@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

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

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

Humans
Czech Republic
*DNA, Ancient/analysis
History, Ancient
*Human Migration/history
Pedigree
Female
Neanderthals/genetics
Animals

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

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

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

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

@article {pmid39637852,
year = {2025},
author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N},
title = {The genomic origin of early maize in eastern North America.},
journal = {Cell},
volume = {188},
number = {1},
pages = {33-43.e16},
doi = {10.1016/j.cell.2024.11.003},
pmid = {39637852},
issn = {1097-4172},
mesh = {*Zea mays/genetics ; *Genome, Plant ; North America ; Domestication ; Genomics ; Phylogeny ; Mexico ; Amylose/metabolism ; },
abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.},
}

*Zea mays/genetics
*Genome, Plant
North America
Domestication
Genomics
Phylogeny
Mexico
Amylose/metabolism

@article {pmid39620136,
year = {2024},
author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, ÅJ and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD},
title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111076},
pmid = {39620136},
issn = {2589-0042},
abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.},
}

@article {pmid39613690,
year = {2025},
author = {Gaul, E and Spyrou, MA},
title = {Historical plague pandemics: perspectives from ancient DNA.},
journal = {Trends in microbiology},
volume = {33},
number = {1},
pages = {7-10},
doi = {10.1016/j.tim.2024.10.008},
pmid = {39613690},
issn = {1878-4380},
mesh = {*Plague/history/microbiology/epidemiology ; *Yersinia pestis/genetics ; *DNA, Ancient/analysis ; Humans ; *Pandemics/history ; Evolution, Molecular ; Animals ; DNA, Bacterial/genetics ; History, Ancient ; },
abstract = {Ancient DNA research has provided important insights into the evolutionary history of Yersinia pestis during the historical plague pandemics. Future work should prioritise a more diversified approach to sampling, to ensure a broader understanding of the factors underlying pandemic onset, spread, and impact across different regions and hosts.},
}

*Plague/history/microbiology/epidemiology
*Yersinia pestis/genetics
*DNA, Ancient/analysis
Humans
*Pandemics/history
Evolution, Molecular
Animals
DNA, Bacterial/genetics
History, Ancient

@article {pmid39612613,
year = {2024},
author = {Ferrando-Bernal, M and Brand, CM and Capra, JA},
title = {Inferring human phenotypes using ancient DNA: from molecules to populations.},
journal = {Current opinion in genetics & development},
volume = {90},
number = {},
pages = {102283},
doi = {10.1016/j.gde.2024.102283},
pmid = {39612613},
issn = {1879-0380},
abstract = {The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes - from the molecular to population scale - with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data.},
}

@article {pmid39606698,
year = {2024},
author = {Zagorc, B and Blanz, M and Gelabert, P and Sawyer, S and Oberreiter, V and Cheronet, O and Chen, HS and Carić, M and Visković, E and Olalde, I and Ivanova-Bieg, M and Novak, M and Reich, D and Pinhasi, R},
title = {Bioarchaeological Perspectives on Late Antiquity in Dalmatia: Paleogenetic, Dietary, and Population Studies of the Hvar - Radošević burial site.},
journal = {Archaeological and anthropological sciences},
volume = {16},
number = {9},
pages = {150},
pmid = {39606698},
issn = {1866-9557},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of those in that region. The Late Antique burial site of Hvar - Radošević, spanning the 3[rd] to 5[th] centuries CE, is located on the Croatian Dalmatian island of Hvar. Given the time frame and location on a busy marine trade route, the study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb and the remaining individuals buried in separate locations in the tomb's proximity. The study aims to provide a new perspective on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. The genetic analysis of the ancestral origins of the individuals buried at Hvar - Radošević revealed a diverse population reflective of the era's genetic variability. The identification of genetic outliers suggests a range of ancestries from distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis (δ[13]C and δ[15]N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties among this specific buried population.},
}

@article {pmid39592000,
year = {2024},
author = {Martínez-García, L and Pulido, A and Ferrari, G and Hufthammer, AK and Vedeler, M and Hirons, A and Kneale, C and Barrett, JH and Star, B},
title = {Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2035},
pages = {20242019},
pmid = {39592000},
issn = {1471-2954},
support = {//European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement, SeaChanges/ ; //Research Council of Norway projects 'FOODIMPACT'/ ; //4-OCEANS Synergy grant agreement/ ; },
mesh = {*Gadus morhua/genetics ; *DNA, Ancient/analysis ; Norway ; Animals ; History, Medieval ; Carbon Isotopes/analysis ; Fisheries ; Nitrogen Isotopes/analysis ; Archaeology ; History, 17th Century ; },
abstract = {Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ[13]C, δ[15]N, non-exchangeable δ[2]H and δ[34]S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ[13]C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries.},
}

