium from the Octagon in Ephesos.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {943},
pmid = {39794407},
issn = {2045-2322},
support = {369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; BE547005//University of Vienna/ ; },
mesh = {Humans ; Male ; *Skull/anatomy & histology ; Turkey ; Child ; Adolescent ; Archaeology ; Femur/anatomy & histology ; },
abstract = {During excavations in 1929, a well-preserved skeleton was discovered in a sarcophagus in the Octagon at Ephesos (Turkey). For the following century, archaeologists have speculated about the identity of this obviously notable person. Repeated claim is that the remains could represent Arsinoë IV, daughter of Ptolemy XII, and younger (half-)sister of Cleopatra VII. To address these questions we undertook state-of-the-art morphological, genetic and dating analyses of the cranium and further analyses of bone samples from a femur and a rib of the skeleton found in the same tomb. We confirm based on genetic analyses from the cranium and the femur that they derive from the same person. [14]C-dating of the cranium provides a most likely time range between 205-36 BC. The connection with Arsinoë IV can be excluded because we confirmed that the individual is a male. The cranium represents an 11-14-year-old boy who suffered from significant developmental disturbances. Genetics suggest an ancestry from the Italian peninsula or Sardinia. The fate of the body of Arsinoë IV, who reportedly was killed in 41 BC in Ephesos, remains open. In contrast, investigations regarding the fate and social background of the boy from the Octagon can now proceed free of speculation.},
}

Humans
Male
*Skull/anatomy & histology
Turkey
Child
Adolescent
Archaeology
Femur/anatomy & histology

@article {pmid39791298,
year = {2025},
author = {Sheng, GL and Zheng, MM and Xiao, B and Yuan, JX},
title = {Progress on ancient DNA investigation of Late Quaternary mammals in China.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {1},
pages = {46-57},
doi = {10.16288/j.yczz.24-193},
pmid = {39791298},
issn = {0253-9772},
mesh = {*DNA, Ancient/analysis ; Animals ; China ; *Mammals/genetics ; Humans ; Evolution, Molecular ; Phylogeny ; Fossils ; },
abstract = {It has been more than 40 years since the beginning of exploring the genetic composition of ancient organisms from the perspective of ancient DNA. In the recent 20 years, with the development and application of high-throughput sequencing technology platforms and the improved efficiency of retrieving highly fragmented DNA molecules, ancient DNA research moved forward to a brand-new era of deep-time paleogenomics. It not only solved many controversial phylogenetic problems, enriched the migration and evolution details of various organisms including humans, but also launched exploration of the molecular responses to climate changes in terms of "whole genomic-big data-multi-species" level. Moreover, it expanded the sample age from no more than 100,000 years to the Early Pleistocene, ~2 million years ago. Recently, Chinese scientists have made many influential breakthroughs in evolution and migration integration of East Asian populations and thus filled an important gap in the evolutionary process of modern human. Compared to the situation in human paleogenomic studies, less attention has been paid to the study of ancient DNA from vertebrates remains. In this review, we introduce a series of advances in ancient DNA investigations of large mammals in Late Quaternary in China, summarize the research breakthroughs in revealing the systematic evolutionary relationship between ancient and extant groups, gene flow, and molecular responses of mammalian populations to climate change, and explore the opportunities and key challenges in the field of mammalian paleogenomics.},
}

*DNA, Ancient/analysis
Animals
China
*Mammals/genetics
Humans
Evolution, Molecular
Phylogeny
Fossils

