Page 151 of 405 FirstFirst ... 51101141149150151152153161201251 ... LastLast
Results 1,501 to 1,510 of 4044

Thread: Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY)

  1. #1501
    Registered Users
    Posts
    1,370
    Sex
    Omitted

    Quote Originally Posted by rozenfeld View Post
    Via Iosif Lazaridis twitter:

    https://twitter.com/iosif_lazaridis/...31752655089665



    https://www.biorxiv.org/content/early/2018/07/04/362566

    The limits of long-term selection against Neandertal introgression

    View ORCID ProfileMartin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot

    doi: https://doi.org/10.1101/362566

    Abstract

    Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans due to deleterious alleles that had accumulated in the Neandertals after they split from the modern human lineage. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45 thousand years. Here we show that this apparent decline is an artifact caused by gene flow between West Eurasians and Africans, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When applying a more robust statistic that takes advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Western Europe over the past 45 thousand years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters, and find that negative selection is not expected to cause a significant long- term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular a depletion of Neandertal ancestry in conserved genomic regions that are likely to be of functional importance. Thus, we find that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.
    What I find highly strange is that this gene flow requires movement of people. Why and how? It seems improbable. This gene flow apparently started around 20.000 year ago. In the middle of the LGM. It simply does not make sense. The other way, West-Eurasian into Africans, is defied by the fact that D-stats seem to be roughly similar for East and West-Africans. But not Central Africans. Maybe Iberomasurians carried part of it?

    What is interesting though is that Villabruna has an affinity with about everybody as Kale recently stated. Everybody including AG3 but excluding MA1, who is pre-LGM.
    Last edited by epoch; 07-05-2018 at 05:14 AM.

  2. The Following User Says Thank You to epoch For This Useful Post:

     Hando (07-05-2018)

  3. #1502
    Registered Users
    Posts
    1,761
    Y-DNA (P)
    I-S336
    mtDNA (M)
    K1c1

    Quote Originally Posted by epoch View Post
    What I find highly strange is that this gene flow requires movement of people. Why and how? It seems improbable. This gene flow apparently started around 20.000 year ago. In the middle of the LGM. It simply does not make sense. The other way, West-Eurasian into Africans, is defied by the fact that D-stats seem to be roughly similar for East and West-Africans. But not Central Africans. Maybe Iberomasurians carried part of it?

    What is interesting though is that Villabruna has an affinity with about everybody as Kale recently stated. Everybody including AG3 but excluding MA1, who is pre-LGM.
    This preprint supposes high Neanderthal in basal because Stuttgart's Neanderthal is within normal European limits and it is assumed to be 44% basal. This has been revised to 25% by more recent papers and one new study has it at 10%. If it's this low it won't bring EEF archaic admixture down significantly even if it has little to no Neanderthal. Additionally there's the matter of pops like Mbuti or Dinka not sharing more drift with western eurasia than with eastern eurasia, as Lazaridis tweeted they should if the supposed migration took place.

  4. The Following User Says Thank You to Shaikorth For This Useful Post:

     Hando (07-06-2018)

  5. #1503
    Registered Users
    Posts
    1,370
    Sex
    Omitted

    Quote Originally Posted by Shaikorth View Post
    This preprint supposes high Neanderthal in basal because Stuttgart's Neanderthal is within normal European limits and it is assumed to be 44% basal. This has been revised to 25% by more recent papers and one new study has it at 10%. If it's this low it won't bring EEF archaic admixture down significantly even if it has little to no Neanderthal. Additionally there's the matter of pops like Mbuti or Dinka not sharing more drift with western eurasia than with eastern eurasia, as Lazaridis tweeted they should if the supposed migration took place.
    However, the idea that a linear demise of Neanderthal admixture can't be due to selection seems correct to me. After only a few generations the chunks of Neanderthal DNA are so small that selection would only target some coding genes. So the demise, if it was due to selection against Neanderthal, would be something like a hyperbole graph, I reckon.

  6. The Following User Says Thank You to epoch For This Useful Post:

     Hando (07-05-2018)

  7. #1504
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    Abstracts from SMBE 2018 are available here: http://smbe2018.jp/mobile_app.html#abstract_pdf

    Some interesting abstracts:

    SY01: Asian population genomics (July 11, 12:30−14:30)

    O-03-AP01

    Northern Asian Genome Project

    JEONG-SUN SEO 1

    1 Gong-Wu Genomic Medicine Institute (G2MI), Seoul National University Bundang Hospital (Republic of Korea)
    We have been working on Northern Asian genome Project. As part of this project, we produced whole-genome sequencing (WGS) data, on average sequencing depth of 15X or 30X, for 1908 samples which composed of 852 Korean, 396 Japanese, 386 Mongolian (the Buryats and the Khalkha Mongols), and 274 Chinese individuals. We discovered millions of novel single nucleotide polymorphism (SNP) and it turned out that large portion of rare SNPs (minor allele frequency < 0.5%) in the 1000 genome project phase 3 were low frequency or even common in our dataset. We were able to construct robust imputation panel for Northern Asian populations which produces great imputation accuracy for rare and low frequency SNPs.

