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

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

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

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

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

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

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

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

@article {pmid40555717,
year = {2025},
author = {Szécsényi-Nagy, A and Virag, C and Jakab, K and Rohland, N and Ringbauer, H and Anders, A and Raczky, P and Hajdu, T and Kiss, K and Szeniczey, T and Évinger, S and Keszi, T and M Virág, Z and Cheronet, O and Mallick, S and Akbari, A and Pinhasi, R and Reich, D and Siklósi, Z},
title = {Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5318},
pmid = {40555717},
issn = {2041-1723},
mesh = {Humans ; *DNA, Ancient/analysis ; Haplotypes ; *Genetics, Population ; History, Ancient ; Genome, Human ; Male ; Genetic Variation ; },
abstract = {Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*DNA, Ancient/analysis
Humans
History, Ancient

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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