@article {pmid40834862,
year = {2025},
author = {Xiong, J and Xu, Y and Chen, G and Yang, L and Zhou, Y and Pan, Y and Wang, Z and Bai, J and Zhang, B and Dong, G and Pei, J and Yang, X and Chen, L and Kang, N and Wu, Y and Wang, B and Zhu, K and Du, P and Li, X and Wen, H and Ma, X and Bai, T and Gu, W and Ye, Y and Wu, Q and Chang, X and Tan, J and Gao, L and Ge, D and Li, B and Yang, Y and Feng, W and Yang, Y and Sheng, P and Meng, H and Wang, R and Zheng, J and Jia, X and Jin, L and Wang, CC and Wen, S},
title = {The genomic history of East Asian Middle Neolithic millet- and rice-agricultural populations.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100976},
doi = {10.1016/j.xgen.2025.100976},
pmid = {40834862},
issn = {2666-979X},
abstract = {The Yellow and Yangtze river basins in China are among the world's oldest independent agricultural centers, known for the domestication of millet and rice, respectively, yet their genetic history is poorly understood. Here, we present genome-wide data from 74 Middle Neolithic genetic samples from these regions, showing marked genetic differentiation but bidirectional gene flow, supporting a demic diffusion model of mixed farming. Yellow River populations exhibit distinct genetic substructures resulting from interactions with surrounding groups during the mid-Neolithic expansion of millet agriculture. Upper Yellow River populations are genetically linked to Tibetan Plateau populations and possess the earliest adaptive EPAS1 haplotype (∼5,800 BP) among modern humans. Meanwhile, Yangtze River rice farmers show genetic affinity with Neolithic to present-day southeast coastal China and Austronesian populations, tracing the origins of proto-Austronesians farther north to the Yangtze River. These findings offer new insights into the impact of mid-Neolithic agricultural expansion on human genetic history.},
}

@article {pmid40834077,
year = {2025},
author = {Tsoupas, A and Reyna-Blanco, CS and Quilodrán, CS and Blöcher, J and Brami, M and Wegmann, D and Burger, J and Currat, M},
title = {Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe.},
journal = {Science advances},
volume = {11},
number = {34},
pages = {eadq9976},
doi = {10.1126/sciadv.adq9976},
pmid = {40834077},
issn = {2375-2548},
mesh = {Humans ; Europe ; *Farmers ; Population Dynamics ; *Human Migration ; Agriculture ; History, Ancient ; Genetics, Population ; Population Density ; },
abstract = {The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into central Europe along the continental route of dispersal. We used spatially explicit simulations of paleogenomic diversity and high-quality paleogenomic data from 67 prehistoric individuals to assess how population dynamics between Indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the continental route. We estimate that the effective population size of farmers was about five times that of hunter-gatherers. In addition, we infer that sporadic long-distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited.},
}

Humans
Europe
*Farmers
Population Dynamics
*Human Migration
Agriculture
History, Ancient
Genetics, Population
Population Density

@article {pmid40831291,
year = {2025},
author = {Yi, W and Delroba, E and Zizzamia, B and Spera, S and Yang, MA},
title = {The AADR Visualizer: An ArcGIS Online Visualizer for ancient human DNA from the Allen Ancient DNA Resource.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioadv/vbaf199},
pmid = {40831291},
issn = {1367-4811},
abstract = {MOTIVATION: The AADR Visualizer is designed to be a public, user-friendly, web-based graphical user interface for visualizing and filtering ancient humans included in the Allen Ancient DNA Resource (AADR), a regularly updated dataset that compiles published human genome-wide ancient DNA for research uses. This tool increases access to the rapidly growing pool of human ancient DNA available for study, facilitating genomic research and education focused on human prehistoric movement and interaction.

RESULTS: The AADR Visualizer provides the ability to 1) view all available individuals and associated metadata, 2) filter individuals using a diverse set of geographic, temporal, and sequencing information, and 3) search for individuals using group nomenclature as described in the Allen Ancient DNA Resource.

The tool is freely available on the web at https://arcg.is/1CyL5n.},
}

@article {pmid40830959,
year = {2025},
author = {Ji, Z and Chen, K and Zheng, J and Qin, C and Cui, S and Shen, Q and Ma, H and Wang, B and Mao, X and Liu, Y and Zhou, H and Zou, X and Wang, X and Tang, J and Ma, T and Wan, W and Zhu, K and Tao, L and He, H and Wang, R and Yang, X and Xu, Y and Xu, M and Bai, T and Jiang, Y and Wen, S and Jin, L and Zhang, Q and Wang, CC},
title = {Genomic formation of lower Yellow River populations in the Han dynasty.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {260},
pmid = {40830959},
issn = {1741-7007},
mesh = {China ; Humans ; Rivers ; *DNA, Ancient/analysis ; *Genome, Human ; History, Ancient ; *Genetics, Population ; Principal Component Analysis ; Genetic Variation ; Human Migration/history ; },
abstract = {BACKGROUND: As a key region in the lower Yellow River Basin, Shandong Province plays a central role in understanding the genetic history of East Asia. However, detailed ancient DNA data across its historical periods remains limited. This study aims to characterise the genomic profiles of Shandong populations during the Western Han Dynasty and trace their genetic connections with neighbouring regions.

RESULTS: Here, we newly generated 14 ancient genomes from the Wenshaobei site of the Western Han dynasty in Shandong Province. Genetic analyses, including principal component analysis (PCA), ADMIXTURE, and f-statistics, revealed that the Wenshaobei population was genetically distinct from Early Neolithic Shandong hunter-gatherers but closely aligned with Middle Neolithic to Iron Age populations from the middle and lower Yellow River Basin. This indicates strong genetic continuity with millet-farming societies from the middle Yellow River, supplemented by minor influences from southern rice-farming groups. Modern Han Chinese in Shandong share a core genetic foundation with ancient populations, such as Wenshaobei.

CONCLUSIONS: Our findings highlight the role of the lower Yellow River Basin as a nexus of genetic exchange between northern millet-farming and southern rice-farming cultures, with sustained genetic influences from the middle Yellow River shaping the demographic landscape from the Neolithic to the Han Dynasty. The study provides critical insights into the formation of East Asian populations, underscoring the interplay between agriculture, migration, and genetic diversity in this cradle of ancient Chinese civilization.},
}

China
Humans
Rivers
*DNA, Ancient/analysis
*Genome, Human
History, Ancient
*Genetics, Population
Principal Component Analysis
Genetic Variation
Human Migration/history

@article {pmid40828789,
year = {2025},
author = {Aborghetti, HP and Collin, SM and Dos Santos, JD and Dos Santos, PB and Zambon, TL and Loureiro, RM and Deps, PD},
title = {Leprosy in skeletons from archaeological sites: A systematic review.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {8},
pages = {e0013374},
doi = {10.1371/journal.pntd.0013374},
pmid = {40828789},
issn = {1935-2735},
abstract = {BACKGROUND: Leprosy (Hansen's disease) is an ancient stigmatising infectious disease that remains endemic in many countries. Leprosy-related bone changes that cause disabilities in affected persons are evident in skeletons from archaeological sites. The aim of our synthesis of paleopathological data was to gain insights into the disease's historical distribution and presentation.

METHODOLOGY: Systematic review of paleopathological studies describing human remains with signs of leprosy published up to December 2023. Extracted data on bone features from skulls and limbs, including rhinomaxillary syndrome (RMS) in cranial bones and post-cranial bone changes (PCBC) in hands and feet, were summarised, together with genomic data from studies of Mycobacterium leprae ancient DNA.

FINDINGS: The 297 skeletons described in 67 studies comprised 264 skeletons from sites in modern-day Europe (117 from England, 68 from Denmark); 23 skeletons from Asia (10 from India), 5 from The Americas, and 4 from the African continent (all from Egypt); 174 (58.6%) were from leprosaria, 255 (85.9%) were adults, 28 (9.4%) adolescent, 14 (4.7%) of indeterminate age. Skeletons dated from 3715 BCE to 1839 CE, peaking around the 15th Century. Probable and possible RMS were identified in 85 (30.5%) and 153 (54.8%) of 279 skeletons with cranial data, respectively. Lower limb pathological PCBC were most prevalent in tarsals (76.6%), metatarsals (81.5%), and feet phalanges (85.6%). In upper limbs, 75.8% of humeri, 65.8% of radii, 61.0% of ulnae and 75.8% of hand phalanges exhibited pathological alterations. From 73 skeletons from 19 genomic studies, M. leprae single nucleotide polymorphism (SNP) type 3 was identified in 59 skeletons (80.8%), SNP type 2 in 11 (15.1%), type 4 in two, and type 1 in one.

