@article {pmid39028337,
year = {2024},
author = {Çubukcu, H and Kılınç, GM},
title = {Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {39028337},
issn = {1432-1777},
abstract = {Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.},
}

@article {pmid39026955,
year = {2024},
author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S},
title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11584},
doi = {10.1002/ece3.11584},
pmid = {39026955},
issn = {2045-7758},
abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.},
}

@article {pmid39024443,
year = {2024},
author = {Gibbons, A},
title = {Oldest human genome comes from a Denisovan.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6706},
pages = {240-241},
doi = {10.1126/science.adr8007},
pmid = {39024443},
issn = {1095-9203},
mesh = {Animals ; Female ; Humans ; Male ; *DNA, Ancient ; Fossils ; *Genome, Human ; *Neanderthals/genetics ; Siberia ; },
abstract = {200,000-year-old DNA shows our now-extinct cousins mated with Neanderthals.},
}

Animals
Female
Humans
Male
*DNA, Ancient
Fossils
*Genome, Human
*Neanderthals/genetics
Siberia

@article {pmid39017314,
year = {2023},
author = {Cosier, S},
title = {Building Knowledge: Scientists sequence DNA from a chunk of a Mesopotamian palace.},
journal = {Scientific American},
volume = {329},
number = {5},
pages = {18},
doi = {10.1038/scientificamerican1223-18a},
pmid = {39017314},
issn = {0036-8733},
mesh = {*Sequence Analysis, DNA ; Humans ; DNA, Ancient/analysis ; DNA/genetics ; Animals ; Fossils ; },
}

*Sequence Analysis, DNA
Humans
DNA, Ancient/analysis
DNA/genetics
Animals
Fossils

@article {pmid39017120,
year = {2023},
author = {Leonard, D},
title = {Quick Hits: A linguistic puzzle, ancient DNA, the origins of bipedalism, and much more in this month's Quick Hits.},
journal = {Scientific American},
volume = {328},
number = {3},
pages = {13},
doi = {10.1038/scientificamerican0323-13},
pmid = {39017120},
issn = {0036-8733},
mesh = {Humans ; *DNA, Ancient/analysis ; Animals ; Linguistics ; Hominidae/genetics ; Biological Evolution ; Language ; },
}

Humans
*DNA, Ancient/analysis
Animals
Linguistics
Hominidae/genetics
Biological Evolution
Language

@article {pmid39013011,
year = {2024},
author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD},
title = {Testing Times: Disentangling Admixture Histories in Recent and Complex Demographies using ancient DNA.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae110},
pmid = {39013011},
issn = {1943-2631},
abstract = {Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches - firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes - and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We observe population differentiation is the primary factor driving qpAdm performance. Notably, whilst complex gene-flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible amongst a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.},
}

@article {pmid39009303,
year = {2024},
author = {Shen, Q and Wu, Z and Zan, J and Yang, X and Guo, J and Ji, Z and Wang, B and Liu, Y and Mao, X and Wang, X and Zou, X and Zhou, H and Peng, Y and Ma, H and He, H and Bai, T and Xu, M and Wen, S and Jin, L and Zhang, Q and Wang, CC},
title = {Ancient genomes illuminate the demographic history of Shandong over the past two millennia.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.008},
pmid = {39009303},
issn = {1673-8527},
abstract = {Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.},
}

@article {pmid39009302,
year = {2024},
author = {Yu, Y and Yang, X and Liu, D and Du, P and Meng, H and Huang, Z and Xiong, J and Ding, Y and Ren, X and Allen, E and Wang, H and Han, S and Jin, L and Wang, CC and Wen, S},
title = {Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.009},
pmid = {39009302},
issn = {1673-8527},
abstract = {China's Northern and Southern Dynasties period (3[rd]-6[th] centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.},
}

@article {pmid39002897,
year = {2024},
author = {Du, S and Chen, J and Li, J and Qian, W and Wu, S and Peng, Q and Liu, Y and Pan, T and Li, Y and Hadi, SS and Tan, J and Yuan, Z and Wang, J and Tang, K and Wang, Z and Wen, Y and Dong, X and Zhou, W and Ruiz-Linares, A and Shi, Y and Jin, L and Liu, F and Zhang, M and Wang, S},
title = {A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.005},
pmid = {39002897},
issn = {1673-8527},
abstract = {Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of Genome-Wide Association Study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited significant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA, and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovan. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.},
}

@article {pmid38996487,
year = {2024},
author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL},
title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.},
journal = {Cell},
volume = {187},
number = {14},
pages = {3541-3562.e51},
doi = {10.1016/j.cell.2024.06.002},
pmid = {38996487},
issn = {1097-4172},
mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; },
abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.},
}

Animals
*Mammoths/genetics
*Genome/genetics
Female
*Skin
Elephants/genetics
Chromatin/genetics
Fossils
DNA, Ancient/analysis
Mice
Humans
X Chromosome/genetics

@article {pmid38996465,
year = {2024},
author = {Sawchuk, EA and Sirak, KA and Manthi, FK and Ndiema, EK and Ogola, CA and Prendergast, ME and Reich, D and Aluvaala, E and Ayodo, G and Badji, L and Bird, N and Black, W and Fregel, R and Gachihi, N and Gibbon, VE and Gidna, A and Goldstein, ST and Hamad, R and Hassan, HY and Hayes, VM and Hellenthal, G and Kebede, S and Kurewa, A and Kusimba, C and Kyazike, E and Lane, PJ and MacEachern, S and Massilani, D and Mbua, E and Morris, AG and Mutinda, C and M'Mbogori, FN and Reynolds, AW and Tishkoff, S and Vilar, M and Yimer, G},
title = {Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.},
journal = {American journal of human genetics},
volume = {111},
number = {7},
pages = {1243-1251},
doi = {10.1016/j.ajhg.2024.05.019},
pmid = {38996465},
issn = {1537-6605},
mesh = {Humans ; *DNA, Ancient/analysis ; *Genetics, Population ; Africa ; Genomics ; Black People/genetics ; },
abstract = {Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.},
}

Humans
*DNA, Ancient/analysis
*Genetics, Population
Africa
Genomics
Black People/genetics

@article {pmid38993187,
year = {2023},
author = {Meng, XY and Wang, QL and Shi, MJ and Zhang, HY},
title = {Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.},
journal = {Bladder cancer (Amsterdam, Netherlands)},
volume = {9},
number = {3},
pages = {211-216},
pmid = {38993187},
issn = {2352-3735},
abstract = {BACKGROUND: The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences.

METHODS: We calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs.

RESULTS: We validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution.

CONCLUSIONS: It is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.},
}

@article {pmid38991076,
year = {2024},
author = {Stone, R},
title = {Stunning 3D chromosomes preserved in thawed mammoths.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {130},
doi = {10.1126/science.adr6185},
pmid = {38991076},
issn = {1095-9203},
mesh = {Animals ; Chromosomes, Mammalian/genetics ; *Fossils ; *Mammoths/genetics ; *DNA, Ancient ; },
abstract = {"New type of fossil" may boost efforts to bring beasts back.},
}

Animals
Chromosomes, Mammalian/genetics
*Fossils
*Mammoths/genetics
*DNA, Ancient

@article {pmid38991073,
year = {2024},
author = {Gibbons, A},
title = {Neanderthals and moderns mingled early and often.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {132-133},
doi = {10.1126/science.adr6187},
pmid = {38991073},
issn = {1095-9203},
mesh = {Animals ; Humans ; Fossils ; *Neanderthals/genetics ; *Extinction, Biological ; DNA, Ancient ; },
abstract = {Study of genes modern humans gave Neanderthals helps explain their end.},
}

Animals
Humans
Fossils
*Neanderthals/genetics
*Extinction, Biological
DNA, Ancient

@article {pmid38987254,
year = {2024},
author = {Bergström, A},
title = {Improving data archiving practices in ancient genomics.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {754},
pmid = {38987254},
issn = {2052-4463},
mesh = {*Genomics ; Humans ; *DNA, Ancient/analysis ; Animals ; Metadata ; },
abstract = {Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.},
}

*Genomics
Humans
*DNA, Ancient/analysis
Animals
Metadata

@article {pmid38986104,
year = {2024},
author = {Jordan, B},
title = {[Ancient DNA speaks].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {6-7},
pages = {563-565},
doi = {10.1051/medsci/2024070},
pmid = {38986104},
issn = {1958-5381},
mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Pedigree ; },
abstract = {Many human DNA sequences have been obtained from ancient remains dating back from several millennia. However, these have low coverage and may contain many errors; this has limited their usefulness for many analyses, in particular the search for Identical By Descent (IBD) segments that is very powerful for detection of kinship. A new method, using imputation from database data and sophisticated statistical analysis, proves able to detect IBD segments (and thus parenthood) in low-quality DNA sequences from individuals linked only by sixth degree parenthood, opening a whole new field of investigation using ancient DNA.},
}

Humans
*DNA, Ancient/analysis
Sequence Analysis, DNA/methods
Pedigree

@article {pmid38981530,
year = {2024},
author = {Goldstein, ST and Mueller, NG and Janzen, A and Ogola, C and Dal Martello, R and Fernandes, R and Li, S and Iminjili, V and Juengst, S and Odera Otwani, A and Sawchuk, EA and Wang, K and Ndiema, E and Boivin, N},
title = {Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2026},
pages = {20232747},
doi = {10.1098/rspb.2023.2747},
pmid = {38981530},
issn = {1471-2954},
support = {//Max-Planck-Institut für Menschheitsgeschichte/ ; },
mesh = {*Crops, Agricultural ; Kenya ; *Archaeology ; *Agriculture ; Animals ; Radiometric Dating ; Africa, Eastern ; },
abstract = {The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.},
}