@article {pmid39791297,
year = {2025},
author = {Zhang, DX and Dai, SR and Cui, YQ},
title = {The migration and evolutionary mechanisms of northern Asian populations from the perspective of ancient genomics.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {1},
pages = {34-45},
doi = {10.16288/j.yczz.24-196},
pmid = {39791297},
issn = {0253-9772},
mesh = {Humans ; *Human Migration ; *Genomics/methods ; *DNA, Ancient/analysis ; Genetics, Population ; Asian People/genetics ; Evolution, Molecular ; China ; },
abstract = {The northern part of Asia, including Siberia, the Mongolian Plateau, and northern China, is not only a crossroads for population exchange on the Eurasian continent but also an important bridge connecting the American continent. This region holds a unique and irreplaceable significance in exploring the origins of humanity, tracking human migration routes, and elucidating evolutionary mechanisms. Despite the limited number of samples unearthed, varying preservation conditions, and constraints of technical means, our understanding of the interactions among populations in northern Asia is still in its infancy. However, the development of high-throughput sequencing technology and its advancement in ancient DNA research have provided us with a new perspective for delving into the genetic history of ancient populations from a molecular level. In this review, we synthesize the changes in the genetic structure of ancient populations in different stages of northern Asia, aiming to reveal the patterns of interaction among ancient populations in this region, the evolutionary process of their genetic structure, and their genetic contributions to modern populations. It will also discuss the adaptive strategies of humans in response to extreme natural conditions. This will not only deepen our understanding of the origins and migration processes of humanity but also provide a solid foundation for studying the evolutionary mechanisms and adaptive strategies of humans under environmental selective pressures.},
}

Humans
*Human Migration
*Genomics/methods
*DNA, Ancient/analysis
Genetics, Population
Asian People/genetics
Evolution, Molecular
China

@article {pmid39791296,
year = {2025},
author = {Ping, WJ and Xue, JY and Fu, QM},
title = {Ancient DNA elucidates the migration and evolutionary history of northern and southern populations in East Asia.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {1},
pages = {18-33},
doi = {10.16288/j.yczz.24-224},
pmid = {39791296},
issn = {0253-9772},
mesh = {Humans ; *DNA, Ancient/analysis ; *Human Migration ; Asia, Eastern ; Genetics, Population ; Asian People/genetics ; Gene Flow ; Genome, Human ; Evolution, Molecular ; China ; },
abstract = {Over the past decade, the continuous development of ancient genomic technology and research has significantly advanced our understanding of human history. Since 2017, large-scale studies of ancient human genomes in East Asia, particularly in China, have emerged, resulting in a wealth of ancient genomic data from various time periods and locations, which has provided new insights into the genetic history of East Asian populations over tens of thousands of years. Especially since 2022, there emerged a series of new research progresses in the genetic histories of the northern and southern Chinese populations within the past 10,000 years. However, there is currently no systematic review focused on these recent ancient genomic studies in East Asia. Therefore, this article emphasizes the study of ancient human genomes in China and systematically reviews the genetic patterns and migration history of populations in East Asia since the Late Paleolithic. Existing research indicates that by at least 19,000 years ago, there was a north-south differentiation among ancient East Asian populations, leading to different genetic lineages divided by the Qinling-Huaihe line. Gene flow and interactions between northern and southern East Asians began in the Early Neolithic and were further strengthened from the Mid-Neolithic. By the historical period, northern East Asian ancestry played a profound role in the genetic components of southern populations, shaping the genetic structure of present-day Chinese populations. Throughout this process, ancient populations in northern and southern China also engaged in extensive interactions through coastal and inland routes with populations from surrounding regions, including Siberia, Japan, Korea, Southeast Asia, and Pacific islands, playing a crucial role in the formation of different linguistic groups. These studies have charted the evolutionary and interaction history of East Asian populations over tens of thousands of years; yet, many unresolved mysteries remain. Further exploration is needed through ancient genomic data from additional time periods and broader geographic areas to facilitate a more comprehensive and detailed investigation, thereby advancing related scientific questions.},
}

Humans
*DNA, Ancient/analysis
*Human Migration
Asia, Eastern
Genetics, Population
Asian People/genetics
Gene Flow
Genome, Human
Evolution, Molecular
China

