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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Humans
Animals
Dogs
*Biological Evolution
Europe

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid39705165,
year = {2024},
author = {Patin, E and Quintana-Murci, L},
title = {Tracing the Evolution of Human Immunity Through Ancient DNA.},
journal = {Annual review of immunology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-immunol-082323-024638},
pmid = {39705165},
issn = {1545-3278},
abstract = {Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.},
}

@article {pmid39703808,
year = {2024},
author = {Veselka, B and Reich, D and Capuzzo, G and Olalde, I and Callan, K and Zalzala, F and Altena, E and Goffette, Q and Ringbauer, H and van der Velde, H and Polet, C and Toussaint, M and Snoeck, C and Cattelain, L},
title = {Assembling Ancestors: the manipulation of Neolithic and Gallo-Roman skeletal remains from Pommerœul, Belgium.},
journal = {Antiquity},
volume = {98},
number = {402},
pages = {1576-1591},
pmid = {39703808},
issn = {0003-598X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {The ancient cemetery of Pommerœul, Belgium, was classified as Gallo-Roman in the 1970s', yielding 76 cremation graves and one inhumation. However, subsequent radiocarbon analyses dated the inhumation to the Late Neolithic (4[th]-3[rd] millennium calBC). We report osteoarchaeological analysis indicating that the inhumation was composed of bones from multiple individuals, afterwards buried as "one". Ancient DNA analyses also finds evidence of multiple individuals and revealed another surprise: the cranium is post-Neolithic and genetically related to a pair of siblings from another Belgian Gallo-Roman site. This composite burial may have been created in Late Neolithic times, with Gallo-Romans adding the cranium, or alternatively the burial may have been fully assembled in the Gallo-Roman periods. This exceptional burial documents unexpected burial practices for both prehistoric and Roman times.},
}

@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@article {pmid39698825,
year = {2024},
author = {Shastry, V and Berg, JJ},
title = {Allele ages provide limited information about the strength of negative selection.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae211},
pmid = {39698825},
issn = {1943-2631},
abstract = {For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by re-weighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson Random Field (PRF) method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.},
}

@article {pmid39697594,
year = {2024},
author = {Wang, B and Hao, D and Xu, Y and Zhu, K and Wang, R and Yang, X and Shen, Q and Xu, M and Bai, T and Ma, H and Zheng, J and Wang, X and Zou, X and Zhou, H and Mao, X and Tang, J and Peng, Y and Tao, L and He, H and Chen, H and Guo, J and Ji, Z and Liu, Y and Wen, S and Jin, L and Zhang, Q and Wang, CC},
title = {Population expansion from central plain to northern coastal China inferred from ancient human genomes.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111405},
pmid = {39697594},
issn = {2589-0042},
abstract = {The population history of the northern coastal Chinese is largely unknown due to the lack of ancient human genomes from the Neolithic to historical periods. In this study, we reported 14 newly generated ancient genomes from Linzi, one of China's densely populated and economically prosperous cities from the Zhou to Han Dynasties. The ancient samples in this study were dated to the Warring States period to the Eastern Han Dynasty (∼2,000 BP). We found the samples derived all their ancestry from Late Bronze Age to Iron Age Middle Yellow River farmers rather than local Neolithic populations. They were genetically homogeneous with present-day Han Chinese of Shandong, suggesting 2,000 years of genetic stability. Our results highlight the role of the eastward migration of Yellow River farmers in the Central Plain to northern coastal China in forming the present-day genetic structure of Han Chinese.},
}

@article {pmid39697469,
year = {2024},
author = {Owsley, DW and Bruwelheide, KS and Harney, É and Mallick, S and Rohland, N and Olalde, I and Barca, KG and Ramsey, AJ and Hull-Walski, DA and Kelso, WM and May, JE and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Simon, VE and Givens, DM and Lavin, MD and Reich, DE},
title = {Historical and Archaeogenomic Identification of High-Status Englishmen at Jamestown, Virginia.},
journal = {Antiquity},
volume = {98},
number = {400},
pages = {1040-1054},
pmid = {39697469},
issn = {0003-598X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {Ancient DNA (aDNA) data are reported for two human skeletons buried within the chancel of the 1608-1616 church at the North American colonial settlement of Jamestown, Virginia. The men are suspected kinsmen of the colony's first Governor, Thomas West, 3[rd] Baron De La Warr based on archaeological, osteological, and documentary evidence. Genomic analyses of these men, Sir Ferdinando Wenman and Captain William West, identify a shared mitochondrial haplogroup, H10e, inferring maternal relatedness. In this unusual case, aDNA prompted further historical research that led to the discovery of illegitimacy, an aspect of identity omitted, likely intentionally, from genealogical records.},
}

