@article {pmid40712582,
year = {2025},
author = {Boast, AP and Wood, JR and Bolstridge, N and Perry, GLW and Wilmshurst, JM},
title = {Long-term parasite decline associated with near extinction and conservation of the critically endangered kākāpō parrot.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.009},
pmid = {40712582},
issn = {1879-0445},
abstract = {Parasite extinction may be a major component of biodiversity loss, as parasites are thought to be biodiverse yet vulnerable to host loss. However, the relative severity of parasite extinction remains poorly understood, as parasites are rarely documented or preserved during the extinction process. The endangered kākāpō parrot (Strigops habroptila) is uniquely represented by a scat and coprolite record spanning its near extinction (c. 1280-1990 AD) and full-population management from c. 1990 onward. Ancient DNA metabarcoding and microfossil data on >200 kākāpō scats and coprolites, from fourteen localities and spanning >800 years to recent in age, revealed a loss of endoparasite richness. Thirteen of the sixteen (81.3%) parasite taxa detected in pre-1990 kākāpō are absent from contemporary populations, with nine losses occurring before, and four after, the management period. Of seven recurrent, and possibly host-specific, parasite taxa found in pre-1990 samples, four (57%) were not detected in contemporary samples and may be extinct. Losses may reflect increasingly unsuccessful host-host transmissions, extinction debt, host removal from infective habitats, and veterinary interventions. Overall, these results suggest that vertebrate population declines can result in permanent parasite loss. Parasite extinctions may be far more prevalent than previous estimates suggest, with unknown impacts on their hosts and their ecosystems.},
}

@article {pmid40705603,
year = {2025},
author = {Zou, Y and Tan, J and Zhou, J and Huang, Z and Yu, X and Han, K and Jin, L and Li, H and Wang, K},
title = {Ancient genomes from the Yellow River Bend reveal long-distance population interactions between the Central Plains, Steppe, and southern China.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116034},
doi = {10.1016/j.celrep.2025.116034},
pmid = {40705603},
issn = {2211-1247},
abstract = {The Yellow River Bend, at the northern frontier of Chinese civilization, has witnessed frequent prehistoric interactions between populations from the Central Plains of China and the northern Steppe. However, the related prehistoric population dynamics in this region remain poorly understood. Here, we generate whole-genome data for 23 individuals from the Late Neolithic to the Bronze-Iron Age. We find that Yangshao-related ancestry from the Central Plains constituted a major component of the local gene pool. During the Late Neolithic period, the Yellow River Bend population received indispensable genetic contributions from the Mongolian Steppe. Meanwhile, the Neolithic outliers presented an unexpected genetic influence from southern China that remains throughout the Bronze-Iron Age, implying a long-distance genetic exchange between northern and southern China. Overall, our study underscores the intricate ancient population interactions between the Central Plains, the Steppe, and southern China at the Yellow River Bend since the Neolithic period.},
}

@article {pmid40704779,
year = {2025},
author = {Garner, RE and Taranu, ZE and Higgins, SN and Paterson, MJ and Gregory-Eaves, I and Walsh, DA},
title = {Eutrophication and Warming Drive Algal Community Shifts in Synchronised Time Series of Experimental Lakes.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70159},
doi = {10.1111/1462-2920.70159},
pmid = {40704779},
issn = {1462-2920},
support = {NETGP-479720//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche du Québec-Nature et technologie/ ; //Canada Research Chairs Program/ ; //Mr. Stephen Bronfman/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; Climate Change ; Ontario ; Ecosystem ; Temperature ; Geologic Sediments/microbiology ; Seasons ; },
abstract = {Lake ecosystems are increasingly impacted by eutrophication and climate change. Whole-lake experiments have provided ecosystem-scale insights into the effects of freshwater stressors, yet these are constrained to the duration of monitoring programmes. Here, we leveraged multidecadal monitoring records and century-scale paleogenetic reconstructions for experimentally fertilised and unmanipulated lakes in the IISD Experimental Lakes Area of northwestern Ontario, Canada, to evaluate the responses of algal communities to nutrient and air temperature variation. We first validated the paleogenetic analysis of sediment DNA by demonstrating the synchrony of algal community changes with monitoring records. Algal communities underwent significant compositional shifts across experimental nutrient loading regimes and climate periods, with baseline assemblages informed by paleogenetics. Nonlinear regression modelling of algal community change in monitoring and paleogenetic time series showed the expected response that nutrients were strong drivers in fertilised lakes. Paleogenetic records reflected the century-scale impacts of climate warming and its combined effects with eutrophication, previously underestimated by monitoring. The synergy between eutrophication and warming points to eutrophic priming of the food web to respond to rising temperatures. Overall, the paleogenetic integration of algal diversity across habitats and seasons enables the detection of slow-acting climate change on lake ecosystems increasingly altered by nutrient pollution.},
}

*Lakes/microbiology/chemistry
*Eutrophication
Climate Change
Ontario
Ecosystem
Temperature
Geologic Sediments/microbiology
Seasons

@article {pmid40694589,
year = {2025},
author = {Fine, AG and Steinrücken, M},
title = {A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.},
journal = {PLoS genetics},
volume = {21},
number = {7},
pages = {e1011769},
doi = {10.1371/journal.pgen.1011769},
pmid = {40694589},
issn = {1553-7404},
abstract = {Detecting and quantifying the strength of selection is a major objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time-series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Here, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which the heterozygote and homozygote fitness are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, a heuristic to account for variable population size, and a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.},
}

@article {pmid40687795,
year = {2025},
author = {Wang, J and Zhang, T and Jia, X and Zhang, Z and He, J and Ning, C and Wang, J and Yang, T and Wang, G and Pang, Y and Huang, Y},
title = {Genomic profiling of a six-generation patrilineal family of the Ming-Qing dynasties in China.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112968},
pmid = {40687795},
issn = {2589-0042},
abstract = {Family cemeteries from historical periods often follow structured burial patterns, but identifying these arrangements is challenging due to limited written records and ambiguities in archaeological interpretation. Archaeogenetics provides a precise means to determine biological kinship, enabling the reconstruction of social relationships and burial customs. Here, we analyzed ancient DNA and contextual data from 34 individuals at Qianweigou, a Ming-Qing dynasty cemetery in Beijing, reconstructing a six-generation patrilineal pedigree. The genomic data revealed strict patrilineal burial customs, with spouses jointly interred and a non-random west-to-east spatial arrangement reflecting generational chronology. Each generation occupied distinct positions, forming an echelon-like burial pattern. This study demonstrates how genetic data can clarify historical kinship organization, refining hypotheses about Ming-Qing burial customs and advancing our understanding of familial structures in late imperial China.},
}

@article {pmid40686088,
year = {2025},
author = {Elliott, L and Boyer, F and Lemane, T and , and Alsos, IG and Coissac, E},
title = {wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70001},
doi = {10.1111/1755-0998.70001},
pmid = {40686088},
issn = {1755-0998},
support = {226134/F50//Norges Forskningsråd/ ; 819192//H2020 European Research Council/ ; },
abstract = {Inferring community composition from shotgun sequencing of environmental DNA is highly dependent on the completeness of reference databases used to assign taxonomic information as well as the pipeline used. While the number of complete, fully assembled reference genomes is increasing rapidly, their taxonomic coverage is generally too sparse to use them to build complete reference databases that span all or most of the target taxa. Low-coverage, whole genome sequencing, or skimming, provides a cost-effective and scalable alternative source of genome-wide information in the interim. Without enough coverage to assemble large contigs of nuclear DNA, much of the utility of a genome skim in the context of taxonomic annotation is found in its short read form. However, previous methods have not been able to fully leverage the data in this format. We demonstrate the utility of wholeskim, a pipeline for the indexing of k-mers present in genome skims and subsequent querying of these indices with short DNA reads. Wholeskim expands on the functionality of kmindex, a software which utilises Bloom filters to efficiently index and query billions of k-mers. Using a collection of thousands of plant genome skims, wholeskim is the only software that is able to index and query the skims in their unassembled form. It is able to correctly annotate 1.16× more simulated reads and 2.48× more true sedaDNA reads in 0.32× of the time required by Holi, another metagenomic pipeline that uses genome skims in their assembled form as its reference database input. We also explore the effects of taxonomic and genomic completeness of the reference database on the accuracy and sensitivity of read assignment. Increasing the genomic coverage of the genome skims used as reference increases the number of correctly annotated reads, but with diminishing returns after ~1× depth of coverage. Increasing taxonomic coverage clearly reduces the number of false negative taxa in the dataset, but we also demonstrate that it does not greatly impact false positive annotations.},
}

@article {pmid40680736,
year = {2025},
author = {Zhang, F and Gao, S and Zhao, X and Wu, Y and Zhang, J and Li, J and Ning, C and Yan, S and Wei, D and Cui, Y},
title = {Bronze and Iron Age genomes reveal the integration of diverse ancestries in the Tarim Basin.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.06.054},
pmid = {40680736},
issn = {1879-0445},
abstract = {The Tarim Basin in Xinjiang functioned as a crucial meeting point for peoples, cultures, and goods across the Eurasian steppe and served as the easternmost edge for western steppe population dispersal.[1][,][2][,][3][,][4][,][5][,][6][,][7] Despite its importance as a historical crossroads, the prehistoric genetic history of the region remains largely unexamined, which results in a major gap in understanding Eurasian population movements and steppe group expansion to the east. Here, we present genome-wide data from 24 individuals from the western Tarim Basin during the Bronze and Iron Ages. Our findings reveal that Bronze Age populations derived most of their ancestry from pastoralist groups, likely tracing back to the rapid eastward expansion of early Andronovo-related cultures in western steppes. As these steppe groups migrated, they first admixed with Bactria-Margiana Archaeological Complex (BMAC)-related agricultural populations and later with indigenous groups represented by the Bronze Age Tarim mummies, ultimately shaping the genetic landscape of the western Tarim Basin. Many of these individuals are genetically distinct from Andronovo-related groups in western Xinjiang,[2] indicating that at least two separate waves facilitated the entry of steppe populations into Xinjiang. Notably, we identified an Iron Age individual from western Tarim Basin who appears largely unaffected by the steppe influx, pointing to a previously unrecognized direct genetic admixture between BMAC and the indigenous ancestors of the Tarim. This underscores the genetic heterogeneity of the Iron Age Tarim and suggests that a long-lasting indigenous legacy endured for more than 1,000 years.},
}

@article {pmid40678522,
year = {2025},
author = {Komluski, J and Filatova, S and Schlütz, F and Claaßen, B and Rösch, M and Krause-Kyora, B and Kirleis, W and Stukenbrock, EH},
title = {Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112716},
pmid = {40678522},
issn = {2589-0042},
abstract = {In medieval central Europe, rye was one of the most important agricultural crops. We combined archaeobotanical methods and ancient DNA sequencing of historical rye material to study patterns of genetic diversity across four centuries. We applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th centuries from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples and compared sequences of historical rye samples to chloroplast genomes of other cereal crops, including a modern rye cultivar. Comparing the aDNA chloroplast samples with modern and non-domesticated rye chloroplast, we show that genetic variation in the historical German rye population was considerably higher. The exceptional difference in levels of genetic variation likely reflects the consequences of late domestication and selective breeding on genetic variation in this important crop in the last few centuries.},
}

@article {pmid40674584,
year = {2025},
author = {Kraft, L and Korneliussen, TS and Sackett, PW and Renaud, G},
title = {AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf407},
pmid = {40674584},
issn = {1367-4811},
abstract = {MOTIVATION: DNA damage patterns, such as increased frequencies of C→T and G→A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In metagenomic studies, fragments can be mapped against multiple references or de novo assembled contigs to identify those likely to be ancient. Generating and comparing damage profiles, however, can be both tedious and time-consuming. Although tools exist for estimating damage in single reference genomes and metagenomic datasets, none efficiently cluster damage patterns.

RESULTS: To address this methodological gap, we developed AdDeam, a tool that combines rapid damage estimation with clustering for streamlined analyses and easy identification of potential contaminants or outliers. Our tool takes aligned aDNA fragments from various samples or contigs as input, computes damage patterns, clusters them and outputs representative damage profiles per cluster, a probability of each sample of pertaining to a cluster as well as a PCA of the damage patterns for each sample for fast visualisation. We evaluated AdDeam on both simulated and empirical datasets. AdDeam effectively distinguishes different damage levels, such as UDG-treated samples, sample-specific damages from specimens of different time periods, and can also distinguish between contigs containing modern or ancient fragments, providing a clear framework for aDNA authentication and facilitating large-scale analyses.

AdDeam is publicly available at https://github.com/LouisPwr/AdDeam and can also be installed via Bioconda. It is implemented in Python and C ++. All analysis scripts and datasets are available at https://github.com/LouisPwr/AdDeamAnalysis and on Zenodo under: 10.5281/zenodo.15052427.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40673342,
year = {2025},
author = {Furness, LH and Sabin, R and Torvanger, MS and Kersten, O and Barrett, JH and Star, B},
title = {Historical Collections of Tropical Marine Mammals Are an Excellent Resource for Ancient DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70015},
doi = {10.1111/1755-0998.70015},
pmid = {40673342},
issn = {1755-0998},
support = {951649//H2020 European Research Council/ ; },
abstract = {The ability to predict ancient DNA sequencing success in natural history collections is critical to reducing the amount of destructive sampling of a finite resource. So far, studies investigating such success have predominantly focused on taxa with ranges restricted to temperate or cold environments at northern latitudes, which likely aids DNA preservation. Here, we report remarkably high aDNA sequencing success in Sirenia, herbivorous marine mammals of which the distribution is currently constrained to the global tropics. We investigate 91 samples from 85 specimens comprising all four contemporary species and one extinct species, comparing different sample types (cranial/post-cranial bone, skin and cartilage), species, collections, and material age. We obtained remarkably high (e.g., > 20%) endogenous DNA preservation for the majority (e.g., ~57% percent) of samples. Sequencing success was linked to sample type, with cranial bones (including petrous and tympanic bones) yielding significantly higher endogenous DNA. Additionally, we obtained variable, but potentially superior DNA results for preserved cartilage and hide samples that can be associated with historical bone. Although such tissue is not always present, this type of material is easy to sample, with very limited destructive impacts on the associated bones, and we therefore highlight its untapped potential as a source of DNA. Overall, our results show the high success of ancient DNA retrieval from historical collections of species with a tropical distribution, expanding on the types of specimens that are available for temporal genomic analyses.},
}

@article {pmid40673184,
year = {2025},
author = {Standeven, FJ and Dahlquist-Axe, G and Hendy, J and Fiddyment, S and Holst, M and McGrath, K and Collins, M and Mundorff, A and Radini, A and Wagner, J and Meehan, CJ and Tedder, A and Speller, CF},
title = {An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111770},
pmid = {40673184},
issn = {2352-3409},
abstract = {Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR).},
}