@article {pmid39789608,
year = {2025},
author = {Koptekin, D and Yapar, E and Vural, KB and Sağlıcan, E and Altınışık, NE and Malaspinas, AS and Alkan, C and Somel, M},
title = {Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {6},
pmid = {39789608},
issn = {1474-760X},
mesh = {Humans ; *Algorithms ; DNA, Ancient/analysis ; Genomics/methods ; Genome, Human ; Software ; },
abstract = {We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine and zenodo.org/records/14234666), masking reads only at positions possibly affected by PMD. We propose graph alignment coupled with bamRefine as a simple strategy to minimize data loss and bias, and urge the community to publish FASTQ files.},
}

Humans
*Algorithms
DNA, Ancient/analysis
Genomics/methods
Genome, Human
Software

@article {pmid39788103,
year = {2025},
author = {Kun, E and Sohail, M and Narasimhan, VM},
title = {The trait-specific timing of accelerated genomic change in the human lineage.},
journal = {Cell genomics},
volume = {5},
number = {1},
pages = {100740},
doi = {10.1016/j.xgen.2024.100740},
pmid = {39788103},
issn = {2666-979X},
mesh = {Humans ; Animals ; *Genome-Wide Association Study ; Neanderthals/genetics ; Evolution, Molecular ; Genome, Human/genetics ; Macaca mulatta/genetics ; Phenotype ; Genomics/methods ; Epigenesis, Genetic ; },
abstract = {Humans exhibit distinct characteristics compared to our primate and ancient hominin ancestors. To investigate genomic bursts in the evolution of these traits, we use two complementary approaches to examine enrichment among genome-wide association study loci spanning diseases and AI-based image-derived brain, heart, and skeletal tissue phenotypes with genomic regions reflecting four evolutionary divergence points. These regions cover epigenetic differences among humans and rhesus macaques, human accelerated regions (HARs), ancient selective sweeps, and Neanderthal-introgressed alleles. Skeletal traits such as pelvic width and limb proportions showed enrichment in evolutionary annotations that mirror morphological changes in the primate fossil record. Additionally, we observe enrichment of loci associated with the longitudinal fasciculus in human-gained epigenetic elements since macaques, the visual cortex in HARs, and the thalamus proper in Neanderthal-introgressed alleles, implying that associated cognitive functions such as language processing, decision-making, sensory signaling, and motor control are enriched at different evolutionary depths.},
}

Humans
Animals
*Genome-Wide Association Study
Neanderthals/genetics
Evolution, Molecular
Genome, Human/genetics
Macaca mulatta/genetics
Phenotype
Genomics/methods
Epigenesis, Genetic

@article {pmid39783862,
year = {2025},
author = {Lubbe, P and Rawlence, NJ and Dussex, N and Kardialsky, O and Knapp, M},
title = {Plio-Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open-Habitat Bird Lineages.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17648},
doi = {10.1111/mec.17648},
pmid = {39783862},
issn = {1365-294X},
support = {16-UOO-096//Marsden Fund/ ; 14-UOO-007//Royal Society Te Apārangi/ ; },
abstract = {In a changing environment, vacant niches can be filled either by adaptation of local taxa or range-expanding invading species. The relative tempo of these patterns is of key interest in the modern age of climate change. Aotearoa New Zealand has been a hotspot of biogeographic research for decades due to its long-term isolation and dramatic geological history. An island with high levels of faunal endemicity, it is a system well suited to studying the relative effects of in situ evolution versus dispersal in determining faunal assemblages, while its turbulent climate and geological history provide valuable insights into the evolutionary impacts of environmental changes. Such investigations are of urgent importance given predicted climate change and human impacts rapidly affecting environments globally. Here, we analyse the divergence dates of nearly all endemic Aotearoa New Zealand bird species from their overseas relatives to assess the role of environmental changes in driving speciation and colonisation, with special regard to cooling climate during the Pliocene and Pleistocene. We uncover a wave of colonisation events by Australian open-habitat adapted species since the Pliocene that peaked at the beginning of the Pleistocene. Furthermore, we highlight an even distribution of divergence dates in forest-adapted taxa through time, consistent with millions of years of extensive forest cover. Finally, we note parallels to the modern-day establishment of new bird populations from Australia and suggest this is largely influenced by anthropogenic land-use patterns. This research contributes to the growing body of work recognising the long-lasting impacts of Pleistocene climate change on Aotearoa New Zealand's avifauna, and reinforces biological invasions as a key evolutionary response to changing environmental conditions.},
}