*Crops, Agricultural
Kenya
*Archaeology
*Agriculture
Animals
Radiometric Dating
Africa, Eastern

@article {pmid38976766,
year = {2024},
author = {Souilmi, Y and Wasef, S and Williams, MP and Conroy, G and Bar, I and Bover, P and Dann, J and Heiniger, H and Llamas, B and Ogbourne, S and Archer, M and Ballard, JWO and Reed, E and Tobler, R and Koungoulos, L and Walshe, K and Wright, JL and Balme, J and O'Connor, S and Cooper, A and Mitchell, KJ},
title = {Ancient genomes reveal over two thousand years of dingo population structure.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {30},
pages = {e2407584121},
doi = {10.1073/pnas.2407584121},
pmid = {38976766},
issn = {1091-6490},
support = {CE170100015//Department of Education and Training | Australian Research Council (ARC)/ ; DP210101960//Department of Education and Training | Australian Research Council (ARC)/ ; FL140100260//Department of Education and Training | Australian Research Council (ARC)/ ; 2021/GNT2011277//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Animals ; Australia ; *Genome ; Dogs/genetics ; Wolves/genetics ; DNA, Ancient/analysis ; Genetics, Population ; },
abstract = {Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.},
}

Animals
Australia
*Genome
Dogs/genetics
Wolves/genetics
DNA, Ancient/analysis
Genetics, Population

@article {pmid38969261,
year = {2024},
author = {Wang, M and Chen, H and Luo, L and Huang, Y and Duan, S and Yuan, H and Tang, R and Liu, C and He, G},
title = {Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.06.016},
pmid = {38969261},
issn = {1673-8527},
abstract = {Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent, to understand kinship, migration patterns, and population dynamics. Within forensic science, forensic investigative genetic genealogy (FIGG) has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources, opening new investigative avenues. In this review, we synthesize current knowledge, underscore recent advancements, and discuss the growing role of FIGG in forensic genomics. FIGG has been pivotal in revitalizing dormant inquiries and offering new genetic leads in numerous cold cases. Its effectiveness relies on the extensive SNP profiles contributed by individuals from diverse populations to specialized genomic databases. Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics, anthropology, and ancient DNA studies. As the field progresses, FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline, shaping the future of forensic investigations.},
}

@article {pmid38965340,
year = {2024},
author = {Gibbon, VE and Thompson, JC and Alves, S},
title = {Informed proxy consent for ancient DNA research.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {815},
pmid = {38965340},
issn = {2399-3642},
mesh = {Humans ; *Informed Consent ; *DNA, Ancient/analysis ; },
abstract = {We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people the research affects. Embracing the underlying principles and process of informed proxy consent has the potential to transform research by (1) enriching outcomes by learning from and collaborating with interested and affected persons; (2) empowering people potentially impacted by research to stipulate evidence for information flow; (3) guarding researchers against actual or perceived violations by providing a common set of guidelines; and (4) highlighting the essential nature of long-term consultation and community partnerships to research outcome success.},
}

Humans
*Informed Consent
*DNA, Ancient/analysis

@article {pmid38963678,
year = {2024},
author = {Coppola Bove, L and Kirkpatrick, CL and Vigil-Escalera Guirado, A and Botella López, MC and Bos, KI},
title = {A morphological and molecular approach to investigating infectious disease in early medieval Iberia: The necropolis of La Olmeda (Palencia, Spain).},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {e24994},
doi = {10.1002/ajpa.24994},
pmid = {38963678},
issn = {2692-7691},
support = {805268/ERC_/European Research Council/International ; //Erasmus+ Traineeship Program Scholarship/ ; //Junta de Andalucía and SEPIE/ ; 756-2023-0246//Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship/ ; },
abstract = {OBJECTIVE: Here we investigate infectious diseases that potentially contribute to osteological lesions in individuals from the early medieval necropolis of La Olmeda (6th-11th c. CE) in North Iberia.

MATERIALS AND METHODS: We studied a minimum number of 268 individuals (33 adult females; 38 adult males, 77 unknown/indeterminate sex; and 120 non-adults), including articulated and commingled remains. Individuals with differential diagnoses suggesting chronic systemic infectious diseases were sampled and bioinformatically screened for ancient pathogen DNA.

RESULTS: Five non-adults (and no adults) presented skeletal evidence of chronic systemic infectious disease (1.87% of the population; 4.67% of non-adults). The preferred diagnoses for these individuals included tuberculosis, brucellosis, and malaria. Ancient DNA fragments assigned to the malaria-causing pathogen, Plasmodium spp., were identified in three of the five individuals. Observed pathology includes lesions generally consistent with malaria; however, additional lesions in two of the individuals may represent hitherto unknown variation in the skeletal manifestation of this disease or co-infection with tuberculosis or brucellosis. Additionally, spondylolysis was observed in one individual with skeletal lesions suggestive of infectious disease.

CONCLUSIONS: This study sheds light on the pathological landscape in Iberia during a time of great social, demographic, and environmental change. Genetic evidence challenges the hypothesis that malaria was absent from early medieval Iberia and demonstrates the value of combining osteological and archaeogenetic methods. Additionally, all of the preferred infectious diagnoses for the individuals included in this study (malaria, tuberculosis, and brucellosis) could have contributed to the febrile cases described in historical sources from this time.},
}

@article {pmid38960861,
year = {2024},
author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Bilal Sharif, M and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD},
title = {Unravelling reference bias in ancient DNA datasets.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae436},
pmid = {38960861},
issn = {1367-4811},
abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome, on mismatch rates across read lengths.

RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read-length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimised mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

AVAILABILITY: AMBER is available for non-commercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyze simulated data sets are available on Github (https://github.com/sdolenz/refbias_scripts).

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

@article {pmid38957694,
year = {2024},
author = {Mousavi-Derazmahalleh, M and Haue, N and Kanstrup, M and Laursen, JT and Lukehurst, SS and Kveiborg, J and Allentoft, ME},
title = {Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11680},
pmid = {38957694},
issn = {2045-7758},
abstract = {An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.},
}

@article {pmid38957308,
year = {2024},
author = {Çokoğlu, SS and Koptekin, D and Fidan, FR and Somel, M},
title = {Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.},
journal = {Evolutionary applications},
volume = {17},
number = {7},
pages = {e13743},
pmid = {38957308},
issn = {1752-4571},
abstract = {The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.},
}

@article {pmid38948161,
year = {2024},
author = {Özdoğan, KT and Gelabert, P and Hammers, N and Altınışık, NE and de Groot, A and Plets, G},
title = {Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past.},
journal = {Archaeological and anthropological sciences},
volume = {16},
number = {7},
pages = {108},
pmid = {38948161},
issn = {1866-9557},
abstract = {Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.},
}

@article {pmid38867050,
year = {2024},
author = {Michel, M and Skourtanioti, E and Pierini, F and Guevara, EK and Mötsch, A and Kocher, A and Barquera, R and Bianco, RA and Carlhoff, S and Coppola Bove, L and Freilich, S and Giffin, K and Hermes, T and Hiß, A and Knolle, F and Nelson, EA and Neumann, GU and Papac, L and Penske, S and Rohrlach, AB and Salem, N and Semerau, L and Villalba-Mouco, V and Abadie, I and Aldenderfer, M and Beckett, JF and Brown, M and Campus, FGR and Chenghwa, T and Cruz Berrocal, M and Damašek, L and Duffett Carlson, KS and Durand, R and Ernée, M and Fântăneanu, C and Frenzel, H and García Atiénzar, G and Guillén, S and Hsieh, E and Karwowski, M and Kelvin, D and Kelvin, N and Khokhlov, A and Kinaston, RL and Korolev, A and Krettek, KL and Küßner, M and Lai, L and Look, C and Majander, K and Mandl, K and Mazzarello, V and McCormick, M and de Miguel Ibáñez, P and Murphy, R and Németh, RE and Nordqvist, K and Novotny, F and Obenaus, M and Olmo-Enciso, L and Onkamo, P and Orschiedt, J and Patrushev, V and Peltola, S and Romero, A and Rubino, S and Sajantila, A and Salazar-García, DC and Serrano, E and Shaydullaev, S and Sias, E and Šlaus, M and Stančo, L and Swanston, T and Teschler-Nicola, M and Valentin, F and Van de Vijver, K and Varney, TL and Vigil-Escalera Guirado, A and Waters, CK and Weiss-Krejci, E and Winter, E and Lamnidis, TC and Prüfer, K and Nägele, K and Spyrou, M and Schiffels, S and Stockhammer, PW and Haak, W and Posth, C and Warinner, C and Bos, KI and Herbig, A and Krause, J},
title = {Ancient Plasmodium genomes shed light on the history of human malaria.},
journal = {Nature},
volume = {631},
number = {8019},
pages = {125-133},
pmid = {38867050},
issn = {1476-4687},
mesh = {Humans ; History, Ancient ; *Genome, Protozoan/genetics ; *Plasmodium falciparum/genetics/isolation & purification ; *Plasmodium vivax/genetics ; *Malaria/parasitology/history/transmission/epidemiology ; Europe ; Genome, Mitochondrial/genetics ; Plasmodium/genetics/classification ; Americas/epidemiology ; DNA, Ancient/analysis ; Malaria, Falciparum/parasitology/history ; Malaria, Vivax/parasitology/history/epidemiology ; Asia ; South America ; },
abstract = {Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species[1]. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe[1,2]. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia[3]. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.},
}