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

@article {pmid39586186,
year = {2025},
author = {Zavala, EI and Rohlfs, RV and Moorjani, P},
title = {Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations.},
journal = {Forensic science international. Genetics},
volume = {75},
number = {},
pages = {103177},
doi = {10.1016/j.fsigen.2024.103177},
pmid = {39586186},
issn = {1878-0326},
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Benchmarking ; *Genotyping Techniques/standards/methods ; *High-Throughput Nucleotide Sequencing ; *DNA Degradation, Necrotic ; *Genotype ; Genetics, Population ; DNA Fingerprinting/methods ; Sequence Analysis, DNA ; Forensic Genetics/methods ; Software ; DNA/genetics ; },
abstract = {Advancements in sequencing and laboratory technologies have enabled forensic genetic analysis on increasingly low quality and degraded DNA samples. However, existing computational methods applied to genotyping and imputation for generating DNA profiles from degraded DNA have not been tested for forensic applications. Here we simulated sequencing data of varying qualities-coverage, fragment lengths, and deamination patterns-from forty individuals of diverse genetic ancestries. We used this dataset to test the performance of commonly used genotype and imputation methods (SAMtools, GATK, ATLAS, Beagle, and GLIMPSE) on five different SNP panels (MPS-plex, FORCE, two extended kinship panels, and the Human Origins array) that are used for forensic and population genetics applications. For genome mapping and variant calling with degraded DNA, we find use of parameters and methods (such as ATLAS) developed for ancient DNA analysis provides a marked improvement over conventional standards used for next generation sequencing analysis. We find that ATLAS outperforms GATK and SAMtools, achieving over 90 % genotyping accuracy for the four largest SNP panels with coverages greater than 10X. For lower coverages, decreased concordance rates are correlated with increased rates of heterozygosity. Genotype refinement and imputation improve the accuracy at lower coverages by leveraging population reference data. For all five SNP panels, we find that using a population reference panel representative of worldwide populations (e.g., the 1000 Genomes Project) results in increased genotype accuracies across genetic ancestries, compared to ancestry-matched population reference panels. Importantly, we find that the low SNP density of commonly used forensics SNP panels can impact the reliability and performance of genotype refinement and imputation. This highlights a critical trade-off between enhancing privacy by using panels with fewer SNPs and maintaining the effectiveness of genomic tools. We provide benchmarks and recommendations for analyzing degraded DNA from diverse populations with widely used genomic methods in forensic casework.},
}

Humans
*Polymorphism, Single Nucleotide
*Benchmarking
*Genotyping Techniques/standards/methods
*High-Throughput Nucleotide Sequencing
*DNA Degradation, Necrotic
*Genotype
Genetics, Population
DNA Fingerprinting/methods
Sequence Analysis, DNA
Forensic Genetics/methods
Software
DNA/genetics

@article {pmid39584937,
year = {2024},
author = {Bragazzi, NL and Lehr, T},
title = {Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {5},
number = {4},
pages = {669-691},
pmid = {39584937},
issn = {2673-3986},
abstract = {Big Epidemiology represents an innovative framework that extends the interdisciplinary approach of Big History to understand disease patterns, causes, and effects across human history on a global scale. This comprehensive methodology integrates epidemiology, genetics, environmental science, sociology, history, and data science to address contemporary and future public health challenges through a broad historical and societal lens. The foundational research agenda involves mapping the historical occurrence of diseases and their impact on societies over time, utilizing archeological findings, biological data, and historical records. By analyzing skeletal remains, ancient DNA, and artifacts, researchers can trace the origins and spread of diseases, such as Yersinia pestis in the Black Death. Historical documents, including chronicles and medical treatises, provide contextual narratives and quantitative data on past disease outbreaks, societal responses, and disruptions. Modern genetic studies reveal the evolution and migration patterns of pathogens and human adaptations to diseases, offering insights into co-evolutionary dynamics. This integrative approach allows for temporal and spatial mapping of disease patterns, linking them to social upheavals, population changes, and economic transformations. Big Epidemiology also examines the roles of environmental changes and socioeconomic factors in disease emergence and re-emergence, incorporating climate science, urban development, and economic history to inform public health strategies. The framework reviews historical and contemporary policy responses to pandemics, aiming to enhance future global health governance. By addressing ethical, legal, and societal implications, Big Epidemiology seeks to ensure responsible and effective epidemiological research and interventions. This approach aims to profoundly impact how we understand, prevent, and respond to diseases, leveraging historical perspectives to enrich modern scientific inquiry and global public health strategies.},
}

@article {pmid39577594,
year = {2024},
author = {Majewski, W and Szczuciński, W and Pawłowska, J and Szymczak-Żyła, M and Lubecki, L and Niedzielski, P},
title = {Environmental degradation and recovery after termination of whaling in sub-Antarctic fjord, South Georgia.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177536},
doi = {10.1016/j.scitotenv.2024.177536},
pmid = {39577594},
issn = {1879-1026},
mesh = {Antarctic Regions ; *Estuaries ; *Geologic Sediments/chemistry ; *Environmental Monitoring ; Ecosystem ; Water Pollutants, Chemical/analysis ; },
abstract = {Polar ecosystems are considered very fragile, however, due to the short observation record it is hard to assess the recovery processes of the coastal and fjord environments after a major disturbance. Here, we provide a unique case study from South Georgia (sub-Antarctic), an area seriously affected by the whaling industry. The study focuses on King Edward Cove, serving as a sheltered harbor for the former whaling station at Grytviken, as well as other parts of Cumberland Bay considered to represent generally pristine areas. We studied [210]Pb dated sediment cores, which were subjected to analysis of sediment geochemical composition, concentrations of anthropogenic organic markers and biomarkers, foraminiferal assemblage changes, as well as sedimentary ancient DNA. Three distinct phases have been identified. The oldest one, predating ca. 1970, recorded the whaling period, and was characterized by anoxic conditions, high organic carbon content, contamination with heavy metals, organic markers, distinct DNA signature and lack of foraminiferal microfossils. It took only a few years to establish a new ecosystem with a fully developed foraminiferal assemblage and decreased contamination characteristic for the middle phase (ca. 1970-2000). Ancient DNA suggests macro-zoobenthic recovery being delayed by a several years in comparison to benthic foraminifera. In the youngest period, around Cumberland Bay, the increase of iceberg rafted debris from rapidly retreating tidewater glaciers was noted, while the improved oxygen availability in bottom waters in King Edward Cove can be likely ascribed to frequent water mixing due to increasing traffic of large cruise vessels. The recorded pace of ecosystem recovery from major anthropogenic disturbance appears similar to that observed in the temperate fjords from the Northern Hemisphere, however, the effects of new anthropogenic threat and the ongoing climate change are already resulting in the new ecosystem disturbance.},
}

Antarctic Regions
*Estuaries
*Geologic Sediments/chemistry
*Environmental Monitoring
Ecosystem
Water Pollutants, Chemical/analysis

@article {pmid39567978,
year = {2024},
author = {Ravasini, F and Kabral, H and Solnik, A and de Gennaro, L and Montinaro, F and Hui, R and Delpino, C and Finocchi, S and Giroldini, P and Mei, O and Beck De Lotto, MA and Cilli, E and Hajiesmaeil, M and Pistacchia, L and Risi, F and Giacometti, C and Scheib, CL and Tambets, K and Metspalu, M and Cruciani, F and D'Atanasio, E and Trombetta, B},
title = {The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {292},
pmid = {39567978},
issn = {1474-760X},
mesh = {Italy ; Humans ; History, Ancient ; *Roman World/history ; DNA, Ancient/analysis ; Genome, Human ; Ethnicity/genetics ; Genetics, Population ; Genomics ; },
abstract = {BACKGROUND: The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9[th] and the 3[rd] century BCE, until the Roman colonization.