CONCLUSIONS: Four out of five archaeological skeletons with leprosy exhibited some degree of RMS, which is pathognomonic of the most severe form of the disease, irrespective of whether the skeleton was excavated from a leprosarium (leprosy hospital) or from a public cemetery or other burial site. The relatively small numbers of remains excavated over a wide geographical area and a long time period, and the focus of archaeological studies on skeletons already identified as having leprosy, mean that it is difficult to prove or disprove theories that aim to explain the decline and eventual disappearance of leprosy as a disease in Europe.},
}

@article {pmid40822357,
year = {2025},
author = {Bonucci, B and de-Dios, T and Barbieri, R and Thompson, JE and Panella, S and Radina, F and Sivilli, S and Kabral, H and Solnik, A and Tafuri, MA and Robb, J and Scheib, CL},
title = {Ancient microbial DNA and proteins preserve in concretions covering human remains.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113182},
pmid = {40822357},
issn = {2589-0042},
abstract = {Archaeological remains covered with concretions, including human bones, are commonly found in certain areas and time periods of interest for understanding the past, but have yet to be investigated for potential ancient DNA (aDNA) and protein content. We extracted aDNA and proteins in tandem from human dental remains and their surrounding concretions and compared them to non-concreted human dental remains from the same site. Concretions appeared homogeneous in color and texture, consisting of a hard dark gray sediment adhered to the bone surfaces, presumably as a result of cyclical waterlogging of the burial deposits. Concretions were found to contain human oral microbial genomes and proteins, probably leached from the original skeletal source, as well as environmental and human proteins. Despite this, both the original teeth and the concretions surrounding them lacked endogenous human aDNA, indicating that the use of this type of material in future molecular archaeological applications is limited.},
}

@article {pmid40820848,
year = {2025},
author = {Güler, MN and Yılmaz, A and Katırcıoğlu, B and Kantar, S and Ünver, TE and Vural, KB and Altınışık, NE and Akbas, E and Somel, M},
title = {DeepKin: Predicting Relatedness From Low-Coverage Genomes and Palaeogenomes With Convolutional Neural Networks.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70032},
doi = {10.1111/1755-0998.70032},
pmid = {40820848},
issn = {1755-0998},
support = {772390//H2020 European Research Council/ ; 952317//H2020 Spreading Excellence and Widening Participation/ ; },
abstract = {DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating relatedness often struggle when genomic data is limited, as with palaeogenomes and degraded forensic samples. DeepKin addresses this challenge by leveraging two CNN models, which are trained solely on simulated genomic data, to classify relatedness up to the third degree and to identify parent-offspring and sibling pairs. Our benchmarking shows DeepKin performs comparably or better than the widely used tool READv2. We validated DeepKin, which uses PLINK's .map and .ped files as input, on empirical palaeogenomes from three archaeological sites, demonstrating its robustness and adaptability across different genetic backgrounds, with accuracy > 90% above 10 K shared SNPs. By capturing information across genomic segments, DeepKin offers a new methodological path for relatedness estimation in settings with highly degraded samples, with applications in ancient DNA, as well as forensic and conservation genetics.},
}

@article {pmid40810211,
year = {2025},
author = {Fleskes, RE and Palacios, HM and Budner, H and Kollmann, D and Newby-Alexander, C and Harder, R and Bolnick, DA and Pollard, M and Pollard, P and Schurr, TG and Brown, DA},
title = {Archaeogenomic Analysis of Nineteenth-Century Burials at Saint Mary's Basilica: An Intersectional Analysis of Religion, Race, and Migration.},
journal = {American journal of biological anthropology},
volume = {187},
number = {4},
pages = {e70110},
pmid = {40810211},
issn = {2692-7691},
support = {SPRF-FR 2105384//National Science Foundation/ ; //Fairfield Foundation/ ; },
abstract = {OBJECTIVES: The Basilica of Saint Mary's of the Immaculate Conception in Norfolk, Virginia, is the only predominantly African American basilica in the United States. A community-based archaeogenomic investigation was carried out at this church to investigate the history of its previous congregants.

MATERIALS AND METHODS: Five burials were selected for excavation and archaeological analysis. The skeletal remains of these past congregants were assessed to determine age, sex, and preservation status. Ancient DNA was extracted at the University of Connecticut's ancient DNA laboratory.

RESULTS: Five burials excavated at the basilica yielded four sets of human remains of variable preservation and sex. Interment location, style, and positioning of the burials suggested that they belong to the earlier Saint Patrick's church (AD 1790s to 1856), which once stood adjacent to the current basilica. Osteological analyses indicated the presence of four adults and one infant. Ancient DNA results for three of the adults indicated that they were genetically affiliated with contemporary populations in Europe, specifically the United Kingdom, France, and Spain. Interestingly, the autosomal and uniparental lineages of two adults showed connections to Spanish populations, with one having a unique L3f1b mitochondrial DNA haplotype tracing back to northern Spain.

CONCLUSIONS: Using an intersectional theoretical framework grounded in historical research, we assess these findings to understand the lived experiences of these past congregants in the context of religion, race, and migration in early nineteenth-century Norfolk. Overall, this study highlights the value of an interdisciplinary archaeogenetic approach in exploring the intersectional lives of historic populations.},
}

@article {pmid40802756,
year = {2025},
author = {Canteri, E and Brown, SC and Post, E and Schmidt, NM and Nogues-Bravo, D and Fordham, DA},
title = {Mismatch in reindeer resilience to past and future warming signals ongoing declines.},
journal = {Science advances},
volume = {11},
number = {33},
pages = {eadu0175},
pmid = {40802756},
issn = {2375-2548},
abstract = {Rangifer tarandus (caribou or reindeer) survived periods of abrupt climatic warming during the last deglaciation but are currently in global decline. Using process-explicit models of likely climate-human-Rangifer interactions and inferences of demographic change from radiocarbon-dated fossils and ancient DNA, we reconstruct and decipher 21,000 years of Rangifer population dynamics. These high-resolution population reconstructions pinpoint ecological characteristics and life-history traits that most likely enabled Rangifer to survive rapid warming events following the Last Glacial Maximum. Projecting these process-driven models into the future reveals that these attributes are unlikely to buffer Rangifer against wide-scale population declines from expected 21st Century climatic warming. Our findings highlight a need to boost investments in the management and conservation of Rangifer, particularly in North America, where projected losses are expected to exceed 80%. This will not only support the survival of the species and the vital services it renders in Arctic ecosystems, but also help sustain the socioeconomic, cultural, and emotional well-being of many Rangifer-dependent communities.},
}

@article {pmid40802463,
year = {2025},
author = {Laine, J and Nickel, J and Romundset, A and Foote, AD},
title = {Ancient stickleback genomes reveal the early stages of parallel adaptation.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf164},
pmid = {40802463},
issn = {1558-5646},
abstract = {The parallel evolution of traits and their underlying genetic basis is well-studied, however, studies of parallel chronology of adaptive genetic changes remain scarce. The probability of parallel genetic change should be increased by the clustering of adaptive alleles in regions of suppressed recombination, particularly for genes that have large fitness or phenotypic effects. Threespine stickleback are a model system for studying parallel evolution. We present genomic data from nine subfossil stickleback bones dated to 14.8-0.7 KYR BP in age. Comparing the four highest coverage genomes, which represent different stages along the marine-freshwater divergence continuum, we find that the accumulation of freshwater ancestry is clustered rather than randomly distributed throughout the marine-freshwater divergent regions of the genome. We consistently find freshwater ancestry on chromosome IV at the early stages of freshwater adaptation. Regions of chromosome IV contain the greatest genetic differentiation between marine and freshwater ecotypes and among the highest density of quantitative trait loci. These include Ectodysplasin (EDA), a large-effect pleiotropic locus associated with defensive armor and variation in neurosensory and behavioral traits. Freshwater ancestry in the subfossils is also consistently found at inversions and X-chromosome early in the adaptive process. Our findings add to emerging evidence that freshwater adaptation in threespine stickleback could have a staggered but predictable temporal dynamic.},
}

@article {pmid40797266,
year = {2025},
author = {Puurand, T and Möls, M and Kaplinski, L and Maal, K and Krjutskov, K and Salumets, A and Kivisild, T and Remm, M},
title = {Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {243},
pmid = {40797266},
issn = {1474-760X},
support = {RE.5.04.23-0214//Estonian Business and Innovation Agency/ ; TEM-TA35, 2021-2027.1.01.24-0627//Estonian Research Council/ ; PRG1076//Estonian Research Council/ ; 101120075//Horizon Europe NESTOR/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence at depths less than 0.1 × at target loci. Leveraging recent advances in telomere-to-telomere sequencing of whole genomes with long reads, we develop a new k-mer based method, Y-mer, and show how information from hundreds of thousands of k-mers in distance-based models enables accurate inference of chrY haplogroup from whole-genome sequence at depth less than 0.01x. We test the performance of Y-mer on ancient DNA and prenatal screening data, showing its potential for genetic ancestry inference for cell-free, forensic and ancient DNA research.},
}

@article {pmid40795857,
year = {2025},
author = {Light-Maka, I and Hermes, TR and Bianco, RA and Semerau, L and Kosintsev, P and Alekseeva, V and Kim, D and Hanage, WP and Herbig, A and Jeong, C and Warinner, C and Key, FM},
title = {Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.07.029},
pmid = {40795857},
issn = {1097-4172},
abstract = {Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover into human populations. However, we lack direct DNA evidence linking animal and human infections during prehistory. Here, we present a Yersinia pestis genome recovered from a 3rd-millennium BCE domesticated sheep from the Eurasian Steppe belonging to the Late Neolithic Bronze Age (LNBA) lineage, until now exclusively identified in ancient humans across Eurasia. We show that this ancient lineage underwent ancestral gene decay paralleling extant lineages, but evolved under distinct selective pressures, contributing to its lack of geographic differentiation. We collect evidence supporting a scenario where the LNBA lineage, unable to efficiently transmit via fleas, spread from an unidentified reservoir to sheep and likely other domesticates, elevating human infection risk. Collectively, our results connect prehistoric livestock with infectious disease in humans and showcase the power of moving paleomicrobiology into the zooarchaeological record.},
}

@article {pmid40792511,
year = {2025},
author = {Pokšāne, A and Ķimsis, J and Pētersone-Gordina, E and Vilcāne, A and Gerhards, G and Ranka, R},
title = {Characterization of ancient DNA preservation in copper-patinated human bone and tooth samples from Latvia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0270524},
doi = {10.1128/spectrum.02705-24},
pmid = {40792511},
issn = {2165-0497},
abstract = {UNLABELLED: Bronze and copper-containing alloys are known to possess antibacterial properties, which, besides mineralization, might contribute to the observation of better preservation of bone, teeth, and other organic materials in close proximity to bronze artifacts in archaeological contexts. Often, the selection of preserved hard tissue material from burials for ancient DNA (aDNA) analysis is limited due to the sampling strategies used at the time of excavations or poor preservation in general. This study assessed the suitability of samples with copper patination for in-depth human and bacterial aDNA analysis. To characterize the difference between patinated and unpatinated samples, a qualitative assessment of human DNA preservation and metagenomic analysis using Kraken2 and MEGAN Alignment Tool was performed. For patinated samples, a very low proportion of endogenous DNA preservation was observed. Only one-the least patinated-out of five analyzed samples could be authenticated to be containing human aDNA with confidence. A patinated sample of specific bacterial genera was affiliated with soil and aquatic, mostly marine environmental, microorganisms. In conclusion, due to mineralization processes that occur during the patination of hard tissue, endogenous DNA preservation is seen to be greatly affected, thus making heavily patinated samples a compromised source of endogenous aDNA. Future in-depth research is needed, including the assessment of chemical composition of patinated tissues.