Humans
History, Ancient
*Genome, Protozoan/genetics
*Plasmodium falciparum/genetics/isolation & purification
*Plasmodium vivax/genetics
*Malaria/parasitology/history/transmission/epidemiology
Europe
Genome, Mitochondrial/genetics
Plasmodium/genetics/classification
Americas/epidemiology
DNA, Ancient/analysis
Malaria, Falciparum/parasitology/history
Malaria, Vivax/parasitology/history/epidemiology
Asia
South America

@article {pmid38946459,
year = {2024},
author = {Özkan, M and Gürün, K and Yüncü, E and Vural, KB and Atağ, G and Akbaba, A and Fidan, FR and Sağlıcan, E and Altınışık, EN and Koptekin, D and Pawłowska, K and Hodder, I and Adcock, SE and Arbuckle, BS and Steadman, SR and McMahon, G and Erdal, YS and Bilgin, CC and Togan, İ and Geigl, EM and Götherström, A and Grange, T and Özer, F and Somel, M},
title = {The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17440},
doi = {10.1111/mec.17440},
pmid = {38946459},
issn = {1365-294X},
support = {772390//European Research Council Consolidator Grant H2020/ ; 952317//European Commission Horizon 2020 TWINNING Programme/ ; 117Z991//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
abstract = {We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.},
}

@article {pmid38942016,
year = {2024},
author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L},
title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.05.033},
pmid = {38942016},
issn = {1097-4172},
abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.},
}

@article {pmid38932149,
year = {2024},
author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS},
title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932149},
issn = {1999-4915},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; },
mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation & purification ; Fossils/virology ; },
abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.},
}

Animals
*Neanderthals/genetics/virology
*Genome, Viral
*DNA, Ancient/analysis
Evolution, Molecular
DNA, Viral/genetics
Sequence Analysis, DNA/methods
Humans
Phylogeny
DNA Viruses/genetics/classification/isolation & purification
Fossils/virology

@article {pmid38927726,
year = {2024},
author = {Zhu, S and Zhang, N and Zhang, J and Shao, X and Guo, Y and Cai, D},
title = {Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060790},
pmid = {38927726},
issn = {2073-4425},
support = {NO.17ZDA221//Major Project of the National Social Science Foundation of China/ ; NO.2020YFC1521606//National Key Research and Development Program of China/ ; NO. 2022M722460//Project funded by China Postdoctoral Science Foundation/ ; NO. 2022CXTD17//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial/genetics ; China ; *DNA, Ancient/analysis ; *Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; History, Ancient ; High-Throughput Nucleotide Sequencing ; Domestication ; },
abstract = {This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.},
}

Animals
Horses/genetics
*Genome, Mitochondrial/genetics
China
*DNA, Ancient/analysis
*Haplotypes
DNA, Mitochondrial/genetics
Phylogeny
History, Ancient
High-Throughput Nucleotide Sequencing
Domestication

@article {pmid38927684,
year = {2024},
author = {Primorac, D and Šarac, J and Havaš Auguštin, D and Novokmet, N and Bego, T and Pinhasi, R and Šlaus, M and Novak, M and Marjanović, D},
title = {Y Chromosome Story-Ancient Genetic Data as a Supplementary Tool for the Analysis of Modern Croatian Genetic Pool.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060748},
pmid = {38927684},
issn = {2073-4425},
mesh = {Humans ; *Chromosomes, Human, Y/genetics ; Croatia ; *Genetics, Population/methods ; Gene Pool ; DNA, Ancient/analysis ; Gene Flow ; Human Migration ; Male ; },
abstract = {Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe's population. SEE, including modern Croatian territory, was a crucial passage from the Near East and even more distant regions and human populations in this region, as almost any other European population represents a remarkable genetic mixture. Modern humans have continuously occupied this region since the Upper Paleolithic era, and different (pre)historical events have left a distinctive genetic signature on the historical narrative of this region. Our views of its history have been mostly renewed in the last few decades by extraordinary data obtained from Y-chromosome studies. In recent times, the international research community, bringing together geneticists and archaeologists, has steadily released a growing number of ancient genomes from this region, shedding more light on its complex past population dynamics and shaping the genetic pool in Croatia and this part of Europe.},
}

Humans
*Chromosomes, Human, Y/genetics
Croatia
*Genetics, Population/methods
Gene Pool
DNA, Ancient/analysis
Gene Flow
Human Migration
Male

@article {pmid38927608,
year = {2024},
author = {Di Stefano, B and Zupanič Pajnič, I and Concato, M and Bertoglio, B and Calvano, MG and Sorçaburu Ciglieri, S and Bosetti, A and Grignani, P and Addoum, Y and Vetrini, R and Introna, F and Bonin, S and Previderè, C and Fattorini, P},
title = {Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060672},
pmid = {38927608},
issn = {2073-4425},
support = {no available//Comunità di Lussino, Trieste, Italy/ ; },
mesh = {Humans ; *Bone and Bones/chemistry ; World War II ; DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats/genetics ; DNA/genetics/isolation & purification ; DNA, Ancient/analysis ; },
abstract = {Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell[®] FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.},
}

Humans
*Bone and Bones/chemistry
World War II
DNA Fingerprinting/methods
Forensic Genetics/methods
Microsatellite Repeats/genetics
DNA/genetics/isolation & purification
DNA, Ancient/analysis

@article {pmid38927588,
year = {2024},
author = {De Iorio, MG and Lazzari, B and Colli, L and Pagnacco, G and Minozzi, G},
title = {Variability and Number of Circulating Complementary Sex Determiner (Csd) Alleles in a Breeding Population of Italian Honeybees under Controlled Mating.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060652},
pmid = {38927588},
issn = {2073-4425},
support = {201801057971 - G44I19001910002//Lombardy Region/ ; 202202375596 - E87F23000000009//Lombardy Region/ ; },
mesh = {Animals ; Bees/genetics ; *Alleles ; Female ; *Sex Determination Processes/genetics ; Male ; Breeding ; Italy ; Insect Proteins/genetics ; Genetic Variation ; },
abstract = {In Apis mellifera, csd is the primary gene involved in sex determination: haploid hemizygous eggs develop as drones, while females develop from eggs heterozygous for the csd gene. If diploid eggs are homozygous for the csd gene, diploid drones will develop, but will be eaten by worker bees before they are born. Therefore, high csd allelic diversity is a priority for colony survival and breeding. This study aims to investigate the variability of the hypervariable region (HVR) of the csd gene in bees sampled in an apiary under a selection scheme. To this end, an existing dataset of 100 whole-genome sequences was analyzed with a validated pipeline based on de novo assembly of sequences within the HVR region. In total, 102 allelic sequences were reconstructed and translated into amino acid sequences. Among these, 47 different alleles were identified, 44 of which had previously been observed, while 3 are novel alleles. The results show a high variability in the csd region in this breeding population of honeybees.},
}

Animals
Bees/genetics
*Alleles
Female
*Sex Determination Processes/genetics
Male
Breeding
Italy
Insect Proteins/genetics
Genetic Variation

@article {pmid38926415,
year = {2024},
author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA},
title = {Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14720},
pmid = {38926415},
issn = {2045-2322},
support = {Pre-doctoral Fellowship//Smithsonian Institution, National Museum of Natural History, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; },
mesh = {*Dental Calculus/microbiology/history ; Humans ; *Metagenomics/methods ; *Paleopathology/methods ; *Tuberculosis/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation & purification ; DNA, Bacterial/genetics ; Male ; Treponema pallidum/genetics/isolation & purification ; Syphilis/diagnosis/microbiology/history ; Female ; Adult ; Metagenome/genetics ; Middle Aged ; },
abstract = {Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.},
}

*Dental Calculus/microbiology/history
Humans
*Metagenomics/methods
*Paleopathology/methods
*Tuberculosis/diagnosis/microbiology
*Mycobacterium tuberculosis/genetics/isolation & purification
DNA, Bacterial/genetics
Male
Treponema pallidum/genetics/isolation & purification
Syphilis/diagnosis/microbiology/history
Female
Adult
Metagenome/genetics
Middle Aged

@article {pmid38916350,
year = {2024},
author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G},
title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266223},
doi = {10.1128/spectrum.02662-23},
pmid = {38916350},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.},
}

@article {pmid38903121,
year = {2024},
author = {Bougiouri, K and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F},
title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38903121},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The multi-millenia long history between dogs and humans has justly placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the huge diversity of breeds today. Although ancient genomes provide valuable information, their use is significantly hindered by low depth of coverage and post-mortem damage, which often inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution afforded by ancient genomic datasets. Imputation accuracy was evaluated by down-sampling 10 high coverage ancient and modern dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We also measured the impact of imputation on principal component analyses (PCA) and runs of homozygosity (ROH). Our findings show high (R[2] > 0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a worldwide dataset of 81 published ancient dog and wolf genomes, in addition to nine newly sequenced medieval and early modern period European dogs, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals, though with some exceptions occurring in ancient Arctic and European dogs. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.},
}

@article {pmid38867041,
year = {2024},
author = {Barquera, R and Del Castillo-Chávez, O and Nägele, K and Pérez-Ramallo, P and Hernández-Zaragoza, DI and Szolek, A and Rohrlach, AB and Librado, P and Childebayeva, A and Bianco, RA and Penman, BS and Acuña-Alonzo, V and Lucas, M and Lara-Riegos, JC and Moo-Mezeta, ME and Torres-Romero, JC and Roberts, P and Kohlbacher, O and Warinner, C and Krause, J},
title = {Ancient genomes reveal insights into ritual life at Chichén Itzá.},
journal = {Nature},
volume = {630},
number = {8018},
pages = {912-919},
pmid = {38867041},
issn = {1476-4687},
mesh = {Humans ; Mexico ; *Genome, Human/genetics ; Male ; *Ceremonial Behavior ; *DNA, Ancient/analysis ; History, Ancient ; Female ; Burial/history ; Archaeology ; Twins/genetics ; History, Medieval ; },
abstract = {The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica[1-4]. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered[2]. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes[5], but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.},
}