@article {pmid39780098,
year = {2025},
author = {Pla-Díaz, M and Akgül, G and Molak, M and du Plessis, L and Panagiotopoulou, H and Doan, K and Bogdanowicz, W and Dąbrowski, P and Oziembłowski, M and Kwiatkowska, B and Szczurowski, J and Grzelak, J and Arora, N and Majander, K and González-Candelas, F and Schuenemann, VJ},
title = {Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {7},
pmid = {39780098},
issn = {1741-7007},
mesh = {*Treponema pallidum/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Humans ; },
abstract = {BACKGROUND: Treponemal diseases are a significant global health risk, presenting challenges to public health and severe consequences to individuals if left untreated. Despite numerous genomic studies on Treponema pallidum and the known possible biases introduced by the choice of the reference genome used for mapping, few investigations have addressed how these biases affect phylogenetic and evolutionary analysis of these bacteria. In this study, we ascertain the importance of selecting an appropriate genomic reference on phylogenetic and evolutionary analyses of T. pallidum.

RESULTS: We designed a multiple-reference-based (MRB) mapping strategy using four different reference genomes and compared it to traditional single-reference mapping. To conduct this comparison, we created a genomic dataset comprising 77 modern and ancient genomes from the three subspecies of T. pallidum, including a newly sequenced seventeenth century genome (35X mean coverage) of a syphilis-causing strain (designated as W86). Our findings show that recombination detection was consistent across different references, but the choice of reference significantly affected ancient genome reconstruction and phylogenetic inferences. The high-coverage W86 genome introduced in this study also provided a new calibration point for Bayesian molecular clock dating, improving the reconstruction of the evolutionary history of treponemal diseases. Additionally, we identified novel recombination events, positive selection targets, and refined dating estimates for key events in the species' history.

CONCLUSIONS: This study highlights the importance of considering methodological implications and reference genome bias in high-throughput sequencing-based whole-genome analysis of T. pallidum, especially of ancient or low-coverage samples, contributing to a deeper understanding of the treponemal pathogen and its subspecies.},
}

*Treponema pallidum/genetics
*Genome, Bacterial
*Phylogeny
*Genomics/methods
Humans

@article {pmid39776197,
year = {2025},
author = {Cuesta-Aguirre, DR and Amor-Jimenez, C and Malgosa, A and Santos, C},
title = {A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14061},
doi = {10.1111/1755-0998.14061},
pmid = {39776197},
issn = {1755-0998},
support = {Ref. 2017 SGR 1630; 2021 SGR 00186//Generalitat de Catalunya/ ; //European Social Fund Plus/ ; //Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya/ ; Ref. PGC2018-096666-B-100//Ministerio de Ciencia, Innovación y Universidades/ ; 2020 FI_B1 00641//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; },
abstract = {Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.},
}

@article {pmid39772917,
year = {2025},
author = {Kishida, T and Sawada, K and Namigata, S and Takabatake, T and Suzuki, M and Takezoe, N and Yamamoto, T and Nakanishi, T and Kitagawa, H},
title = {Hidden population turnover of small odontocetes in the northwestern North Pacific during the Holocene.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240525},
pmid = {39772917},
issn = {1744-957X},
support = {23K23956//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Dolphins ; Pacific Ocean ; Japan ; Porpoises/physiology ; Fossils ; Population Dynamics ; Radiometric Dating ; },
abstract = {Despite numerous studies on the rise and fall of terrestrial megafauna in the late Quaternary, knowledge about marine megafauna from this period remains limited. In this study, we performed radiocarbon dating and partial mitochondrial DNA sequencing from the skeletal remains of three species of small odontocetes (Pacific white-sided dolphins, Dall's porpoises and harbour porpoises) excavated from prehistoric archaeological sites around the Japanese shore dating back to 8500-1000 years ago (ya). Pacific white-sided dolphins that habituated the eastern coast of Hokkaido around 2000 ya belonged to different maternal groups than those from over 5000 ya and today. Furthermore, the species composition excavated from eastern Hokkaido sites varies between 5000 and 2000 ya. These findings suggest two significant population turnovers of small odontocetes on the east coast of Hokkaido, a transitional zone between the coastal area of East Asia and the offshore North Pacific. Notably, the first turnover, occurring between 5000 and 2000 ya, represents the oldest evidence of local population turnovers of marine megafauna during the late Quaternary.},
}