IMPORTANCE: Ancient DNA research has recently become a very powerful tool for archaeological and historical research, enabling the discovery of information about various aspects of our predecessors' lives, but it is limited by the availability of material to be sampled. To our knowledge, there is no previous study focused on effects of copper patination on ancient DNA preservation and metagenomic profiles of archaeological teeth and bone samples. Our results suggest that patination should be considered an influential factor during sample selection, as it affected human endogenous DNA preservation and metagenomic diversity within analyzed samples.},
}

@article {pmid40778146,
year = {2025},
author = {Karim, LM and Martínez-Martínez, FJ and O'Farrell, A and Hinrichs, AS and Sanderson, T and Iqbal, Z and Kozyreva, VK and Bell, JM and López, MG and Comas, I and Corbett-Detig, R},
title = {UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis of Mycobacterium tuberculosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40778146},
support = {/WT_/Wellcome Trust/United Kingdom ; T32 HG012344/HG/NHGRI NIH HHS/United States ; U01 CK000539/CK/NCEZID CDC HHS/United States ; },
abstract = {Mycobacterium tuberculosis, the bacterium responsible for the Tuberculosis (TB) disease, remains a leading global infectious disease killer, and genomic epidemiology is essential for understanding its transmission dynamics. Computational limitations prevent comprehensive phylogenetic analysis of the publicly available Mycobacterium tuberculosis genomes. Here, we create UShER-TB, a comprehensive pipeline for scalable phylogenomic MTB analysis. We processed 129,312 MTB genomes to construct a comprehensive global phylogeny capturing unprecedented genomic diversity. UShER-TB achieved high accuracy in transmission cluster reconstruction. The comprehensive phylogeny also facilitated identification of putative novel lineages and sublineages, and successful placement of ancient DNA samples. The UShER-TB platform enables real-time phylogenomic analysis of new genomes, revealing transmission hotspots and introduction patterns at global scales. Our approach overcomes longstanding computational barriers, providing researchers with efficient tools for TB genomic surveillance especially for resource-limited settings where TB burden is highest.},
}

@article {pmid40766232,
year = {2025},
author = {Nebet, ER and Aprea, C and Zoodsma, JD and Raab, W and Sirotkin, HI and Wollmuth, LP},
title = {Conservation of human NMDA receptor subunits and disease variants in zebrafish.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {40766232},
issn = {2693-5015},
support = {R01 NS088479/NS/NINDS NIH HHS/United States ; },
abstract = {BACKGROUND: NMDA receptors (NMDARs) are widely expressed, glutamate-gated ion channels that play key roles in brain development and function. Variants have been identified in the GRIN genes encoding NMDAR subunits that are linked to neurodevelopmental disorders, among other manifestations. Zebrafish are a powerful model to study brain development and function given their rapid development and ease of genetic manipulation. As a result of an ancient genome duplication, zebrafish possess two paralogues for most human NMDAR subunits. To evaluate the degree of conservation between human NMDAR subunits and their respective zebrafish paralogues, we carried out detailed in silico analyses, with an emphasis on key functional elements. To further assess the suitability of zebrafish for modeling NMDAR-associated neurodevelopmental disorders, we analyzed the conservation of positions with identified missense variants.

RESULTS: We find that the human NMDAR subunits are generally well conserved across zebrafish paralogs. Moreover, variants classified as pathogenic and putatively pathogenic are highly conserved, reflecting the importance of key protein regions to neurotypical receptor function. Positions with putatively benign and benign variants are less conserved. Across NMDAR domains, the transmembrane domain is most highly conserved, followed by the ligand-binding domain, which maintains conservation of amino acids that participate in the binding of ligands. The N-terminal domain is less well conserved but aligned homology models show high degrees of structural similarity. The C-terminal domain is the most poorly conserved region across zebrafish paralogs, but certain key regions that undergo phosphorylation, palmitoylation, and ubiquitylation as well as protein-binding motifs are better conserved.

CONCLUSIONS: Our findings highlight a strong conservation of human NMDAR subunits in zebrafish, with some exceptions. The ligand-binding domain, the transmembrane domain forming the ion channel and the short polypeptide linkers that connect them are highly conserved. The N- and C-terminal domains are less conserved but functional motifs in general, except for the Zn[2+] binding site in GluN2A paralogues, are more highly conserved relative to the entire domain. Overall, our findings support the utility of zebrafish as a model for studying neurodevelopment and disease mechanisms and provide a template for rigorously considering the relationship between human and zebrafish paralogues.},
}

@article {pmid40758875,
year = {2025},
author = {Walker, SJ and Boilard, A and Henriksen, M and Lord, E and Robu, M and Buylaert, JP and Beijersbergen, LMT and Halvorsen, LS and Cintrón-Santiago, AM and Onshuus, EK and Cockerill, CA and Ujvari, G and Palcsu, L and Temovski, M and Maccali, J and Linge, H and Olsen, J and Aksnes, S and Bertheussen, A and Lygre, O and Alsos, IG and Dalén, L and Star, B and Hufthammer, AK and van Kolfschoten, T and Lauritzen, SE and Lødøen, TK and Boessenkool, S},
title = {A 75,000-y-old Scandinavian Arctic cave deposit reveals past faunal diversity and paleoenvironment.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2415008122},
pmid = {40758875},
issn = {1091-6490},
support = {314464//Norges Forskningsråd (Forskningsrådet)/ ; PFSS23\230009//British Academy (The British Academy)/ ; Doctoral Fellowship//FRQ | Fonds de recherche du Québec - Nature et technologies (FRQNT)/ ; 819192 (IceAGenT)//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {Arctic Regions ; Animals ; *Biodiversity ; *Caves ; Geologic Sediments/analysis ; Phylogeny ; Bone and Bones/chemistry ; Fossils ; Norway ; Ice Cover ; Paleontology ; },
abstract = {During the last glacial period (~118 to 11.7 ka), the Arctic has been characterized by a major redistribution of flora and fauna as a consequence of extreme climatic fluctuations, with associated glacial advances and retreats, sea-level changes, and shifting sea ice extent. In the high-latitude regions of Northern Europe that are currently subject to rapid climate warming, we lack a comprehensive understanding of faunal biodiversity in the last glacial period due to the extreme rarity of preserved organic remains. Here, we present a stratified sediment deposit with a diverse faunal composition preserved in a bone-bearing layer in Arne Qvamgrotta, part of the Storsteinhola cave system (68.10° N 16.38° E) in Northern Norway. Chronological analyses of sediments and bones including radiocarbon, optically stimulated luminescence, uranium-thorium, and phylogenetic dating place the faunal assemblage in Marine Isotope Stage 5a (MIS 5a, Odderade interstadial, ~85 to 71 ka). Combining comparative osteology and bulk-bone metabarcoding, we identify 46 taxa, including mammals, birds, and fish, with several species not previously found in Fennoscandia. The fauna implies a nonanalogous cold-adapted coastal community, with close proximity to sea ice and nearby freshwater bodies. Mitogenome analyses of a subset of taxa identify extinct lineages which attest to a lack of habitat tracking and the absence of a local refugium during the subsequent fully glaciated periods. This faunal record demonstrates long-term faunal dynamics and coastal environmental conditions during MIS 5a in the European Arctic.},
}

Arctic Regions
Animals
*Biodiversity
*Caves
Geologic Sediments/analysis
Phylogeny
Bone and Bones/chemistry
Fossils
Norway
Ice Cover
Paleontology

@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},
pmid = {40694589},
issn = {1553-7404},
support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; },
mesh = {*Diploidy ; *Selection, Genetic ; *Models, Genetic ; *Genetics, Population/methods ; Algorithms ; Humans ; Markov Chains ; Computer Simulation ; Genetic Variation ; },
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.},
}

*Diploidy
*Selection, Genetic
*Models, Genetic
*Genetics, Population/methods
Algorithms
Humans
Markov Chains
Computer Simulation
Genetic Variation

@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 = {41},
number = {8},
pages = {},
pmid = {40674584},
issn = {1367-4811},
support = {NNF20OC0062491//Novo Nordisk Data Science Investigator/ ; //Department for Health Technology at DTU/ ; },
mesh = {*Software ; *DNA Damage ; Cluster Analysis ; Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; *DNA, Ancient/analysis ; Algorithms ; },
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 ancient DNA (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 pertaining to a cluster, as well as a Principal Component Analysis 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 uracil-DNA glycosylase-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.},
}