@article {pmid40671036,
year = {2025},
author = {Williams, MP and Huber, CD},
title = {The genomic footprints of migration: how ancient DNA reveals our history of mobility.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {206},
pmid = {40671036},
issn = {1474-760X},
support = {R35GM146886//National Institute of Health/ ; R35GM146886//National Institute of Health/ ; },
mesh = {Humans ; *DNA, Ancient/analysis ; *Human Migration ; *Genetics, Population/methods ; *Genome, Human ; *Genomics/methods ; },
abstract = {Ancient DNA has emerged as a powerful tool for studying human migration through the detection of admixture signatures. Here, we present the theoretical principles and methodologies for admixture analysis, with an emphasis on f-statistics and qpAdm. We review case studies from the literature demonstrating how these methods uncover patterns of human mobility, and discuss challenges related to data quality, demographic complexity, and sample representativeness on admixture and migration inferences. Finally, we highlight promising advancements in admixture analysis and underscore the importance of integrating genetic, archaeological, and historical data to achieve a more interdisciplinary and nuanced reconstruction of human history.},
}

Humans
*DNA, Ancient/analysis
*Human Migration
*Genetics, Population/methods
*Genome, Human
*Genomics/methods

@article {pmid40663601,
year = {2025},
author = {Perretti, S and Santos, P and Vizzari, MT and Tassani, E and Benazzo, A and Ghirotto, S and Barbujani, G},
title = {Inference of human pigmentation from ancient DNA by genotype likelihoods.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {29},
pages = {e2502158122},
doi = {10.1073/pnas.2502158122},
pmid = {40663601},
issn = {1091-6490},
support = {2020HJXCK9//Italian Ministry of University (MUR) PRIN 2020/ ; 2020TACEZR//Italian Ministry of University (MUR) PRIN 2020/ ; P20228M8ZN//Italian Ministry of University (PRIN) 2022-PNRR/ ; },
mesh = {Humans ; *DNA, Ancient/analysis ; Genotype ; *Skin Pigmentation/genetics ; *Hair Color/genetics ; Eye Color/genetics ; Likelihood Functions ; *Pigmentation/genetics ; },
abstract = {Light eyes, hair, and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in three high-coverage ancient samples, the Paleolithic Ust'-Ishim from Russia, the Mesolithic SF12 from Sweden, and the Neolithic I5077 from current Croatia. We could thus compare three approaches to pigmentation inference, concluding that for suboptimal levels of coverage (<8×), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye, and hair color evolved over the past 45,000 y. The shift toward lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Bronze and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.},
}

Humans
*DNA, Ancient/analysis
Genotype
*Skin Pigmentation/genetics
*Hair Color/genetics
Eye Color/genetics
Likelihood Functions
*Pigmentation/genetics

@article {pmid40662803,
year = {2025},
author = {Yılmaz, MA and Ceylan, AA and Kaynar, G and Çiçek, AE},
title = {LYCEUM: learning to call copy number variants on low-coverage ancient genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i285-i293},
doi = {10.1093/bioinformatics/btaf244},
pmid = {40662803},
issn = {1367-4811},
mesh = {*DNA Copy Number Variations ; Humans ; *Machine Learning ; *DNA, Ancient/analysis ; *Software ; Algorithms ; Genome, Human ; },
abstract = {MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions.

RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection.

LYCEUM is available at https://github.com/ciceklab/LYCEUM.},
}

*DNA Copy Number Variations
Humans
*Machine Learning
*DNA, Ancient/analysis
*Software
Algorithms
Genome, Human

@article {pmid40655309,
year = {2025},
author = {De Jonge, C and Dubois, N and Ladd, SN and Deng, L and Gajendra, N and Haghipour, N and Schubert, CJ and Lever, M},
title = {Holocene environmental change in Rotsee and its impact on sedimentary carbon storage.},
journal = {Journal of paleolimnology},
volume = {73},
number = {4},
pages = {311-327},
pmid = {40655309},
issn = {0921-2728},
abstract = {To assess the long-term impact of climate change and human influence on lakes and their sedimentary carbon storage, paleo-environmental approaches using well-dated lake sediment cores can be employed. Here, we reconstruct carbon mass accumulation rates for organic and inorganic carbon since 13 ka BP in Rotsee, a perialpine lake near the Swiss Alps, using a 12-m sediment core. A multiproxy approach (XRF, carbon and nitrogen isotopes, organic macromolecule chemical compositions, aDNA) was used to explore changes in the lake system that affect sedimentary carbon storage. The Early Holocene (11.8-7 cal ka BP) was characterized by a mixed phytoplankton and watershed-derived provenance of organic matter, and the deposition of inorganic and organic sedimentary carbon. Warming during the Holocene Thermal Maximum (9.8-8.8 cal ka BP) increased sedimentary carbon storage. In the Mid- to Late Holocene (7-1 cal ka BP), the sedimentary record indicates an increased influx of allochthonous, vascular plant-derived organic matter, and low production or conservation of phytoplankton-derived carbon. Organic carbon storage increased, while inorganic carbon became negligible. Larger deforestation events, potentially during Neolithic times (around 4 ka BP), but especially during Roman times (2 ka BP), coincided with further increased organic carbon MARs. Recent sediments, influenced by eutrophication in the last century, show higher carbon accumulation rates compared to earlier Holocene periods. Rotsee serves as a case study of how climate warming and human land use changes have influenced lake development and sedimentary carbon6 storage, with broader implications for understanding carbon dynamics in high altitude lakes and their future carbon balance.},
}

@article {pmid40644297,
year = {2025},
author = {Wang, K},
title = {Q&A with Ke Wang.},
journal = {Cell reports},
volume = {44},
number = {7},
pages = {115968},
doi = {10.1016/j.celrep.2025.115968},
pmid = {40644297},
issn = {2211-1247},
abstract = {In this interview, Dr. Jorge Santos discusses with Dr. Ke Wang her research focusing on the evolutionary history of human ancient populations through the study of ancient DNA and sociocultural innovations. Dr. Wang recently published in Cell Reports on the prehistoric population interactions and dynamics along the Yellow River Bend of China.},
}

@article {pmid40640605,
year = {2025},
author = {Bundell, S and Petrić Howe, N},
title = {Ancient DNA reveals farming led to more human diseases.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-025-02179-5},
pmid = {40640605},
issn = {1476-4687},
}

@article {pmid40635430,
year = {2025},
author = {Campbell, MA and Ward, I and Blyth, A and Allentoft, ME},
title = {Using sedimentary ancient DNA in coastal and marine contexts to explore past human-environmental interactions in Australia.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1930},
pages = {20240032},
pmid = {40635430},
issn = {1471-2970},
mesh = {Australia ; *Geologic Sediments/chemistry/analysis ; *DNA, Ancient/analysis ; Humans ; *Ecosystem ; Biodiversity ; Oceans and Seas ; },
abstract = {Over the 65 000 years of human occupation in Australia, sea levels have fluctuated significantly, notably rising from -120 m around 21 000 years ago, submerging vast areas of the continental shelf. Current coastal ecosystems stabilized about 5000 years ago, leaving many early cultural landscapes underwater, complicating the study of ancient human activity. Sedimentary ancient DNA (sedaDNA) analysis, a powerful tool for monitoring ecological changes and human-environment interactions, has recently gained attention but its exploration is still in its early stages in Australia. This approach holds great potential for investigating shifts in resource and land-use changes, the introduction of non-native species and distinguishing between human and natural impacts on biodiversity. Despite challenges with DNA preservation due to Australia's harsh climate, organic-rich coastal and marine sediments may provide favourable conditions for sedaDNA. We review case studies across Australia, showcasing how sedaDNA offers valuable insights into past coastal ecologies and can contribute to developing a sustainable biocultural landscape.This article is part of the theme issue 'Shifting seas: understanding deep-time human impacts on marine ecosystems'.},
}

Australia
*Geologic Sediments/chemistry/analysis
*DNA, Ancient/analysis
Humans
*Ecosystem
Biodiversity
Oceans and Seas

@article {pmid40635429,
year = {2025},
author = {Zampirolo, G and McCarthy, ML and Živaljević, I and Penezić, K and Vuković, S and Mladenović, T and Marković, D and Marković, N and Radmanović, D and Orton, D and Tange Olsen, M and Pedersen, MW},
title = {Continuous mitochondrial diversity of Danube sturgeon species over millennia: insights from ancient DNA.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1930},
pages = {20240034},
pmid = {40635429},
issn = {1471-2970},
support = {//Horizon 2020 Framework Programme/ ; //Carlsberg Semper Ardens Accelerate fellowship/ ; //Danmarks Grundforskningsfond/ ; //H2020 Marie Skłodowska-Curie Actions/ ; //Carlsbergfondet/ ; },
mesh = {Animals ; *Fishes/genetics/classification ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics/analysis ; *Genetic Variation ; },
abstract = {Sturgeons, an iconic group of large fishes inhabiting marine and freshwater ecosystems, have historically had significant economic and cultural value, particularly prized for their meat and roe (caviar). Furthermore, sturgeons play a vital ecological role as mesopredators of prey fish and invertebrates. In the Danube basin, the European (Acipenser sturio) and fringebarbel or ship sturgeon (Acipenser nudiventris) are locally extinct, while beluga (Huso huso), Russian (Acipenser gueldenstaedtii), stellate (Acipenser stellatus) and sterlet (Acipenser ruthenus) sturgeon have significantly declined since the nineteenth century owing to overfishing, habitat loss and pollution. Archaeological evidence suggests that sturgeon exploitation along the Danube began as early as 11.6 thousand years before the present. This study explores the genetic landscape of Danube sturgeons over the past approximately 10 000 years using ancient DNA (aDNA) from archaeological specimens. Despite challenges posed by limited sample size, phylogenetic analyses of mitochondrial genomes and the D-loop reveal high genetic diversity within beluga, Russian and ship sturgeon populations. In addition, shared haplotypes between modern and historical specimens of both beluga and Russian sturgeons suggest genetic continuity within each species over time. This study provides, to our knowledge, the first high-coverage sequencing of ancient sturgeon mitogenomes establishing the foundation for future aDNA research.This article is part of the theme issue 'Shifting seas: understanding deep-time human impacts on marine ecosystems'.},
}

Animals
*Fishes/genetics/classification
*DNA, Ancient/analysis
*DNA, Mitochondrial/genetics/analysis
*Genetic Variation

@article {pmid40634615,
year = {2025},
author = {Green, DR and Uno, KT and Miller, ER and Feibel, CS and Aoron, EE and Beck, CC and Grossman, A and Kirera, FM and Kirinya, MM and Leakey, LN and Liutkus-Pierce, C and Manthi, FK and Ndiema, EK and Nengo, IO and Nyete, C and Rowan, J and Russo, GA and Sanders, WJ and Smiley, TM and Princehouse, P and Vitek, NS and Cleland, TP},
title = {Eighteen million years of diverse enamel proteomes from the East African Rift.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634615},
issn = {1476-4687},
abstract = {Research into the palaeobiology of extinct taxa through ancient DNA and proteomics has been mostly limited to Plio-Pleistocene fossils[1-9], due to molecular breakdown over time, which is exacerbated in tropical settings[1-3]. Here we sample small proteomes from the interior enamel of fossils at palaeontological sites from the Pleistocene to the Oligocene in the Turkana Basin, Kenya, which has produced a rich record of Cenozoic mammalian evolution[10]. Through a mass-spectrometry-based proteomic workflow, and using criteria to locate diagenetiforms derived from enamel, we recover fragments of enamelin, ameloblastin, matrix metalloprotease-20 and dentin matrix acidic phosphoprotein 1 from an Early Miocene rhinocerotid and several proboscideans collected from the sites of Buluk (16 million years ago; Ma) and Loperot (18 Ma). Diagenetiform counts decline in progressively older fossils, and we observe variability in Early Miocene preservation across sites. Phylogenetic analyses reveal the contribution of these sequences to the systematic placement of extinct taxa, although we caution that this approach must account for sparse fragments, uncertainty in fragment identification and possible sequence diagenesis. We identify likely modifications that support the ancient age of these proteins, and some of the oldest examples of advanced glycation end-products yet known. The discovery of protein sequences within dense enamel tissues in one of the persistently warmest regions on Earth promises the discovery of much older proteomes that will aid in the study of the palaeobiology and evolutionary relationships of extinct taxa.},
}

@article {pmid40611166,
year = {2025},
author = {Davidson, R and Roca-Rada, X and Ravishankar, S and Taufik, L and Haarkötter, C and Collen, E and Williams, MP and Webb, P and Mahmud, MI and Djami, ENI and Purnomo, GA and Santos, C and Malgosa, A and Manzanilla, LR and Silva, AM and Tereso, S and Matos, V and Carvalho, PC and Fernandes, T and Maurer, AF and Teixeira, JC and Tobler, R and Fehren-Schmitz, L and Llamas, B},
title = {Optimized in-solution enrichment of over a million ancient human SNPs.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {190},
pmid = {40611166},
issn = {1474-760X},
support = {PTDC/HAR-ARQ/6273/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; FPU 20/01967//Ministerio de Universidades/ ; DE190101069//Australian Research Council/ ; CE170100015//Australian Research Council/ ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA, Ancient/analysis ; High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Sequence Analysis, DNA/methods ; Genome, Human ; },
abstract = {BACKGROUND: In-solution hybridization enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmark the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancient human samples of diverse demographic origin with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment and assessed performance compared to deep shotgun sequencing.

RESULTS: We find that the "Twist Ancient DNA" assay provides robust enrichment of approximately 1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity.