    Series of analyses demonstrated distinctive population structure of the Mongolians from the other East Asians. We identified significant gene flow from the Buryats to the Finnish and we found that Buryat admixture existed in the Finnish genome. Since part of these samples was included in the GA100K (Genome Asia 100K ) pilot project, we firstly analyzed the mitochondrial haplogroups, which show a clear differentiation between Northern and Southern part of Asian haplogroups. These observations suggest that at least two waves of maternal lineage migration from North Asia to South Asia.

    O-03-AP02

    High-coverage sequencing of diverse human populations in the HGDP-CEPH panel

    Anders Bergstrom 1, Shane A McCarthy 1, 2, Ruoyun Hui 2, Qasim Ayub 1, 3, 4, Petr Danecek 1, Mohamed A Almarri 1, Javier Prado-Martinez 1, Yuan Chen 1, John A Kamm 1, 2, Joshua Randall 1, Swapan Mallick 5, 6, 8, Pontus Skoglund 7, Manjinder S Sandhu 1, David Reich 5, 6, 8, Scally Aylwyn 2, Yali Xue 1, Richard Durbin 1, 2, Chris Tyler-Smith 1

    1 Wellcome Sanger Institute (United Kingdom),
    2 University of Cambridge (United Kingdom),
    3 Monash University Malaysia (Malaysia),
    4 Monash University Malaysia (Malaysia),
    5 Harvard Medical School (United States),
    6 Broad Institute of Harvard and MIT (United States),
    7 The Francis Crick Institute (United Kingdom),
    8 Harvard Medical School (United States)

    The Human-Genome Diversity Project (HGDP-CEPH) panel consists of samples from 53 diverse human populations from six continents, including many of particular evolutionary, anthropological, and linguistic interest. We have generated a dataset consisting of 929 high-coverage genome sequences from this panel, including 120 samples previously sequenced as part of the Simons Genome Diversity Project. We have also sequenced 26 of the individuals using 10x Genomics linked-read technology, enabling physical haplotype phasing. We perform analyses of detailed effective population size histories, including in the last 10 thousand years, genetic split times, archaic admixture and patterns of rare variant sharing, to further our understanding of human population history and genetic variation. The data is open access with no analysis restrictions, and we hope it will be constitute a useful resource for the human genetics community.

    O-03-AP03

    Back migrations of Southeast Asian ancestors to South Asia during the Last Glacial Maximum

    Namrata Kalsi 1, Stephan Schuster 1, Hie Lim Kim 1, 2, The GenomeAsia 100K consortium

    1 Nanyang Technological University (Singapore),
    2 Nanyang Technological University (Singapore)

    The ancestor of the South Asian tribal people, the oldest groups in the region, has not been clearly known, due to lack of genome data. Our study used more than 800 high coverage and whole genome data, including 470 South Asians and 280 Southeast Asians, generated by the GenomeAsia 100K project. We found admixture signals between tribal South Asians and indigenous people living in the Malay Peninsula, Kensiu and Kintak, who are the earliest settlers in the region and also speak Austroasiatic languages. According to the MSMC analysis, the Malay groups have once increased their population size during the Last Glacial Maximum. During this period, the sea level in the Southeast Asia region was dramatically increased. In the same time period, the South Asian tribes show admixture signal and higher cross-coalescence rate with Kensiu than other South Asian groups. These results support the possible contacts between the ancestors of South and Southeast Asian groups, during the Last Glacial Maximum. Based on analyses using sex chromosomes and mitochondrial genomes, we found abundant male Southeast Asian ancestries in the South Asian tribal groups, which is consistent with previous studies. Overall, our study suggests the possibility of male-driven migrations from Southeast Asia to South Asia and noticeable contacts between them, with the sea level rise in Southeast Asia.

    O-03-AP04

    Human population history in the southwestern coastal region of Sea of Okhotsk, inferred from ancient genome analysis

    Takehiro Sato 1, Noboru Adachi 2, Ryosuke Kimura 3, Minoru Yoneda 4, Hiroki Oota 5, Atsushi Tajima 1, Atsushi Toyoda 6, Hiromi Matsumae 7, 8, Kae Koganebuchi 3, Kentaro K Shimizu 7, 8, Tsunehiko Hanihara 4, Andrzej Weber 9, Hirofumi Kato 10, Hajime Ishida 3

    1 Kanazawa University (Japan),
    2 University of Yamanashi (Japan),
    3 University of the Ryukyus (Japan),
    4 The University of Tokyo (Japan),
    5 Kitasato University (Japan),
    6 National Institute of Genetics (Japan),
    7 University of Zurich (Switzerland),
    8 Yokohama City University (Japan),
    9 University of Alberta (Canada),
    10 Hokkaido University (Japan)