Humans
Mexico
*Genome, Human/genetics
Male
*Ceremonial Behavior
*DNA, Ancient/analysis
History, Ancient
Female
Burial/history
Archaeology
Twins/genetics
History, Medieval

@article {pmid38913897,
year = {2024},
author = {Sasso, S and Saag, L and Spros, R and Beneker, O and Molinaro, L and Biagini, SA and Lehouck, A and Van De Vijver, K and Hui, R and D'Atanasio, E and Kushniarevich, A and Kabral, H and Metspalu, E and Guellil, M and Ali, MQA and Geypen, J and Hoebreckx, M and Berk, B and De Winter, N and Driesen, P and Pijpelink, A and Van Damme, P and Scheib, CL and Deschepper, E and Deckers, P and Snoeck, C and Dewilde, M and Ervynck, A and Tambets, K and Larmuseau, MHD and Kivisild, T},
title = {Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {27},
pages = {e2406734121},
doi = {10.1073/pnas.2406734121},
pmid = {38913897},
issn = {1091-6490},
support = {NA//agentschap Onroerend Erfgoed Archeologie syntheseproject/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; STG/18/021//KU Leuven start-up grant/ ; ZKD6488 C24M/19/075//KU Leuven BOF-C24/ ; NA//EWI-Vlaanderen citizien science project "MamaMito"/ ; PRG1027//Estonian Research fundation grant/ ; NA//Sapienza University Rome fellowship/ ; },
mesh = {Humans ; History, Medieval ; *Pedigree ; Belgium ; Burial/history ; Genetics, Population/methods ; Female ; Male ; DNA, Ancient/analysis ; England ; Human Migration ; Archaeology ; Netherlands ; Genome, Human ; },
abstract = {The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.},
}

Humans
History, Medieval
*Pedigree
Belgium
Burial/history
Genetics, Population/methods
Female
Male
DNA, Ancient/analysis
England
Human Migration
Archaeology
Netherlands
Genome, Human

@article {pmid38904838,
year = {2024},
author = {Kumar, S and Singh, PP and Pasupuleti, N and Shendre, SS and Sequeira, JJ and Babu, I and Mustak, MS and Rai, N and Chaubey, G},
title = {Correction: Genetic evidence for a single founding population of the Lakshadweep Islands.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {63},
doi = {10.1007/s00438-024-02154-1},
pmid = {38904838},
issn = {1617-4623},
}

@article {pmid38900796,
year = {2024},
author = {Aldeias, V and Stahlschmidt, MC},
title = {Sediment DNA can revolutionize archaeology-if it is used the right way.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {26},
pages = {e2317042121},
doi = {10.1073/pnas.2317042121},
pmid = {38900796},
issn = {1091-6490},
support = {101041245//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 101042570//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {*Archaeology/methods ; *Geologic Sediments ; Humans ; DNA ; DNA, Ancient/analysis ; },
}

*Archaeology/methods
*Geologic Sediments
Humans
DNA
DNA, Ancient/analysis

@article {pmid38896620,
year = {2024},
author = {Parasayan, O and Laurelut, C and Bôle, C and Bonnabel, L and Corona, A and Domenech-Jaulneau, C and Paresys, C and Richard, I and Grange, T and Geigl, EM},
title = {Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome.},
journal = {Science advances},
volume = {10},
number = {25},
pages = {eadl2468},
doi = {10.1126/sciadv.adl2468},
pmid = {38896620},
issn = {2375-2548},
mesh = {Humans ; *Genome, Human ; *Burial/history ; *Haplotypes ; White People/genetics ; Genetics, Population ; History, Ancient ; Human Migration ; Europe ; DNA, Ancient/analysis ; Population Dynamics ; France ; },
abstract = {The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives' genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.},
}

Humans
*Genome, Human
*Burial/history
*Haplotypes
White People/genetics
Genetics, Population
History, Ancient
Human Migration
Europe
DNA, Ancient/analysis
Population Dynamics
France

@article {pmid38891676,
year = {2024},
author = {Abdelmanova, AA and Deniskova, TE and Kharzinova, VR and Chinarov, RY and Boronetskaya, OI and Sölkner, J and Brem, G and Ai, H and Huang, L and Trukhachev, VI and Zinovieva, NA},
title = {Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {11},
pages = {},
pmid = {38891676},
issn = {2076-2615},
support = {23-46-00014//Russian Science Foundation/ ; },
abstract = {The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.},
}

@article {pmid38885310,
year = {2024},
author = {Wang, M and Huang, Y and Liu, K and Wang, Z and Zhang, M and Yuan, H and Duan, S and Wei, L and Yao, H and Sun, Q and Zhong, J and Tang, R and Chen, J and Sun, Y and Li, X and Su, H and Yang, Q and Hu, L and Yun, L and Yang, J and Nie, S and Cai, Y and Yan, J and Zhou, K and , and Wang, C and Zhu, B and Liu, C and He, G},
title = {Multiple human population movements and cultural dispersal events shaped the landscape of Chinese paternal heritage.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae122},
pmid = {38885310},
issn = {1537-1719},
abstract = {Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations, that have shaped the Chinese paternal landscape. Firstly, the expansion of early East Asians and millet farmers from the Yellow River Basin, predominantly carrying O2/D subclades, significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Secondly, the dispersal of rice farmers from the Yangtze River Valley, carrying O1 and certain O2 sublineages, reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Thirdly, Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourthly, J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.},
}

@article {pmid38883810,
year = {2024},
author = {Pathak, AK and Simonian, H and Ibrahim, IAA and Hrechdakian, P and Behar, DM and Ayub, Q and Arsanov, P and Metspalu, E and Yepiskoposyan, L and Rootsi, S and Endicott, P and Villems, R and Sahakyan, H},
title = {Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.},
journal = {iScience},
volume = {27},
number = {6},
pages = {110016},
pmid = {38883810},
issn = {2589-0042},
abstract = {West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.},
}

@article {pmid38871872,
year = {2024},
author = {Callaway, E},
title = {Ancient DNA from Maya ruins tells story of ritual human sacrifices.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38871872},
issn = {1476-4687},
}

@article {pmid38870299,
year = {2024},
author = {Curry, A},
title = {Sacrificed Maya boys tied to myth of 'Hero Twins'.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6701},
pages = {1160-1161},
doi = {10.1126/science.adr0288},
pmid = {38870299},
issn = {1095-9203},
mesh = {Humans ; *DNA, Ancient ; History, Ancient ; Male ; Twins/genetics ; Female ; },
abstract = {Ancient DNA shows continuity between living and ancient Maya communities.},
}

Humans
*DNA, Ancient
History, Ancient
Male
Twins/genetics
Female

@article {pmid38862782,
year = {2024},
author = {Childebayeva, A and Fricke, F and Rohrlach, AB and Huang, L and Schiffels, S and Vesakoski, O and Mannermaa, K and Semerau, L and Aron, F and Solodovnikov, K and Rykun, M and Moiseyev, V and Khartanovich, V and Kovtun, I and Krause, J and Kuzminykh, S and Haak, W},
title = {Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {723},
pmid = {38862782},
issn = {2399-3642},
mesh = {Siberia ; Humans ; History, Ancient ; *Metallurgy/history ; DNA, Ancient/analysis ; Human Migration ; Archaeology ; Genetics, Population ; },
abstract = {The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.},
}

Siberia
Humans
History, Ancient
*Metallurgy/history
DNA, Ancient/analysis
Human Migration
Archaeology
Genetics, Population

@article {pmid38845985,
year = {2024},
author = {Tejero, JM and Cheronet, O and Gelabert, P and Zagorc, B and Álvarez-Fernández, E and Arias, P and Averbouh, A and Bar-Oz, G and Barzilai, O and Belfer-Cohen, A and Bosch, MD and Brück, F and Cueto, M and Dockner, M and Fullola, JM and Gárate, D and Giannakoulis, M and González, C and Jakeli, N and Mangado, X and Meshveliani, T and Neruda, P and Nigst, P and Ontañón, R and Shemer, M and Šimková, PG and Tapia, J and Sánchez de la Torre, M and Schwab, C and Weber, G and Pinhasi, R},
title = {Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e31858},
pmid = {38845985},
issn = {2405-8440},
abstract = {Antler is one of the primary animal raw materials exploited for technical purposes by the hunter-gatherer groups of the Eurasian Upper Palaeolithic (UP) all over the ecological range of deers, and beyond. It was exhaustively employed to produce one of the most critical tools for the survival of the UP societies: hunting weapons. However, antler implements can be made from diverse deer taxa, with different ecological requirements and ethological behaviours. Identifying the antler's origin at a taxonomic level is thus essential in improving our knowledge of humans' functional, practical and symbolic choices, as well as the human-animal interface during Prehistoric times. Nevertheless, palaeogenetics analyses have focused mainly on bone and teeth, with genetic studies of antler generally focused on modern deer conservation. Here we present the results of the first whole mitochondrial genome ancient DNA (aDNA) analysis by means of in-solution hybridisation capture of antlers from pre-Holocene archaeological contexts. We analysed a set of 50 Palaeolithic and Neolithic (c. 34-8ka) antler and osseous objects from South-Western Europe, Central Europe, South-Western Asia and the Caucasus. We successfully obtained aDNA, allowing us to identify the exploited taxa and demonstrate the archaeological relevance of those finds. Moreover, as most of the antlers were sampled using a minimally-invasive method, further analyses (morphometric, technical, genetic, radiometric and more) remain possible on these objects.},
}

@article {pmid38844121,
year = {2024},
author = {Amer, K and Soliman, NA and Soror, S and Gad, YZ and Moustafa, A and Elmonem, MA and Amer, M and Ragheb, A and Kotb, A and Taha, T and Ali, W and Sakr, M and Ghaffar, KA and , },
title = {Egypt genome: Towards an African new genomic era.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.06.003},
pmid = {38844121},
issn = {2090-1224},
abstract = {BACKGROUND: Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future.