CONCLUSIONS: In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimizing experimental protocols.},
}

Humans
*Polymorphism, Single Nucleotide
*DNA, Ancient/analysis
High-Throughput Nucleotide Sequencing/methods
Gene Library
Sequence Analysis, DNA/methods
Genome, Human

@article {pmid40609663,
year = {2025},
author = {Muschick, M and Rüber, L and Matschiner, M},
title = {Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae).},
journal = {Molecular phylogenetics and evolution},
volume = {211},
number = {},
pages = {108406},
doi = {10.1016/j.ympev.2025.108406},
pmid = {40609663},
issn = {1095-9513},
abstract = {Lophichthys boschmai, the only member of the family Lophichthyidae, is an elusive lophiiform fish whose phylogenetic associations are debated. This family is among the last two vertebrate families lacking DNA sequence data, primarily due to the species' rarity, lack of fresh material and challenges associated with sequencing formalin-treated museum specimens. In this study, we provide mitochondrial and nuclear DNA sequences obtained from two museum specimens of Lophichthys boschmai. Employing ancient DNA techniques, we successfully extracted and analyzed the degraded and fragmented DNA. Our findings, derived from both mitochondrial genomes and nuclear ultra-conserved elements (UCE), reveal the Lophichthyidae as sister lineage to Tathicarpidae within the Antennarioidei. This study showcases the use of whole-genome "shotgun" sequencing data from formalin-fixed museum specimens in the context of an available UCE dataset. Given the enhanced versatility in data reusability this approach offers, we suggest it should be a favored approach when studying rare specimens.},
}

@article {pmid40608932,
year = {2025},
author = {Liu, JH and Ruan, QJ and Ge, JY and Huang, YJ and Zhang, XL and Liu, J and Li, SF and Shen, H and Wang, Y and Stidham, TA and Deng, CL and Li, SH and Han, F and Jin, YS and O'Gorman, K and Li, B and Dennell, R and Gao, X},
title = {300,000-year-old wooden tools from Gantangqing, southwest China.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6755},
pages = {78-83},
doi = {10.1126/science.adr8540},
pmid = {40608932},
issn = {1095-9203},
mesh = {China ; Animals ; Archaeology ; *Fossils ; Hominidae ; Wood ; Bone and Bones ; History, Ancient ; },
abstract = {Evidence of Early and Middle Pleistocene wooden implements is exceptionally rare, and existing evidence has been found only in Africa and western Eurasia. We report an assemblage of 35 wooden implements from the site of Gantangqing in southwestern China, which was found associated with stone tools, antler billets (soft hammers), and cut-marked bones and is dated from ~361,000 to ~250,000 years at a 95% confidence interval. The wooden implements include digging sticks and small, complete, hand-held pointed tools. The sophistication of many of these tools offsets the seemingly "primitive" aspects of stone tool assemblages in the East Asian Early Paleolithic. This discovery suggests that wooden implements might have played an important role in hominin survival and adaptation in Middle Pleistocene East Asia.},
}

China
Animals
Archaeology
*Fossils
Hominidae
Wood
Bone and Bones
History, Ancient

@article {pmid40604287,
year = {2025},
author = {Zeng, TC and Vyazov, LA and Kim, A and Flegontov, P and Sirak, K and Maier, R and Lazaridis, I and Akbari, A and Frachetti, M and Tishkin, AA and Ryabogina, NE and Agapov, SA and Agapov, DS and Alekseev, AN and Boeskorov, GG and Derevianko, AP and Dyakonov, VM and Enshin, DN and Fribus, AV and Frolov, YV and Grushin, SP and Khokhlov, AA and Kiryushin, KY and Kiryushin, YF and Kitov, EP and Kosintsev, P and Kovtun, IV and Makarov, NP and Morozov, VV and Nikolaev, EN and Rykun, MP and Savenkova, TM and Shchelchkova, MV and Shirokov, V and Skochina, SN and Sherstobitova, OS and Slepchenko, SM and Solodovnikov, KN and Solovyova, EN and Stepanov, AD and Timoshchenko, AA and Vdovin, AS and Vybornov, AV and Balanovska, EV and Dryomov, S and Hellenthal, G and Kidd, K and Krause, J and Starikovskaya, E and Sukernik, R and Tatarinova, T and Thomas, MG and Zhabagin, M and Callan, K and Cheronet, O and Fernandes, D and Keating, D and Candilio, F and Iliev, L and Kearns, A and Özdoğan, KT and Mah, M and Micco, A and Michel, M and Olalde, I and Zalzala, F and Mallick, S and Rohland, N and Pinhasi, R and Narasimhan, VM and Reich, D},
title = {Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40604287},
issn = {1476-4687},
abstract = {The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples, but much of their history is poorly understood. In particular, the genomic formation of populations that speak Uralic and Yeniseian languages today is unknown. Here, by generating genome-wide data for 180 ancient individuals spanning this region, we show that the Early-to-Mid-Holocene hunter-gatherers harboured a continuous gradient of ancestry from fully European-related in the Baltic, to fully East Asian-related in the Transbaikal. Contemporaneous groups in Northeast Siberia were off-gradient and descended from a population that was the primary source for Native Americans, which then mixed with populations of Inland East Asia and the Amur River Basin to produce two populations whose expansion coincided with the collapse of pre-Bronze Age population structure. Ancestry from the first population, Cis-Baikal Late Neolithic-Bronze Age (Cisbaikal_LNBA), is associated with Yeniseian-speaking groups and those that admixed with them, and ancestry from the second, Yakutia Late Neolithic-Bronze Age (Yakutia_LNBA), is associated with migrations of prehistoric Uralic speakers. We show that Yakutia_LNBA first dispersed westwards from the Lena River Basin around 4,000 years ago into the Altai-Sayan region and into West Siberian communities associated with Seima-Turbino metallurgy-a suite of advanced bronze casting techniques that expanded explosively from the Altai[1]. The 16 Seima-Turbino period individuals were diverse in their ancestry, also harbouring DNA from Indo-Iranian-associated pastoralists and from a range of hunter-gatherer groups. Thus, both cultural transmission and migration were key to the Seima-Turbino phenomenon, which was involved in the initial spread of early Uralic-speaking communities.},
}

@article {pmid40603668,
year = {2025},
author = {},
title = {Ancient DNA helps trace stinky Roman fish sauce to its source.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40603668},
issn = {1476-4687},
}

@article {pmid40598853,
year = {2025},
author = {Fan, GY and Tian-Ge, J and Zhu, Y},
title = {Decoding the Han paternal legacy: a Y chromosomal genealogy of Xuzhou as the cradle of the Han civilization.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {},
number = {},
pages = {},
doi = {10.1127/anthranz/1857},
pmid = {40598853},
issn = {0003-5548},
abstract = {Xuzhou, hailed as the Oriental Athens, holds a pivotal position in the development of Han Chinese culture. This study delves into the genetic makeup of the Xuzhou Han population utilizing Y-chromosomal markers, aiming to enrich population genetics and forensic science research. We analyzed 638 unrelated males from Pei County, Xuzhou, through the SureID[®] PathFinder Plus Kit. The pairwise genetic relationships were compared between the Xuzhou Han and 52 other Chinese population. We employed the k-nearest neighbor algorithm for Y-SNP haplogroup prediction and Linear Discriminant Analysis (LDA) for category forecasting. Most Y-STR loci exhibited high polymorphism, with the exception of DYS645. The Xuzhou Han population showcased a haplotype diversity of 0.9997 and a discrimination capacity of 0.9708. Genetic similarities were detected among Han populations across the nation, with the Xuzhou Han revealing a prevalence of Y haplogroups O2a2 and O2a1. Comparisons of haplogroup distributions across 55 contemporary Chinese ethnic groups and ancient DNA from 59 archaeological sites unveiled the widespread presence of the O2 haplogroup before the Han Dynasty. Our research also underscores the Y chromosomal genealogy continuity of the O2 population in northern China from the Neolithic to modern times. Meanwhile, LDA hints a long history of integration between Jiangsu Han groups. Nevertheless, the Xuzhou Han still exhibited an extremely high O2a2 ratio, reflecting the rapid expansion of this patrilineal familys population base throughout history. Our study is not only expected to have a positive impact on the reconstruction of the local patrilineal history, but also defined forensic applications and deepens the understanding of Han Chinese culture through the lens of paternal genetics.},
}

@article {pmid40597195,
year = {2025},
author = {Sun, L and Ma, H and Wang, R and Wu, Z and Qiu, L and Chen, H and Wang, CC},
title = {The demic expansion of Yangshao culture inferred from ancient human genomes.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {186},
pmid = {40597195},
issn = {1741-7007},
mesh = {Humans ; China ; *Genome, Human ; *Human Migration/history ; *DNA, Ancient/analysis ; Archaeology ; },
abstract = {BACKGROUND: Originating from the middle Yellow River, Yangshao culture is one of the most influential archaeological cultures in Neolithic China. It has long been debated whether there was a genetic substructure between the core Yangshao sites and those representing regional variants of the Yangshao culture, such as the Qinwangzhai culture. The excavated human remains from the burials at the Zhanmatun site, which belonged to the Qinwangzhai culture, present ideal material for inferring the population dynamics accompanying the cultural expansion.

RESULTS: In this study, we analyzed genome-wide data from 12 human remains obtained from the Zhanmatun site. The results indicated that Zhanmatun individuals were genetically homogeneous with all published Yangshao culture-related individuals from the core region of Yangshao and its periphery as well as Late Dawenkou culture-related Xixiahou people in the east, with no tracts of genetic influence from Neolithic Southern East Asian in the south.

CONCLUSIONS: Our findings support a demic diffusion model for Yangshao culture expansion, where human migration, rather than mere cultural diffusion, played a dominant role in spreading Yangshao-related ancestry across northern China.},
}

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

@article {pmid40590317,
year = {2025},
author = {Champney, TH and Smith, HF and Hildebrandt, S and Cornwall, J},
title = {Human, Animal, or Mineral? Ethical Considerations for Studies of Fossilized Hominin Remains.},
journal = {American journal of biological anthropology},
volume = {187},
number = {3},
pages = {e70085},
pmid = {40590317},
issn = {2692-7691},
mesh = {*Fossils ; Humans ; *Hominidae ; Animals ; *Paleontology/ethics ; },
abstract = {Ethical considerations around research and education with modern human subjects, use of human tissue, and studies involving humans are ubiquitous within the global scientific community. This commentary explores considerations around how and whether these types of ethical considerations may apply to hominin fossils. While some might propose that the age of a fossil could be the basis for decisions around their ethical handling, it may be that characteristics or behaviors of the hominins are a more appropriate measure to determine their ethical status. These types of ethical considerations have recently been examined in other historical human tissues, such as mummies and ancient DNA, with these ethical explorations being driven by a recognition of evolving ethical perspectives around the world. Thus, there is both the precedent and stimulus for the paleoanthropology community to revisit current ethical practices within the profession. Doing so would help identify and establish standards that are reflective of global perspectives around the contemporary ethical management of hominin fossils, and potentially assist in aligning these practices with other disciplines that work with both hominin fossils and human tissues.},
}

*Fossils
Humans
*Hominidae
Animals
*Paleontology/ethics

@article {pmid40578321,
year = {2025},
author = {Li, R and Zang, Y and Liu, Z and Yang, J and Wang, N and Liu, J and Wu, E and Wu, R and Sun, H},
title = {clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf055},
pmid = {40578321},
issn = {2210-3244},
abstract = {The detection of identity-by-descent (IBD) segments is widely used to infer relatedness in many fields, including forensics and ancient DNA analysis. However, existing methods are often ineffective for poor-quality DNA samples. Here, we propose a method, clusIBD, which can robustly detect IBD segments using unphased genetic data with a high rate of genotype error. We evaluated and compared the performance of clusIBD with that of IBIS, TRUFFLE, and IBDseq using simulated data, artificial poor-quality materials, and ancient DNA samples. The results show that clusIBD outperforms these tools and could be used for kinship inference in fields such as ancient DNA analysis and criminal investigation. ClusIBD is publicly available at GitHub (https://github.com/Ryan620/clusIBD/) and BioCode (https://ngdc.cncb.ac.cn/biocode/tool/BT007882).},
}

@article {pmid40568545,
year = {2025},
author = {Turvey, ST and Ortiz, A and Granger, M and Brace, S and Henriksen, RA and Yang, Q and Nguyễn, TA and Buck, LT and Ma, H and Hansford, JP and Booth, T and Chatterjee, HJ and Fan, P and Chen, X},
title = {Morphometric characterization of Holocene mandibles expands the ecological baseline for understanding gibbon extinction dynamics.},
journal = {Royal Society open science},
volume = {12},
number = {6},
pages = {242065},
pmid = {40568545},
issn = {2054-5703},
abstract = {Human activities have driven biodiversity loss for millennia, and conservation of 'refugee species' that survive as remnant populations requires insights from historical baselines. However, reconstructing the past distribution and ecology of such species is challenging due to data limitations with specimen-based archives. Here, we assess the taxonomic identity of two gibbon mandibles from the Wumingshan Neolithic site in Guangxi, China. Although ancient DNA extraction was unsuccessful, a suite of linear and geometric morphometric analyses using dental and mandibular characters reveals that these mandibles fall within or close to variation shown by extant Chinese Nomascus gibbons and can be assigned to the cao vit gibbon N. nasutus. This is now one of the world's rarest mammals, with a surviving population of 74 individuals in one site. Comparative assessment of bioclimatic, abiotic and anthropogenic parameters for Wumingshan and other sites where N. nasutus historically occurred reveals the species was formerly a landscape generalist but is now restricted to a high-elevation refugium with reduced human pressures. Our multidisciplinary analyses provide a new baseline on niche requirements and vulnerability for N. nasutus with implications for population management, demonstrating the importance of integrating environmental archives into conservation planning.},
}

@article {pmid40565531,
year = {2025},
author = {Zhu, Y and Hou, X and Zhao, J and Xiao, B and Song, S and Zou, X and Liu, S and Hofreiter, M and Lai, X},
title = {Revisiting Aurochs Haplogroup C: Paleogenomic Perspectives from Northeastern China.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
pmid = {40565531},
issn = {2073-4425},
support = {41972001//National Natural Science Foundation of China/ ; 2016-2041//the "PPP" project jointly funded by China Scholarship Council and DAAD, Germany, funded by German Academic Exchange Service/ ; },
mesh = {Animals ; *Haplotypes/genetics ; China ; Cattle/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; Fossils ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND/OBJECTIVES: Aurochs (Bos primigenius), one of the earliest and largest herbivores domesticated by humans, were widely distributed in Eurasia and North Africa during the Pleistocene and Holocene. Studies of aurochs in China have focused mainly on the Northeastern region. Previous studies have suggested that haplogroup C is a haplogroup unique to China, but recent studies have shown that this is not the case. We have compiled all data on haplogroup C to revisit the classification of the aurochs haplogroup C.

METHODS: In this study, we obtained 13 nearly complete mitochondrial genomes from Late Pleistocene to early Holocene bovine samples from Northeastern China through fossil sample collection, ancient DNA extraction, library construction, and high-throughput sequencing. Based on the acquired ancient DNA data and in combination with previously published bovine data, the phylogenetic status, lineage divergence time, and population dynamics of aurochs in Northeastern China were analyzed.

RESULTS: Phylogenetic analyses and divergence time estimations suggest that the current definition of haplogroup C is overly inclusive, necessitating a refined reclassification of this haplogroup. We also estimated the population dynamics of aurochs in Northeastern China using Bayesian skyline plots found that the maternal effective population size of the aurochs increased significantly during Marine Isotope Stage 5 (MIS5), but began to decrease in the second half of MIS3 before they eventually became extinct.

