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Thread: Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)

  1. #3191
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    Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments

    https://science.sciencemag.org/conte.../6542/eabf1667

    Structured Abstract
    INTRODUCTION
    The study of hominin history has progressed through both archaeological and genetic insights. Although DNA sequencing from hominin skeletal remains allows the association of ancient populations with specific places in time and space, many archaeological sites lack associated hominin remains, limiting the scope of genetic analyses. Even when ancient hominin remains are found, they often do not cover the full time span of a site or sampling them for DNA may not be possible. The fossil record is particularly sparse for Pleistocene hominins, leaving large gaps in our understanding of the genetic histories of archaic and early modern humans.

    RATIONALE
    Recent work has demonstrated the feasibility of sequencing ancient mammalian mitochondrial DNA (mtDNA), including that of hominins, from Pleistocene cave sediments. However, mtDNA represents only the maternal lineage and thus provides limited data for the resolution of population relationships. It is therefore desirable to complement mtDNA analysis with the retrieval of nuclear DNA, but no strategies are in place to enrich hominin nuclear DNA from a background of related sequences from other mammals present in most sedimentary deposits. To close this gap, we developed a set of probes for hybridization capture that targets 1.6 million ancestry-informative positions in the hominin nuclear genome, specifically at loci with high mammalian sequence divergence. We then developed computational methods to deplete residual microbial and faunal DNA sequences, along with methods to account for such non-hominin DNA in population genetic analyses.

    RESULTS
    We applied these methods to explore the history of Neanderthal populations in western Europe and southern Siberia using sediment samples from three Pleistocene caves: Galería de las Estatuas, a site in northern Spain with 40 thousand years of Neanderthal occupation but that is genetically unexplored, and Chagyrskaya and Denisova Caves, which have previously yielded high-coverage genomes of two Neanderthals and one Denisovan hominin. In total, we recovered Neanderthal or Denisovan mtDNA from >60 sediment samples and nuclear DNA from 30 of these. For Chagyrskaya and Denisova Caves, our phylogenetic results from sediment DNA were consistent with previously published results from skeletal remains, confirming the accuracy of our approach. At Galería de las Estatuas, we recovered Neanderthal DNA from layers spanning nearly the entire stratigraphy, and identified a population turnover ~100,000 years ago accompanied by a loss of mtDNA diversity. By incorporating genetic data from previously published skeletal samples, we associated this turnover with two putative radiations in Neanderthal history.

    CONCLUSION
    We developed methods for the effective retrieval and analysis of ancient hominin nuclear DNA from sediments and used them to uncover previously unknown events in Neanderthal history. This work demonstrates that detailed genetic analyses are now possible for many more archaeological sites than previously thought, with DNA from abundant sediments allowing dense time-series studies that are independent of the fossil record.

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  3. #3192
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    https://www.eurekalert.org/pub_relea...-fmo050521.php

    News Release 6-May-2021

    First member of ill-fated 1845 Franklin expedition is identified by DNA analysis

    With a living descendant's DNA sample, a team of researchers have identified the remains of John Gregory, engineer aboard HMS Erebus

    ...

    "We are extremely grateful to the Gregory family for sharing their family history with us and for providing DNA samples in support of our research. We'd like to encourage other descendants of members of the Franklin expedition to contact our team to see if their DNA can be used to identify the other 26 individuals," says Stenton.


    Article itself:

    https://www.cambridge.org/core/journ...6A8F978072EE02

    DNA identification of a sailor from the 1845 Franklin northwest passage expedition

    Published online by Cambridge University Press: 28 April 2021

    Douglas R. Stenton, Stephen Fratpietro, Anne Keenleyside and Robert W. Park

    Abstract

    The 1845 British polar expedition in search of a northwest passage through the Canadian Arctic under the command of Sir John Franklin resulted in the greatest loss of life event in the history of polar exploration. The names of the 129 officers and crew who sailed and died on the catastrophic voyage are known, but the identification of their skeletons found scattered along the route of their attempted escape is problematic. Here, we report DNA analyses from skeletal remains from King William Island, where the majority of the expedition fatalities occurred, and from a paternal descendant of a member of the expedition. A match was found between an archaeological sample and a presumed descendant sample using Y-chromosome haplotyping. We conclude that DNA and genealogical evidence confirm the identity of the remains as those of Warrant Officer John Gregory, Engineer, HMS Erebus. This is the first member of the 1845 Franklin expedition whose identity has been confirmed through DNA and genealogical analyses.

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  5. #3193
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    Evidence for early dispersal of domestic sheep into Central Asia

    Shnaider et al April 2021
    The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized. Archaeological and biomolecular investigations of ancient sheep remains from the site of Obishir V in southern Kyrgyzstan reveal that domestic livestock and Neolithic lifeways reached the heart of Central Asia by ca. 6,000 BCE, thousands of years earlier than previously recognized.
    https://www.researchgate.net/publica...o_Central_Asia

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  7. #3194
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    https://www.cell.com/current-biology...21)00535-2#%20

    Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula

    Tina Saupe 26, 27
    Francesco Montinaro 26
    Cinzia Scaggion
    Nicola Carrara
    Toomas Kivisild
    Eugenia D’Atanasio
    Ruoyun Hui
    Anu Solnik
    Ophélie Lebrasseur
    Greger Larson
    Luca Alessandri
    Ilenia Arienzo
    Flavio De Angelis
    Mario Federico Rolfo
    Robin Skeates
    Letizia Silvestri
    Jessica Beckett
    Sahra Talamo
    Andrea Dolfini
    Monica Miari
    Mait Metspalu
    Stefano Benazzi
    Cristian Capelli 26
    Luca Pagani 26
    Christiana L. Scheib 26

    Open Access

    Published:May 10, 2021DOI:https://doi.org/10.1016/j.cub.2021.04.022


    Highlights

    • 22 genomes from Northeastern and Central Italy dated between 3200 and 1500 BCE
    • Arrival of Steppe-related ancestry in the central Italian Peninsula by 1600 BCE
    • Close patrilineal kinship patterns within commingled Chalcolithic cave burials
    • Roman Imperial period had a stronger effect on phenotype shifts than the Bronze Age

    Summary

    Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001–1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200–900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen’s disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.