AIM OF REVIEW: The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG.

KEY SCIENTIFIC CONCEPTS: EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.},
}

@article {pmid38664113,
year = {2024},
author = {Gresky, J},
title = {Assessing autosomal aneuploidy in ancient genomes.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {6},
pages = {463-464},
doi = {10.1016/j.tig.2024.04.006},
pmid = {38664113},
issn = {0168-9525},
mesh = {*Aneuploidy ; Humans ; *Genome, Human/genetics ; DNA, Ancient/analysis ; },
abstract = {Using genetic methods, aneuploidies can be detected in ancient human remains, which is so far the only way to reliably prove their existence in the past. As highlighted in recent studies by Rohrlach et al. and by Anastasiadou et al., this initial step enables a deeper exploration of the history of rare diseases, encompassing the social and historical contexts of the afflicted individuals.},
}

*Aneuploidy
Humans
*Genome, Human/genetics
DNA, Ancient/analysis

@article {pmid38831280,
year = {2024},
author = {Sandhu, S and Sharma, V and Kumar, S and Rai, N and Chand, P},
title = {Quantifying variations associated with dental caries reveals disparity in effect allele frequencies across diverse populations.},
journal = {BMC genomic data},
volume = {25},
number = {1},
pages = {50},
pmid = {38831280},
issn = {2730-6844},
support = {No. 5/4/2-9/Oral Health/2021-NCD-II//Indian Council of Medical Research/ ; No. 5/4/2-9/Oral Health/2021-NCD-II//Indian Council of Medical Research/ ; },
mesh = {Humans ; *Dental Caries/genetics/epidemiology ; *Gene Frequency ; *Genome-Wide Association Study ; Genetic Predisposition to Disease ; Alleles ; Polymorphism, Single Nucleotide ; India/epidemiology/ethnology ; Asian People/genetics ; },
abstract = {BACKGROUND: Dental caries (DC) is a multifaceted oral condition influenced by genetic and environmental factors. Recent advancements in genotyping and sequencing technologies, such as Genome-Wide Association Studies (GWAS) have helped researchers to identify numerous genetic variants associated with DC, but their prevalence and significance across diverse global populations remain poorly understood as most of the studies were conducted in European populations, and very few were conducted in Asians specifically in Indians.

AIM: This study aimed to evaluate the genetic affinity of effect alleles associated with DC to understand the genetic relationship between global populations with respect to the Indian context.

METHODOLOGY: This present study used an empirical approach in which variants associated with DC susceptibility were selected. These variants were identified and annotated using the GWAS summary. The genetic affinity was evaluated using Fst.

RESULTS: The effect of allele frequencies among different populations was examined, revealing variations in allele distribution. African populations exhibited higher frequencies of specific risk alleles, whereas East Asian and European populations displayed distinct profiles. South Asian populations showed a unique genetic cluster.

CONCLUSION: Our study emphasises the complex genetic landscape of DC and highlights the need for population-specific research as well as validation of GWAS-identified markers in Indians before defining them as established candidate genes.},
}

Humans
*Dental Caries/genetics/epidemiology
*Gene Frequency
*Genome-Wide Association Study
Genetic Predisposition to Disease
Alleles
Polymorphism, Single Nucleotide
India/epidemiology/ethnology
Asian People/genetics

@article {pmid38830089,
year = {2024},
author = {Fordham, DA and Brown, SC and Canteri, E and Austin, JJ and Lomolino, MV and Haythorne, S and Armstrong, E and Bocherens, H and Manica, A and Rey-Iglesia, A and Rahbek, C and Nogués-Bravo, D and Lorenzen, ED},
title = {52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {24},
pages = {e2316419121},
doi = {10.1073/pnas.2316419121},
pmid = {38830089},
issn = {1091-6490},
support = {DP180102392//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Extinction, Biological ; *Perissodactyla ; *Population Dynamics ; *Fossils ; Ecosystem ; DNA, Ancient/analysis ; Paleontology ; },
abstract = {The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.},
}

Animals
*Extinction, Biological
*Perissodactyla
*Population Dynamics
*Fossils
Ecosystem
DNA, Ancient/analysis
Paleontology

@article {pmid38813936,
year = {2024},
author = {Arsuaga, JL and Martínez, I and Gracia-Téllez, A and Carretero, JM and Esquivel, A and García, N and Lorenzo, C and Quam, R and Aramburu, A and Sala, N and Trueba, J},
title = {How the Sima de los Huesos was won.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25509},
pmid = {38813936},
issn = {1932-8494},
support = {PID2021-122355NB-C31 supported by MCIN/AEI/10.1303//Government of Spain/ ; //Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá)/ ; EPU-INV-UAH/2022/006//Universidad de Alcalá/ ; },
abstract = {Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.},
}

@article {pmid38811785,
year = {2024},
author = {},
title = {Ancient DNA reveals extinct flightless bird's superpowers.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38811785},
issn = {1476-4687},
}

@article {pmid38806487,
year = {2024},
author = {Bagnasco, G and Marzullo, M and Cattaneo, C and Biehler-Gomez, L and Mazzarelli, D and Ricciardi, V and Müller, W and Coppa, A and McLaughlin, R and Motta, L and Prato, O and Schmidt, F and Gaveriaux, F and Marras, GB and Millet, MA and Madgwick, R and Ballantyne, R and Makarewicz, CA and Trentacoste, A and Reimer, P and Mattiangeli, V and Bradley, DG and Malone, C and Esposito, C and Breslin, EM and Stoddart, S},
title = {Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11895},
pmid = {38806487},
issn = {2045-2322},
mesh = {Italy ; Humans ; *Archaeology ; History, Ancient ; Male ; DNA, Ancient/analysis ; Female ; },
abstract = {Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.},
}

Italy
Humans
*Archaeology
History, Ancient
Male
DNA, Ancient/analysis
Female

@article {pmid38798346,
year = {2024},
author = {Fine, AG and Steinrücken, M},
title = {A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.10.593575},
pmid = {38798346},
abstract = {Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Thus, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which heterozygote and homozygote fitnesses are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, as well as a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years, and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.},
}

@article {pmid38796876,
year = {2024},
author = {Nikolaos, P and Despoina, V and Argyro, N and Eugenia, T and Pavlos, P and Alexandros, S and Nikos, P},
title = {Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes.},
journal = {Forensic science international. Genetics},
volume = {71},
number = {},
pages = {103060},
doi = {10.1016/j.fsigen.2024.103060},
pmid = {38796876},
issn = {1878-0326},
abstract = {In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.},
}

@article {pmid38795367,
year = {2024},
author = {Larsson, MNA and Morell Miranda, P and Pan, L and Başak Vural, K and Kaptan, D and Rodrigues Soares, AE and Kivikero, H and Kantanen, J and Somel, M and Özer, F and Johansson, AM and Storå, J and Günther, T},
title = {Ancient Sheep Genomes reveal four Millennia of North European Short-Tailed Sheep in the Baltic Sea region.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae114},
pmid = {38795367},
issn = {1759-6653},
abstract = {Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia less than 6000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from Late Neolithic (∼4100 calBP) to historical times (∼1600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.},
}

@article {pmid38788981,
year = {2024},
author = {Ketagoda, DHK and Varga, P and Fitzsimmons, TR and Moore, NE and Weyrich, LS and Zilm, PS},
title = {Development of an in vitro biofilm model of the human supra-gingival microbiome for Oral microbiome transplantation.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {106961},
doi = {10.1016/j.mimet.2024.106961},
pmid = {38788981},
issn = {1872-8359},
abstract = {The high prevalence of dental caries and periodontal disease place a significant burden on society, both socially and economically. Recent advances in genomic technologies have linked both diseases to shifts in the oral microbiota - a community of >700 bacterial species that live within the mouth. The development of oral microbiome transplantation draws on the success of fecal microbiome transplantation for the treatment of gut pathologies associated with disease. Many current in vitro oral biofilm models have been developed but do not fully capture the complexity of the oral microbiome which is required for successful OMT. To address this, we developed an in vitro biofilm system that maintained an oral microbiome with 252 species on average over 14 days. Six human plaque samples were grown in 3D printed flow cells on hydroxyapatite discs using artificial saliva medium (ASM). Biofilm composition and growth were monitored by high throughput sequencing and confocal microscopy/SEM, respectively. While a significant drop in bacterial diversity occurred, up to 291 species were maintained in some flow cells over 14 days with 70% viability grown with ASM. This novel in vitro biofilm model represents a marked improvement on existing oral biofilm systems and provides new opportunities to develop oral microbiome transplant therapies.},
}

@article {pmid38781957,
year = {2024},
author = {Bai, F and Liu, Y and Wangdue, S and Wang, T and He, W and Xi, L and Tsho, Y and Tsering, T and Cao, P and Dai, Q and Liu, F and Feng, X and Zhang, M and Ran, J and Ping, W and Payon, D and Mao, X and Tong, Y and Tsring, T and Chen, Z and Fu, Q},
title = {Ancient genomes revealed the complex human interactions of the ancient western Tibetans.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.04.068},
pmid = {38781957},
issn = {1879-0445},
abstract = {The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.},
}