CONCLUSIONS: Our results provide new molecular evidence on the phylogenetic status, divergence time, and population dynamics of aurochs in Northeastern China.},
}

Animals
*Haplotypes/genetics
China
Cattle/genetics
Phylogeny
*Genome, Mitochondrial/genetics
Fossils
DNA, Ancient/analysis
DNA, Mitochondrial/genetics

@article {pmid40564233,
year = {2025},
author = {Katanyuphan, Y and Krajaejun, P and Wattanapituksakul, A and Surat, W},
title = {The First Report of Rhino DNA in Thailand: A Possible Extinct Indian Javan Subspecies, Rhinoceros sondaicus inermis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121678},
pmid = {40564233},
issn = {2076-2615},
support = {B4301-00121-65//Kasetsart University, Bangkok, Thailand/ ; N42A650275//the National Research Council of Thailand (NRCT)/ ; },
abstract = {The Javan rhino is a critically endangered species that has become extinct in several Asian countries, including Thailand. There are three Javan rhino subspecies: Rhinoceros sondaicus sondaicus, R. s. annamiticus, and R. s. inermis, and the first two subspecies existed in Thailand decades ago. However, no genetic study on Thai rhinos has been reported. In this study, we amplified a partial D-loop region of two ancient rhino specimens dated to approximately 100 years before present, from southwest Thailand. Then, we constructed phylogenetic trees and a haplotype network based on the D-loop sequences of the Thai rhinos and 39 Javan, Sumatran, and Indian rhinos from the GenBank database. The ancient Thai rhino DNA belonged to Javan rhinos and was clearly separated from R. s. annamiticus and R. s. sondaicus. The nucleotide differences among the ancient Thai, R. s. annamiticus, and R. s. sondaicus rhino DNA were 5.14-8.30%, similar to those between two white rhino subspecies. Moreover, species delimitation analyses confirmed that the ancient Thai rhinos should belong to another Javan rhino subspecies, possibly the extinct Indian Javan rhino. This is the first report of rhino DNA from Thailand and possibly the Indian Javan rhino DNA, which could be used for evolutionary studies.},
}

@article {pmid40559445,
year = {2025},
author = {Rbbani, G and Siriyappagouder, P and Murshed, R and Joshi, R and Nedoluzhko, A and Galindo-Villegas, J and Fernandes, JMO},
title = {Optimization of Nile Tilapia Artificial Breeding Using Human Chorionic Gonadotropin (hCG) Hormone.},
journal = {Methods and protocols},
volume = {8},
number = {3},
pages = {},
pmid = {40559445},
issn = {2409-9279},
support = {683210, 101081935/ERC_/European Research Council/International ; 250548, 310103, 311799//Research Council of Norway/ ; 817992//EU H2020/ ; },
abstract = {Nile tilapia (Oreochromis niloticus) is the most widely farmed tilapia species globally, making it one of the most important aquaculture species. To meet increasing demand, hatcheries occasionally use artificial breeding techniques such as hormonal induction to synchronize breeding. Despite the common use of human chorionic gonadotropin (hCG) in fish breeding, no detailed protocol has been established specifically for Nile tilapia. The objective of this study is to establish an effective hCG-induced artificial breeding protocol for gene editing and aquaculture production, optimizing fertilization, hatching, and survival rates. We employed a single intramuscular injection of 2 IU/g hCG to induce ovulation. The protocol achieved an average fertilization rate of 88.3% and a larval survival rate of 90.5%, demonstrating its potential for obtaining high-quality embryos for functional studies and enhancing reproductive performance on a commercial scale.},
}

@article {pmid40556972,
year = {2025},
author = {Andreeva, TV and Soshkina, AD and Kunizheva, SS and Manakhov, AD and Pezhemsky, DV and Rogaev, EI},
title = {Great Bolgar's historical genetics: a genomic study of individuals from burials close to the Greek Chamber in the 14th century.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {3},
pages = {423-432},
doi = {10.18699/vjgb-25-45},
pmid = {40556972},
issn = {2500-0462},
abstract = {Bolgar was one of the most significant mediaeval cities in Eastern Europe. Before the Mongol conquest, it served as a major administrative centre of Volga Bulgaria, and after 1236, it temporarily functioned as the capital of the Golden Horde. Historical, archaeological, and paleoanthropological evidence indicates a mixed population of this city during the 13th-15th centuries; however, the contributions of exact ethnic groups into its genetic structure remain unclear. To date, there are no genetic data for this medieval group. For the first time, using massive parallel sequencing methods, we determined whole-genome sequences for three individuals from Bolgar who were buried in the early 14th century close to the so-called "Greek Chamber". The average coverage of the studied genomes ranged from x0.5 to x1.5. We identified the genetic sex of the people (two men and one woman), and performed a population genetic analysis. The authenticity of the DNA studied and the low level of contamination were confirmed, and the mitochondrial DNA haplogroups of all three individuals as well as the Y-chromosome haplogroups of two male individuals were determined. We used more than 2.7 thousand DNA samples from representatives of ancient and modern populations that had been previously published to perform a comparative population-genetic analysis. Whole-genome data analysis employing uniparental markers (mitochondrial DNA and Y chromosome) and autosomal markers revealed genetic heterogeneity in this population. Based on PCA and f4- statistics analysis, a genetic connection was identified between one of the individuals (female) and modern Finno-Ugric peoples of the Volga-Ural region. Genomic analysis of the other two individuals suggests their Armenian origin and indicates migrant influx from the Caucasus or Anatolia. The results align well with archaeological and paleoanthropological findings and significantly enhance them by reconstructing the contributions of the indigenous population to the formation of the mediaeval Bolgar population structure.},
}

@article {pmid40555717,
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 M Virág, Z 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 = {Nature communications},
volume = {16},
number = {1},
pages = {5318},
pmid = {40555717},
issn = {2041-1723},
mesh = {Humans ; *DNA, Ancient/analysis ; Haplotypes ; *Genetics, Population ; History, Ancient ; Genome, Human ; Male ; Genetic Variation ; },
abstract = {Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 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 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.},
}

Humans
*DNA, Ancient/analysis
Haplotypes
*Genetics, Population
History, Ancient
Genome, Human
Male
Genetic Variation

@article {pmid40534706,
year = {2025},
author = {Skinner, L and Felix, M and Rodrigues, CL and Iñiguez, AM},
title = {Genotyping specimens of human lice from a centenary entomological collection.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {7},
number = {},
pages = {100276},
pmid = {40534706},
issn = {2667-114X},
abstract = {Pediculus humanus has been infesting humans since their origin. This obligatory hematophagous and monoxenic parasite has co-evolved with its hosts, carrying genetic information that reflects this long evolutionary history. The ecotypes of P. humanus are divided into six phylogenetic clades (A-F) with distinct geographical distributions. Paleoparasitological studies have revealed a high lice infestation rate in mummies from various chronological periods and cultures worldwide. In this study, we conducted a paleogenetic analysis of head lice specimens from the Entomological Collection of Oswaldo Cruz Institute, collected in Suriname in 1941, to investigate the P. humanus mitochondrial haplotypes that were circulating in that population at that time. Ancient DNA was extracted from adult lice specimens, and paleogenetic analysis was performed using PCR-Sanger sequencing targeting the mitochondrial cytochrome b (cytb) gene. Our results identified sequences belonging to the cosmopolitan clade A, specifically the haplotype A17. A17 is the second largest cosmopolitan haplotype within clade A, with representatives found across all continents, but never found in South America. In 1941, Suriname, as part of the Kingdom of the Netherlands, experienced various socio-political changes and movements of populations due to World War II. This finding reflects both the colonial activities of that time and the global conflicts influencing human migrations. Specimens housed in collections for many decades often exhibit degraded DNA due to preservation techniques being inappropriate for molecular studies, posing challenges for genetic analysis. Our findings highlight the importance of biological collections as valuable repositories of genetic information that can shed light on the past distributions and interactions of parasitic species.},
}

@article {pmid40527453,
year = {2025},
author = {Manin, A and Debruyne, R and Lin, A and Lebrasseur, O and Dimopoulos, EA and González Venanzi, L and Charlton, S and Scarsbrook, L and Hogan, A and Linderholm, A and Boyko, AR and Joncour, P and Berón, M and González, P and Castro, JC and Cornero, S and Cantarutti, G and López Mendoza, P and Martínez, I and Mendoza España, V and Pavlovic, D and Prates, L and Prevosti, F and Rogan, J and Oyaneder, A and Power, X and deFrance, S and Wylde, M and Gutierrez, B and Grouard, S and Freiwald, C and Awe, JJ and Ebert, CE and Hoggarth, JA and Equihua, JC and Pereira, G and Parker, H and Lefèvre, C and Goepfert, N and Ostrander, E and Larson, G and Frantz, L and Hitte, C and Ollivier, M},
title = {Ancient dog mitogenomes support the dual dispersal of dogs and agriculture into South America.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20242443},
pmid = {40527453},
issn = {1471-2954},
support = {//Natural Environment Research Council/ ; //Région Bretagne/ ; //Muséum National d'Histoire Naturelle/ ; //the Intramural Program of the National Human Genome Research Institute of the U.S, National Institute of Health/ ; },
mesh = {Animals ; Dogs/genetics ; *Genome, Mitochondrial ; South America ; *Agriculture ; Phylogeny ; *Animal Distribution ; Archaeology ; },
abstract = {Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.},
}

Animals
Dogs/genetics
*Genome, Mitochondrial
South America
*Agriculture
Phylogeny
*Animal Distribution
Archaeology

@article {pmid40499537,
year = {2025},
author = {Añorve-Garibay, V and Huerta-Sanchez, E and Sohail, M and Ortega-Del Vecchyo, D},
title = {Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2025.05.009},
pmid = {40499537},
issn = {1537-6605},
abstract = {The prediction of phenotypes from ancient humans has gained interest due to its potential to investigate the evolution of complex traits. These predictions are commonly performed using polygenic scores computed with DNA information from ancient humans along with genome-wide association study (GWAS) data from present-day humans. However, numerous evolutionary processes could impact these phenotypic predictions. In this work, we investigate how natural selection shapes the temporal dynamics of variants with an effect on the trait and how these changes impact phenotypic predictions for ancient individuals using polygenic scores. We find that stabilizing selection accelerates the loss of large-effect alleles contributing to trait variation. Conversely, directional selection accelerates the loss of small- and large-effect alleles that drive individuals farther away from the optimal phenotypic value. These phenomena result in specific shared genetic variation patterns between ancient and modern populations that hamper the accuracy of polygenic scores to predict phenotypes. Our results assume perfectly estimated effect sizes at the causal loci of complex traits segregating in a GWAS performed in the present and, therefore, provide a putatively loose upper bound on the polygenic score portability to predict traits in the past. Furthermore, we show how natural selection could impact the predictive accuracy of ancient polygenic scores for two widely studied traits: height and body mass index. Our results emphasize the importance of considering decreases on the reliability of polygenic scores to perform phenotypic predictions in ancient individuals due to allele frequency changes driving the loss of alleles via natural selection.},
}

@article {pmid40497055,
year = {2025},
author = {Wu, X and Liu, P and Yan, F and Jin, R and Zhong, C and Wang, L and Chen, K and Yang, F and Nie, L and Liang, J and Zhou, Y and Ding, B},
title = {Ancient genomes reveal the genetic structure and population interaction in the Central Plains of China during the Eastern Zhou Period.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602625},
pmid = {40497055},
issn = {1664-302X},
abstract = {The Eastern Zhou period (770-256 BCE) was a transformative era in ancient China, marked by intensified social stratification, frequent warfare, and increased population movements. The Western Guo State, as an important vassal state during the Western Zhou period, migrated eastward with King Ping of Zhou and was eventually conquered by the Jin State. Due to limited genomic data, the genetic history of the Guo State population remains unclear. The Shangshihe cemetery, located in Yima City, Henan Province, is hypothesized to be associated with the Guo State and provides an opportunity to understand the genetic dynamics of this period. In our study, we successfully obtained 13 ancient genomes from the Shangshihe cemetery. Our findings suggest notable maternal and paternal genetic diversity within the Shangshihe population, although this observation is limited by the small sample size. Population genomic analysis shows that the Shangshihe individuals are predominantly of Yellow River Basin-related ancestry, with minor contributions from Southern East Asian-related and Eurasian Steppe-related sources. This genetic profile reflects extensive interactions between the Central Plains and surrounding populations during the Eastern Zhou period. Additionally, while distinct Y-chromosome haplogroups were observed among individuals with different burial orientations, autosomal analysis did not detect significant genetic differentiation, indicating overall genetic homogeneity within the population. These results not only elucidate the genetic characteristics of the Guo State population but also provide a new genetic perspective on the population dynamics and cultural exchanges in the Central Plains during the Eastern Zhou period.},
}

@article {pmid40493646,
year = {2025},
author = {Ledger, ML and Murchie, TJ and Dickson, Z and Kuch, M and Haddow, SD and Knüsel, CJ and Stein, GJ and Pearson, MP and Ballantyne, R and Knight, M and Deforce, K and Carroll, M and Rice, C and Franconi, T and Šarkić, N and Redžič, S and Rowan, E and Cahill, N and Poblome, J and Palma, MF and Brückner, H and Mitchell, PD and Poinar, H},
title = {Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {6},
pages = {e0013135},
pmid = {40493646},
issn = {1935-2735},
mesh = {Humans ; *DNA, Ancient/analysis ; Animals ; *Geologic Sediments/parasitology ; Enzyme-Linked Immunosorbent Assay ; *Parasitic Diseases/history/parasitology/epidemiology ; *Parasites/genetics/isolation & purification/classification ; History, Ancient ; Roman World ; Feces/parasitology ; Paleopathology/methods ; Microscopy ; Helminths/genetics/isolation & purification/classification ; DNA, Protozoan/genetics ; High-Throughput Nucleotide Sequencing ; Parasitology/methods ; Trichuris/genetics/isolation & purification ; },
abstract = {The detection of parasite infections in past populations has classically relied on microscopic analysis of sediment samples and coprolites. In recent years, additional methods have been integrated into paleoparasitology such as enzyme-linked immunosorbent assay (ELISA) and ancient DNA (aDNA). The aim of this study was to evaluate a multimethod approach for paleoparasitology using microscopy, ELISA, and sedimentary ancient DNA (sedaDNA) with a parasite-specific targeted capture approach and high-throughput sequencing. Using 26 samples dating from c. 6400 BCE to 1500 CE that were previously analyzed with microscopy and ELISA, we aimed to more accurately detect and reconstruct parasite diversity in the Roman Empire and compare this diversity to earlier and later time periods to explore temporal changes in parasite diversity. Microscopy was found to be the most effective technique for identifying the eggs of helminths, with 8 taxa identified. ELISA was the most sensitive for detecting protozoa that cause diarrhea (notably Giardia duodenalis). Parasite DNA was recovered from 9 samples, with no parasite DNA recovered from any pre-Roman sites. Sedimentary DNA analysis identified whipworm at a site where only roundworm was visible on microscopy, and also revealed that the whipworm eggs at another site came from two different species (Trichuris trichiura and Trichuris muris). Our results show that a multimethod approach provides the most comprehensive reconstruction of parasite diversity in past populations. In the pre-Roman period, taxonomic diversity included a mixed spectrum of zoonotic parasites, together with whipworm, which is spread by ineffective sanitation. We see a marked change during the Roman and medieval periods with an increasing dominance of parasites transmitted by ineffective sanitation, especially roundworm, whipworm and protozoa that cause diarrheal illness.},
}

Humans
*DNA, Ancient/analysis
Animals
*Geologic Sediments/parasitology
Enzyme-Linked Immunosorbent Assay
*Parasitic Diseases/history/parasitology/epidemiology
*Parasites/genetics/isolation & purification/classification
History, Ancient
Roman World
Feces/parasitology
Paleopathology/methods
Microscopy
Helminths/genetics/isolation & purification/classification
DNA, Protozoan/genetics
High-Throughput Nucleotide Sequencing
Parasitology/methods
Trichuris/genetics/isolation & purification