*Software
*DNA Damage
Cluster Analysis
Metagenomics/methods
*Sequence Analysis, DNA/methods
Humans
*DNA, Ancient/analysis
Algorithms

@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 = {644},
number = {8075},
pages = {122-132},
pmid = {40604287},
issn = {1476-4687},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *DNA, Ancient/analysis ; History, Ancient ; Siberia/ethnology ; Human Migration/history ; Genome, Human/genetics ; *Language/history ; *Asian People/genetics ; *Ethnicity/genetics ; Haplotypes/genetics ; White People/genetics ; Male ; Genetics, Population ; Chromosomes, Human, Y/genetics ; White ; },
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.},
}

Humans
*DNA, Ancient/analysis
History, Ancient
Siberia/ethnology
Human Migration/history
Genome, Human/genetics
*Language/history
*Asian People/genetics
*Ethnicity/genetics
Haplotypes/genetics
White People/genetics
Male
Genetics, Population
Chromosomes, Human, Y/genetics
White

@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 = {15},
number = {8},
pages = {},
pmid = {40476363},
issn = {2160-1836},
support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; //Leakey Foundation Research/ ; R01GM146051/NH/NIH HHS/United States ; //University of Chicago/ ; },
mesh = {*Diploidy ; *Software ; *Selection, Genetic ; Models, Genetic ; Computer Simulation ; Gene Frequency ; Humans ; },
abstract = {Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA sequences and data from evolve-and-resequence experiments are generated at a rapid pace. Such data present 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.},
}

*Diploidy
*Software
*Selection, Genetic
Models, Genetic
Computer Simulation
Gene Frequency
Humans

@article {pmid39222521,
year = {2024},
author = {Garcia-Heras, J},
title = {The Discovery of Common Chromosome Aneuploidies with Medical Implications Through Innovative Analysis of Ancient DNA (aDNA).},
journal = {Journal of the Association of Genetic Technologists},
volume = {50},
number = {3},
pages = {96-99},
pmid = {39222521},
issn = {1523-7834},
abstract = {Two recent studies that re-examined through novel approaches previous shotgun sequencing data from prehistoric/historic Europeans uncovered several autosomal and sex chromosome aneuploidies (Anastasiadou et al., 2024; Rohrlach et al., 2024). These disorders, which are common in contemporary humans, were trisomies 18 and 21, Klinefelter syndrome (47,XXY), 47,XYY syndrome, and mosaic Turner syndrome X/XX. These discoveries about prehistoric/historic occurrence of constitutional chromosomal syndromes with high clinical significance in modern medical genetics are an important breakthrough. They contribute to a more comprehensive genetic delineation of past human populations and give impetus to perform more historic/prehistoric studies to discover other contemporary genetic disorders. A molecular profiling of ancient DNA (aDNA) from human remains added to anthropological and archaeological data may also give a broader picture of the social and historical contexts of individuals who were affected by genetic diseases. These advances in the detection of chromosome aneuploidies and previous discoveries of current monogenic syndromes in archaic hominins also highlight the possibility of detecting other genetic diseases of present-day occurrence in our ancestors. As a result, it might be feasible to delineate the evolutionary history of modern genetic diseases, establishing a timeline of their emergence, patterns of mutations, putative mechanisms of selection, and genomic mechanisms involved.},
}

@article {pmid39105137,
year = {2024},
author = {de Vos, JM and Streiff, SJR and Bachelier, JB and Epitawalage, N and Maurin, O and Forest, F and Baker, WJ},
title = {Phylogenomics of the pantropical Connaraceae: revised infrafamilial classification and the evolution of heterostyly.},
journal = {Plant systematics and evolution = Entwicklungsgeschichte und Systematik der Pflanzen},
volume = {310},
number = {4},
pages = {29},
pmid = {39105137},
issn = {0378-2697},
abstract = {UNLABELLED: Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.},
}

@article {pmid38798346,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38798346},
issn = {2692-8205},
support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; },
abstract = {Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. 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 {pmid37905072,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37905072},
issn = {2692-8205},
support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; },
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 userfriendly 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 {pmid36993413,
year = {2023},
author = {Barton, AR and Santander, CG and Skoglund, P and Moltke, I and Reich, D and Mathieson, I},
title = {Insufficient evidence for natural selection associated with the Black Death.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36993413},
issn = {2692-8205},
support = {FC001595/WT_/Wellcome Trust/United Kingdom ; R01 HG012287/HG/NHGRI NIH HHS/United States ; R35 GM133708/GM/NIGMS NIH HHS/United States ; },
abstract = {Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2, for which they estimate a selection coefficient of 0.39-several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis, we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.},
}

@article {pmid34475454,
year = {2021},
author = {Kehlmaier, C and López-Jurado, LF and Hernández-Acosta, N and Mateo-Miras, A and Fritz, U},
title = {"Ancient DNA" reveals that the scientific name for an extinct tortoise from Cape Verde refers to an extant South American species.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17537},
pmid = {34475454},
issn = {2045-2322},
mesh = {Animals ; Cabo Verde ; DNA, Ancient/*analysis ; *Ecosystem ; *Extinction, Biological ; Genome, Mitochondrial ; Phylogeny ; South America ; Turtles/classification/*genetics ; },
abstract = {We examined the type material of the extinct tortoise species Geochelone atlantica López-Jurado, Mateo and García-Márquez, 1998 from Sal Island, Cape Verde, using aDNA approaches and AMS radiocarbon dating. High-quality mitochondrial genomes obtained from the three type specimens support that all type material belongs to the same individual. In phylogenetic analyses using mitochondrial genomes of all species groups and genera of extant and some recently extinct tortoises, the type material clusters within the extant South American red-footed tortoise Chelonoidis carbonarius (Spix, 1824). Our radiocarbon date indicates that the tortoise from which the type series of G. atlantica originates was still alive during 1962 and 1974. These results provide firm evidence that the type material of G. atlantica does not belong to the Quaternary tortoise bones excavated on Sal Island in the 1930s, as originally thought. Thus, the extinct tortoise species remains unstudied and lacks a scientific name, and the name G. atlantica has to be relegated into the synonymy of C. carbonarius. The circumstances that led to this confusion currently cannot be disentangled.},
}

Animals
Cabo Verde
DNA, Ancient/*analysis
*Ecosystem
*Extinction, Biological
Genome, Mitochondrial
Phylogeny
South America
Turtles/classification/*genetics

@article {pmid33723011,
year = {2021},
author = {Crump, SE and Fréchette, B and Power, M and Cutler, S and de Wet, G and Raynolds, MK and Raberg, JH and Briner, JP and Thomas, EK and Sepúlveda, J and Shapiro, B and Bunce, M and Miller, GH},
title = {Ancient plant DNA reveals High Arctic greening during the Last Interglacial.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {13},
pages = {},
pmid = {33723011},
issn = {1091-6490},
mesh = {Arctic Regions ; *Climate Change ; DNA, Ancient/*analysis ; DNA, Plant/*analysis ; Fossils ; Geologic Sediments/analysis ; Lakes ; Paleontology ; *Plant Dispersal ; Pollen/*genetics ; },
abstract = {Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.},
}

Arctic Regions
*Climate Change
DNA, Ancient/*analysis
DNA, Plant/*analysis
Fossils
Geologic Sediments/analysis
Lakes
Paleontology
*Plant Dispersal
Pollen/*genetics

@article {pmid33717442,
year = {2021},
author = {Seersholm, FV and Hansen, KL and Heydenrych, M and Hansen, AJ and Bunce, M and Allentoft, ME},
title = {Ancient DNA preserved in small bone fragments from the P.W. Lund collection.},
journal = {Ecology and evolution},
volume = {11},
number = {5},
pages = {2064-2071},
pmid = {33717442},
issn = {2045-7758},
abstract = {The Lund collection is one of the oldest subfossil collections in the world. The vast assemblage of subfossils was collected in the 1830s and 1840s by Peter Wilhelm Lund in Lagoa Santa, Brazil, and was shipped to Copenhagen in 1848, where it was stored in various locations around the city with little attention for the future preservation of the collection. So far, successful genetic research on the material collected by Lund has been limited to two samples of human petrous bone. However, less is known about the preservation conditions of the vast amounts of small and fragmentary bones stored in the collection. To address this, we studied ancient DNA from bulk bone samples of approximately 100 bone fragments from the P.W. Lund collection from boxes with varying degrees of physical preservation conditions. Using bulk bone metabarcoding, we found a high species diversity in all samples. In total, we identified 17 species, representing 11 mammals, two birds, one fish, and three frogs. Of these, two species are new to the collection. Collectively, these results exhibit the potential of future genetic studies on the famous P.W. Lund collection and suggest that the effects of poor storage conditions are probably negligible compared with the long-term in situ degradation that specimens undergo before excavation.},
}

@article {pmid33189847,
year = {2021},
author = {Froment, C and Zanolli, C and Hourset, M and Mouton-Barbosa, E and Moreira, A and Burlet-Schiltz, O and Mollereau, C},
title = {Protein sequence comparison of human and non-human primate tooth proteomes.},
journal = {Journal of proteomics},
volume = {231},
number = {},
pages = {104045},
doi = {10.1016/j.jprot.2020.104045},
pmid = {33189847},
issn = {1876-7737},
mesh = {Animals ; *Hominidae ; Humans ; Phylogeny ; Primates ; Proteome ; *Tooth ; },
abstract = {In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.},
}

Animals
*Hominidae
Humans
Phylogeny
Primates
Proteome
*Tooth

@article {pmid31523131,
year = {2019},
author = {Ishiya, K and Mizuno, F and Wang, L and Ueda, S},
title = {MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.},
journal = {Bioinformatics and biology insights},
volume = {13},
number = {},
pages = {1177932219873884},
pmid = {31523131},
issn = {1177-9322},
abstract = {The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.},
}