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

CONCLUSIONS: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula.},
}

Italy
Humans
History, Ancient
*Roman World/history
DNA, Ancient/analysis
Genome, Human
Ethnicity/genetics
Genetics, Population
Genomics

@article {pmid39567925,
year = {2024},
author = {Lv, M and Ma, H and Wang, R and Li, H and Zhang, X and Zhang, W and Zeng, Y and Qin, Z and Zhai, H and Lou, Y and Lin, Y and Tao, L and He, H and Yang, X and Zhu, K and Zhou, Y and Wang, CC},
title = {Ancient genomes from the Tang Dynasty capital reveal the genetic legacy of trans-Eurasian communication at the eastern end of Silk Road.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {267},
pmid = {39567925},
issn = {1741-7007},
mesh = {Humans ; China ; *Genome, Human ; DNA, Ancient/analysis ; History, Ancient ; Asian People/genetics ; Gene Flow ; Genetic Variation ; Human Migration/history ; },
abstract = {BACKGROUND: Ancient Chang'an in the Tang Dynasty (618-907 AD) was one of the world's largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang'an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city.

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

CONCLUSIONS: Our study underlined the widespread distribution of the YR_LN-related ancestry alongside the Silk Road within the territory of China during the historical era and provided direct evidence of trans-Eurasian communication in Chang'an from a genetic perspective.},
}

Humans
China
*Genome, Human
DNA, Ancient/analysis
History, Ancient
Asian People/genetics
Gene Flow
Genetic Variation
Human Migration/history

@article {pmid39567757,
year = {2025},
author = {Mathov, Y and Nissim-Rafinia, M and Leibson, C and Galun, N and Marques-Bonet, T and Kandel, A and Liebergal, M and Meshorer, E and Carmel, L},
title = {Inferring DNA methylation in non-skeletal tissues of ancient specimens.},
journal = {Nature ecology & evolution},
volume = {9},
number = {1},
pages = {153-165},
pmid = {39567757},
issn = {2397-334X},
support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; 61739//John Templeton Foundation (JTF)/ ; },
mesh = {*DNA Methylation ; Humans ; *DNA, Ancient/analysis ; Algorithms ; Animals ; Fossils ; },
abstract = {Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.},
}

*DNA Methylation
Humans
*DNA, Ancient/analysis
Algorithms
Animals
Fossils

@article {pmid39532856,
year = {2024},
author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM},
title = {Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9772},
pmid = {39532856},
issn = {2041-1723},
mesh = {*DNA, Ancient/analysis ; *Selection, Genetic ; Humans ; Europe ; *Genetic Drift ; *Gene Frequency ; Haplotypes/genetics ; Animals ; Lactase/genetics ; Genetics, Population/methods ; Evolution, Molecular ; Genotype ; },
abstract = {Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.},
}

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

@article {pmid39515325,
year = {2024},
author = {Pilli, E and Vai, S and Moses, VC and Morelli, S and Lari, M and Modi, A and Diroma, MA and Amoretti, V and Zuchtriegel, G and Osanna, M and Kennett, DJ and George, RJ and Krigbaum, J and Rohland, N and Mallick, S and Caramelli, D and Reich, D and Mittnik, A},
title = {Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {5307-5318.e7},
pmid = {39515325},
issn = {1879-0445},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *DNA, Ancient/analysis ; Male ; Female ; History, Ancient ; Archaeology ; Roman World/history ; Adult ; },
abstract = {The eruption of Somma-Vesuvius in 79 CE buried several nearby Roman towns, killing the inhabitants and burying under pumice lapilli and ash deposits a unique set of civil and private buildings, monuments, sculptures, paintings, and mosaics that provide a rich picture of life in the empire. The eruption also preserved the forms of many of the dying as the ash compacted around their bodies. Although the soft tissue decayed, the outlines of the bodies remained and were recovered by excavators centuries later by filling the cavities with plaster. From skeletal material embedded in the casts, we generated genome-wide ancient DNA and strontium isotopic data to characterize the genetic relationships, sex, ancestry, and mobility of five individuals. We show that the individuals' sexes and family relationships do not match traditional interpretations, exemplifying how modern assumptions about gendered behaviors may not be reliable lenses through which to view data from the past. For example, an adult wearing a golden bracelet with a child on their lap-often interpreted as mother and child-is genetically an adult male biologically unrelated to the child. Similarly, a pair of individuals who were thought to have died in an embrace-often interpreted as sisters-included at least one genetic male. All Pompeiians with genome-wide data consistently derive their ancestry largely from recent immigrants from the eastern Mediterranean, as has also been seen in contemporaneous ancient genomes from the city of Rome, underscoring the cosmopolitanism of the Roman Empire in this period.},
}

Humans
*DNA, Ancient/analysis
Male
Female
History, Ancient
Archaeology
Roman World/history
Adult