@article {pmid40490443,
year = {2025},
author = {Noda, M and Kishida, T and Kitagawa, H and Fukuyama, I and Nishikawa, K},
title = {Ancient DNA integrates fossil and modern giant salamander taxonomy.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18642},
pmid = {40490443},
issn = {2045-2322},
support = {JPMJSP2110//JST SPRING/ ; 23K23956//Japan Society for the Promotion of Science/ ; JPMEERF20204002//the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency of Japan/ ; },
mesh = {Animals ; *Fossils ; *Caudata/genetics/classification ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics ; Phylogeny ; Japan ; },
abstract = {The genus Andrias includes the largest extant salamanders, and is comprised of one Japanese species A. japonicus and four Chinese species. The fossil record of the giant salamander is incomplete and modern giant salamanders are not differentiated osteologically among species, making it difficult to identify bones at the species level. In this study, we re-examined a fossil series of giant salamander discovered from a cave on Shikoku Island, Japan. We obtained ancient DNA from the fossil and confirmed that the partial sequence of mitochondrial DNA was identical to that of extant A. japonicus. These remains were dated to the Late Pleistocene, however, the result of carbon-14 dating in this study estimated the age as more recent, approximately 3,500-4,100 years ago. Currently, there is a small population of A. japonicus in Shikoku, but it is far removed from the fossil discovery area. Our findings suggest that wild A. japonicus in western Shikoku may have been extirpated very recently.},
}

Animals
*Fossils
*Caudata/genetics/classification
*DNA, Ancient/analysis
*DNA, Mitochondrial/genetics
Phylogeny
Japan

@article {pmid40476363,
year = {2025},
author = {Cheng, X and Steinrücken, M},
title = {diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf123},
pmid = {40476363},
issn = {2160-1836},
abstract = {Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA (aDNA) sequences and data from evolve-and-resequence (E&R) experiments are generated at a rapid pace. Such data presents unprecedented opportunities to elucidate the dynamics of genetic variation under selection. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications. Here, we present diplo-locus, an open-source Python package that provides functionality to simulate and perform inference from time-series data under the Wright-Fisher diffusion with general diploid selection. The package includes Python modules as well as command-line tools and is available at: https://github.com/steinrue/diplo_locus.},
}

@article {pmid40475634,
year = {2025},
author = {Brand, CM and Capra, JA},
title = {A catalog of ancient proxies for modern genetic variants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.19.654975},
pmid = {40475634},
issn = {2692-8205},
abstract = {The ability to observe the genomes of past human populations using ancient DNA provides an extraordinary perspective on many fundamental questions in human genetics, including understanding the evolutionary history of variants that underlie human disease and other phenotypes. However, ancient DNA is often damaged and degraded, yielding low-coverage of most nucleotides. Further, many publicly available genotypes for ancient humans are limited to ∼1.23 million specific loci. Thus, variants of interest often fall outside these specific positions, limiting the ability of ancient DNA to shed light on many loci. Here, we address this challenge by quantifying linkage disequilibrium (LD) between modern variants and ancient genotyped variants (AGVs) to generate a catalog enabling rapid identification of proxy variants. We identified 260,732,675 pairs of AGVs and modern variants with a minimum LD threshold hold of R [2] ≥ 0.2. Even at R [2] ≥ 0.9, ≥ 60% of common variants were linked to an AGV in non-African ancestry groups, as were 34% of common variants in Africans. We evaluated the accuracy of the genotypes inferred from proxy variants in two high-coverage ancient genomes finding that > 90% of genotypes were correctly predicted, even in a 45,000 year old individual. We also find that AGVs are significantly older than expected and that many likely are evolving neutrally. We integrate these results in a database that researchers can easily query to identify ancient proxy variants if their variant of interest is not directly genotyped in ancient humans.},
}

@article {pmid40468069,
year = {2025},
author = {Wang, J and Yan, S and Li, Z and Zan, J and Zhao, Y and Zhao, J and Chen, K and Wang, X and Ji, T and Zhang, C and Yang, T and Zhang, T and Qiao, R and Guo, M and Rao, Z and Zhang, J and Wang, G and Ran, Z and Duan, C and Zhang, F and Song, Y and Wu, X and Mace, R and Sun, B and Pang, Y and Huang, Y and Zhang, H and Ning, C},
title = {Ancient DNA reveals a two-clanned matrilineal community in Neolithic China.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40468069},
issn = {1476-4687},
abstract = {Studies of ancient DNA from cemeteries provide valuable insights into early human societies, and have strongly indicated patrilocality[1-10]. Here, we analysed ancient DNA alongside archaeological contexts and multiple stable isotopic data from 60 individuals in 2 separate cemeteries at the Fujia archaeological site in eastern China, dating between 2750 and 2500 BCE. Our findings suggest the existence of an early-described matrilineal community in the Neolithic period, characterized by high endogamy and a population practicing millet agriculture near the coast. Evidence of intermarriage between individuals in the two cemeteries and the presence of both primary and secondary burials, organized strictly according to maternal clans, underscore a strong sense of social cohesion and identity at Fujia. Bayesian modelling of radiocarbon dates indicates that the two cemeteries were used for approximately 250 years, implying a stable matrilineal lineage spanning at least 10 generations. This study contributes to the ongoing debate in anthropology and archaeology[11], not only suggesting the existence of a matrilineal society in early human history but also revealing a pair of Neolithic cemeteries organized around two matrilineal clans, furthering our understanding of the early evolution of human societies through kinship systems.},
}

@article {pmid40467681,
year = {2025},
author = {Bonczarowska, JH and Wysocka, J and Drupka, B and da Silva, NA and Krause-Kyora, B and Krzepkowski, M},
title = {The outcasts, the sick, and the undead: atypical burials of the late medieval to modern greater Poland.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19608},
pmid = {40467681},
issn = {2045-2322},
support = {EXC 2167 - 390884018//International Max Planck Research School for Evolutionary Biology in Ploen, Germany and the Precision Medicine in Chronic Inflammation (PMI) Cluster/ ; CRC 1266 - 290391021//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Past burial practices can provide insights into the social status of the inhumed and inform us of how the individuals were perceived by their community. Atypical or "deviant" burials may indicate that the deceased was considered an outcast, either due to disease, different provenance, criminal activity, or religious beliefs. To explore the importance of atypical burial practices in medieval and modern Poland, an interdisciplinary study was conducted on three Polish cemeteries (Dzwonowo, Skoki, and Wągrowiec) dating to the 14th -18th centuries CE. Twelve individuals were examined using archaeological evidence, anthropological analysis, and ancient DNA (aDNA) analysis. This study aimed to determine the underlying reasons behind the atypical nature of the burials (i.e., whether the individuals were outsiders, outcasts, relatives, or victims of infectious disease) and shed light on the complex interplay between health, social status, and community perception in medieval and modern Poland. The results revealed that a non-adult male and a middle-aged female, who were holding hands in a double burial in Skoki, possibly died from the plague. Yersinia pestis DNA was recovered from the non-adult individual, making it the third confirmed case of plague in Poland. Using the nonmetric skeletal traits, archaeological assemblage, and aDNA analysis, we identified several individuals as likely "outsiders" in the community. The results of this study expand our knowledge of past societal structures and cultural responses to disease as well as provide crucial context for interpreting burial patterns elsewhere in Europe.},
}

@article {pmid40465848,
year = {2025},
author = {Wang, R and Zhu, L and Ma, H and Song, M and Ma, G and Wang, B and Fu, L and Hao, J and Fu, G and Wang, J and Wang, Q and Zhu, K and Yang, X and Xu, Y and Tao, L and He, H and Li, S and Jiang, J and Zhang, W and Wang, CC and Cong, B},
title = {Genetic formation of Neolithic Hongshan people and demic expansion of Hongshan culture inferred from ancient human genomes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf139},
pmid = {40465848},
issn = {1537-1719},
abstract = {The Hongshan culture, situated at the crossroads of northern and northeast China, represented one of the earliest complex societies in Neolithic East Asia. The remains of Hongshan culture have been found in an area stretching from today's Inner Mongolia Autonomous Region to Liaoning Province, covering an area of over 200,000 square kilometers. However, the question of how Hongshan culture occupied such a vast geographical location, following either the demic diffusion (i.e., genetic interaction accompanied by cultural expansion) or cultural diffusion model (i.e., local groups adopting new culture without receiving genetic influence), remains unanswered due to a lack of ancient genomes. Here, we report genome-wide data from 19 individuals associated with the Hongshan culture, from the Zhengjiagou site in Hebei Province, the westernmost and southernmost Hongshan culture-related site discovered to date. We co-analyzed our newly generated Hebei Hongshan genomes with previously published 3 Hongshan culture-related genomes from the Banlashan site in Liaoning Province, located in the core region of Hongshan culture and about 473 km away from the Zhengjiagou site. Our genetic results revealed strong genetic links between the Hebei Hongshan and Liaoning Hongshan people, supporting the demic diffusion of the Hongshan culture. Both Liaoning and Hebei Hongshan people harboured Ancient Northeast Asian-related (possibly related to the local earlier Zhaobaogou culture) and Neolithic Yangshao culture-related millet farmer ancestries. Interestingly, our ancestral modelling suggested that Yangshao culture-related ancestry in the Hongshan people was more likely introduced by middle Neolithic Dawenkou culture-related farmers from Shandong, who carried about 40% of an early Neolithic Shandong hunter-gatherer-related lineage and 60% of a Yangshao culture-related lineage. Our findings highlight a complex interconnected gene pool among the West Liao River, the Central Plain, and Shandong during the middle Neolithic period.},
}

@article {pmid40461538,
year = {2025},
author = {Santana, J and Del Pino Curbelo, M and Iriarte, E and Morales, J and Caro, JL and Fregel, R and Hagenblad, J and García González, R and Rodríguez Rodríguez, A},
title = {Climate, biogeography, and human resilience in the demographic history of the Canary Islands during the Amazigh period.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19485},
pmid = {40461538},
issn = {2045-2322},
support = {851733//H2020 European Research Council/ ; RTI2018-101923-J-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Humans ; Spain ; *Climate ; Climate Change ; Population Dynamics ; History, Medieval ; History, Ancient ; History, 15th Century ; Radiometric Dating ; Agriculture ; Islands ; Demography ; },
abstract = {This study explores the dynamic interplay between biogeography, climate variability, and human agency in shaping the population trajectories of Amazigh communities in the Canary Islands (1st to fifteenth centuries cal CE). Using radiocarbon dating as a proxy for population size, this research suggests potential links between demographic trends and environmental factors, highlighting how climatic phases influence agricultural productivity and settlement patterns. Favorable conditions during the Roman Warm Period (RWP) facilitated population expansion, whereas climatic stress during positive phases of the North Atlantic oscillation (NAO) (700-800 cal CE) led to significant demographic declines, particularly on smaller and more arid islands. Larger and ecologically more diverse islands, such as Gran Canaria and Tenerife, showed resilience due to their ecological diversity, agricultural innovations, and food security strategies, which supported sustained growth even during challenging periods such as the Early Medieval Climate Anomaly (MCA, 800-1150 cal CE). From 1150 to 1350 cal CE, cooler sea surface temperatures and a prevailing negative NAO phase increased marine productivity, enabling demographic recovery across islands. However, the arrival of Europeans in the fourteenth-fifteenth centuries introduced external disruptions, including slave raids, novel pathogens, and land seizures, leading to societal collapse. Overall, this study highlights the critical role of environmental diversity and agricultural adaptability in supporting human populations through climatic change and offers valuable perspectives on the relationships among climate, biogeography and human societies.},
}

Humans
Spain
*Climate
Climate Change
Population Dynamics
History, Medieval
History, Ancient
History, 15th Century
Radiometric Dating
Agriculture
Islands
Demography

@article {pmid40460935,
year = {2025},
author = {Qi, B and Dou, H and Liu, W and Bennett, A and Rao, H and Yang, Y},
title = {Differentiating goose eggshells through proteomics: A case study from Xitou, North China.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105467},
doi = {10.1016/j.jprot.2025.105467},
pmid = {40460935},
issn = {1876-7737},
abstract = {Eggshells are significant cultural symbols linked to funeral customs and social development. Identifying their species is crucial in archaeological research. However, their small fragment size makes eggshells difficult to accurately identify using traditional methods. Recent mass spectrometry advances have significantly enhanced eggshell species identification in archaeological research, but their success remains limited. For example, Anser cygnoides and Anser anser eggshells cannot yet be reliably distinguished. This paleoproteomic study uses Zooarchaeology by Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry to identify by proteotyping the species of eggshells from the Xitou site in China. We established a series of peptide markers and amino acid variants to distinguish A. cygnoides from A. anser, and with this method attribute three Xitou eggshell specimens to the graylag goose. Carbon isotope analysis and shell thickness measurements were conducted to understand the domestication of the geese associated with these eggshells. The isotope results indicate that these geese primarily ate C3 plants, and shell thickness results suggest they were possibly domesticated. These findings firstly provide direct molecular evidence of possibly domesticated graylag geese in China and offer new insights into poultry domestication and cultural practices. SIGNIFICANCE: Combing ZooMS and LC-MS/MS analysis, we have identified novel peptide markers to distinguish the eggshells of swan goose (Anser cygnoides) from those of graylag goose (Anser anser). Using a series of ZooMS markers and amino acid variations, the eggshells from Xitou site (north China) were identified to be derived from graylag goose. Further eggshells thickness and isotope analysis show that these geese were likely domesticated and primarily fed on C3 plants, offering valuable insights into early geese farming and sustainable practices during the Western Zhou period. Furthermore, the discovery of eggs as burial items highlights the important role that geese played in ancient Chinese culture and rituals.},
}

@article {pmid40447800,
year = {2025},
author = {Bythell-Douglas, R and van Twest, S and Abbouche, L and Dunn, E and Coulthard, RJ and Briggs, DC and Murphy, V and Zhang, X and Tan, W and Henrikus, SS and Qian, D and Wu, Y and Wolf, J and Rigoreau, L and Shakeel, S and Chapman, KL and McDonald, NQ and Deans, AJ},
title = {Structural basis of Fanconi anemia pathway activation by FANCM.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40447800},
issn = {1460-2075},
support = {GNT1181110//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; CC2068/WT_/Wellcome Trust/United Kingdom ; },
abstract = {FANCM is crucial in genome maintenance, functioning in the Fanconi anemia (FA) pathway, alternative lengthening of telomeres (ALT), and replication fork protection. FANCM recognizes branched DNA structures and promotes their remodeling through ATP-dependent branch migration. The protein has emerged as a promising therapeutic target due to synthetic lethal interactions with BRCA1, SMARCAL1, and RAD52, and in ALT-positive cancers. Here we present crystal structures of FANCM's N-terminal ATP-dependent translocase domain (2.2 Å) and C-terminal FAAP24-bound region (2.4 Å), both complexed with branched DNA. Through structural analysis, biochemical reconstitution, and cellular studies, we demonstrate that FANCM employs two distinct mechanisms: an ATP-dependent branch migration activity essential for DNA damage survival, and a branched DNA-binding mode that enhances FANCD2-FANCI monoubiquitination through FA core complex interaction. The N-terminal translocase domain specifically recognizes DNA junctions through multiple key elements, while the C-terminal FAAP24-binding domain engages adjacent double-stranded DNA. Our results reveal how FANCM evolved from an ancient DNA repair motor into a sophisticated sensor that couples DNA damage recognition to selective pathway activation, providing a structural framework for developing targeted therapeutics.},
}