Animals
*DNA, Mitochondrial/genetics
Dolphins
Pacific Ocean
Japan
Porpoises/physiology
Fossils
Population Dynamics
Radiometric Dating

@article {pmid39765596,
year = {2024},
author = {Anaya, G and Garrido, JM and Riquelme, JA and Martínez, RM and Membrillo, A and Caro, JA and Pajuelo, A and Ruiz, A and Martín de la Cruz, JC and Molina, A},
title = {Ancient DNA Reveals the Earliest Evidence of Sheep Flocks During the Late Fourth and Third Millennia BC in Southern Iberia.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {24},
pages = {},
pmid = {39765596},
issn = {2076-2615},
abstract = {The Spanish Merino is the most significant sheep breed globally due to its economic and cultural importance in human history. It has also had a substantial influence on the development of other Merino and Merino-derived breeds. Historical sources indicate that crossbreeding to produce finer, higher-quality wool was already taking place in the south of the Iberian Peninsula during the Roman era. This evidence suggests that individuals with a racial pattern very similar to that of the modern Merino may have already existed on the peninsula. The presence of the skeletal remains of these animals at various human settlements dated to the late fourth and third millennia BC could provide insights into the genomics of these ancestral sheep. This study analyses ancient DNA extracted from nine skeletal remains from three archaeological sites in Southern Iberia, dated to the third millennium BC. The samples were sequenced and aligned with the ovine genome. The genetic distances observed among the samples indicate a closer relationship between several animals from the Marinaleda (Seville) and Grañena Baja (Jaén) sites. The study of the slaughter/death age profiles identified at La Minilla (La Rambla, Córdoba) suggests an approach centred on meat exploitation, while the data from Marinaleda (Seville) and Grañena Baja (Jaén) indicate the potential exploitation of secondary resources. A review of the composition of these small ruminant herds could provide insights into the type of secondary resource exploitation that may have been prioritised. Our aim is to investigate the presence of distinct production systems, differentiating between those aimed primarily at meat use and those focused on secondary products. This is the first approach to exploring the genetic evidence for sheep livestock related to its productive use during this period and in this geographical area.},
}

@article {pmid39762943,
year = {2025},
author = {Swiel, Y and Kelso, J and Peyrégne, S},
title = {Resolving the source of branch length variation in the Y chromosome phylogeny.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {4},
pmid = {39762943},
issn = {1474-760X},
mesh = {*Chromosomes, Human, Y/genetics ; Humans ; *Phylogeny ; Animals ; *Evolution, Molecular ; Genetic Variation ; Neanderthals/genetics ; Male ; },
abstract = {BACKGROUND: Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome lineages has been observed, notably amongst those that are highly diverged from the human reference Y chromosome. Understanding the origin of this variation, which has previously been attributed to changes in generation time, mutation rate, or efficacy of selection, is important for accurately reconstructing human evolutionary and demographic history.

RESULTS: Here, we analyze Y chromosomes from present-day and ancient modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination of branch lengths in the Y chromosome phylogeny.