@article {pmid39514086,
year = {2024},
author = {Geršak, ŽM and Golob, A and Kravanja, P and Concato, M and Leskovar, T and Pajnič, IZ},
title = {Patellae as a source of DNA in forensic and archaeological analysis.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {39514086},
issn = {1437-1596},
support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; },
abstract = {Analysing genetic material from skeletonised human remains has become valuable in forensic and archaeological contexts. While the petrous bone is often preferred for DNA extraction, its availability is not guaranteed, and because of destructive sampling, it is not frequently used in forensic cases. This study explores the potential of patellae as an alternative source of bone material for genetic investigations. Forty-five patellae were sampled from a post-World War II mass grave and an archaeological Christian cemetery dated from the 13th to 19th centuries. A full demineralisation extraction method was used to obtain the DNA, and real-time PCR quantification was used to determine the quantity and quality of DNA. To evaluate the suitability of patellae for forensic and archaeological analyses, short tandem repeat (STR) typing was performed using the ESI17 Fast PCR amplification kit (Promega). To explore the difference in DNA yield, DNA degradation and STR typing success between the post-World War II and archaeological patellae, statistical analysis was performed. The results revealed significantly higher DNA yield and STR typing success in WWII patellae and higher degradation of DNA in archaeological patellae, highlighting the impact of environmental exposure time on genetic material preservation. Almost all WWII patellae achieved a high success rate in STR typing with full profiles generated. More than half of the archaeological patellae showed high STR typing performance and highly informative partial profiles were obtained, indicating the suitability of patellae not only for forensic purposes but also for archaeological genetic analyses.},
}

@article {pmid39509486,
year = {2024},
author = {Chandrashekhar, V},
title = {India looks to ancient DNA to track migrations.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6722},
pages = {607},
doi = {10.1126/science.adu4090},
pmid = {39509486},
issn = {1095-9203},
mesh = {Humans ; Bone and Bones ; *DNA, Ancient/analysis ; *Human Migration/history ; India ; *South Asian People/history ; },
abstract = {Findings from analyses of human bones could be politically sensitive.},
}

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

@article {pmid39500721,
year = {2024},
author = {Hong, JH and Fujita, H and Kim, J and Shin, DH},
title = {Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis.},
journal = {Anatomy & cell biology},
volume = {},
number = {},
pages = {},
doi = {10.5115/acb.24.125},
pmid = {39500721},
issn = {2093-3665},
abstract = {Ancient DNA (aDNA) analysis has developed rapidly since it first emerged in the 1980s, becoming an almost indispensable tool in anthropological and archaeological sciences. Earlier aDNA study was based on the polymerase chain reaction (PCR) technique, with which, unfortunately, modern DNA contamination and other authenticity issues were often incurred. These technical hurdles were soon overcome by application of advancements in the forms of the next generation sequencing (NGS) technique and others. However, since NGS requires money, time, and, in the case of large projects, manpower as well, genetic analysis of some ancient samples considered to be insignificant is commonly delayed or, in the worst cases, neglected entirely. We acknowledge that as a diagnostic tool in aDNA analysis, PCR is less accurate than NGS and more easily affected by modern DNA contamination; but it also has advantages, such as simplicity, time-saving, and greater ease of interpretation, among others. The role of PCR in aDNA analysis, then, should be reconsidered.},
}

@article {pmid39493412,
year = {2024},
author = {Sedig, J and Snow, M and Searcy, M and Diaz, JLP and LeBlanc, S and Ramos, F and Eccles, L and Reich, D},
title = {High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico.},
journal = {Antiquity},
volume = {98},
number = {400},
pages = {1023-1039},
pmid = {39493412},
issn = {0003-598X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.},
}

@article {pmid39481771,
year = {2025},
author = {Brambilla, L and Ibarra, DA and Barboza, MC and Bresso, EG and Rosano, G and Pérez, G and Straccia, P and Scian, RD and Brun, LR},
title = {Mitochondrial genome of Neuryurus rudis (Xenarthra, Cingulata); contribution to phylogeny and origin of glyptodonts.},
journal = {Gene},
volume = {936},
number = {},
pages = {149059},
doi = {10.1016/j.gene.2024.149059},
pmid = {39481771},
issn = {1879-0038},
mesh = {*Phylogeny ; Animals ; *Genome, Mitochondrial ; Evolution, Molecular ; Xenarthra/genetics/classification ; Fossils ; DNA, Mitochondrial/genetics ; Armadillos/genetics ; },
abstract = {The remarkable glyptodonts have sparked the interest of evolutionary biologists since the 19th century, in their attempts to elucidate the phylogenetic relationships among the various species of these armored giants and their relationship with other xenarthrans. In recent years, the molecular analysis of the first glyptodont has included them within the cingulates, as a special group of armadillos that lost the mobility of the bands of their armor during their evolutionary history. In this research, we obtained the mitochondrial DNA sequence of the elusive and poorly known glyptodont Neuryurus rudis, inferring its phylogenetic position with respect to the glyptodont Doedicurus sp. and extant armadillos. This study reaffirms glyptodonts as a subgroup of cingulates, with Neuryurus and Doedicurus sharing a common ancestor from the late Oligocene or early Miocene and traces the group's origin back to an armadillo ancestor in the Eocene.},
}

*Phylogeny
Animals
*Genome, Mitochondrial
Evolution, Molecular
Xenarthra/genetics/classification
Fossils
DNA, Mitochondrial/genetics
Armadillos/genetics

@article {pmid39478221,
year = {2024},
author = {Ghalichi, A and Reinhold, S and Rohrlach, AB and Kalmykov, AA and Childebayeva, A and Yu, H and Aron, F and Semerau, L and Bastert-Lamprichs, K and Belinskiy, AB and Berezina, NY and Berezin, YB and Broomandkhoshbacht, N and Buzhilova, AP and Erlikh, VR and Fehren-Schmitz, L and Gambashidze, I and Kantorovich, AR and Kolesnichenko, KB and Lordkipanidze, D and Magomedov, RG and Malek-Custodis, K and Mariaschk, D and Maslov, VE and Mkrtchyan, L and Nagler, A and Fazeli Nashli, H and Ochir, M and Piotrovskiy, YY and Saribekyan, M and Sheremetev, AG and Stöllner, T and Thomalsky, J and Vardanyan, B and Posth, C and Krause, J and Warinner, C and Hansen, S and Haak, W},
title = {The rise and transformation of Bronze Age pastoralists in the Caucasus.},
journal = {Nature},
volume = {635},
number = {8040},
pages = {917-925},
pmid = {39478221},
issn = {1476-4687},
mesh = {*Agriculture/history ; *Archaeology ; Eastern European People/genetics ; *Farmers/history ; *Gene Flow ; *Genetics, Population ; *Genome, Human/genetics ; Genomics ; Georgia (Republic)/ethnology ; *Grassland ; History, Ancient ; Human Migration/history ; Hunting/history ; Russia/ethnology ; West Asian People/genetics ; },
abstract = {The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age[1] and the birthplace of the earliest steppe pastoralist societies[2]. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies[3-5]. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry[4,6] in the north, and a distinct Caucasus hunter-gatherer ancestry[7] with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex[8]. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.},
}