@article {pmid38781323,
year = {2024},
author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ},
title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.},
journal = {Science advances},
volume = {10},
number = {21},
pages = {eadj6823},
doi = {10.1126/sciadv.adj6823},
pmid = {38781323},
issn = {2375-2548},
mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; },
abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.},
}

Animals
*Birds/genetics
*Genome
*Extinction, Biological
Cell Nucleus/genetics
Phylogeny
Fossils
Genome, Mitochondrial
Flight, Animal
New Zealand
Male
DNA Transposable Elements/genetics
Genomics/methods

@article {pmid38777837,
year = {2024},
author = {Saltré, F and Chadœuf, J and Higham, T and Ochocki, M and Block, S and Bunney, E and Llamas, B and Bradshaw, CJA},
title = {Environmental conditions associated with initial northern expansion of anatomically modern humans.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4364},
pmid = {38777837},
issn = {2041-1723},
mesh = {Humans ; *Human Migration/history ; *Archaeology ; Environment ; Europe ; Americas ; History, Ancient ; Temperature ; Asia ; Rivers ; Forests ; Grassland ; },
abstract = {The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.},
}

Humans
*Human Migration/history
*Archaeology
Environment
Europe
Americas
History, Ancient
Temperature
Asia
Rivers
Forests
Grassland

@article {pmid38769390,
year = {2024},
author = {Borbély, N and Dudás, D and Tapasztó, A and Dudás-Boda, E and Csáky, V and Szeifert, B and Mende, BG and Egyed, B and Szécsényi-Nagy, A and Pamjav, H},
title = {Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11480},
pmid = {38769390},
issn = {2045-2322},
support = {FK 127938//Hungarian National Research, Development, and Innovation Office/ ; },
mesh = {Humans ; *Phylogeny ; *Chromosomes, Human, Y/genetics ; Hungary ; *Genome, Mitochondrial ; Male ; Genetics, Population ; Female ; DNA, Mitochondrial/genetics ; DNA, Ancient/analysis ; Microsatellite Repeats/genetics ; Haplotypes ; },
abstract = {This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.},
}

Humans
*Phylogeny
*Chromosomes, Human, Y/genetics
Hungary
*Genome, Mitochondrial
Male
Genetics, Population
Female
DNA, Mitochondrial/genetics
DNA, Ancient/analysis
Microsatellite Repeats/genetics
Haplotypes

@article {pmid38756579,
year = {2024},
author = {Wang, Z and Wang, M and Hu, L and He, G and Nie, S},
title = {Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e30067},
pmid = {38756579},
issn = {2405-8440},
abstract = {Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.},
}

@article {pmid38754423,
year = {2024},
author = {Yuan, J and Hu, J and Liu, W and Chen, S and Zhang, F and Wang, S and Zhang, Z and Wang, L and Xiao, B and Li, F and Hofreiter, M and Lai, X and Westbury, MV and Sheng, G},
title = {Camelus knoblochi genome reveals the complex evolutionary history of Old World camels.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.04.050},
pmid = {38754423},
issn = {1879-0445},
abstract = {Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.[1][,][2] Although many remains have been unearthed,[3][,][4][,][5] we know neither whether the prevalent hybridization observed between extant Camelus species[2][,][6][,][7] also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.},
}

@article {pmid38750053,
year = {2024},
author = {Cabrera, VM},
title = {New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11150},
pmid = {38750053},
issn = {2045-2322},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *DNA, Ancient/analysis ; *Phylogeography ; Spain ; Phylogeny ; Genetics, Population ; Indigenous Peoples/genetics ; Archaeology ; Human Migration ; History, Ancient ; High-Throughput Nucleotide Sequencing ; },
abstract = {Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.},
}

Humans
*DNA, Mitochondrial/genetics
*DNA, Ancient/analysis
*Phylogeography
Spain
Phylogeny
Genetics, Population
Indigenous Peoples/genetics
Archaeology
Human Migration
History, Ancient
High-Throughput Nucleotide Sequencing

@article {pmid38745401,
year = {2024},
author = {Ekram, MA and Campbell, M and Kose, SH and Plet, C and Hamilton, R and Bijaksana, S and Grice, K and Russell, J and Stevenson, J and Vogel, H and Coolen, MJL},
title = {A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).},
journal = {Geobiology},
volume = {22},
number = {3},
pages = {e12599},
doi = {10.1111/gbi.12599},
pmid = {38745401},
issn = {1472-4669},
support = {DP15102587//Australian Research Council/ ; //International Continental Scientific Drilling Program (ICDP)/ ; //U.S. National Science Foundation (NSF)/ ; 200021_153053/SNSF_/Swiss National Science Foundation/Switzerland ; //PT Vale Indonesia/ ; //Ministry of Research, Education, and Higher Technology of Indonesia (RISTEK)/ ; //Brown University/ ; //The Institute for Geoscience Research (TIGeR)/ ; //Research Office at Curtin University (ROC)/ ; },
mesh = {*Lakes/chemistry ; *Geologic Sediments ; Indonesia ; *DNA, Ancient/analysis ; Plants ; Tropical Climate ; Ecosystem ; DNA, Plant/genetics ; },
abstract = {Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.},
}

*Lakes/chemistry
*Geologic Sediments
Indonesia
*DNA, Ancient/analysis
Plants
Tropical Climate
Ecosystem
DNA, Plant/genetics

@article {pmid38742634,
year = {2024},
author = {Harris, KD and Greenbaum, G},
title = {DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae373},
pmid = {38742634},
issn = {1362-4962},
abstract = {The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.},
}

@article {pmid38739117,
year = {2024},
author = {Dahlquist-Axe, G and Standeven, FJ and Speller, CF and Tedder, A and Meehan, CJ},
title = {Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001251},
pmid = {38739117},
issn = {2057-5858},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Anti-Bacterial Agents/pharmacology ; History, Ancient ; Diet ; Bacteria/genetics/classification/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; History, Medieval ; History, 17th Century ; History, 18th Century ; History, 16th Century ; },
abstract = {The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.},
}

Humans
*Microbiota
*Mouth/microbiology
*Anti-Bacterial Agents/pharmacology
History, Ancient
Diet
Bacteria/genetics/classification/drug effects
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics
History, Medieval
History, 17th Century
History, 18th Century
History, 16th Century

@article {pmid38662789,
year = {2024},
author = {Erven, JAM and Scheu, A and Verdugo, MP and Cassidy, L and Chen, N and Gehlen, B and Street, M and Madsen, O and Mullin, VE},
title = {A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation.},
journal = {Molecular biology and evolution},
volume = {41},
number = {5},
pages = {},
doi = {10.1093/molbev/msae076},
pmid = {38662789},
issn = {1537-1719},
support = {406.18.HW.026//Dutch Research Council Open Competition/ ; },
mesh = {Animals ; Cattle/genetics ; *Polymorphism, Single Nucleotide ; *Genome ; DNA, Ancient/analysis ; Haplotypes ; Genotype ; Genomics/methods ; },
abstract = {Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.},
}

Animals
Cattle/genetics
*Polymorphism, Single Nucleotide
*Genome
DNA, Ancient/analysis
Haplotypes
Genotype
Genomics/methods

@article {pmid38703773,
year = {2024},
author = {Urban, C and Blom, AA and Avanzi, C and Walker-Meikle, K and Warren, AK and White-Iribhogbe, K and Turle, R and Marter, P and Dawson-Hobbis, H and Roffey, S and Inskip, SA and Schuenemann, VJ},
title = {Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.04.006},
pmid = {38703773},
issn = {1879-0445},
abstract = {Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.[1][,][2] Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,[3][,][4][,][5] the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.[6][,][7] However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.},
}

@article {pmid38691462,
year = {2024},
author = {Zhu, K and He, H and Tao, L and Ma, H and Yang, X and Wang, R and Guo, J and Wang, CC},
title = {Protocol for a comprehensive pipeline to study ancient human genomes.},
journal = {STAR protocols},
volume = {5},
number = {2},
pages = {102985},
doi = {10.1016/j.xpro.2024.102985},
pmid = {38691462},
issn = {2666-1667},
abstract = {Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.[1].},
}

@article {pmid38684896,
year = {2024},
author = {Elmonem, MA and Soliman, NA and Moustafa, A and Gad, YZ and Hassan, WA and Taha, T and El-Feky, G and Sakr, M and Amer, K},
title = {The Egypt Genome Project.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38684896},
issn = {1546-1718},
}

@article {pmid38676702,
year = {2024},
author = {Aktürk, Ş and Mapelli, I and Güler, MN and Gürün, K and Katırcıoğlu, B and Vural, KB and Sağlıcan, E and Çetin, M and Yaka, R and Sürer, E and Atağ, G and Çokoğlu, SS and Sevkar, A and Altınışık, NE and Koptekin, D and Somel, M},
title = {Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13960},
doi = {10.1111/1755-0998.13960},
pmid = {38676702},
issn = {1755-0998},
abstract = {There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.},
}

@article {pmid38671208,
year = {2024},
author = {Taurozzi, AJ and Rüther, PL and Patramanis, I and Koenig, C and Sinclair Paterson, R and Madupe, PP and Harking, FS and Welker, F and Mackie, M and Ramos-Madrigal, J and Olsen, JV and Cappellini, E},
title = {Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38671208},
issn = {1750-2799},
support = {17649//Villum Fonden (Villum Foundation)/ ; 17649//Villum Fonden (Villum Foundation)/ ; 722606//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 722606//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 948365//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 722606//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PROTEIOS (DNRF128)//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.},
}