CONCLUSION: We show that our approach allows us to estimate the age of ancient samples from Y chromosome sequence data and provide updated estimates for the time to the most recent common ancestor using the portion of the Y chromosome where the effect of reference bias is minimized.},
}

*Chromosomes, Human, Y/genetics
Humans
*Phylogeny
Animals
*Evolution, Molecular
Genetic Variation
Neanderthals/genetics
Male

@article {pmid39755798,
year = {2025},
author = {Llanos-Lizcano, A and Hämmerle, M and Sperduti, A and Sawyer, S and Zagorc, B and Özdoğan, KT and Guellil, M and Cheronet, O and Kuhlwilm, M and Pinhasi, R and Gelabert, P},
title = {Intra-individual variability in ancient plasmodium DNA recovery highlights need for enhanced sampling.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {757},
pmid = {39755798},
issn = {2045-2322},
support = {P-36433//Austrian Science Fund (FWF)/ ; FW547002//Austrian Science Fund (FWF)/ ; ISID_2019//Infravec/ ; 10.47379/VRG20001//Vienna Science and Technology Fund/ ; },
mesh = {Humans ; *Plasmodium falciparum/genetics ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Malaria, Falciparum/parasitology ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Malaria has been a leading cause of death in human populations for centuries and remains a major public health challenge in African countries, especially affecting children. Among the five Plasmodium species infecting humans, Plasmodium falciparum is the most lethal. Ancient DNA research has provided key insights into the origins, evolution, and virulence of pathogens that affect humans. However, extensive screening of ancient skeletal remains for Plasmodium DNA has shown that such genomic material is rare, with no studies so far addressing potential intra-individual variability. Consequently, the pool of ancient mitochondrial DNA (mtDNA) or genomic sequences for P. falciparum is extremely limited, with fewer than 20 ancient sequences available for genetic analysis, and no complete P. falciparum mtDNA from Classical antiquity published to date. To investigate intra-individual diversity and genetic origins of P. falciparum from the Roman period, we generated 39 sequencing libraries from multiple teeth and two from the femur of a Roman malaria-infected individual. The results revealed considerable variability in P. falciparum recovery across different dental samples within the individual, while the femur samples showed no preservation of Plasmodium DNA. The reconstructed 43-fold P. falciparum mtDNA genome supports the hypothesis of an Indian origin for European P. falciparum and suggests mtDNA continuity in Europe over the past 2000 years.},
}

Humans
*Plasmodium falciparum/genetics
*DNA, Ancient/analysis
*DNA, Mitochondrial/genetics
DNA, Protozoan/genetics
Malaria, Falciparum/parasitology
Genetic Variation
Phylogeny
Sequence Analysis, DNA/methods

@article {pmid39755464,
year = {2024},
author = {Chen, S and Xia, H and Chen, F},
title = {Paleogenomic research reintroduces extinct East Asian aurochs to our sights.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.12.028},
pmid = {39755464},
issn = {2095-9281},
}

@article {pmid39747910,
year = {2025},
author = {Gelabert, P and Oberreiter, V and Straus, LG and Morales, MRG and Sawyer, S and Marín-Arroyo, AB and Geiling, JM and Exler, F and Brueck, F and Franz, S and Cano, FT and Szedlacsek, S and Zelger, E and Hämmerle, M and Zagorc, B and Llanos-Lizcano, A and Cheronet, O and Tejero, JM and Rattei, T and Kraemer, SM and Pinhasi, R},
title = {A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {107},
pmid = {39747910},
issn = {2041-1723},
mesh = {Spain ; Humans ; *DNA, Ancient/analysis ; Animals ; *Caves ; *Fossils ; *Neanderthals/genetics ; Archaeology ; Phylogeny ; Carnivora/genetics ; DNA, Mitochondrial/genetics ; Geologic Sediments ; History, Ancient ; },
abstract = {Caves are primary sites for studying human and animal subsistence patterns and genetic ancestry throughout the Palaeolithic. Iberia served as a critical human and animal refugium in Europe during the Last Glacial Maximum (LGM), 26.5 to 19 thousand years before the present (cal kya). Therefore, it is a key location for understanding human and animal population dynamics during this event. We recover and analyse sedimentary ancient DNA (sedaDNA) data from the lower archaeological stratigraphic sequence of El Mirón Cave (Cantabria, Spain), encompassing the (1) Late Mousterian period, associated with Neanderthals, and (2) the Gravettian (c. 31.5 cal kya), Solutrean (c. 24.5-22 cal kya), and Initial Magdalenian (d. 21-20.5 cal kya) periods, associated with anatomically modern humans. We identify 28 animal taxa including humans. Fifteen of these taxa had not been identified from the archaeozoological (i.e., faunal) record, including the presence of hyenas in the Magdalenian. Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. Finally, we recover three human mtDNA sequences from the Solutrean levels. These sequences, along with published data, suggest mtDNA haplogroup continuity in Iberia throughout the Solutrean/Last Glacial Maximum period.},
}