*Agriculture/history
*Archaeology
Eastern European People/genetics
*Farmers/history
*Gene Flow
*Genetics, Population
*Genome, Human/genetics
Genomics
Georgia (Republic)/ethnology
*Grassland
History, Ancient
Human Migration/history
Hunting/history
Russia/ethnology
West Asian People/genetics

@article {pmid39478147,
year = {2024},
author = {Yavuz, OE and Oxilia, G and Silvestrini, S and Tassoni, L and Reiter, E and Drucker, DG and Talamo, S and Fontana, F and Benazzi, S and Posth, C},
title = {Biomolecular analysis of the Epigravettian human remains from Riparo Tagliente in northern Italy.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1415},
pmid = {39478147},
issn = {2399-3642},
mesh = {Italy ; Humans ; *Radiometric Dating ; Fossils ; Male ; Body Remains/chemistry ; Femur/chemistry/metabolism ; },
abstract = {The Epigravettian human remains from Riparo Tagliente in northern Italy represent some of the earliest evidence of human occupation in the southern Alpine slopes after the Last Glacial Maximum. Genomic analyses of the 17,000-year-old Tagliente 2 mandible revealed the oldest presence of a genetic profile with affinities to the Near East in the Italian peninsula, which later became the most widespread hunter-gatherer ancestry across Europe. However, a comparable biomolecular characterization of the Tagliente 1 burial remains unavailable, preventing us from defining its biological relationships with Tagliente 2. Here, we apply paleogenomic, isotopic, and radiocarbon dating analyses on a femur fragment of Tagliente 1 and compare the reconstructed data with previously reported results from Tagliente 2. Despite their different isotopic signatures and non-overlapping radiocarbon dates, we reveal that the two human remains belong to the same male individual. We determine that the distinct isotopic values can be explained by different dietary practices during lifetime, whereas the non-overlapping radiocarbon dates can be caused by minimal radiocarbon contamination, possibly deriving from chemical treatments for conservation purposes. These findings highlight the importance of interdisciplinary biomolecular studies in offering new perspectives on the Palaeolithic fossil record and addressing long-standing bioarchaeological questions.},
}

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

@article {pmid39468234,
year = {2024},
author = {Słowakiewicz, M and Borkowski, A and Perri, E and Działak, P and Tagliasacchi, E and Gradziński, M and Kele, S and Reuning, L and Kibblewhite, T and Whitaker, F and Reid, RP and Tucker, ME},
title = {Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {25889},
pmid = {39468234},
issn = {2045-2322},
support = {2019/35/B/ST10/02190//Narodowe Centrum Nauki/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; },
mesh = {*Biofilms/growth & development ; *Fresh Water/microbiology/virology ; *Calcium Carbonate/metabolism/chemistry ; Geologic Sediments/microbiology/virology ; Viruses/genetics/metabolism ; Principal Component Analysis ; Metagenomics/methods ; },
abstract = {Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.},
}

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

@article {pmid39440313,
year = {2024},
author = {Malyarchuk, BA},
title = {Genetic aspects of lactase deficiency in indigenous populations of Siberia.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {6},
pages = {650-658},
doi = {10.18699/vjgb-24-72},
pmid = {39440313},
issn = {2500-0462},
abstract = {The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.},
}

@article {pmid39438503,
year = {2024},
author = {Feinauer, IS and Lord, E and von Seth, J and Xenikoudakis, G and Ersmark, E and Dalén, L and Meleg, IN},
title = {Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24917},
pmid = {39438503},
issn = {2045-2322},
mesh = {*Ursidae/genetics ; Animals ; Scandinavian and Nordic Countries ; *Genome, Mitochondrial ; *Haplotypes ; *Genetic Variation ; *Phylogeny ; Female ; DNA, Mitochondrial/genetics ; Genetics, Population ; },
abstract = {Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.},
}

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

@article {pmid39437846,
year = {2024},
author = {Kaptan, D and Atağ, G and Vural, KB and Morell Miranda, P and Akbaba, A and Yüncü, E and Buluktaev, A and Abazari, MF and Yorulmaz, S and Kazancı, DD and Küçükakdağ Doğu, A and Çakan, YG and Özbal, R and Gerritsen, F and De Cupere, B and Duru, R and Umurtak, G and Arbuckle, BS and Baird, D and Çevik, Ö and Bıçakçı, E and Gündem, CY and Pişkin, E and Hachem, L and Canpolat, K and Fakhari, Z and Ochir-Goryaeva, M and Kukanova, V and Valipour, HR and Hoseinzadeh, J and Küçük Baloğlu, F and Götherström, A and Hadjisterkotis, E and Grange, T and Geigl, EM and Togan, İZ and Günther, T and Somel, M and Özer, F},
title = {The Population History of Domestic Sheep Revealed by Paleogenomes.},
journal = {Molecular biology and evolution},
volume = {41},
number = {10},
pages = {},
pmid = {39437846},
issn = {1537-1719},
support = {772390/ERC_/European Research Council/International ; //University Paris Diderot/ ; DGE20111123014//Fondation pour la Recherche Médicale/ ; 11015901//Région Ile-de-France/ ; 2017-05267//Swedish Research Council Vetenskapsrådet/ ; F20-0274//Helge Ax:son Johnson Stiftelse/ ; 075-15-2019-1879//Government of Russian Federation/ ; BCS-0530699//National Science Foundation/ ; },
mesh = {Animals ; *Sheep, Domestic/genetics ; *Domestication ; Sheep/genetics ; Genome ; DNA, Ancient/analysis ; Europe ; },
abstract = {Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not.},
}