@article {pmid38671010,
year = {2024},
author = {Heraclides, A and Aristodemou, A and Georgiou, AN and Antoniou, M and Ilgner, E and Davranoglou, LR},
title = {Palaeogenomic insights into the origins of early settlers on the island of Cyprus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9632},
pmid = {38671010},
issn = {2045-2322},
mesh = {Cyprus ; Humans ; *Archaeology ; Human Migration/history ; Genome, Human ; History, Ancient ; DNA, Ancient/analysis ; Genetics, Population ; },
abstract = {Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c. 7600-6800 cal BCE). These appear to derive roughly 80% of their ancestry from Aceramic Neolithic Central Anatolians residing in or near the Konya plain, and the remainder from a genetically basal Levantine population. Based on genome-wide weighted ancestry covariance analysis, we infer that this admixture event took place roughly between 14,000 and 10,000 BCE, coinciding with the transition from the Cypriot late Epipaleolithic to the Pre-Pottery Neolithic A (PPNA). Additionally, we identify strong genetic affinities between the examined Cypro-LPPNB individuals and later northwestern Anatolians and the earliest European Neolithic farmers. Our results inform archaeological evidence on prehistoric demographic processes in the Eastern Mediterranean, providing important insights into early seafaring, maritime connections, and insular settlement.},
}

Cyprus
Humans
*Archaeology
Human Migration/history
Genome, Human
History, Ancient
DNA, Ancient/analysis
Genetics, Population

@article {pmid38659893,
year = {2024},
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, PN 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 Malikovich, MA 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 Serikovna, MR 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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.17.589597},
pmid = {38659893},
abstract = {The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.},
}

@article {pmid38658749,
year = {2024},
author = {Gnecchi-Ruscone, GA and Rácz, Z and Samu, L and Szeniczey, T and Faragó, N and Knipper, C and Friedrich, R and Zlámalová, D and Traverso, L and Liccardo, S and Wabnitz, S and Popli, D and Wang, K and Radzeviciute, R and Gulyás, B and Koncz, I and Balogh, C and Lezsák, GM and Mácsai, V and Bunbury, MME and Spekker, O and le Roux, P and Szécsényi-Nagy, A and Mende, BG and Colleran, H and Hajdu, T and Geary, P and Pohl, W and Vida, T and Krause, J and Hofmanová, Z},
title = {Network of large pedigrees reveals social practices of Avar communities.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38658749},
issn = {1476-4687},
abstract = {From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years[1]. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies[2]. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.},
}

@article {pmid38658715,
year = {2024},
author = {Cassidy, LM},
title = {Ancient DNA traces family lines and political shifts in the Avar empire.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38658715},
issn = {1476-4687},
}

@article {pmid38642939,
year = {2024},
author = {Zhu, S and Chen, Z and Hu, S and Wang, W and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Fu, Q},
title = {Corrigendum to "Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis)" [Journal of Genetics and Genomics (2022) 49, 1076-1079].},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {4},
pages = {466},
doi = {10.1016/j.jgg.2024.03.002},
pmid = {38642939},
issn = {1673-8527},
}

@article {pmid38640342,
year = {2024},
author = {Lin, Q and Zhang, K and Giguet-Covex, C and Arnaud, F and McGowan, S and Gielly, L and Capo, E and Huang, S and Ficetola, GF and Shen, J and Dearing, JA and Meadows, ME},
title = {Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2321303121},
doi = {10.1073/pnas.2321303121},
pmid = {38640342},
issn = {1091-6490},
support = {2022YFF0801101//MOST | National Key Research and Development Program of China (NKPs)/ ; 42230507//MOST | National Natural Science Foundation of China (NSFC)/ ; 42361144717//MOST | National Natural Science Foundation of China (NSFC)/ ; 42111530229//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20201099//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
abstract = {Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.},
}

@article {pmid38636619,
year = {2024},
author = {Sun, Z and Pan, L and Tian, A and Chen, P},
title = {Critically-ill COVID-19 susceptibility gene CCR3 shows natural selection in sub-Saharan Africans.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105594},
doi = {10.1016/j.meegid.2024.105594},
pmid = {38636619},
issn = {1567-7257},
abstract = {The prevalence of COVID-19 critical illness varies across ethnicities, with recent studies suggesting that genetic factors may contribute to this variation. The aim of this study was to investigate natural selection signals of genes associated with critically-ill COVID-19 in sub-Saharan Africans. Severe COVID-19 SNPs were obtained from the HGI website. Selection signals were assessed in 661 sub-Sahara Africans from 1000 Genomes Project using integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and fixation index (Fst). Allele frequency trajectory analysis of ancient DNA samples were used to validate the existing of selection in sub-Sahara Africans. We also used Mendelian randomization to decipher the correlation between natural selection and critically-ill COVID-19. We identified that CCR3 exhibited significant natural selection signals in sub-Sahara Africans. Within the CCR3 gene, rs17217831-A showed both high iHS (Standardized iHS = 2) and high XP-EHH (Standardized XP-EHH = 2.5) in sub-Sahara Africans. Allele frequency trajectory of CCR3 rs17217831-A revealed natural selection occurring in the recent 1,500 years. Natural selection resulted in increased CCR3 expression in sub-Sahara Africans. Mendelian Randomization provided evidence that increased blood CCR3 expression and eosinophil counts lowered the risk of critically ill COVID-19. Our findings suggest that sub-Saharan Africans are resistant to critically ill COVID-19 due to natural selection and identify CCR3 as a potential novel therapeutic target.},
}

@article {pmid38626302,
year = {2024},
author = {Ghimire, P and Palacios, C and Trimble, J and Lamichhaney, S},
title = {Museum Genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae081},
pmid = {38626302},
issn = {2160-1836},
abstract = {The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia sps.) and examine their genetic composition, taxonomic status, and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences, however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian sub-species C. e. neglecta and C. e. episcopus suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.},
}

@article {pmid38623594,
year = {2024},
author = {Meijer, H},
title = {Janus faced: The co-evolution of war and peace in the human species.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {e22027},
doi = {10.1002/evan.22027},
pmid = {38623594},
issn = {1520-6505},
abstract = {The human species presents a paradox. No other species possesses the propensity to carry out coalitionary lethal attacks on adult conspecifics coupled with the inclination to establish peaceful relations with genetically unrelated groups. What explains this seemingly contradictory feature? Existing perspectives, the "deep roots" and "shallow roots" of war theses, fail to capture the plasticity of human intergroup behaviors, spanning from peaceful cooperation to warfare. By contrast, this article argues that peace and war have both deep roots, and they co-evolved through an incremental process over several million years. On the one hand, humans inherited the propensity for coalitionary lethal violence from their chimpanzee-like ancestor. Specifically, having first inherited the skills to engage in cooperative hunting, they gradually repurposed such capacity to execute coalitionary killings of adult conspecifics and subsequently enhanced it through technological innovations like the use of weapons. On the other hand, they underwent a process of cumulative cultural evolution and, subsequently, of self-domestication which led to heightened cooperative communication and increased prosocial behavior within and between groups. The combination of these two biocultural evolutionary processes-coupled with feedback loop effects between self-domestication and Pleistocene environmental variability-considerably broadened the human intergroup behavioral repertoire, thereby producing the distinctive combination of conflictual and peaceful intergroup relations that characterizes our species. To substantiate this argument, the article synthesizes and integrates the findings from a variety of disciplines, leveraging evidence from evolutionary anthropology, primatology, archeology, paleo-genetics, and paleo-climatology.},
}

@article {pmid38617445,
year = {2024},
author = {Zhang, J and Li, X and Li, L and Chen, A and Zhang, S},
title = {Y-STR analysis of highly degraded DNA from skeletal remains over 70 years old.},
journal = {Forensic sciences research},
volume = {9},
number = {2},
pages = {owae020},
pmid = {38617445},
issn = {2471-1411},
abstract = {The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery. Considering that information about distant relatives is more relevant for long-term missing persons and alleged family members are male, Y-STR loci analysis is considered the most appropriate and informative approach for determining paternal lineage relationship. In this study, Y-STR genotypes obtained from these alleged relatives were identical to each other and to the alleles of missing persons' consensus profiles at more than 22 loci examined, whilst not being found in Y-STR population database from Y-Chromosome STR Haplotype Reference Database. Therefore, Missing Person No.7 and Missing Person No.18 have a patrilineal relationship with reference samples from Family1 and Family2, respectively. In addition, the fact that Y-STR haplotypes obtained from skeletal remains of missing persons and reference samples are not found in the Han Chinese people from East Asian demonstrates its rarity and further supports a paternal lineage relationship amongst them.},
}

@article {pmid38612593,
year = {2024},
author = {Ferreira, RC and Rodrigues, CR and Broach, JR and Briones, MRS},
title = {Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25073785},
pmid = {38612593},
issn = {1422-0067},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; },
abstract = {The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.},
}

@article {pmid38611559,
year = {2024},
author = {Di Pasquale, GM and Stagnati, L and Lezzi, A and Lanubile, A and Marocco, A and Rossi, G and Busconi, M},
title = {Morphological and Genetic Characterization of Maize Landraces Adapted to Marginal Hills in North-West Italy.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/plants13071030},
pmid = {38611559},
issn = {2223-7747},
support = {PSR2014-2020. Project number 5015253, RICOLMA//Regione Emilia-Romagna/ ; ECS00000036, NODES//Ministero dell'Università e della Ricerca/ ; },
abstract = {The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a FST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area.},
}