@article {pmid30464240,
year = {2018},
author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA},
title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17208},
pmid = {30464240},
issn = {2045-2322},
support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/International ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/International ; },
mesh = {Animals ; Chile ; *Climate Change ; DNA, Ancient/*isolation & purification ; DNA, Fungal/*isolation & purification ; Desert Climate ; Feces/chemistry ; *Fossils ; Fungi/*classification/*genetics ; Metagenomics/methods ; Plant Diseases/*microbiology ; RNA, Ribosomal, 18S/genetics ; Rodentia ; },
abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.},
}

Animals
Chile
*Climate Change
DNA, Ancient/*isolation & purification
DNA, Fungal/*isolation & purification
Desert Climate
Feces/chemistry
*Fossils
Fungi/*classification/*genetics
Metagenomics/methods
Plant Diseases/*microbiology
RNA, Ribosomal, 18S/genetics
Rodentia

@article {pmid26805936,
year = {2016},
author = {Li, G and Dong, H and Hou, W and Wang, S and Jiang, H and Yang, J and Wu, G},
title = {Temporal Succession of Ancient Phytoplankton Community in Qinghai Lake and Implication for Paleo-environmental Change.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {19769},
pmid = {26805936},
issn = {2045-2322},
mesh = {*Biodiversity ; China ; Climate Change ; Environment ; *Environmental Monitoring ; Geography ; *Lakes ; *Phytoplankton/classification/genetics ; RNA, Ribosomal, 23S/genetics ; },
abstract = {Tibetan lake sediments in NW China are sensitive recorders of climate change. However, many important plankton members do not leave any microscopic features in sedimentary records. Here we used ancient DNA preserved in Qinghai Lake sediments to reconstruct the temporal succession of plankton communities in the past 18,500 years. Our results showed that seven classes and sixteen genera of phytoplankton in the lake underwent major temporal changes, in correlation with known climatic events. Trebouxiophyceae and Eustigmatophyceae were predominant during the cold periods, whereas Chlorophyceae, Phaeophyceae, Xanthophyceae, Bacillariophyceae, and Cyanophyceae were abundant during the warm periods. The inferred changes in temperature, nutrients, precipitation, and salinity, as driven by the Westerlies and summer Monsoon strength, likely contributed to these observed temporal changes. Based on these correlations, we propose the phytoplankton index as a proxy to reconstruct the stadial versus interstadial climate change history in Qinghai Lake. This taxon-specific index is free of terrestrial contamination, sensitive to short-term climatic oscillations, and continuous in recording all climatic events in the lake. The validity of this index and its applicability to other lakes is demonstrated by its good correlations with multiple climate records of Qinghai Lake and another lake on the Tibetan Plateau, Kusai Lake.},
}

*Biodiversity
China
Climate Change
Environment
*Environmental Monitoring
Geography
*Lakes
*Phytoplankton/classification/genetics
RNA, Ribosomal, 23S/genetics

@article {pmid25944642,
year = {2015},
author = {Olalde, I and Capote, J and Del-Arco, MC and Atoche, P and Delgado, T and González-Anton, R and Pais, J and Amills, M and Lalueza-Fox, C and Ramírez, O},
title = {Ancient DNA sheds light on the ancestry of pre-hispanic Canarian pigs.},
journal = {Genetics, selection, evolution : GSE},
volume = {47},
number = {1},
pages = {40},
pmid = {25944642},
issn = {1297-9686},
mesh = {Animals ; Cytochromes b/genetics ; DNA/chemistry ; Genetic Variation ; Haplotypes ; Spain ; Sus scrofa/genetics ; Swine/*genetics ; },
abstract = {BACKGROUND: Canarian Black (CB) pigs belong to an autochthonous and endangered breed, which is spread throughout the Canarian archipelago. It is commonly accepted that they represent a relic of the pig populations that were bred by the Berbers in North Africa over millennia. It is important to note that the geographic isolation of the Canary Islands has preserved this genetic legacy intact from foreign introgressions until the Spanish conquest of the archipelago in the 15(th) century. Ten years ago, it was demonstrated that, in CB pigs, the frequency of the Asian A2 cytochrome-b haplogroup reached 73%. The current work aimed at investigating whether this observation is explained by either a recent or an ancient introgression of CB pigs with Far Eastern pigs.

RESULTS: Genetic analyses of 23 ancient samples from pre-hispanic Canarian pigs (420 to 2500 years before present) showed that Near Eastern and Far Eastern genetic signatures were totally absent in the primitive Canarian pre-hispanic pigs. Indeed, the haplotypes detected in these pigs were closely related to those of North African and European wild boars.

CONCLUSIONS: Our results demonstrate that the high frequency of the Far Eastern mitochondrial cytochrome B A2 haplotype in modern Canarian Black pigs probably corresponds to a relatively recent introgression with British breeds.},
}

Animals
Cytochromes b/genetics
DNA/chemistry
Genetic Variation
Haplotypes
Spain
Sus scrofa/genetics
Swine/*genetics

@article {pmid25422439,
year = {2014},
author = {Xiang, H and Gao, J and Yu, B and Zhou, H and Cai, D and Zhang, Y and Chen, X and Wang, X and Hofreiter, M and Zhao, X},
title = {Early Holocene chicken domestication in northern China.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {49},
pages = {17564-17569},
pmid = {25422439},
issn = {1091-6490},
mesh = {Animal Husbandry/*history ; Animals ; Archaeology/methods ; Bayes Theorem ; *Biological Evolution ; Bone and Bones ; Chickens/*genetics ; China ; DNA, Mitochondrial/*analysis ; Gene Pool ; Geography ; Haplotypes ; History, Ancient ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to ∼ 10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China.},
}

Animal Husbandry/*history
Animals
Archaeology/methods
Bayes Theorem
*Biological Evolution
Bone and Bones
Chickens/*genetics
China
DNA, Mitochondrial/*analysis
Gene Pool
Geography
Haplotypes
History, Ancient
Models, Genetic
Molecular Sequence Data
Phylogeny
Species Specificity

@article {pmid25418693,
year = {2015},
author = {Reynolds, AW and Raff, JA and Bolnick, DA and Cook, DC and Kaestle, FA},
title = {Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley.},
journal = {American journal of physical anthropology},
volume = {156},
number = {3},
pages = {434-448},
doi = {10.1002/ajpa.22668},
pmid = {25418693},
issn = {1096-8644},
mesh = {DNA, Mitochondrial/*genetics ; Female ; *Genetics, Population ; Haplotypes ; *Human Migration ; Humans ; Illinois ; Male ; Mississippi ; Paleontology ; Rivers ; },
abstract = {Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.},
}

DNA, Mitochondrial/*genetics
Female
*Genetics, Population
Haplotypes
*Human Migration
Humans
Illinois
Male
Mississippi
Paleontology
Rivers

@article {pmid22563371,
year = {2012},
author = {Hervella, M and Izagirre, N and Alonso, S and Fregel, R and Alonso, A and Cabrera, VM and de la Rúa, C},
title = {Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e34417},
pmid = {22563371},
issn = {1932-6203},
mesh = {Agriculture ; Archaeology ; DNA, Mitochondrial/*genetics/history ; Europe ; Genetic Heterogeneity ; Genetic Variation ; Genetics, Population/classification ; Haplotypes ; History, Ancient ; Humans ; *Models, Theoretical ; Phylogeny ; Spain ; },
abstract = {BACKGROUND/PRINCIPAL FINDINGS: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.

METHODOLOGY/SIGNIFICANCE: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.

CONCLUSION: The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.},
}

Agriculture
Archaeology
DNA, Mitochondrial/*genetics/history
Europe
Genetic Heterogeneity
Genetic Variation
Genetics, Population/classification
Haplotypes
History, Ancient
Humans
*Models, Theoretical
Phylogeny
Spain

@article {pmid22237531,
year = {2012},
author = {Stiller, M and Fulton, TL},
title = {Multiplex PCR amplification of ancient DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {840},
number = {},
pages = {133-141},
doi = {10.1007/978-1-61779-516-9_17},
pmid = {22237531},
issn = {1940-6029},
mesh = {Animals ; DNA/*genetics ; DNA Primers/genetics ; Electrophoresis, Agar Gel/methods ; *Fossils ; Multiplex Polymerase Chain Reaction/*methods ; },
abstract = {Multiplex PCR allows the simultaneous amplification of up to dozens of target fragments in a single PCR. It is therefore a powerful tool to obtain many kilobases of continuous sequence from minute amounts of ancient DNA (aDNA), which usually must be amplified in multiple short and overlapping fragments. Because significantly less template is required compared to amplifying each fragment separately, multiplex PCR is particularly beneficial when the fossil material itself, or access to the fossil material, is limited. The recently refined two-step multiplex PCR protocol consists of a first-step reaction (the actual multiplex PCR) that then acts as the template for the second-step PCR. During the second step, nested primers are used in individual amplification reactions. Although the same set of primers can be used in both steps, using a nested set in the second step adds an additional level of selectivity and specificity, minimizing PCR artifacts. This is particularly important when complex mixtures of template DNA, such as aDNA extracts, are amplified.},
}

Animals
DNA/*genetics
DNA Primers/genetics
Electrophoresis, Agar Gel/methods
*Fossils
Multiplex Polymerase Chain Reaction/*methods