Spain
Humans
*DNA, Ancient/analysis
Animals
*Caves
*Fossils
*Neanderthals/genetics
Archaeology
Phylogeny
Carnivora/genetics
DNA, Mitochondrial/genetics
Geologic Sediments
History, Ancient

@article {pmid39723543,
year = {2024},
author = {Atmore, LM and van der Jagt, I and Boilard, A and Häberle, S and Blevis, R and Dierickx, K and Quinlan, LM and Orton, DC and Hufthammer, AK and Barrett, JH and Star, B},
title = {The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA.},
journal = {Global change biology},
volume = {30},
number = {12},
pages = {e70010},
pmid = {39723543},
issn = {1365-2486},
support = {951649//H2020 European Research Council/ ; 813383//H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {*DNA, Ancient/analysis ; Animals ; *Fishes/genetics ; *Polymorphism, Single Nucleotide ; *Fisheries ; Archaeology ; Europe ; },
abstract = {Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools-including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)-that can accurately detect the population identity of individual fish. However, the biological relevance of such tools over longer periods of time remains unknown. Here, we demonstrate that diagnostic SNP panels designed for contemporary MSA in Atlantic herring have a millennium-long biological relevance and applicability. We assign the population identity of ancient Atlantic herring specimens-obtained through famously profitable historic fisheries-up to 1300 years old from eight archaeological sites across Europe. Analyzing contemporary and ancient whole-genome data, we obtain evidence for the long-term mixed-stock exploitation of Atlantic herring. Despite such mixed-stock exploitation, we exclusively identify autumn-spawning herring amongst these archaeological remains, indicative of a specific biological availability or cultural preference for certain herring ecotypes in the past. Moreover, our results show that herring demographic patterns were relatively stable until the dramatic disruptions and stock collapses during the 20th century. We find small but significant reductions in genetic diversity over time, indicating long-term evolutionary consequences from 20th-century stock declines. The long-term applicability of diagnostic SNP panels underscores their biological relevance and cost-effective application for the genetic monitoring of herring stocks and highlights the utility of ancient DNA to obtain insights in herring ecology and population dynamics.},
}

*DNA, Ancient/analysis
Animals
*Fishes/genetics
*Polymorphism, Single Nucleotide
*Fisheries
Archaeology
Europe

@article {pmid39723349,
year = {2025},
author = {Brandl, M and Martinez, MM and Hauzenberger, C and Filzmoser, P and Milić, B and Horejs, B},
title = {Unveiling Neolithic Economic Behavior: A Novel Approach to Chert Procurement at Çukuriçi Höyük, Western Anatolia.},
journal = {Journal of archaeological method and theory},
volume = {32},
number = {1},
pages = {16},
pmid = {39723349},
issn = {1573-7764},
abstract = {UNLABELLED: The expansion of the Neolithic way of life triggered the most profound changes in peoples' socioeconomic behaviors, including how critical resources for everyday life were managed. Recent research spearheaded by ancient DNA analysis has greatly contributed to our understanding of the main direction of Neolithisation spreading from western Anatolia into central Europe. Due to the diverse processes involved in Neolithisation, which resulted in a high diversity of regional and local phenomena, the underlying mechanisms of these developments are still largely unexplored. One of these mechanisms is economic behavior and resource management. Neolithic economic behavior is the result of social processes involving the physical actions of the procurement, processing, use, discard, and distribution of raw materials as well as finished products for utilitarian needs and to create and maintain social relations. Within this continuum, the key for tracing meaningful behavioral patterns is the identification of raw material procurement. Since stone tools are among the most ubiquitous and stable finds at Neolithic sites, they are ideally suited for this endeavor. Here, we present the results of a case study from the Neolithic site of Çukuriçi Höyük in western Anatolia tracing lithic raw material procurement. We employ a novel approach using geochemical provenance analyses coupled with quantitative technological and econometric methods. The key finding of this diachronic study covering almost 700 years revealed patterns of socioeconomic dynamics undetectable through conventional analytical approaches. We demonstrate that technological concepts fluctuate over time and are subject to innovations, whereas raw material procurement remains a stable element.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10816-024-09681-6.},
}