@article {pmid40444660,
year = {2025},
author = {Lopez-Valdivia, I and Vallebueno-Estrada, M and Rangarajan, H and Swarts, K and Benz, BF and Blake, M and Sidhu, JS and Perez-Limon, S and Sawers, RJH and Schneider, H and Lynch, JP},
title = {In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacán.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70245},
pmid = {40444660},
issn = {1469-8137},
support = {847548//European Union's Framework Programme for Research and Innovation Horizon 2020/ ; 602757//Foundation for Food and Agriculture Research/ ; //Social Sciences and Humanities Research Council of Canada/ ; 0091490//National Science Foundation/ ; PEN04732//United States Department of Agriculture-National Institiute of Food and Agriculture/ ; },
abstract = {Roots are essential for plant adaptation to changing environments, yet the role of roots in crop domestication remains unclear. This study examined the evolution of root phenotypes from teosinte to maize, a transition resulting in reduced nodal root number (NRN), multiseriate cortical sclerenchyma (MCS), and increased seminal root number (SRN). We reconstructed the root phenotypes of maize and teosinte, as well as the environments of the Tehuacán Valley over the last 18 000 yr using a combination of ancient DNA, paleobotany, and functional-structural modeling. Our models reveal that increasing Holocene atmospheric CO2 concentrations favored the appearance of reduced NRN and MCS between 12 000 and 8000 yr before present (yrBP), promoting deeper root systems. The advent of irrigation by 6000 yrBP switched nitrogen distribution from topsoil to subsoil domains, a change that increased the utility of reduced NRN and MCS. Comparison of allelic frequencies among ancient samples ranging from 5500 to 500 yrBP suggests that increased SRN may have appeared c. 3500 yrBP, coinciding with a period of increased human population, agricultural intensification, and soil degradation. Our results suggest that root phenotypes that enhance plant performance under nitrogen stress are important for maize adaptation to changing agricultural practices in the Tehuacán Valley.},
}

@article {pmid40441135,
year = {2025},
author = {Murray, M and Nakamura, S and Fuentes, M and Canizales, R and Talavera, O and Varela, S and Madrid, Z and Carbajal, C and Ogawa, M and Yoneda, M and Cassidy, LM and Gakuhari, T and Nakagome, S},
title = {Ancient genomes reveal demographic trajectories during the Classic Maya period.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.05.002},
pmid = {40441135},
issn = {1879-0445},
abstract = {Copán was a major capital at the southeasternmost extreme of the Classic Maya civilization, serving as a crossroads connecting Central and South America. In 426/427 CE, the city witnessed the establishment of a royal dynasty, which endured for approximately 400 years. Despite extensive historical and archaeological records, there remains limited information regarding the genetic profile of people who resided in Copán. Here, we present genomes from seven Classic Copán individuals, including a potential member of the ruling dynasty and an accompanying sacrificial burial. Our analysis shows that the population associated with the Classic Copán culture forms a genetic cluster with the Late Archaic population from Belize, as well as with the Terminal Classic Maya from Chichén Itzá, the Colonial Maya from Campeche, and present-day Maya, all from Mexico. Using Late Archaic Belize as a source of local ancestry, we identify an influx of ancestry associated with highland Mexican populations from the Early-to-Middle Classic period onward, underscoring the role of gene flow in the formation of the Classic Maya state. Estimates of effective population size suggest a decline at the end of the Classic period, when Classic Maya civilization experienced widespread destabilization and collapse.},
}

@article {pmid40440428,
year = {2025},
author = {Lopopolo, M and Avanzi, C and Duchene, S and Luisi, P and de Flamingh, A and Ponce-Soto, GY and Tressieres, G and Neumeyer, S and Lemoine, F and Nelson, EA and Iraeta-Orbegozo, M and Cybulski, JS and Mitchell, J and Marks, VT and Adams, LB and Lindo, J and DeGiorgio, M and Ortiz, N and Wiens, C and Hiebert, J and Bonifaz, A and Montes de Oca, G and Paredes-Solis, V and Franco-Paredes, C and Vera-Cabrera, L and Pereira Brunelli, JG and Jackson, M and Spencer, JS and Salgado, CG and Han, XY and Pearce, CM and Warren, AK and Rosa, PS and de Finardi, AJ and Belone, AFF and Ferreira, C and Suffys, PN and Fontes, ANB and Vasconcellos, SEG and Schaub, R and Couppié, P and Drak Alsibai, K and Hernández-Castro, R and Silva Miranda, M and Estrada-Garcia, I and Jurado-Santacruz, F and Orlando, L and Schroeder, H and Quintana-Murci, L and Del Papa, M and Lahiri, R and Malhi, RS and Rasmussen, S and Rascovan, N},
title = {Pre-European contact leprosy in the Americas and its current persistence.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadu7144},
doi = {10.1126/science.adu7144},
pmid = {40440428},
issn = {1095-9203},
abstract = {Leprosy, primarily caused by Mycobacterium leprae, is considered a disease introduced into the Americas during European colonization. However, the recent discovery of a second pathogen causing leprosy, M. lepromatosis, mainly found in the Americas, challenges this view. Here, we show that M. lepromatosis infected humans in the Americas before European contact. By screening 389 ancient and 408 contemporary samples, we have expanded the genetic data available for the species. Phylogenetic analyses revealed distinct human-infecting clades of M. lepromatosis, with one dominating North America since colonial times. The presence of millennia-old strains in North and South America indicates M. lepromatosis may have been widespread during the Late Holocene, demonstrating M. lepromatosis leprosy has a long-standing history in the Americas before European arrival.},
}

@article {pmid40440389,
year = {2025},
author = {Sidhu, RK and Mas Fiol, G and Lê-Bury, P and Demeure, CE and Bougit, E and Beau, R and Balière, C and Kwasiborski, A and Caro, V and Klunk, J and Salkeld, DJ and Carmichael, A and Varlık, N and Poinar, D and Earn, DJD and Bolker, BM and Dushoff, J and Golding, GB and Rascovan, N and Dussurget, O and Holmes, EC and Pizarro-Cerdá, J and Poinar, HN},
title = {Attenuation of virulence in Yersinia pestis across three plague pandemics.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6750},
pages = {eadt3880},
doi = {10.1126/science.adt3880},
pmid = {40440389},
issn = {1095-9203},
mesh = {*Yersinia pestis/pathogenicity/genetics ; *Plague/epidemiology/microbiology/mortality ; Animals ; Mice ; Virulence/genetics ; *Pandemics ; *Bacterial Proteins/genetics ; Humans ; Plasmids/genetics ; *Pore Forming Cytotoxic Proteins/genetics ; *Plasminogen Activators/genetics ; Rodentia/microbiology ; Gene Deletion ; Female ; Disease Models, Animal ; },
abstract = {Yersinia pestis has spilled over from wild rodent reservoirs to commensal rodents and humans, causing three historically recorded pandemics. Depletion in the copy number of the plasmid-encoded virulence gene pla occurred in later-dated strains of the first and second pandemics, yet the biological relevance of the pla deletion has been difficult to test. We identified modern Y. pestis strains that independently acquired the same pla depletion as ancient strains and herein show that excision of pla from the multicopy pPCP1 plasmid is accompanied by the integration of a separate full pPCP1 harboring pla into the single-copy pCD1 plasmid, reducing pla dosage. Moreover, we demonstrate that this depletion decreases the mortality of mice in models of bubonic plague but not in the pneumonic and septicemic forms of the disease. We hypothesize that pla depletion may have been selectively advantageous in bubonic plague, owing to rodent fragmentation after pandemic-induced mortality.},
}

*Yersinia pestis/pathogenicity/genetics
*Plague/epidemiology/microbiology/mortality
Animals
Mice
Virulence/genetics
*Pandemics
*Bacterial Proteins/genetics
Humans
Plasmids/genetics
*Pore Forming Cytotoxic Proteins/genetics
*Plasminogen Activators/genetics
Rodentia/microbiology
Gene Deletion
Female
Disease Models, Animal

@article {pmid40439179,
year = {2025},
author = {Zhang, M and Wang, C and Zheng, Y and Ni, X and Hu, S and Zhuang, L and Guo, M and Dai, Q and Cao, P and Ren, L and Dong, G and Yang, R and Liu, F and Feng, X and Hou, H and Wang, H and Wang, W and Zhang, L and Bennett, EA and Fu, Q},
title = {Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Gray Wolves (Canis lupus).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.13005},
pmid = {40439179},
issn = {1749-4877},
support = {41925009//National Natural Science Foundation of China/ ; 41625005//National Natural Science Foundation of China/ ; 2022YFE0203800//National Key R&D Program of China/ ; 2024RS-CXTD-74//Science and Technology Innovation Team of Shaanxi Province/ ; YSBR-019//Ministry of Finance of the People's Republic of China/ ; },
abstract = {The gray wolf (Canis lupus) is the only wild ancestor of dogs (Canis lupus familiaris) and serves a crucial role in understanding the highly controversial issue of dog origins. Recently, ancient DNA studies on gray wolves from different regions of the Eurasian continent have achieved significant breakthroughs, providing important clues about the dog origins. As one of the potential origin areas for dogs, East Asia has seen some research on ancient dogs; however, reports related to gray wolves remain limited. In this study, we sequenced seven new mitogenomes of ancient gray wolves from Northern China, integrating them with 497 ancient and modern canid mitogenomes from published data. Our results reveal the following: (1) East Asian gray wolves have maintained high genetic diversity from ancient times to the present; (2) multiple haplogroup A gray wolves from Northern China support the hypothesis that Northeastern Eurasia is a core region for dog origins; (3) a deep gray wolf lineage in East Asia has been identified in this study; (4) different mitogenomes concentrated at the Jinchankou site indicate that admixture may have frequently occurred in the northeastern edge of the Tibetan Plateau. These findings enhance our understanding of the maternal genetic history of gray wolves in East Asia.},
}

@article {pmid40435234,
year = {2025},
author = {Krettek, KL and Casas-Vargas, A and Mas-Sandoval, A and Alvis, LA and Reiter, E and Madero, JM and Urban, M and Vargas, JCN and Usaquén, W and Cuenca, JVR and Posth, C},
title = {A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia.},
journal = {Science advances},
volume = {11},
number = {22},
pages = {eads6284},
pmid = {40435234},
issn = {2375-2548},
mesh = {Colombia ; Humans ; *Genomics/methods ; *Genetics, Population ; *Genome, Human ; *Indians, South American/genetics ; Phylogeny ; },
abstract = {Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.},
}

Colombia
Humans
*Genomics/methods
*Genetics, Population
*Genome, Human
*Indians, South American/genetics
Phylogeny

@article {pmid40431178,
year = {2025},
author = {Ekram, MA and Wuchter, C and Bijaksana, S and Grice, K and Russell, J and Stevenson, J and Vogel, H and Coolen, MJL},
title = {A Quaternary Sedimentary Ancient DNA (sedaDNA) Record of Fungal-Terrestrial Ecosystem Dynamics in a Tropical Biodiversity Hotspot (Lake Towuti, Sulawesi, Indonesia).},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051005},
pmid = {40431178},
issn = {2076-2607},
abstract = {Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi-soil-plant interactions, particularly in undersampled, floristically diverse tropical forests. We recently conducted trnL-P6 amplicon sequencing to generate a sedimentary ancient DNA (sedaDNA) record of the regional catchment vegetation of the tropical waterbody Lake Towuti (Sulawesi, Indonesia), spanning over one million years (Myr) of the lake's developmental history. In this study, we performed 18SV9 amplicon sequencing to create a parallel paleofungal record to (a) infer the composition, origins, and functional guilds of paleofungal community members and (b) determine the extent to which downcore changes in fungal community composition reflect the late Pleistocene evolution of the Lake Towuti catchment. We identified at least 52 members of Ascomycota (predominantly Dothiodeomycetes, Eurotiomycetes, and Leotiomycetes) and 12 members of Basidiomycota (primarily Agaricales and Polyporales). Spearman correlation analysis of the relative changes in fungal community composition, geochemical parameters, and paleovegetation assemblages revealed that the overwhelming majority consisted of soil organic matter and wood-decaying saprobes, except for a necrotrophic phytopathogenic association between Mycosphaerellaceae (Cadophora) and wetland herbs (Alocasia) in more-than-1-Myr-old silts and peats deposited in a pre-lake landscape, dominated by small rivers, wetlands, and peat swamps. During the lacustrine stage, vegetation that used to grow on ultramafic catchment soils during extended periods of inferred drying showed associations with dark septate endophytes (Ploettnerulaceae and Didymellaceae) that can produce large quantities of siderophores to solubilize mineral-bound ferrous iron, releasing bioavailable ferrous iron needed for several processes in plants, including photosynthesis. Our study showed that sedaDNA metabarcoding paired with the analysis of geochemical parameters yielded plausible insights into fungal-plant-soil interactions, and inferred changes in the paleohydrology and catchment evolution of tropical Lake Towuti, spanning more than one Myr of deposition.},
}

@article {pmid40426041,
year = {2025},
author = {Zabel, S and Breitling, S and Posth, C and Nieselt, K},
title = {A probabilistic approach to visualize the effect of missing data on PCA in ancient human genomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {537},
pmid = {40426041},
issn = {1471-2164},
support = {16DHBKI086//Federal Ministry of Education and Research, Germany/ ; W73/2022//Leibniz ScienceCampus "Geogenomic Archaeology Campus Tübingen (GACT)"/ ; },
mesh = {Humans ; *Genomics/methods ; *DNA, Ancient/analysis ; *Principal Component Analysis ; *Genome, Human ; Genotype ; Genetics, Population ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Principal Component Analysis (PCA) is widely used in population genetics to visualize genetic relationships and population structures. In ancient genomics, genotype information may in parts remain unresolved due to the low abundance and degraded quality of ancient DNA. While methods like SmartPCA allow the projection of ancient samples despite missing data, they do not quantify projection uncertainty. The reliability of PCA projections for often very sparse ancient genotype samples is not well understood. Ignoring this uncertainty may lead to overconfident conclusions about the observed genetic relationships and population structure.

RESULTS: This study systematically investigates the impact of missing loci on PCA projections using both simulated and real ancient human genotype data. Through extensive simulations with high-coverage ancient samples, we demonstrate that increasing levels of missing data can lead to less accurate SmartPCA projections, highlighting the importance of considering uncertainty when interpreting PCA results from ancient samples. To address this, we developed a probabilistic framework to quantify the uncertainty in PCA projections due to missing data. By applying our methodology to modern and ancient West Eurasian genotype samples from the Allen Ancient DNA Resource database, we could show a high concordance between our predicted projection and empirically derived distributions. Applying this framework to real-world data, we demonstrate its utility in predicting and visualizing embedding uncertainties for ancient samples of varying SNP coverages.