@article {pmid38601034,
year = {2024},
author = {Abbona, CC and Lebrasseur, O and Prevosti, FJ and Peralta, E and González Venanzi, L and Frantz, L and Larson, G and Gil, AF and Neme, GA},
title = {Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities.},
journal = {Royal Society open science},
volume = {11},
number = {4},
pages = {231835},
pmid = {38601034},
issn = {2054-5703},
abstract = {The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ[13]Ccol and δ[15]N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.},
}

@article {pmid38589385,
year = {2024},
author = {Mills, KK and Hildebrandt, KPB and Everson, KM and Horstmann, L and Misarti, N and Olson, LE},
title = {Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8257},
pmid = {38589385},
issn = {2045-2322},
support = {Walrus Adaptability and Long-term Responses; Using multi-proxy data to project Sustainability, Award #1263848//National Science Foundation/ ; OIA-1826801//National Science Foundation/ ; },
abstract = {Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.},
}

@article {pmid38586998,
year = {2024},
author = {Brack, J and Biran, M and Amitai, R},
title = {Plague and the Mongol conquest of Baghdad (1258)? A reevaluation of the sources.},
journal = {Medical history},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/mdh.2023.38},
pmid = {38586998},
issn = {2048-8343},
abstract = {This paper reexamines the sources used by N. Fancy and M.H. Green in "Plague and the Fall of Baghdad (1258)" (Medical History, 65/2 (2021), 157-177). Fancy and Green argued that the Arabic and Persian descriptions of the Mongol sieges in Iran and Iraq, and in particular, in the conquest of Baghdad in 1258, indicate that the besieged fortresses and cities were struck by Plague after the Mongol sieges were lifted. This, they suggested, is part of a recurrent pattern of the outbreak of Plague transmitted by the Mongol expansion across Eurasia. Fancy and Green concluded that the primary sources substantiate the theory driven by recent paleogenetic studies indicating that the Mongol conquests of the thirteenth century set the stage for the massive pandemic of the mid-fourteenth century. The link between the Plague outbreak and the Mongol siege of Baghdad relies on three near-contemporaneous historical accounts. However, our re-examination of the sources shows that the main text (in Persian) has been significantly misunderstood, and that the two other texts (in Syriac and Arabic) have been mis-contextualized, and thus not understood properly. They do not support the authors' claim regarding Plague epidemic in Baghdad in 1258, nor do other contemporary and later Arabic texts from Syria and Egypt adduced by them, which we re-examine in detail here. We conclude that there is no evidence for the appearance of Plague during or immediately after the Mongol conquests in the Middle East, certainly not for its transmission by the Mongols.},
}

@article {pmid38583481,
year = {2024},
author = {Alsos, IG and Boussange, V and Rijal, DP and Beaulieu, M and Brown, AG and Herzschuh, U and Svenning, JC and Pellissier, L},
title = {Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1902},
pages = {20230017},
doi = {10.1098/rstb.2023.0017},
pmid = {38583481},
issn = {1471-2970},
abstract = {Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.},
}

@article {pmid38567866,
year = {2024},
author = {Miles, LS and Waterman, H and Ayoub, NA and Garb, JE and Haney, RA and Rosenberg, MS and Krabbenhoft, TJ and Verrelli, BC},
title = {Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esae018},
pmid = {38567866},
issn = {1465-7333},
support = {//Virginia Commonwealth University/ ; //University at Buffalo/ ; },
abstract = {Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.},
}

@article {pmid38559769,
year = {2024},
author = {Bellini, G and Schrieber, K and Kirleis, W and Erfmeier, A},
title = {Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1307364},
doi = {10.3389/fpls.2024.1307364},
pmid = {38559769},
issn = {1664-462X},
abstract = {Pre-adaptation to anthropogenic disturbance is broadly considered key for plant invasion success. Nevertheless, empirical evidence remains scarce and fragmentary, given the multifaceted nature of anthropogenic disturbance itself and the complexity of other evolutionary forces shaping the (epi)-genomes of recent native and invasive plant populations. Here, we review and critically revisit the existing theory and empirical evidence in the field of evolutionary ecology and highlight novel integrative research avenues that work at the interface with archaeology to solve open questions. The approaches suggested so far focus on contemporary plant populations, although their genomes have rapidly changed since their initial introduction in response to numerous selective and stochastic forces. We elaborate that a role of pre-adaptation to anthropogenic disturbance in plant invasion success should thus additionally be validated based on the analyses of archaeobotanical remains. Such materials, in the light of detailed knowledge on past human societies could highlight fine-scale differences in the type and timing of past disturbances. We propose a combination of archaeobotanical, ancient DNA and morphometric analyses of plant macro- and microremains to assess past community composition, and species' functional traits to unravel the timing of adaptation processes, their drivers and their long-term consequences for invasive species. Although such methodologies have proven to be feasible for numerous crop plants, they have not been yet applied to wild invasive species, which opens a wide array of insights into their evolution.},
}

@article {pmid38552628,
year = {2024},
author = {Du, P and Zhu, K and Qiao, H and Zhang, J and Meng, H and Huang, Z and Yu, Y and Xie, S and Allen, E and Xiong, J and Zhang, B and Chang, X and Ren, X and Xu, Y and Zhou, Q and Han, S and Jin, L and Wei, P and Wang, CC and Wen, S},
title = {Ancient genome of the Chinese Emperor Wu of Northern Zhou.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.02.059},
pmid = {38552628},
issn = {1879-0445},
abstract = {Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.[1][,][2] Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.},
}

@article {pmid38552017,
year = {2024},
author = {Boilard, A and Walker, SJ and Lødøen, TK and Henriksen, M and Takken Beijersbergen, LM and Star, B and Robu, M and Tøssebro, C and Albrektsen, CM and Soleng, Y and Aksnes, S and Jørgensen, R and Hufthammer, AK and van Kolfschoten, T and Lauritzen, SE and Boessenkool, S},
title = {Ancient DNA and osteological analyses of a unique paleo-archive reveal Early Holocene faunal expansion into the Scandinavian Arctic.},
journal = {Science advances},
volume = {10},
number = {13},
pages = {eadk3032},
doi = {10.1126/sciadv.adk3032},
pmid = {38552017},
issn = {2375-2548},
abstract = {Paleo-archives are essential for our understanding of species responses to climate warming, yet such archives are extremely rare in the Arctic. Here, we combine morphological analyses and bulk-bone metabarcoding to investigate a unique chronology of bone deposits sealed in the high-latitude Storsteinhola cave system (68°50' N 16°22' E) in Norway. This deposit dates to a period of climate warming from the end of the Late Glacial [~13 thousand calibrated years before the present (ka cal B.P.)] to the Holocene thermal maximum (~5.6 ka cal B.P.). Paleogenetic analyses allow us to exploit the 1000s of morphologically unidentifiable bone fragments resulting in a high-resolution sequence with 40 different taxa, including species not previously found here. Our record reveals borealization in both the marine and terrestrial environments above the Arctic Circle as a naturally recurring phenomenon in past periods of warming, providing fundamental insights into the ecosystem-wide responses that are ongoing today.},
}

@article {pmid38538568,
year = {2024},
author = {Kumar, S and Singh, PP and Pasupuleti, N and Tripathi, VM and Chauley, MK and Chaubey, G and Rai, N},
title = {The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddae054},
pmid = {38538568},
issn = {1460-2083},
support = {EMBO-STF-8028:2019//European Molecular Biology Organisation-Short Term Fellowship/ ; SERB-CRG/20-21/006762//Science and Engineering Research Board/ ; 2021-6389//Indian Council of Medical Research/ ; 2021-11289//Banaras Hindu University/ ; //Archaeological Survey of India/ ; //Directorate of Archaeology, Government of Assam/ ; },
abstract = {The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations.},
}

@article {pmid38533900,
year = {2024},
author = {Jackson, I and Woodman, P and Dowd, M and Fibiger, L and Cassidy, LM},
title = {Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.},
journal = {Molecular biology and evolution},
volume = {41},
number = {3},
pages = {},
doi = {10.1093/molbev/msae017},
pmid = {38533900},
issn = {1537-1719},
support = {IRCLA/2022/126//Wellcome Trust Institutional Strategic Support Fund/ ; 18/CRT/6214//Science Foundation Ireland Centre for Research Training in Genomics Data Science/ ; },
abstract = {Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.},
}

@article {pmid38530148,
year = {2024},
author = {Yaka, R and Maja Krzewińska, and Lagerholm, VK and Linderholm, A and Özer, F and Somel, M and Götherström, A},
title = {Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2023-0107},
pmid = {38530148},
issn = {1940-9818},
support = {STF 7909//EMBO (short-term fellowship)/ ; 772390//ERC (consolidator grant)/ ; 117Z229//TUBITAK of Turkey/ ; NAISS 2023/22-504, NAISS 2023/23-262//Uppsala Multidisciplinary Center for Advanced Computational Science/ ; },
abstract = {Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.},
}

@article {pmid38527214,
year = {2024},
author = {Nelder, MP and Schats, R and Poinar, HN and Cooke, A and Brickley, MB},
title = {Pathogen prospecting of museums: Reconstructing malaria epidemiology.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {15},
pages = {e2310859121},
doi = {10.1073/pnas.2310859121},
pmid = {38527214},
issn = {1091-6490},
support = {231563//Canada Research Chairs (Chaires de recherche du Canada)/ ; 016.Veni.195.195//Dutch Research Council (NWO)/ ; W18357-6-EM//Elise Mathilde Fund/Leiden University Fund/ ; },
abstract = {Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.},
}

@article {pmid38526010,
year = {2024},
author = {Gill, H and Lee, J and Jeong, C},
title = {Reconstructing the genetic relationship between ancient and present-day Siberian populations.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae063},
pmid = {38526010},
issn = {1759-6653},
abstract = {Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 years ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.},
}