@article {pmid39715432,
year = {2025},
author = {Quilter, J and Harkins, K and Fanco Jordan, R and Marsh, E and Prieto, G and Verano, J and LeBlanc, S and Broomandkhoshbacht, N and Krigbaum, J and Fehren-Schmitz, L},
title = {Family relations of Moche elite burials on the North Coast of Peru (~500 CE): Analyses of the Señora de Cao and relatives.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2416321121},
pmid = {39715432},
issn = {1091-6490},
support = {NGS- HJ-142R-17//National Geographic Society (NGS)/ ; NGS-52945R-19//National Geographic Society (NGS)/ ; NGS-7844-05//National Geographic Society (NGS)/ ; NGS-7961-05//National Geographic Society (NGS)/ ; },
mesh = {Peru ; Humans ; *Burial/history ; Male ; *Archaeology ; Female ; Family Relations ; History, Medieval ; Family ; History, Ancient ; },
abstract = {The Moche archaeological culture flourished along Peru's North Coast between the 4th and 10th centuries CE and was characterized by a complex social hierarchy dominated by political and religious elites. Previous archaeological evidence suggests kinship was a key factor in maintaining political authority within Moche society. To test this hypothesis, we applied archaeological, genetic, and isotopic methods to examine familial relationships between six individuals, including the prominent Señora de Cao (~500 CE), buried together in a pyramid-like, painted temple, Huaca Cao Viejo, in the Chicama Valley, Peru. Our findings reveal that all six individuals were biologically related, with varying degrees of kinship. The Señora de Cao was interred with a sacrificed juvenile, identified as a possible niece, and at least one, and potentially two siblings and a grandparent in separate tombs nearby. One of the male siblings was accompanied in death by his sacrificed son. Isotopic analysis indicates that while most individuals had diets rich in maize and animal protein and spent their childhoods in or near the Chicama Valley, the sacrificed juvenile accompanying the Señora had a distinct diet and geographic origin. These results demonstrate that Moche elites were interred with family members, including some raised far from their parental homes. This supports the hypothesis that kinship was central to transmitting status and authority. Moreover, sacrificing family members to accompany deceased elites underscores the significance of ritual sacrifice in reinforcing familial ties and linking the deceased to both ancestors and the divine.},
}

Peru
Humans
*Burial/history
Male
*Archaeology
Female
Family Relations
History, Medieval
Family
History, Ancient

@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},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
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},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
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 = {2025},
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 = {35},
number = {1},
pages = {145-153.e4},
doi = {10.1016/j.cub.2024.11.029},
pmid = {39689706},
issn = {1879-0445},
mesh = {*Vitis/microbiology/genetics ; *Plant Diseases/microbiology ; *Phylogeny ; *Xylella/genetics/pathogenicity ; Genome, Fungal ; },
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.},
}

*Vitis/microbiology/genetics
*Plant Diseases/microbiology
*Phylogeny
*Xylella/genetics/pathogenicity
Genome, Fungal

@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 Martin, AM 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 Sampò, MC and Trucco, F and Pando, AP and Schjellerup Jørkov, ML and Courtaud, P and Peake, R and Bao, JFG and Parditka, G and Stenderup, J and Sjögren, KG and Staring, J and Olsen, L and Deyneko, IV and Pálfi, G and Aldana, PML 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 = {},
pmid = {39677618},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM153400/GM/NIGMS NIH HHS/United States ; },
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