CONCLUSION: Our results emphasize the importance of accounting for projection uncertainty in ancient population studies. We therefore make our probabilistic model available through TrustPCA, a user-friendly web tool that provides researchers with uncertainty estimates alongside PCA projections, facilitating data exploration in ancient human genomic studies and enhancing transparency in data quality reporting.},
}

Humans
*Genomics/methods
*DNA, Ancient/analysis
*Principal Component Analysis
*Genome, Human
Genotype
Genetics, Population
Polymorphism, Single Nucleotide

@article {pmid40411280,
year = {2025},
author = {Grasso, G and Debruyne, R and Adamo, M and Rué, O and Lejzerowicz, F and Bittner, L and Bianciotto, V and Marmeisse, R},
title = {Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14122},
doi = {10.1111/1755-0998.14122},
pmid = {40411280},
issn = {1755-0998},
support = {//Sorbonne Université/ ; //Università Italo Francese/ ; //Università degli Studi di Torino/ ; ATM2021//Muséum National d'Histoire Naturelle/ ; //CNR: Short-Term Mobility (2023) program/ ; },
abstract = {Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.},
}

@article {pmid40403731,
year = {2025},
author = {Zhang, Y and Wang, J and Yi, C and Su, Y and Yin, Z and Zhang, S and Jin, L and Stoneking, M and Yang, J and Wang, K and Huang, H and Li, J and Fan, S},
title = {An ancient regulatory variant of ACSF3 influences the coevolution of increased human height and basal metabolic rate via metabolic homeostasis.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100855},
doi = {10.1016/j.xgen.2025.100855},
pmid = {40403731},
issn = {2666-979X},
abstract = {Anatomically modern humans (AMHs) exhibit a significant increase in basal metabolic rate (BMR) and height compared to non-human apes. This study investigates the genetic basis underlying these traits. Our analyses reveal a strong genetic correlation between height and BMR. A regulatory mutation, rs34590044-A, was found to be associated with the increased height and BMR in AMHs. rs34590044-A upregulates the expression of ACSF3 by increasing its enhancer activity, leading to increased body length and BMR in mice fed essential amino acids which are characteristic of meat-based diets. In the British population, rs34590044-A has been under positive selection over the past 20,000 years, with a particularly strong signal in the last 5,000 years, as also evidenced by ancient DNA analysis. These results suggest that the emergence of rs34590044-A may have facilitated the adaptation to a meat-enriched diet in AMHs, with increased height and BMR as consequences of this dietary shift.},
}

@article {pmid40392844,
year = {2025},
author = {Andrews, AJ and Eriksen, EF and Star, B and Præbel, K and Di Natale, A and Malca, E and Onar, V and Aniceti, V and Carenti, G and Piquès, G and Nielsen, SV and Persson, P and Piattoni, F and Fontani, F and Atmore, LM and Kersten, O and Tinti, F and Cilli, E and Cariani, A},
title = {Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2409302122},
doi = {10.1073/pnas.2409302122},
pmid = {40392844},
issn = {1091-6490},
support = {813383//EU Horizion 2020/ ; },
mesh = {Animals ; *Tuna/genetics ; *DNA, Ancient/analysis ; Genetic Variation ; Population Dynamics ; Atlantic Ocean ; Conservation of Natural Resources ; },
abstract = {Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n = 49) and ancient (n = 41) specimens dating up to 5,000 y ago, uncovering several findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.},
}

Animals
*Tuna/genetics
*DNA, Ancient/analysis
Genetic Variation
Population Dynamics
Atlantic Ocean
Conservation of Natural Resources

@article {pmid40392669,
year = {2025},
author = {Letsch, H and Greve, C and Hundsdoerfer, AK and Irisarri, I and Moore, JM and Espeland, M and Wanke, S and Arifin, U and Blom, MPK and Corrales, C and Donath, A and Fritz, U and Köhler, G and Kück, P and Lemer, S and Mengual, X and Salas, NM and Meusemann, K and Palandačić, A and Printzen, C and Sigwart, JD and Silva-Brandão, KL and Simões, M and Stange, M and Suh, A and Szucsich, N and Tilic, E and Töpfer, T and Böhne, A and Janke, A and Pauls, S},
title = {Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf040},
pmid = {40392669},
issn = {1076-836X},
abstract = {Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species. While the results of genome sequencing are often connected to a physical voucher specimen, they are rarely derived from the ultimate taxonomic reference for a species, i.e., the name-bearing type specimens. This is a known but under-appreciated problem for ensuring the replicability of findings, especially those that affect the interpretation of biodiversity distributions and phylogenetic relationships. Destructive sampling of museum specimens, particularly of type material, often carries a high risk of sequencing failure, and thus the cost of damage to the specimen may outweigh the resulting benefit. Both taxonomic work and genome sequencing require specialist skills and there are often communication gaps between the respective experts. A new, harmonised approach, maximising information extraction while minimising risk to type specimens, is a critical step forward toward linking disciplines across biodiversity research and promoting a better taxonomic and systematic understanding of eukaryotic diversity. The genetic make-up of a type specimen is a fundamental part of its biological information, which can and should be made freely and digitally available through type genomics. Here we describe guidelines for the use of nomenclatural types in genome sequencing approaches considering different kinds of types in different stages of preservation and different data types.},
}

@article {pmid40390081,
year = {2025},
author = {Beneker, O and Molinaro, L and Guellil, M and Sasso, S and Kabral, H and Bonucci, B and Gaens, N and D'Atanasio, E and Mezzavilla, M and Delbrassine, H and Braet, L and Lambert, B and Deckers, P and Biagini, SA and Hui, R and Becelaere, S and Geypen, J and Hoebreckx, M and Berk, B and Driesen, P and Pijpelink, A and van Damme, P and Vanhoutte, S and De Winter, N and Saag, L and Pagani, L and Tambets, K and Scheib, CL and Larmuseau, MHD and Kivisild, T},
title = {Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {127},
pmid = {40390081},
issn = {1474-760X},
support = {G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; S003422N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; ZKD6488 C24M/19/075//KU Leuven/ ; ZKD6488 C24M/19/075//KU Leuven/ ; ZKD6488 C24M/19/075//KU Leuven/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; 10.55776/ESP162//Austrian Science Fund/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; 885137/ERC_/European Research Council/International ; CZ.02.01.01/00/22_008/0004593//Czech Ministry of Education, Youth and Sports/ ; 3M220588//Agentschap Onroerend Erfgoed/ ; },
mesh = {Humans ; History, Medieval ; *Urbanization/history ; Belgium ; Genetic Variation ; Genetics, Population ; Genomics ; Plague/epidemiology/history/genetics ; Genome, Human ; },
abstract = {BACKGROUND: Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes.

RESULTS: We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes.

CONCLUSIONS: This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.},
}

Humans
History, Medieval
*Urbanization/history
Belgium
Genetic Variation
Genetics, Population
Genomics
Plague/epidemiology/history/genetics
Genome, Human

@article {pmid40383374,
year = {2025},
author = {Chen, Y and Xu, Y and Zhu, K and Wang, CC},
title = {ADGAP: a user-friendly online Ancient DNA Database and Genome Analysis Platform.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2025.05.006},
pmid = {40383374},
issn = {1673-8527},
}

@article {pmid40374632,
year = {2025},
author = {Schreiber, L and Ribeiro, S and Jackson, R and Kvorning, AB and Nota, K and O'Regan, M and Pearce, C and Seersholm, F and Seidenkrantz, MS and Zimmermann, HH and Lorenzen, ED},
title = {Holocene shifts in marine mammal distributions around Northern Greenland revealed by sedimentary ancient DNA.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4543},
pmid = {40374632},
issn = {2041-1723},
mesh = {Animals ; Greenland ; *Geologic Sediments/chemistry ; *Mammals/genetics/physiology ; Fossils ; *DNA, Ancient/analysis ; Ecosystem ; Climate Change ; Ice Cover ; Arctic Regions ; *Aquatic Organisms/genetics ; Temperature ; },
abstract = {Arctic marine ecosystems have undergone notable reconfigurations in response to Holocene climate and environmental changes. Yet our understanding of how marine mammal occurrence was impacted remains limited, due to their relative scarcity in the fossil record. We reconstruct the occurrence of marine mammals across the past 12,000 years through detections based on sedimentary ancient DNA from four marine sediment cores collected around Northern Greenland, and integrate the findings with local and regional environmental proxy records. Our findings indicate a close association between marine mammals at densities detectable in marine sediments and the deglaciation of high Arctic marine environments at the onset of the Holocene. Further, we identify air temperature and changes in sea ice cover as significant drivers of community change across time. Several marine mammals are detected in the sediments earlier than in the fossil record, for some species by several thousand years. During the Early-to-Mid Holocene, a period of warmer climate, we record northward distribution shifts of temperate and low-arctic marine mammal species. Our findings provide unique, long-term baseline data on the occurrence of marine mammals around Northern Greenland, enabling insights into past community dynamics and the effects of Holocene climatic shifts on the region's marine ecosystems.},
}

Animals
Greenland
*Geologic Sediments/chemistry
*Mammals/genetics/physiology
Fossils
*DNA, Ancient/analysis
Ecosystem
Climate Change
Ice Cover
Arctic Regions
*Aquatic Organisms/genetics
Temperature

@article {pmid40368150,
year = {2025},
author = {Mascarenhas, S and Hodgins, HP and Doxey, AC},
title = {Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {108405},
doi = {10.1016/j.toxicon.2025.108405},
pmid = {40368150},
issn = {1879-3150},
abstract = {BACKGROUND: Ancient DNA collected from archaeological specimens not only provides a window into ancient human genetic diversity but also contains a rich mixture of associated microbial DNA including potential pathogens. In recent work, we identified C. tetani and tetanus neurotoxin (TeNT) genes in ancient DNA datasets collected from human archaeological specimens. However, the reasons underlying the occurrence of these toxin genes and the extent to which other toxin genes are present in ancient DNA is unclear.

METHODS: Here, we performed a large-scale analysis of 6,435 ancient DNA (aDNA) sequencing datasets including human and non-human sources, searching for 49 clostridial neurotoxin types and subtypes, as well as 3 additional unrelated toxins.

RESULTS: Our search identified a total of 105 ancient DNA datasets (1.6%) containing significant matches to one or more neurotoxin genes. Consistent with our earlier work, TeNT genes were most common, found in 50 ancient DNA datasets. In addition, we identified sequences encoding diverse botulinum neurotoxins including BoNT/C (40 samples), BoNT/D (6 samples), BoNT/B (4 samples), BoNT/E (1 sample), and the Enterococcus-associated BoNT/En (10 samples). TeNT genes were detected in a broad range of ancient samples including human and animal (horse, wild bear, chimpanzee, gorilla, dog) remains, whereas the largest diversity of toxins was detected in aDNA from Egyptian mummies. Phylogenetic and sequence analysis of the identified matches revealed close identity to modern forms of these toxins. Damage analysis revealed several toxin genes with hallmarks of ancient DNA associated damage, indicative of an ancient origin.

CONCLUSIONS: Our work reveals that clostridial neurotoxin genes occur frequently in aDNA samples, including human and animal-associated toxin variants. We conclude that the frequent association of these genes with aDNA likely reflects a strong ecological association of pathogenic clostridia with decaying human and animal remains and possible post-mortem colonization of these samples.},
}

@article {pmid40367347,
year = {2025},
author = {Liu, L and Zhu, S and Gu, Y and Tao, S and Krock, B and Wang, C and Shi, X and Yan, Q and Pan, X and Chen, J and Lin, S and Luo, Z},
title = {Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf095},
pmid = {40367347},
issn = {1751-7370},
abstract = {Existing data and models suggest increasing prominence of dinoflagellates and their blooms in future warmer ocean but supporting long-term data are sparse. Here, we used 18S rRNA gene sequencing to investigate sedimentary ancient dinoflagellate communities in northern South China Sea and compared them with contemporary dinoflagellate data from global oceans (TARA Oceans data) and 40 years of dinoflagellate bloom records in China. We found a continuous warming (by ~4.3°C in mean annual sea surface temperature) from 12 to 4.3 kiloyears before present (kyr BP), which caused an initial increase in the relative abundance and diversity of dinoflagellates, followed by a decrease reaching the lowest value, probably due to thermal stress. However, dinoflagellates flourished again after 4.3 kyr BP, coinciding with a rapid increase in human activities. Further analyses indicated that warming and environmental changes during the Holocene favored dinoflagellate generalists over specialists. These generalists have also been abundant throughout contemporary low- and mid-latitude regions, whereas specialists were more abundant at higher latitudes. The predominant generalist genera Noctiluca, Gymnodinium, and Prorocentrum in core sediment corresponded to taxa responsible for most dinoflagellate blooms in the contemporary China Seas over the past 40 years. The success of generalists during warmer periods suggests that dinoflagellate blooms are likely to expand geographically rather than simply shift toward high latitudes under global warming. Moreover, the homogenization of dinoflagellate communities resulting from generalist expansion may significantly reduce the complexity of marine plankton interactions and compromise ecosystem services under global warming.},
}

@article {pmid40360796,
year = {2025},
author = {Amjadi, MA and Özdemir, YC and Ramezani, M and Jakab, K and Megyes, M and Bibak, A and Salehi, Z and Hayatmehar, Z and Taheri, MH and Moradi, H and Zargari, P and Hasanpour, A and Jahani, V and Sharifi, AM and Egyed, B and Mende, BG and Tavallaie, M and Szécsényi-Nagy, A},
title = {Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16530},
pmid = {40360796},
issn = {2045-2322},
mesh = {Iran ; *DNA, Ancient/analysis ; Humans ; History, Ancient ; *Genetics, Population ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Archaeology ; },
abstract = {In this study, we present new ancient DNA data from prehistoric and historic populations of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously published ancient DNA datasets from Western and South-Central Asia, enhancing our understanding of genetic continuity and diversity within ancient Iranian populations. A new Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-term cultural and biological continuity in and around the Zagros area, alongside evidence of some western genetic influence. Our sample selection prioritizes northern Iran, with a particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE-460 CE). The genetic profiles of historical samples from this region position them as intermediates on an east-west genetic cline across the Persian Plateau. They also exhibit strong connections to local and South-Central Asian Bronze Age populations, underscoring enduring genetic connections across these regions. Diachronic analyses of uniparental lineages on the Iranian Plateau further highlight population stability from prehistoric to modern times.},
}

Iran
*DNA, Ancient/analysis
Humans
History, Ancient
*Genetics, Population
*DNA, Mitochondrial/genetics
Genetic Variation
Archaeology

@article {pmid40352621,
year = {2025},
author = {Bro-Jørgensen, MH and Ahlgren, H and Glykou, A and Ruiz-Puerta, EJ and Lõugas, L and Gotfredsen, AB and Olsen, MT and Lidén, K},
title = {The Evolutionary History of the Extinct Baltic Sea Harp Seal Population.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71322},
pmid = {40352621},
issn = {2045-7758},
abstract = {The now-extinct harp seal population that inhabited the Baltic Sea from the Mesolithic to the Iron Age is an enigma. It occurred outside the species' contemporary Arctic range, likely deviated from typical harp seal migratory behaviour, and experienced body size reductions and dramatic population fluctuations leading up to its extinction. Here we use ancient DNA analyses to shed more light on the evolutionary history of the Baltic Sea harp seal population, including its origin, timing of colonisation, diversity and factors contributing to its demise. We generated 49 ancient Baltic and eight ancient Arctic harp seal mitogenomes, which we analysed together with 53 contemporary Arctic harp seal mitogenomes. We detected limited phylogeographic resolution among ancient and contemporary populations, which we interpret as a late Pleistocene range expansion from a common refugial population with subsequent gene flow. Ancient Baltic harp seals were significantly genetically differentiated from contemporary harp seal populations and retained their own genetic composition throughout time. The genetic diversity of Baltic harp seals decreased over time, yet was comparable to that of contemporary populations. This suggests that Baltic harp seals formed a distinct breeding population, which may occasionally have received immigrants from the Arctic but was itself confined in the Baltic Sea until the end. We hypothesise that loss of genetic diversity and the ultimate extinction of the Baltic harp seal population was a consequence of population fluctuations caused by climatic change, reduced salinity and biological productivity, and periodic intense human harvest.},
}

@article {pmid40349970,
year = {2025},
author = {Domingo, P and Prieto, P and Pons, L},
title = {A plague like no other Beyond the buboes in Thucydides' account of the plague of Athens.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.05.001},
pmid = {40349970},
issn = {1469-0691},
abstract = {BACKGROUND: The Athens Plague (430-427 BCE) was a devastating outbreak during the Peloponnesian War, described in detail by Thucydides. Although there is ongoing discussion, the specific cause of the epidemic remains undetermined.