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

@article {pmid39432055,
year = {2025},
author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS},
title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14029},
pmid = {39432055},
issn = {1755-0998},
support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; },
abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.},
}

*DNA, Ancient/analysis
DNA Damage
Sequence Analysis, DNA/methods
Likelihood Functions
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
Humans

@article {pmid39429655,
year = {2024},
author = {Farhud, DD and Azari, M and Rahbar, M},
title = {Tuberculosis in Human Bones from 4000 Years Ago, Iran.},
journal = {Iranian journal of public health},
volume = {53},
number = {9},
pages = {2103-2112},
pmid = {39429655},
issn = {2251-6093},
abstract = {BACKGROUND: Tuberculosis is caused by a bacterium called Mycobacterium tuberculosis, which is a contagious and infectious disease; in the first stage, it destroys the lungs and in the next stage other body organs, such as the spine and long bones. This disease is transmitted through an infected person and due to the weakness of the immune system, the infection intensifies. Tuberculosis has two stages: low activity and high activity. In this article, we have discussed the signs of tuberculosis destruction with high intensity on the bones of prehistory human remains.

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

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

CONCLUSION: We found tuberculosis among the bones. This common ancient disease existed even among Neanderthals.},
}

@article {pmid39415996,
year = {2024},
author = {Rubin, J and van Waaij, J and Kraft, L and Sirén, J and Sackett, PW and Renaud, G},
title = {SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39415996},
issn = {2692-8205},
support = {R01 HG010485/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; },
abstract = {Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C→T and G→A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI, an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.},
}

@article {pmid39408629,
year = {2024},
author = {Herbert, A},
title = {A Compendium of G-Flipon Biological Functions That Have Experimental Validation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
pmid = {39408629},
issn = {1422-0067},
mesh = {*G-Quadruplexes ; Animals ; Humans ; Transcription Factors/metabolism/genetics ; DNA/metabolism/genetics ; RNA, Untranslated/genetics/metabolism ; DNA Repair ; Caenorhabditis elegans/genetics/metabolism ; },
abstract = {As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G3N1-7)3G3, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate.},
}

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

@article {pmid39395415,
year = {2024},
author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS},
title = {Compacted hair in broken teeth reveals dietary prey of historic lions.},
journal = {Current biology : CB},
volume = {34},
number = {21},
pages = {5104-5111.e4},
doi = {10.1016/j.cub.2024.09.029},
pmid = {39395415},
issn = {1879-0445},
mesh = {Animals ; *Lions/genetics ; *Hair/chemistry ; Kenya ; Predatory Behavior ; Tooth/chemistry ; Diet/veterinary ; Phylogeny ; },
abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.},
}

Animals
*Lions/genetics
*Hair/chemistry
Kenya
Predatory Behavior
Tooth/chemistry
Diet/veterinary
Phylogeny

@article {pmid39390557,
year = {2024},
author = {Sawyer, S and Gelabert, P and Yakir, B and Llanos-Lizcano, A and Sperduti, A and Bondioli, L and Cheronet, O and Neugebauer-Maresch, C and Teschler-Nicola, M and Novak, M and Pap, I and Szikossy, I and Hajdu, T and Moiseyev, V and Gromov, A and Zariņa, G and Meshorer, E and Carmel, L and Pinhasi, R},
title = {Improved detection of methylation in ancient DNA.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {261},
pmid = {39390557},
issn = {1474-760X},
mesh = {*DNA Methylation ; *DNA, Ancient/analysis ; Humans ; *Sulfites ; Sequence Analysis, DNA/methods ; },
abstract = {Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.},
}

*DNA Methylation
*DNA, Ancient/analysis
Humans
*Sulfites
Sequence Analysis, DNA/methods

@article {pmid39383567,
year = {2025},
author = {Wu, Y and Ma, Q and Han, B and Shen, Y and Wen, S},
title = {Familial hypodontia in bronze age Northwest China (1046-771BC).},
journal = {Archives of oral biology},
volume = {169},
number = {},
pages = {106104},
doi = {10.1016/j.archoralbio.2024.106104},
pmid = {39383567},
issn = {1879-1506},
mesh = {Humans ; China/epidemiology ; *Anodontia/genetics/epidemiology ; Male ; History, Ancient ; Female ; DNA, Ancient/analysis ; Cemeteries ; Prevalence ; },
abstract = {OBJECTIVE: This research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals.

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

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

CONCLUSIONS: The prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals.},
}

Humans
China/epidemiology
*Anodontia/genetics/epidemiology
Male
History, Ancient
Female
DNA, Ancient/analysis
Cemeteries
Prevalence

@article {pmid39357284,
year = {2024},
author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C},
title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.},
journal = {Journal of human evolution},
volume = {196},
number = {},
pages = {103599},
doi = {10.1016/j.jhevol.2024.103599},
pmid = {39357284},
issn = {1095-8606},
mesh = {*Neanderthals/anatomy & histology/genetics ; Animals ; France ; *Fossils/anatomy & histology ; Male ; Tooth/anatomy & histology ; Dentition ; X-Ray Microtomography ; },
abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.},
}

*Neanderthals/anatomy & histology/genetics
Animals
France
*Fossils/anatomy & histology
Male
Tooth/anatomy & histology
Dentition
X-Ray Microtomography