    Reminder: all the discussion should be done in other threads, not here.

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  9. #3195
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    https://www.nature.com/articles/s41431-021-00897-8

    Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes

    Anne-Mai Ilumäe, Helen Post, Rodrigo Flores, Monika Karmin, Hovhannes Sahakyan, Mayukh Mondal, Francesco Montinaro, Lauri Saag, Concetta Bormans, Luisa Fernanda Sanchez, Adam Ameur, Ulf Gyllensten, Mart Kals, Reedik Mägi, Luca Pagani, Doron M. Behar, Siiri Rootsi & Richard Villems

    European Journal of Human Genetics (2021)Cite this article

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    Abstract

    The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1–3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.

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  11. #3196
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    Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe

    Twenty-four palaeogenomes from Mokrin, a major Early Bronze Age necropolis in southeastern Europe, were sequenced to analyse kinship between individuals and to better understand prehistoric social organization. 15 investigated individuals were involved in genetic relationships of varying degrees. The Mokrin sample resembles a genetically unstructured population, suggesting that the community’s social hierarchies were not accompanied by strict marriage barriers. We find evidence for female exogamy but no indications for strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. We further show that sons had the possibility to acquire status during their lifetimes, but not necessarily to inherit it. Taken together, these findings suggest that Southeastern Europe in the Early Bronze Age had a significantly different family and social structure than Late Neolithic and Early Bronze Age societies of Central Europe.

    https://www.nature.com/articles/s415...-89090-x#Sec25

    Genomic data are available at the European Nucleotide Archive under the accession no. PRJEB38643 in BAM and fastq format.
    Last edited by VladimirTaraskin; 05-12-2021 at 10:27 AM.

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  13. #3197
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    Mitochondrial DNA analysis of Chitrali population of Pakistan from ancient human bones
    Ghani Rehman
    Kunming University of Science and Technology

    February 2021
    Meta Gene 27(5806):100821

    Abstract
    Ancient human DNA has various applications in molecular evolution and studies the genetic relationship between the archaic human population and the modern human population. Many ancient human remains are stored in the archeological museum and can be used for DNA sequence analysis. The current study was ever first attempt in Pakistan to use old biological specimens for molecular characterization to trace the population of Chitral district in KP Pakistan. Due to the low quantity and quality of ancient DNA, it is challenging to isolate DNA profiles from ancient human samples. A protocol was optimized for the extraction of degraded DNA from the ancient human bone's specimens. Different Bioinformatics analyses like online servers, Mitomastar and James lick, Phylogenetic Tree, and Genetic Diversity were used for the molecular characterization of the Chitrali population. Our results show that the Ancient Chitrali population has admixture with Europeans and Neolithic European populations.

    https://www.researchgate.net/publica...nt_human_bones
    Last edited by Kapisa; 05-15-2021 at 04:13 AM.

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  15. #3198
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    Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.
    Emma Svensson, Torsten Günther, Alexander Hoischen, Montserrat Hervella, Arielle R. Munters, Mihai Ioana, Florin Ridiche, Hanna Edlund, Rosanne C. van Deuren, Andrei Soficaru, Concepción de-la-Rua, Mihai G. Netea, Mattias Jakobsson,
    Current Biology, 2021,ISSN 0960-9822,

    https://doi.org/10.1016/j.cub.2021.04.045.
    (https://www.sciencedirect.com/scienc...60982221005923)

    Highlights

    • Peştera Muierii woman is related to Europeans, but she is not a direct ancestor
    • Reduced diversity in Europe caused by Last Glaciation, not out-of-Africa bottleneck
    • Genetic load appears indifferent across 40,000 years of European history
    • New DNA extraction approach recovers up to 33 times more DNA from ancient remains

    Summary - Few comlete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from “Peştera Muierii,” Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
    Keywords: Upper Palaeolithic; population size; bottleneck; genetic load; palaeogenomics
    J1 FGC5987 to FGC6175 (188 new SNPs)
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    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  17. #3199
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    Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes

    Abstract

    Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggests that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.

    https://academic.oup.com/mbe/advance...sab147/6277411

    Last edited by Waldemar; 05-18-2021 at 06:21 PM.

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    Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe
    Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced.
    Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from ‘‘Pesxtera
    Muierii,’’ Romania who lived 34,000 years ago to 13.53 coverage. The genome shows similarities to modern-
    day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and
    Neanderthal features, the genome shows similar levels of Neanderthal admixture (3.1%) to most EUP
    humans but only half compared to the 40,000-year-old Pesxtera Oase 1. All EUP European hunter-gatherers
    display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the
    Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic
    diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant
    from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed
    among Europeans.
    Pdf:
    https://www.cell.com/action/showPdf?...2821%2900592-3

  20. The Following 13 Users Say Thank You to David Bush For This Useful Post:

     anglesqueville (05-19-2021),  grumpydaddybear (05-20-2021),  Hando (05-20-2021),  J1 DYS388=13 (05-20-2021),  Lenny Nero (05-20-2021),  Nganasankhan (05-19-2021),  parasar (05-19-2021),  Piquerobi (05-19-2021),  RP48 (05-20-2021),  sheepslayer (05-23-2021),  Shuzam87 (05-20-2021),  teepean47 (05-20-2021),  theplayer (05-20-2021)

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