OBJECTIVES: This review reexamines the Athenian plague through historical and microbiological lenses, reassessing diagnostic hypotheses and proposing the plausibility of an ancient pneumonic strain ofYersinia pestis.

SOURCES: We analyzed Thucydides' original account alongside interdisciplinary literature from classical studies, paleopathology, epidemiology, and microbiology. We gathered sources from PubMed, JSTOR, Google Scholar, and the Perseus Digital Library, covering works from 1634 to 2024.

CONTENT: The clinical progression described by Thucydides-fever, conjunctivitis, bloody cough, gastrointestinal symptoms, rash, and high mortality-is compared to the presentations of typhoid fever, smallpox, epidemic typhus, measles, and plague. This review considers archaeological and paleogenomic findings, including controversial evidence of Salmonella enterica and the evolutionary history of Y. pestis. Special emphasis is placed on early strains of Y. pestis that lacked flea-borne virulence factors but may have caused pneumonic forms transmitted between humans.

IMPLICATIONS: The epidemic's significant demographic, political, and social impacts highlight the broader consequences of infectious diseases in ancient history. This review emphasizes the necessity of employing a multidisciplinary approach in historical epidemiology and advocates for reassessing pneumonic plague as a likely contributor to the outbreak that occurred in Athens.},
}

@article {pmid40341774,
year = {2025},
author = {Ralf, A and Zandstra, D and van Wersch, B and Köksal, Z and Larmuseau, MHD and Rosa, A and Jobling, MA and D'Amato, ME and Courts, C and Gysi, M and Haas, C and Flores, R and Neis, M and Wetton, JH and Kiesler, K and Ameur, A and Azonbakin, S and Bôžiková, A and Choma, A and De Ungria, MC and Corradini, B and Cruz, C and Dunkelmann, B and Ferri, G and Fleckhaus, J and Fragou, D and Gaens, N and Gonçalves, R and Havaš Auguštin, D and Helm, K and Hölzl-Müller, P and Kaliszan, M and Kasu, M and Kovatsi, L and Lesaoana, M and Mizuno, N and Neuhuber, F and Nováčková, J and Ňuňuková, A and Pamjav, H and Parson, W and Ramankulov, Y and Rangel Villalobos, H and Rębała, K and Rootsi, S and Salvador, J and Šarac, J and Steffen, CR and Stenzl, V and Török, T and Villems, R and Watahiki, H and Zhabagin, M and Schneider, PM and Kayser, M},
title = {UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups.},
journal = {European journal of human genetics : EJHG},
volume = {},
number = {},
pages = {},
pmid = {40341774},
issn = {1476-5438},
support = {101080117//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PRG1071//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1071//Eesti Teadusagentuur (Estonian Research Council)/ ; },
abstract = {For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.},
}

@article {pmid40333974,
year = {2025},
author = {von Hippel, B and Stoof-Leichsenring, KR and Çabuk, U and Liu, S and Melles, M and Herzschuh, U},
title = {Postglacial bioweathering, soil nutrient cycling, and podzolization from palaeometagenomics of plants, fungi, and bacteria.},
journal = {Science advances},
volume = {11},
number = {19},
pages = {eadj5527},
pmid = {40333974},
issn = {2375-2548},
mesh = {*Soil/chemistry ; *Fungi/genetics/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics ; *Plants/metabolism/genetics ; *Ice Cover ; Geologic Sediments/microbiology ; *Nutrients/metabolism ; DNA, Ancient/analysis ; },
abstract = {Warming-induced glacier retreat exposes bare rocks and glacial sediments, facilitating the establishment of soils. The dynamic interplay between climate, vegetation cover, and soil formation is poorly understood as time-series data are lacking. Here, we present postglacial soil formation during the past 23,000 years inferred from ancient DNA shotgun analyses of Lake Lama sediments targeting plants, soil-associated fungi, and bacteria showing postmortem damage signatures that verify their ancient origin. In the Late Glacial, we reveal basaltic weathering with high abundances of lichens, carbon, and arsenic cyclers, shifting to mycorrhizae domination and N cycling in the Holocene. We reconstruct podzolization starting with spruce forest migration in the Holocene, resulting in soil acidification and increased iron cycling. Our reconstruction of soil formation also contributes basic knowledge for the design of carbon-capture strategies using basalt weathering.},
}

*Soil/chemistry
*Fungi/genetics/metabolism
*Soil Microbiology
*Bacteria/metabolism/genetics
*Plants/metabolism/genetics
*Ice Cover
Geologic Sediments/microbiology
*Nutrients/metabolism
DNA, Ancient/analysis

@article {pmid40309111,
year = {2025},
author = {Zhang, X and Zhang, F},
title = {Island ancient genomes reveal dynamic populations interactions in the northern China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584315},
pmid = {40309111},
issn = {1664-302X},
abstract = {The Longshan period (2500-1900 BC) was a transformative era in central China, marked by the emergence of complex social structures and early state formation. While human mobility likely played a role in these developments, the scale and nature of migration during this period remain poorly understood. Previous ancient DNA studies on Longshan culture populations have focused on individuals from inland Shandong, with no ancient DNA data available from island populations. In this study, we present the first ancient DNA analysis from individuals associated with the Longshan and subsequent Yueshi cultures on the Tuoji Island. Our findings indicate that, despite the widespread cultural influence of the inland Longshan culture in Shandong, the genetic ancestry of the Tuoji Island individuals primarily reflects connections to the preceding Dawenkou culture, with additional ancestry linked to the coastal regions of southern China. This suggests an earlier population movement into Tuoji Island before the Longshan period. However, during the Longshan period, the spread of Longshan cultural materials on Tuoji Island appears to represent the diffusion of ideas rather than significant population admixture from the inland. Additionally, our study shows genetic continuity of Longshan and Yueshi cultures in Tuoji Island highlighting the dynamic nature of coastal migration, as the Tuoji Island populations exhibit more genetic influence from coastal regions than from the inland. In contrast, inland populations during the Longshan period show no significant genetic influx from neighboring regions. This study not only advances our understanding of the prehistoric populations in Neolithic China but also provides new insights into patterns of migration and cultural exchange during this critical period.},
}

@article {pmid40307544,
year = {2025},
author = {Pinotti, T and Adler, MA and Mermejo, R and Bitz-Thorsen, J and McColl, H and Scorrano, G and Feizabadifarahani, M and Gandy, D and Boulanger, M and Gaunitz, C and Stenderup, J and Ramsøe, A and Korneliussen, T and Demeter, F and Santos, FR and Vinner, L and Sikora, M and Meltzer, DJ and Moreno-Mayar, JV and Quanchello, C and Willerslev, E},
title = {Picuris Pueblo oral history and genomics reveal continuity in US Southwest.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40307544},
issn = {1476-4687},
abstract = {Indigenous groups often encounter significant challenges when asserting ancestral claims and cultural affiliations based on oral histories, particularly in the USA where such narratives have historically been undervalued. Although ancient DNA offers a tool to complement traditional knowledge and address gaps in oral history, longstanding disregard for Indigenous sovereignty and beliefs has understandably led many Indigenous communities to distrust DNA studies[1-4]. Earlier research often focused on repatriation claims[5-7], whereas more recent work has increasingly moved towards enhancing Tribal histories[8,9]. Here we present a collaborative study initiated by a federally recognized Native American tribe, the sovereign nation of Picuris Pueblo in the Northern Rio Grande region of New Mexico, USA, to address gaps in traditional knowledge and further their understanding of their population history and ancestry. We generated genomes from 16 ancient Picuris individuals and 13 present-day members of Picuris Pueblo, providing genomic data spanning the last millennium. We show genetic continuity between ancient and present-day Picuris, and more broadly with Ancestral Puebloans from Pueblo Bonito in Chaco Canyon[10], 275 km to the west. This suggests a firm spatiotemporal link among these Puebloan populations of the North American Southwest. Furthermore, we see no evidence of population decline before European arrival[11-13], and no Athabascan ancestry in individuals predating 1500 CE, challenging earlier migration hypotheses[14-16]. This work prioritizes Indigenous control of genetic data and brings together oral tradition, archaeology, ethnography and genetics.},
}

@article {pmid40296056,
year = {2025},
author = {Oteo-Garcia, G and Silva, M and Foody, MGB and Yau, B and Fichera, A and Alapont, L and Justeau, P and Rodrigues, S and Monteiro, R and Gandini, F and Rovira Gomar, ML and Ribera I Lacomba, A and Pascual Beneyto, J and Mattiangeli, V and Bradley, DG and Edwards, CJ and Pala, M and Richards, MB},
title = {Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {108},
pmid = {40296056},
issn = {1474-760X},
support = {N°101034324//European Union's Horizon 2020 research and innovation programme/ ; 205072/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Africa, Northern ; Spain ; *Genome, Human ; History, Medieval ; *Gene Flow ; DNA, Ancient/analysis ; Genetics, Population ; Black People/genetics ; },
abstract = {BACKGROUND: The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late medieval period through ancient DNA.

RESULTS: Our comprehensive genomic analysis uncovers gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncover one of the earliest dated Islamic burials in Spain, which shows high levels of consanguinity. For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from North Africa.

CONCLUSIONS: This study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade, underscores the low impact of the Reconquista in the genetic landscape, and shows the lasting impact of post-medieval events, such as the Expulsion of the Moriscos in 1609 CE, on the region's genetic and cultural landscape, through mass population displacement and replacement.},
}

Humans
Africa, Northern
Spain
*Genome, Human
History, Medieval
*Gene Flow
DNA, Ancient/analysis
Genetics, Population
Black People/genetics

@article {pmid40287785,
year = {2025},
author = {Bai, F and He, W and Gao, Y and Ping, WJ and Fu, QM},
title = {Ancient genomes revealed the genetic history and interaction of prehistoric populations in the Ngari region of the western Tibetan Plateau.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {5},
pages = {501-512},
doi = {10.16288/j.yczz.24-368},
pmid = {40287785},
issn = {0253-9772},
mesh = {Humans ; Tibet ; Archaeology ; *Genetics, Population ; Human Migration/history ; *DNA, Ancient/analysis ; *Genome, Human ; *Asian People/genetics ; History, Ancient ; },
abstract = {The Ngari Prefecture is located in the western part of the Tibetan Plateau. Despite its high altitude and harsh natural environment, it occupies a strategic position adjacent to northern Nepal, India, and Ladakh. As a crossroads connecting the Tibetan Plateau, Xinjiang Autonomous Region, Central Asia, and South Asia, it likely played an important role in early human migration. Archaeological studies in recent years have revealed that even before the establishment of the Tubo Dynasty in the seventh century, the Ngari region maintained extensive cultural connections with Kashmir, Nepal, Xinjiang, and other regions. Furthermore, its subsistence economy reflected strong interactions between Ngari and northern South Asia. Recent paleogenetic studies have demonstrated that the genetic components of the ancient population in the Ngari region originated from the southern part of the plateau, with multiple population expansions occurring from south to west. These studies have also confirmed that alongside cultural exchanges, the Ngari region began experiencing complex genetic interactions with ancient populations from neighboring Central and South Asia at least 2,300 years ago. In this review, we integrate findings from paleogenetics, archaeology, archaeobotany, and zooarchaeology in the Ngari region to systematically examine the genetic origins of the ancient western plateau population and analyze both intraregional cultural-genetic interactions within the Tibetan Plateau and those between Ngari populations and external groups. This synthesis provides important insights for understanding the complex relationships between ancient population movements and interactions in the western Tibetan Plateau, as well as the transformation patterns of regional archaeological cultures and subsistence economies.},
}

Humans
Tibet
Archaeology
*Genetics, Population
Human Migration/history
*DNA, Ancient/analysis
*Genome, Human
*Asian People/genetics
History, Ancient

@article {pmid40280921,
year = {2025},
author = {Garcés-Pastor, S and Heintzman, PD and Zetter, S and Lammers, Y and Yoccoz, NG and Theurillat, JP and Schwörer, C and Tribsch, A and Walsh, K and Vannière, B and Wangensteen, OS and Heiri, O and Coissac, E and Lavergne, S and van Vugt, L and Rey, F and Giguet-Covex, C and Ficetola, GF and Karger, DN and Pellissier, L and Schabetsberger, R and Haas, JN and Strasser, M and Koinig, KA and Goslar, T and Szidat, S and , and Brown, AG and Tinner, W and Alsos, IG},
title = {Wild and domesticated animal abundance is associated with greater late-Holocene alpine plant diversity.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3924},
pmid = {40280921},
issn = {2041-1723},
support = {819192//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; KAW 2021.0048//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2022.0033//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LCF/BQ/PI24/12040011//"la Caixa" Foundation (Caixa Foundation)/ ; FP7/2007-2013//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
mesh = {Animals ; *Biodiversity ; *Animals, Domestic ; *Plants/genetics/classification ; Cattle ; Ecosystem ; *Animals, Wild ; Sheep ; Goats ; Europe ; Geologic Sediments ; Climate Change ; Herbivory ; },
abstract = {In the face of human land use and climate dynamics, it is essential to know the key drivers of plant species diversity in montane regions. However, the relative roles of climate and ungulates in alpine ecosystem change is an open question. Neither observational data nor traditional palaeoecological data have the power to resolve this issue over decadal to centennial timescales, but sedimentary ancient DNA (sedaDNA) does. Here we record 603 plant taxa, as well as 5 wild, and 6 domesticated mammals from 14 lake sediment records over the last 14,000 years in the European Alps. Sheep were the first domesticated animals detected (at 5.8 ka), with cattle appearing at the early Bronze Age (4.2 ka) and goats arriving later (3.5 ka). While sheep had an impact similar to wild ungulates, cattle have been associated with increased plant diversity over the last 2 ka by promoting the diversity of forbs and graminoids. Modelling of the sedaDNA data revealed a significantly larger effect of cattle and wild ungulates than temperature on plant diversity. Our findings highlight the significant alteration of alpine vegetation and the entire ecosystem in the Alps by wild and domesticated herbivores. This study has immediate implications for the maintenance and management of high plant species diversity in the face of ongoing anthropogenic changes in the land use of montane regions.},
}

Animals
*Biodiversity
*Animals, Domestic
*Plants/genetics/classification
Cattle
Ecosystem
*Animals, Wild
Sheep
Goats
Europe
Geologic Sediments
Climate Change
Herbivory

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*DNA, Ancient/analysis
Humans
History, Ancient

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

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

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

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

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

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

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

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

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

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

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