@article {pmid39345259,
year = {2024},
author = {Wu, X and Ding, B and Nie, L and Zhong, C and Liu, P and Liang, J and Wang, L and Gao, X and Wei, J and Zhou, Y},
title = {Genomic insights into the complex demographic history and inbreeding phenomena during Zhou Dynasty on the Central Plains of China.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1471740},
pmid = {39345259},
issn = {1664-302X},
abstract = {In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population's genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization's multiethnic.},
}

@article {pmid39343094,
year = {2024},
author = {Wei, X and Zhang, M and Min, R and Jiang, Z and Xue, J and Zhu, Z and Yuan, H and Li, X and Zhao, D and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Wu, X and Hu, C and Ma, M and Liu, X and Wan, Y and Yang, F and Zhou, R and Kang, L and Dong, G and Ping, W and Wang, T and Miao, B and Bai, F and Zheng, Y and Liu, Y and Yang, MA and Wang, W and Bennett, EA and Fu, Q},
title = {Neolithic to Bronze Age human maternal genetic history in Yunnan, China.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.09.013},
pmid = {39343094},
issn = {1673-8527},
abstract = {Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Xizang, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 and 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.},
}

@article {pmid39333293,
year = {2024},
author = {Petrova, TV and Panitsina, VA and Bodrov, SY and Abramson, NI},
title = {The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22259},
pmid = {39333293},
issn = {2045-2322},
support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Phylogeny ; *Genome, Mitochondrial ; Endangered Species ; Rodentia/genetics/classification ; },
abstract = {Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.},
}

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

@article {pmid39326418,
year = {2024},
author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q},
title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.},
journal = {Cell},
volume = {187},
number = {21},
pages = {5891-5900.e8},
doi = {10.1016/j.cell.2024.08.008},
pmid = {39326418},
issn = {1097-4172},
mesh = {Humans ; *Cheese/microbiology ; *Lactobacillus/genetics ; Kefir/microbiology ; History, Ancient ; Phylogeny ; China ; Biological Evolution ; Fermentation ; Asia, Eastern ; },
abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.},
}

Humans
*Cheese/microbiology
*Lactobacillus/genetics
Kefir/microbiology
History, Ancient
Phylogeny
China
Biological Evolution
Fermentation
Asia, Eastern

@article {pmid39322456,
year = {2024},
author = {Hou, J and Guan, X and Xia, X and Lyu, Y and Liu, X and Mazei, Y and Xie, P and Chang, F and Zhang, X and Chen, J and Li, X and Zhang, F and Jin, L and Luo, X and Sinding, MS and Sun, X and Achilli, A and Migliore, NR and Zhang, D and Lenstra, JA and Han, J and Fu, Q and Liu, X and Zhang, X and Chen, N and Lei, C and Zhang, H},
title = {Evolution and legacy of East Asian aurochs.},
journal = {Science bulletin},
volume = {69},
number = {21},
pages = {3425-3433},
doi = {10.1016/j.scib.2024.09.016},
pmid = {39322456},
issn = {2095-9281},
mesh = {Animals ; Cattle/genetics ; Asia, Eastern ; Biological Evolution ; Evolution, Molecular ; Gene Flow ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; *Phylogeny ; Phylogeography ; *Ruminants/genetics ; Extinction, Biological ; },
abstract = {Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.},
}

Animals
Cattle/genetics
Asia, Eastern
Biological Evolution
Evolution, Molecular
Gene Flow
Genetic Variation/genetics
Genome, Mitochondrial/genetics
*Phylogeny
Phylogeography
*Ruminants/genetics
Extinction, Biological

@article {pmid39314480,
year = {2024},
author = {Akbari, A and Barton, AR and Gazal, S and Li, Z and Kariminejad, M and Perry, A and Zeng, Y and Mittnik, A and Patterson, N and Mah, M and Zhou, X and Price, AL and Lander, ES and Pinhasi, R and Rohland, N and Mallick, S and Reich, D},
title = {Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39314480},
issn = {2692-8205},
support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.},
}

@article {pmid39305897,
year = {2024},
author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M},
title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.},
journal = {Current biology : CB},
volume = {34},
number = {20},
pages = {4650-4661.e4},
doi = {10.1016/j.cub.2024.08.047},
pmid = {39305897},
issn = {1879-0445},
mesh = {*DNA, Ancient/analysis ; Animals ; *Archaeology ; Forests ; Sheep/genetics ; Microbiota/genetics ; Agriculture/history ; Geologic Sediments/analysis ; Europe ; },
abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."},
}

*DNA, Ancient/analysis
Animals
*Archaeology
Forests
Sheep/genetics
Microbiota/genetics
Agriculture/history
Geologic Sediments/analysis
Europe

@article {pmid39302159,
year = {2024},
author = {Leppälä, K and da Silva Coelho, FA and Richter, M and Albert, VA and Lindqvist, C},
title = {Five-leaf Generalizations of the D-statistic Reveal the Directionality of Admixture.},
journal = {Molecular biology and evolution},
volume = {41},
number = {11},
pages = {},
pmid = {39302159},
issn = {1537-1719},
mesh = {*Models, Genetic ; Polymorphism, Single Nucleotide ; Hybridization, Genetic ; Animals ; Phylogeny ; Genetic Introgression ; Alleles ; },
abstract = {Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use five leaves to evaluate admixture. Among these, the DFOIL method ("FOIL", a mnemonic for "First-Outer-Inner-Last"), which tests allelic patterns on the "symmetric" tree S=(((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the "asymmetric" tree A=((((1,2),3),4),5) and the "quasisymmetric" tree Q=(((1,2),3),(4,5)), which can considerably supplement the "symmetric" S=(((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently, DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality.},
}

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

@article {pmid39300260,
year = {2024},
author = {Gretzinger, J and Gibbon, VE and Penske, SE and Sealy, JC and Rohrlach, AB and Salazar-García, DC and Krause, J and Schiffels, S},
title = {9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter.},
journal = {Nature ecology & evolution},
volume = {8},
number = {11},
pages = {2121-2134},
pmid = {39300260},
issn = {2397-334X},
mesh = {Humans ; South Africa ; *DNA, Ancient/analysis ; Genetic Variation ; },
abstract = {Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 BP, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.},
}