@article {pmid12167530,
year = {2002},
author = {Zink, AR and Reischl, U and Wolf, H and Nerlich, AG},
title = {Molecular analysis of ancient microbial infections.},
journal = {FEMS microbiology letters},
volume = {213},
number = {2},
pages = {141-147},
doi = {10.1111/j.1574-6968.2002.tb11298.x},
pmid = {12167530},
issn = {0378-1097},
mesh = {Animals ; Biological Evolution ; Communicable Diseases/*history ; DNA, Bacterial/analysis/genetics ; History, Ancient ; Humans ; Mummies ; Paleopathology ; Tuberculosis/epidemiology/*history/microbiology ; },
abstract = {The detection of ancient microbial DNA offers a new approach for the study of infectious diseases, their occurrence, frequency and host-pathogen interaction in historic times and populations. Moreover, data obtained from skeletal and mummified tissue may represent an important completion of contemporary phylogenetic analyses of pathogens. In the last few years, a variety of bacterial, protozoal and viral infections have been detected in ancient tissue samples by amplification and characterization of specific DNA fragments. This holds particularly true for the identification of the Mycobacterium tuberculosis complex, which seems to be more robust than other microbes due to its waxy, hydrophobic and lipid-rich cell wall. These observations provided useful information about the occurrence, but also the frequency of tuberculosis in former populations. Moreover, these studies suggest new evolutionary models and indicate the route of transmission between human and animals. Until now, other pathogens, such as Mycobacterium leprae, Yersinia pestis, Plasmodium falciparum and others, have occasionally been identified - mostly in single case studies or small sample sizes - as well, although much less information is available on these pathogens in ancient settings. The main reason therefore seems to be the degradation and modification of ancient DNA by progressive oxidative damage. Furthermore, the constant risk of contamination by recent DNA forces to take time and cost effective measures and renders the analysis of ancient microbes difficult. Nevertheless, the study of microbial ancient DNA significantly contributes to the understanding of transmission and spread of infectious diseases, and potentially to the evolution and phylogenetic pathways of pathogens.},
}

Animals
Biological Evolution
Communicable Diseases/*history
DNA, Bacterial/analysis/genetics
History, Ancient
Humans
Mummies
Paleopathology
Tuberculosis/epidemiology/*history/microbiology

@article {pmid9667992,
year = {1998},
author = {Smith, AB},
title = {What does palaeontology contribute to systematics in a molecular world?.},
journal = {Molecular phylogenetics and evolution},
volume = {9},
number = {3},
pages = {437-447},
doi = {10.1006/mpev.1998.0488},
pmid = {9667992},
issn = {1055-7903},
mesh = {Animals ; DNA/chemistry/*genetics/isolation & purification ; *Evolution, Molecular ; Fishes/classification/genetics ; *Fossils ; Genetic Variation ; *Paleontology ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/*methods ; Time ; Vertebrates/classification/genetics ; },
abstract = {Palaeontology provides the only direct record for morphological and genetic change through time and uniquely contributes to systematics in two ways: by providing access to denser taxon sampling than is otherwise possible and by dating divergence times. Claims that ancient DNA has survived millions of years in certain fossils suggested the possibility that palaeontology could contribute directly to molecular systematic studies. Unfortunately, none of the supposed geologically ancient DNA records stands up to detailed scrutiny and fossils therefore contribute primarily through the morphological information they preserve. Denser taxon sampling can improve the accuracy of phylogenetic estimates primarily through allowing better discrimination of homoplasy from homology. This in turn leads to more accurate hypotheses of character transformation. Denser taxon sampling also offers the opportunity for more accurate rooting, since more characters can be polarized by reference to a stem-group taxon than to an extant sister-group taxon. Missing data can be a problem for fossils, but is not crippling. Finally the temporal order of clade appearances in the fossil record can provide ancillary evidence for selecting a working phylogeny from among a number of equally most parsimonious cladograms.},
}

Animals
DNA/chemistry/*genetics/isolation & purification
*Evolution, Molecular
Fishes/classification/genetics
*Fossils
Genetic Variation
*Paleontology
*Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal/genetics
Sequence Analysis, DNA/*methods
Time
Vertebrates/classification/genetics

@article {pmid40826367,
year = {2025},
author = {Roca-Rada, X and Davidson, R and Williams, MP and Villalba-Mouco, V and Carvalho, AF and Ravishankar, S and Collen, E and Haarkötter, C and Taufik, L and Cuesta-Aguirre, DR and Tente, C and Calleja, ÁMM and MacRoberts, RA and Melo, L and Purnomo, GA and Souilmi, Y and Tobler, R and Cunha, E and Tereso, S and Matos, VMJ and Fernandes, TM and Maurer, AF and Silva, AM and Carvalho, PC and Llamas, B and Teixeira, JC},
title = {The genetic history of Portugal over the past 5,000 years.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {248},
pmid = {40826367},
issn = {1474-760X},
support = {I.P./MCTES (PTDC/HAR-ARQ/6273/2020)//Fundação para a Ciência e a Tecnologia/ ; FPU 20/01967//Spanish Ministry of Universities/ ; DE210101235//Australian Research Council/ ; },
abstract = {BACKGROUND: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of Portuguese ancient genome-wide data, from 67 individuals spanning 5000 years of human history, from the Neolithic to the nineteenth century.

RESULTS: We identify early admixture between local hunter-gatherers and Anatolian-related farmers in Neolithic Portugal, with a northeastern-southwestern gradient of increasing Magdalenian-associated ancestry persistence in Iberia. This profile continues into the Chalcolithic, though Bell Beaker-associated sites reveal Portugal's first evidence of Steppe-related ancestry. Such ancestry has a broader demographic impact during the Bronze Age, despite continuity of local Chalcolithic genetic ancestry and limited Mediterranean connections. The village of Idanha-a-Velha emerges in the Roman period as a site of significant migration and interaction, presenting a notably diverse genetic profile that includes North African and Eastern Mediterranean ancestries. The Early Medieval period is marked by the arrival of Central European genetic diversity, likely linked to migrations of Germanic tribes, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant additional African admixture in the south. The latter remains stable during the post-Islamic period, suggesting enduring African influences.

CONCLUSIONS: We reveal dynamic patterns of migration in line with cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archeological data, enhancing our understanding of Iberia's biological and cultural heritage.},
}

@article {pmid40801890,
year = {2025},
author = {Libedinsky, I and Wei, Y and de Leeuw, C and Rilling, JK and Posthuma, D and van den Heuvel, MP},
title = {The emergence of genetic variants linked to brain and cognitive traits in human evolution.},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
volume = {35},
number = {8},
pages = {},
pmid = {40801890},
issn = {1460-2199},
support = {VI.C.241.074//VICI/ ; //Netherlands Organization for Scientific Research/ ; 101001062//European Research Council consolidator/ ; 024.004.012//BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology/ ; 834057/ERC_/European Research Council/International ; },
abstract = {Human evolution involved major anatomical transformations, including a rapid increase in brain volume over the last 2 million years. Examination of fossil records provides insight into these physical changes but offers limited information on the evolution of brain function and cognition. A complementary approach integrates genome dating from the Human Genome Dating Project with genome-wide association studies to trace the emergence of genetic variants linked to human traits over 5 million years. We find that genetic variants underlying cortical morphology (~300,000 years, P = 4 × 10-28), fluid intelligence (~500,000 years, P = 1.4 × 10-4), and psychiatric disorders (~475,000 years, P = 5.9 × 10-33) emerged relatively recently in hominin evolution. Among psychiatric phenotypes, variants associated with depression (~24,000 years, P = 1.6 × 10-4) and alcoholism-related traits (~40,000 years, P = 5.2 × 10-12) are the youngest. Genes with recent evolutionary modifications are involved in intelligence (P = 1.7 × 10-6) and cortical area (P = 3.5 × 10-4) and exhibit elevated expression in language-related areas (P = 7.1 × 10-4), a hallmark of human cognition. Our findings suggest that recently evolved genetic variants shaped the human brain, cognition, and psychiatric traits.},
}

@article {pmid40780196,
year = {2025},
author = {Skourtanioti, E and Jia, X and Tavartkiladze, N and Bitadze, L and Shengelia, R and Tushabramishvili, N and Aslanishvili, V and Gasparyan, B and Kandel, AW and Naumann, D and Neumann, GU and Bianco, RA and Mötsch, A and Prüfer, K and Lamnidis, TC and Traverso, L and Ghalichi, A and Ellingvåg, S and Stockhammer, PW and Krause, J and Ringbauer, H},
title = {The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.07.013},
pmid = {40780196},
issn = {1097-4172},
abstract = {The Caucasus was a hub for cultural and technological innovation in prehistory, yet the population history between the Greater and Lesser Caucasus remains insufficiently understood. We present genome-wide data of 205 individuals from modern Georgia and 25 from Armenia, spanning the period from the Bronze Age (BA) to the "Migration Period" (c. 3500 BCE-700 CE). Our results reveal a persisting local gene pool that, during the Middle-Late BA, absorbed additional ancestry from Anatolia and the neighboring Eurasian Steppe. In subsequent periods, we document population growth and increasing genetic diversity, supported by a high rate of individual ancestry outliers, particularly in urban centers of eastern Georgia. Among 20 Medieval individuals with artificially deformed skulls, 15 were part of local mating networks and five derived ancestry from the Eurasian Steppe, suggesting that cranial modification arrived with nomadic groups but became a locally adopted cultural practice.},
}