@article {pmid39694065,
year = {2024},
author = {Barquera, R and Sitter, TL and Kirkpatrick, CL and Ramirez, DA and Kocher, A and Spyrou, MA and Couoh, LR and Talavera-González, JA and Castro, M and von Hunnius, T and Guevara, EK and Hamilton, WD and Roberts, P and Scott, E and Fabra, M and Da Peña, GV and Pacheco, A and Rodriguez, M and Aspillaga, E and Tiliakou, A and Nelson, EA and Giffin, KL and Bianco, RA and Rohrlach, AB and de Los Ángeles García Martínez, M and Ballesteros Solís, FA and Sajantila, A and Saunders, SR and Nores, R and Herbig, A and Krause, J and Bos, KI},
title = {Ancient genomes reveal a deep history of treponemal disease in the Americas.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-024-08515-5},
pmid = {39694065},
issn = {1476-4687},
abstract = {Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most famously, syphilis[1]. Debates on both a common origin for these pathogens and the history of syphilis itself has weighed evidence for the "Columbian hypothesis"[2], which argues for an American origin, against that for the "pre-Columbian hypothesis"[3], which argues for presence of the disease in Eurasia in the Medieval period and possibly earlier. While molecular data has provided a genetic basis for distinction of the typed subspecies[4], deep evolution of the complex has remained unresolved due to limitations in the conclusions that can be drawn from the sparse paleogenomic data currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the T. pallidum pallidum (syphilis), T. pallidum pertenue (yaws) and T. pallidum endemicum (bejel) lineages. Our data indicate unexplored diversity and an emergence of T. pallidum that post-dates human occupation in the Americas. Together these results support an American origin for all T. pallidum characterized at the genomic level, both modern and ancient.},
}

@article {pmid39689706,
year = {2025},
author = {Donegan, MA and Kahn, AK and Becker, N and Castillo Siri, A and Campos, PE and Boyer, K and Colwell, A and Briand, M and Almeida, RPP and Rieux, A},
title = {Century-old herbarium specimen provides insights into Pierce's disease of grapevines emergence in the Americas.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {145-153.e4},
doi = {10.1016/j.cub.2024.11.029},
pmid = {39689706},
issn = {1879-0445},
mesh = {*Vitis/microbiology/genetics ; *Plant Diseases/microbiology ; *Phylogeny ; *Xylella/genetics/pathogenicity ; Genome, Fungal ; },
abstract = {Fossils and other preserved specimens are integral for informing timing and evolutionary history in every biological system. By isolating a plant pathogen genome from herbarium-preserved diseased grapevine material from 1906 (Herb_1906), we were able to answer questions about an enigmatic system. The emergence of Pierce's disease (PD) of grapevine has shaped viticultural production in North America; yet, there are uncertainties about the geographic origin of the pathogen (Xylella fastidiosa subsp. fastidiosa, Xff) and the timing and route of its introduction. We produced a high-quality, de novo genome assembly of this historical plant pathogen and confirmed degradation patterns unique to ancient DNA. Due to the inclusion of the Herb_1906 sample, we were able to generate a significant temporal signal in the genomic data. This allowed us to build a time-calibrated phylogeny, where we estimate the introduction of Xff into the US between 1734 and 1741 CE, an earlier time frame than previously inferred. In a large collection of >300 Xff genomes, the Herb_1906 sample was genetically most similar to a small population from Northern California but not basal to the entire Xff California clade. Based on phylogenetic placement and a phylogeographic reconstruction, our data support a single introduction of Xff into the Southeastern US from Central America, with multiple subsequent introductions into California.},
}

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

@article {pmid39677618,
year = {2024},
author = {Yediay, FE and Kroonen, G and Sabatini, S and Frei, KM and Frank, AB and Pinotti, T and Wigman, A and Thorsø, R and Vimala, T and McColl, H and Moutafi, I and Altinkaya, I and Ramsøe, A and Gaunitz, C and Renaud, G and Martin, AM and Demeter, F and Scorrano, G and Canci, A and Fischer, P and Duyar, I and Serhal, C and Varzari, A and Türkteki, M and O'Shea, J and Rahmstorf, L and Polat, G and Atamtürk, D and Vinner, L and Omura, S and Matsumura, K and Cao, J and Valeur Seersholm, F and Morillo Leon, JM and Voutsaki, S and Orgeolet, R and Burke, B and Herrmann, NP and Recchia, G and Corazza, S and Borgna, E and Sampò, MC and Trucco, F and Pando, AP and Schjellerup Jørkov, ML and Courtaud, P and Peake, R and Bao, JFG and Parditka, G and Stenderup, J and Sjögren, KG and Staring, J and Olsen, L and Deyneko, IV and Pálfi, G and Aldana, PML and Burns, B and Paja, L and Mühlenbock, C and Cavazzuti, C and Cazzella, A and Lagia, A and Lambrinoudakis, V and Kolonas, L and Rambach, J and Sava, E and Agulnikov, S and Castañeda Fernández, V and Broné, M and Peña Romo, V and Molina González, F and Cámara Serrano, JA and Jiménez Brobeil, S and Nájera Molino, T and Rodríguez Ariza, MO and Galán Saulnier, C and González Martín, A and Cauwe, N and Mordant, C and Roscio, M and Staniaszek, L and Tafuri, MA and Yıldırım, T and Salzani, L and Sand Korneliussen, T and Moreno-Mayar, JV and Allentoft, ME and Sikora, M and Nielsen, R and Kristiansen, K and Willerslev, E},
title = {Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39677618},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM153400/GM/NIGMS NIH HHS/United States ; },
abstract = {The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious[1-5]. It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age[6,7]. However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages[8,9]. To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic[10,11] and Graeco-Armenian[1,12,13] hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.},
}

@article {pmid39674265,
year = {2024},
author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B},
title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39674265},
issn = {1477-4054},
support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; },
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; },
abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Sequence Analysis, DNA/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome
Workflow
DNA Contamination

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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