Humans
South Africa
*DNA, Ancient/analysis
Genetic Variation

@article {pmid39294129,
year = {2024},
author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS},
title = {Towards predicting the geographical origin of ancient samples with metagenomic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21794},
pmid = {39294129},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; },
abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.},
}

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

@article {pmid39292210,
year = {2024},
author = {Atağ, G and Waldman, S and Carmi, S and Somel, M},
title = {An explanation for the sister repulsion phenomenon in Patterson's f-statistics.},
journal = {Genetics},
volume = {228},
number = {3},
pages = {},
pmid = {39292210},
issn = {1943-2631},
support = {772390//H2020 ERC Consolidator/ ; 952317//H2020-WIDESPREAD-05-2020 TWINNING/ ; //Scientific and Technological Research Council of Turkey (TÜBİTAK)/ ; },
mesh = {Humans ; *Models, Genetic ; *Gene Flow ; *Gene Frequency ; Genetics, Population ; Genome, Human ; Greece ; },
abstract = {Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.},
}

Humans
*Models, Genetic
*Gene Flow
*Gene Frequency
Genetics, Population
Genome, Human
Greece

@article {pmid39291130,
year = {2024},
author = {Song, G and Wang, Y and Ruan, Q and Cai, DE},
title = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {9},
pages = {1232-1236},
pmid = {39291130},
issn = {2380-2359},
abstract = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.},
}

@article {pmid39280844,
year = {2024},
author = {Modina, SA and Kusliy, MA and Malikov, DG and Molodtseva, AS},
title = {Phylogeography of the woolly mammoth (Mammuthus primigenius) in the Minusinsk Depression of southern Siberia in the Late Pleistocene.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {5},
pages = {571-577},
doi = {10.18699/vjgb-24-63},
pmid = {39280844},
issn = {2500-0462},
abstract = {To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100-150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.},
}

@article {pmid39279684,
year = {2024},
author = {Pan, J and Liu, X and Baca, M and Calvière-Tonasso, L and Schiavinato, S and Chauvey, L and Tressières, G and Perdereau, A and Aury, JM and Oliveira, PH and Wincker, P and Abdykanova, A and Arsuaga, JL and Bayarsaikhan, J and Belinskiy, AB and Carbonell, E and Davoudi, H and Lira Garrido, J and Gilbert, AS and Hermes, T and Warinner, C and Kalmykov, AA and Lordkipanidze, D and Mackiewicz, P and Mohaseb, AF and Richter, K and Sayfullaev, N and Shapiro, B and Shnaider, S and Southon, J and Stefaniak, K and Summers, GD and van Asperen, EN and Vanishvili, N and Hill, EA and Kuznetsov, P and Reinhold, S and Hansen, S and Mashkour, M and Berthon, R and Taylor, WTT and Houle, JL and Hekkala, E and Popović, D and Orlando, L},
title = {Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.},
journal = {Molecular ecology},
volume = {33},
number = {19},
pages = {e17527},
doi = {10.1111/mec.17527},
pmid = {39279684},
issn = {1365-294X},
support = {101027750//European Union's Horizon 2020 research and innovation programme/ ; 101062645//European Union's Horizon 2020 research and innovation programme/ ; //Agricultural Science and Technology Innovation Program (ASTIP-05)/ ; //CNRS and University Paul Sabatier (AnimalFarm IRP)/ ; //Spanish Ministerio de Educación, Cultura y Deporte (Archaeological Projects Abroad 2017)/ ; //Wroclaw Centre of Biotechnology programme ('The Leading National Research Center [KNOW]')/ ; 681605//HORIZON EUROPE European Research Council/ ; 834616//HORIZON EUROPE European Research Council/ ; 101071707//HORIZON EUROPE European Research Council/ ; ANR-10-INBS-09//Agence Nationale pour la Recherche/ ; 19-78-10053//Russian Science Foundation/ ; 22-18-00194//Russian Science Foundation/ ; },
mesh = {Animals ; *Equidae/genetics ; *Genetics, Population ; Mongolia ; Genome/genetics ; Phylogeny ; Fossils ; Horses/genetics ; Adaptation, Physiological/genetics ; },
abstract = {The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.},
}

Animals
*Equidae/genetics
*Genetics, Population
Mongolia
Genome/genetics
Phylogeny
Fossils
Horses/genetics
Adaptation, Physiological/genetics

@article {pmid39278943,
year = {2024},
author = {Sun, Y and Lorenzen, ED and Westbury, MV},
title = {Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {826},
pmid = {39278943},
issn = {1471-2164},
support = {37352//Villum Fonden/ ; 9064-00025B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Ursidae/genetics ; Animals ; Arctic Regions ; *Alleles ; *Genome ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; },
abstract = {The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.},
}

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

@article {pmid39268685,
year = {2024},
author = {Scheib, CL and Hui, R and Rose, AK and D'Atanasio, E and Inskip, SA and Dittmar, J and Cessford, C and Griffith, SJ and Solnik, A and Wiseman, R and Neil, B and Biers, T and Harknett, SJ and Sasso, S and Biagini, SA and Runfeldt, G and Duhig, C and Evans, C and Metspalu, M and Millett, MJ and O'Connell, TC and Robb, JE and Kivisild, T},
title = {Low Genetic Impact of the Roman Occupation of Britain in Rural Communities.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
pmid = {39268685},
issn = {1537-1719},
support = {2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; //St John's College, Cambridge/ ; 2014-2020.4.01.15-0012//European Regional Development Fund/ ; PRG243//Estonian Research Council/ ; 2014-2020.4.01.16-0030//European Union through the European Regional Development Fund/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; United Kingdom ; *Human Migration ; *Rural Population ; History, Ancient ; DNA, Ancient/analysis ; Genetics, Population ; },
abstract = {The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.},
}

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