@article {pmid40762062,
year = {2025},
author = {Llamas, B and van Loenen, AL and Mitchell, KJ and Hofman-Kamińska, E and Bocherens, H and Heiniger, H and Pacher, M and Makowiecki, D and Piličiauskienė, G and Drucker, DG and Brown, D and Thomas, ZA and Turney, CSM and Kowalczyk, R and Cooper, A},
title = {Coexistence, Extinction and Survival-The Evolutionary History of Bison Species in Western Eurasia.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70354},
pmid = {40762062},
issn = {1365-2486},
support = {//Narodowe Centrum Nauki/ ; },
mesh = {*Bison/genetics/physiology ; Animals ; Europe ; *Extinction, Biological ; *Biological Evolution ; Phylogeny ; *Genome, Mitochondrial ; Climate Change ; Ecosystem ; },
abstract = {European bison (Bison bonasus) are one of the few European megafaunal species to survive the Late Pleistocene mass megafaunal extinction. Current conservation management efforts have proceeded in the absence of information about their evolutionary history, which has been obscured by recent severe population bottlenecks. We characterized mitochondrial genomes from 135 ancient bison samples spanning > 50,000 years (> 50 ka) across the Eurasian continent and detected three distinct phylogenetic groups: two distinct clades of European bison and the extinct steppe bison (Bison priscus). The geographical distributions and dietary/ecological signatures of the three groups overlapped during the Late Pleistocene climate cycles and tracked environmental changes including vegetation cover and human impacts. The abundance of European bison specimens responded negatively to the extent of forest cover, including Holocene cycles of abrupt atmospheric-ocean circulation changes originating in the North Atlantic. European bison remain preferentially adapted to an open environment, but with today's anthropogenic landscapes, are now largely restricted to forest habitats with negative implications under scenarios of future environmental change.},
}

*Bison/genetics/physiology
Animals
Europe
*Extinction, Biological
*Biological Evolution
Phylogeny
*Genome, Mitochondrial
Climate Change
Ecosystem

@article {pmid40760046,
year = {2025},
author = {Le Geay, M and Mayers, K and Sytiuk, A and Dorrepaal, E and Küttim, M and Lamentowicz, M and Tuittila, ES and Lauga, B and Jassey, VEJ},
title = {Uncovering diversity and abundance patterns of CO2-fixing microorganisms in peatlands.},
journal = {npj biodiversity},
volume = {4},
number = {1},
pages = {30},
pmid = {40760046},
issn = {2731-4243},
support = {ANR- 18-EURE-0018//Agence Nationale de la Recherche/ ; ANR-23-ERCC-0001-01//Agence Nationale de la Recherche/ ; },
abstract = {Microorganisms play a crucial role in the carbon (C) dynamics of peatlands - a major terrestrial C reservoir. Because of their role in C emissions, heterotrophic microorganisms have attracted much attention over the past decades. CO2-fixing microorganisms (CFMs) remained largely overlooked, while they could attenuate C emissions. Here, we use metabarcoding and digital droplet PCR to survey microorganisms that potentially fix CO2 in different peatlands. We demonstrate that CFMs are abundant and diverse in peatlands, with on average 1021 CFMs contributing up to 40% of the total bacterial abundance. Using a joint-species distribution model, we identified a core and a specific CFM microbiome, the latter being influenced by temperature and nutrients. Our findings highlight that ASV richness and community structure were direct drivers of CFM abundance, while environmental parameters were indirect drivers. These results provide the basis for a better understanding of the role of CFMs in peatland C cycle inputs.},
}

@article {pmid40751194,
year = {2025},
author = {Kim, J and Blazyte, A and Choi, JP and Kim, C and Sharko, F and Jeon, S and Kim, EM and Sohn, H and Lee, JH and Kim, HW and Yoo, MH and Lee, K and Nedoluzhko, A and Bhak, J},
title = {Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {234},
pmid = {40751194},
issn = {1741-7007},
support = {[P0016195, P0016193] (1425156792, 1425157301) (2.220035.01, 2.220036.01)//Promotion of Innovative Business for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea)/ ; [P0016195, P0016193] (1425156792, 1425157301) (2.220035.01, 2.220036.01)//Promotion of Innovative Business for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea)/ ; [P0016195, P0016193] (1425156792, 1425157301) (2.220035.01, 2.220036.01)//Promotion of Innovative Business for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea)/ ; [P0016195, P0016193] (1425156792, 1425157301) (2.220035.01, 2.220036.01)//Promotion of Innovative Business for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea)/ ; 1.200047.01//Ulsan City Research Fund/ ; 1.200047.01//Ulsan City Research Fund/ ; 1.200047.01//Ulsan City Research Fund/ ; 1.200047.01//Ulsan City Research Fund/ ; R2020024, R2021030, R2022033, R2024004//National Institute of Fisheries Science, Ministry of Ocean and Fisheries, Korea/ ; R2020024, R2021030, R2022033, R2024004//National Institute of Fisheries Science, Ministry of Ocean and Fisheries, Korea/ ; R2020024, R2021030, R2022033, R2024004//National Institute of Fisheries Science, Ministry of Ocean and Fisheries, Korea/ ; R2020024, R2021030, R2022033, R2024004//National Institute of Fisheries Science, Ministry of Ocean and Fisheries, Korea/ ; R2020024, R2021030, R2022033, R2024004//National Institute of Fisheries Science, Ministry of Ocean and Fisheries, Korea/ ; },
mesh = {Animals ; *Sea Lions/genetics ; *Genome ; *Extinction, Biological ; Republic of Korea ; Phylogeny ; *Biological Evolution ; *Evolution, Molecular ; Genetic Variation ; Gene Flow ; },
abstract = {BACKGROUND: The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and the Japanese sea lion internationally, was endemic to the Northwest Pacific before its extinction in the 1950s. However, its origins, speciation, and genetic diversity remain poorly understood.

RESULTS: To address this, we sequenced DNA from 16 Z. japonicus bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our genome-wide SNP analyses reveal Z. japonicus as the earliest diverged species within its genus, redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. Our research further elucidates the phylogeny of Z. japonicus, shedding light on the complexity of the genetic isolation process within its genus that was prompted by the geographic isolation of the three populations of Zalophus ancestral stock. Conversely, the genetic signature of the Dokdo sea lion genome can be modeled as an evolutionary pathway involving gene flow from Otariidae species with shared range. In addition, we discovered that the population decline of Z. japonicus started already over 100,000 years ago; however, Z. japonicus genome maintained a relatively high heterozygosity despite nearing extinction.

CONCLUSIONS: Our genome-scale analysis sheds light on the phylogeny of Z. japonicus, the evolutionary pathways underlying its speciation, and its genetic diversity before extinction. Broadly, we elucidate Zalophus gene flow complexity and genetic diversities among extant species. Furthermore, this study offers retrospective genomic insights into the extinction process of a carnivorous marine mammal, information that could aid conservation efforts for extant Otariidae species.},
}

Animals
*Sea Lions/genetics
*Genome
*Extinction, Biological
Republic of Korea
Phylogeny
*Biological Evolution
*Evolution, Molecular
Genetic Variation
Gene Flow

@article {pmid40737495,
year = {2025},
author = {Günther, T and Goldberg, A and Schraiber, JG},
title = {Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf172},
pmid = {40737495},
issn = {2160-1836},
abstract = {Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-read, high-throughput sequencing data, mapping sequencing reads to a linear reference genome can bias population genetic inference due to mismatches in reads carrying non-reference alleles. In this study, we investigate the impact of mapping bias on allele frequency estimates from pseudohaploid data and genotype likelihoods, two approaches commonly used in ultra-low to medium coverage sequencing. To mitigate mapping bias, we propose an empirical adjustment to genotype likelihoods. Using data from the 1000 Genomes Project, we find that our new method improves allele frequency estimation. To test a downstream application, we simulate ancient DNA data with realistic post-mortem damage to compare widely used methods for estimating ancestry proportions under different scenarios, including reference genome selection, population divergence, and sequencing depth. Our findings reveal that mapping bias can lead to differences in estimated admixture proportion of up to 4% depending on the reference population. However, the choice of method has a much stronger impact, with some methods showing differences of 10%. qpAdm appears to perform best at estimating simulated ancestry proportions, but it is sensitive to mapping bias and its applicability may vary across species due to its requirement for additional populations beyond the sources and target population. Our adjusted genotype likelihood approach largely mitigates the effect of mapping bias on genome-wide ancestry estimates from genotype likelihood-based tools. However, it cannot account for the bias introduced by the method itself or the noise in individual site allele frequency estimates due to low sequencing depth. Overall, our study provides valuable insights for obtaining more precise estimates of allele frequencies and ancestry proportions in empirical studies.},
}

@article {pmid40720742,
year = {2025},
author = {Ravasini, F and Conati Barbaro, C and Scheib, CL and Tambets, K and Metspalu, M and Cruciani, F and Trombetta, B and D'Atanasio, E},
title = {A New Perspective on the Arrival of the Eastern Mediterranean Genetic Influx in Central Italy Before the Onset of the Roman Empire.},
journal = {Genome biology and evolution},
volume = {17},
number = {8},
pages = {},
pmid = {40720742},
issn = {1759-6653},
support = {PID15152//EASI-Genomics 3rd Call for Transnational Access/ ; //Gerda Henkel Foundation/ ; RM12117A81385C5A//Sapienza University of Rome/ ; RM122181691E0881//Sapienza University of Rome/ ; RM123188F697BDAE//Sapienza University of Rome/ ; RM12218167749457//Sapienza University of Rome/ ; RM12218167749457//Sapienza University of Rome/ ; PRIN2022 2022PC2TSX//Italian Ministry of Research/ ; 2022E8NN2N//Italian Ministry of Research/ ; //European Union/ ; E53D23007590006//Next Generation EU/ ; H53D23003260006//Next Generation EU/ ; },
mesh = {Humans ; Italy ; *Human Migration ; History, Ancient ; Roman World ; Mediterranean Region ; *Genetics, Population ; DNA, Ancient/analysis ; Gene Pool ; Haplotypes ; },
abstract = {Italian genetic history was profoundly shaped by the Romans. While the Iron Age Central Italian gene pool was comparable to that of other coeval Central/Western European regions, during the Imperial age, it was significantly influenced by Eastern Mediterranean ancestries. To explain this genetic shift, it has been proposed that people from eastern provinces of the Empire migrated toward its political center: Rome and its surroundings. In this study, by presenting a new Roman Republic individual (1.25×) and comparing it to other published Republican samples, we propose a novel perspective for the presence of the Eastern Mediterranean ancestry in the Imperial gene pool. We show that the spread of this genetic ancestry may have taken place earlier than previously thought, during the Late Republican period, therefore predating the onset of the Empire by ∼200 years. The diffusion of this ancestry occurred due to early East-to-West movements, either because Eastern Mediterranean regions were under Roman political influence since the Late Republican period or even as a result of internal movements from Southern Italy where several Greek and Phoenician settlements were established during the 1st millennium BCE.},
}

Humans
Italy
*Human Migration
History, Ancient
Roman World
Mediterranean Region
*Genetics, Population
DNA, Ancient/analysis
Gene Pool
Haplotypes

@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},
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 {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 = {35},
number = {15},
pages = {3759-3766.e4},
doi = {10.1016/j.cub.2025.06.054},
pmid = {40680736},
issn = {1879-0445},
mesh = {Humans ; China ; *Genome, Human ; *DNA, Ancient/analysis ; *Human Migration/history ; History, Ancient ; Archaeology ; },
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.},
}

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

@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 {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},
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},
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},
mesh = {Humans ; China ; *DNA, Ancient/analysis ; },
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.},
}

Humans
China
*DNA, Ancient/analysis

@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 = {643},
number = {8072},
pages = {712-718},
pmid = {40634615},
issn = {1476-4687},
mesh = {Animals ; *Dental Enamel/chemistry/metabolism ; Dental Enamel Proteins/analysis ; East African People ; *Fossils ; Kenya ; Mammals/classification/metabolism ; Phylogeny ; *Proteome/analysis ; Proteomics ; },
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.},
}

Animals
*Dental Enamel/chemistry/metabolism
Dental Enamel Proteins/analysis
East African People
*Fossils
Kenya
Mammals/classification/metabolism
Phylogeny
*Proteome/analysis
Proteomics

@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},
mesh = {Animals ; *Phylogeny ; *Fishes/genetics/classification ; Genome, Mitochondrial ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; Museums ; Cell Nucleus/genetics ; },
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.},
}

Animals
*Phylogeny
*Fishes/genetics/classification
Genome, Mitochondrial
Sequence Analysis, DNA
DNA, Mitochondrial/genetics
Museums
Cell Nucleus/genetics

@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 = {Animals ; Archaeology ; Bone and Bones ; China ; *Fossils ; History, Ancient ; *Hominidae ; *Occupations/history ; *Wood ; *Technology/history ; },
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.},
}

Animals
Archaeology
Bone and Bones
China
*Fossils
History, Ancient
*Hominidae
*Occupations/history
*Wood
*Technology/history

@article {pmid40603668,
year = {2025},
author = {},
title = {Ancient DNA helps trace stinky Roman fish sauce to its source.},
journal = {Nature},
volume = {643},
number = {8071},
pages = {307},
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 = {82},
number = {3},
pages = {309-317},
doi = {10.1127/anthranz/1857},
pmid = {40598853},
issn = {0003-5548},
mesh = {Humans ; *Chromosomes, Human, Y/genetics ; Male ; China/ethnology ; Haplotypes/genetics ; *Asian People/genetics ; *Ethnicity/genetics ; Genetics, Population ; },
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.},
}

Humans
*Chromosomes, Human, Y/genetics
Male
China/ethnology
Haplotypes/genetics
*Asian People/genetics
*Ethnicity/genetics
Genetics, Population

@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 = {},
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},
support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; },
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 = {112},
number = {7},
pages = {1547-1561},
pmid = {40499537},
issn = {1537-6605},
mesh = {Humans ; *Selection, Genetic ; *Multifactorial Inheritance/genetics ; Genome-Wide Association Study ; Phenotype ; Alleles ; Models, Genetic ; Polymorphism, Single Nucleotide ; Genetic Variation ; },
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.},
}

Humans
*Selection, Genetic
*Multifactorial Inheritance/genetics
Genome-Wide Association Study
Phenotype
Alleles
Models, Genetic
Polymorphism, Single Nucleotide
Genetic Variation

@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 {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 = {},
pmid = {40475634},
issn = {2692-8205},
support = {R35 GM127087/GM/NIGMS NIH HHS/United States ; },
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 = {643},
number = {8074},
pages = {1304-1311},
pmid = {40468069},
issn = {1476-4687},
mesh = {*DNA, Ancient/analysis ; Humans ; China ; History, Ancient ; Bayes Theorem ; Burial/history ; Radiometric Dating ; *Cemeteries/history ; Female ; Male ; Archaeology ; Agriculture/history ; Millets ; },
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.},
}

*DNA, Ancient/analysis
Humans
China
History, Ancient
Bayes Theorem
Burial/history
Radiometric Dating
*Cemeteries/history
Female
Male
Archaeology
Agriculture/history
Millets

@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/ ; },
mesh = {Humans ; Poland ; *Burial/history ; Male ; Female ; History, Medieval ; Archaeology ; DNA, Ancient/analysis ; Cemeteries ; Middle Aged ; Adult ; History, 15th Century ; Plague/history ; History, 18th Century ; },
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.},
}

Humans
Poland
*Burial/history
Male
Female
History, Medieval
Archaeology
DNA, Ancient/analysis
Cemeteries
Middle Aged
Adult
History, 15th Century
Plague/history
History, 18th Century

@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 = {42},
number = {6},
pages = {},
pmid = {40465848},
issn = {1537-1719},
mesh = {Humans ; *Genome, Human ; China ; DNA, Ancient/analysis ; *Cultural Evolution ; *Asian People/genetics ; History, Ancient ; Human Migration ; },
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.},
}

Humans
*Genome, Human
China
DNA, Ancient/analysis
*Cultural Evolution
*Asian People/genetics
History, Ancient
Human Migration

@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 {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 = {44},
number = {14},
pages = {4013-4036},
pmid = {40447800},
issn = {1460-2075},
support = {CC2068/WT_/Wellcome Trust/United Kingdom ; GNT1181110//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Fanconi Anemia/metabolism/genetics ; *DNA Helicases/metabolism/chemistry/genetics ; Crystallography, X-Ray ; DNA Damage ; DNA/metabolism/chemistry ; Models, Molecular ; Protein Binding ; Fanconi Anemia Complementation Group D2 Protein/metabolism/genetics/chemistry ; Fanconi Anemia Complementation Group Proteins/metabolism/chemistry ; Ubiquitination ; DNA Repair ; DNA-Binding Proteins ; },
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.},
}

Humans
*Fanconi Anemia/metabolism/genetics
*DNA Helicases/metabolism/chemistry/genetics
Crystallography, X-Ray
DNA Damage
DNA/metabolism/chemistry
Models, Molecular
Protein Binding
Fanconi Anemia Complementation Group D2 Protein/metabolism/genetics/chemistry
Fanconi Anemia Complementation Group Proteins/metabolism/chemistry
Ubiquitination
DNA Repair
DNA-Binding Proteins

@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 = {35},
number = {11},
pages = {2709-2719.e5},
doi = {10.1016/j.cub.2025.05.002},
pmid = {40441135},
issn = {1879-0445},
mesh = {Humans ; *DNA, Ancient/analysis ; *Genome, Human ; History, Ancient ; Gene Flow ; Belize ; Archaeology ; Mexico ; Human Migration ; },
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.},
}

Humans
*DNA, Ancient/analysis
*Genome, Human
History, Ancient
Gene Flow
Belize
Archaeology
Mexico
Human Migration

@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 = {389},
number = {6758},
pages = {eadu7144},
doi = {10.1126/science.adu7144},
pmid = {40440428},
issn = {1095-9203},
mesh = {Humans ; Europe/epidemiology ; History, Ancient ; *Leprosy/history/microbiology ; *Leprosy, Lepromatous/microbiology/history/epidemiology ; *Mycobacterium leprae/genetics/classification/isolation & purification ; North America/epidemiology ; Phylogeny ; South America/epidemiology ; *Mycobacterium/classification/genetics/isolation & purification ; },
abstract = {Leprosy, caused primarily 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 that M. lepromatosis may have been widespread during the Late Holocene, demonstrating that M. lepromatosis leprosy has a long-standing history in the Americas before European arrival.},
}

Humans
Europe/epidemiology
History, Ancient
*Leprosy/history/microbiology
*Leprosy, Lepromatous/microbiology/history/epidemiology
*Mycobacterium leprae/genetics/classification/isolation & purification
North America/epidemiology
Phylogeny
South America/epidemiology
*Mycobacterium/classification/genetics/isolation & purification

@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 = {Animals ; Female ; Humans ; Mice ; *Bacterial Proteins/genetics ; Disease Models, Animal ; Gene Deletion ; *Pandemics ; *Plague/microbiology/mortality/transmission ; Plasmids/genetics ; *Plasminogen Activators/genetics ; *Pore Forming Cytotoxic Proteins/genetics ; Rodentia/microbiology ; Virulence/genetics ; *Yersinia pestis/pathogenicity/genetics ; },
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.},
}

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

@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 = {},
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.},
}