    In 2013, an ancient human skeleton (NAT002) of the prehistoric Okhotsk culture was excavated from Hamanaka 2 site, Rebun Island, northern Japan. Radiocarbon age of NAT002 was 1060-1155 (68.2%) calAD. Some bones of this individual were affected by severe hyperostosis, suggesting SAPHO syndrome. To investigate the genetic features of the Okhotsk people, we extracted DNA from 3rd molars of NAT002 and performed whole genome sequencing. As a result of sequencing for 18 NGS libraries, the sequence data with 35-fold coverage was obtained. The typical deamination pattern and sufficiently low contamination rate were observed, ensuring the DNA authenticity. The mtDNA haplotype of NAT002 was assigned to haplogroup G1b, which is commonly observed among the modern North Asian populations. Results of outgroup f3 test, PCA, and ADMIXTURE analysis indicated that NAT002 was genetically close to the modern Nivkh and Ulch, who are living around the northern Sakhalin and the Lower Amur Basin. In addition, TREEMIX analysis indicated gene flow from the Ainu to NAT002. These findings suggest the past human migration from the Lower Amur region to the northern part of the Japanese archipelago and the admixture between the Okhotsk and Ainu lineages, corresponding to the archaeological evidences. HLA typing indicated that NAT002 possessed HLA-B40 allele, which has been reported as one of the risk factors of ankylosing spondylitis, reactive arthritis, and undifferentiated spondyloarthritis. These diseases are classified into seronegative arthritis as well as SAPHO syndrome. Therefore, HLA type of NAT002 might be one of the cause of the hyperostosis.

    O-03-AP06

    Evolutionary history and adaptation from whole-genome sequences of a pygmy population of Flores Island, Indonesia

    Serena Tucci 1, 2, 3, Sam H. Vohr 4, Rajiv C. McCoy 1, 2, Benjamin Vernot 5, Matthew R. Robinson 6, 7, Chiara Barbieri 8, Wenqing Fu 9, Gludhug A. Purnomo 10, Herawati Sudoyo 10, 11, Guido Barbujani 3, Peter M. Visscher 12, 13, Joshua M. Akey 1, 2, Richard E. Green 4

    1 Princeton University (United States),
    2 Princeton University (United States),
    3 University of Ferrara (Italy),
    4 University of California, Santa Cruz (United States),
    5 Max Planck Institute for Evolutionary Anthropology (Germany),
    6 University of Lausanne (Switzerland),
    7 Quatier Sorge, Lausanne (Switzerland),
    8 Max Planck Institute for the Science of Human History (Germany),
    9 University of Washington, Seattle (United States),
    10 Eijkman Institute for Molecular Biology, Jakarta (Indonesia),
    11 University of Indonesia, Jakarta (Indonesia),
    12 The University of Queensland, Brisbane (Australia),
    13 The University of Queensland, Brisbane (Australia)

    Despite the pivotal role that Flores Island (Eastern Indonesia) plays in understanding human evolutionary history, genomic data from this region is lacking. Here we generate genome-scale data for over 2 million SNPs and the first whole-genome sequences from a pygmy population living on Flores, near the Liang Bua cave where remains of the enigmatic small-bodied hominin species, Homo floresiensis, were recently found. The genomes of the Flores pygmies reveal a complex history of hominin admixture east of the Wallace's line and a striking signature of recent positive selection encompassing the FADS gene cluster on chromosome 11, encoding for fatty acid desaturases that regulate the metabolism of long-chain polyunsaturated fatty acids (LC-PUFA). Our results add to emerging evidence that the FADS region has been a recurrent target of selection in diverse human populations, possibly in response to changing diets. Further, we find that polygenic selection acting on standing variation contributed to the short-stature phenotype of the Flores pygmies, which suggests that multiple, independent instances of hominin insular dwarfism occurred on Flores Island.

  8. The Following 15 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  blackflash16 (07-06-2018),  bmoney (07-06-2018),  epoch (07-06-2018),  ffoucart (07-06-2018),  Hando (07-06-2018),  Helen (07-08-2018),  Judith (07-06-2018),  KSDA (07-06-2018),  Menchaca (07-06-2018),  MikkaK (07-06-2018),  parasar (07-08-2018),  RCO (07-06-2018),  Silesian (07-06-2018),  Varun R (07-06-2018)

  9. #1505
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    SY06: Evolutionary epigenomics, progress and prospects (July 12, 9:30−11:30)

    O-04-EE03

    Reconstructing Denisovan Anatomy Using DNA Methylation Maps

    David Gokhman 1, Nadav Mishol 1, Marc de Manuel Montero 2, David de Juan 2, Jonathan Shuqrun 1, Tomas Marques-Bonet 2, 3, Yoel Rak 4, Liran Carmel 1

    1 The Hebrew University of Jerusalem (Israel),
    2 UPF-CSIC (Spain),
    3 ICREA (Spain),
    4 Tel Aviv University (Israel)

    The Denisovan is a human group unique for having its DNA sequence and methylation mapped, but whose morphology remains almost completely unknown. Here, we present a method to reconstruct anatomical profiles from DNA methylation patterns, based on linking unidirectional promoter methylation changes to loss-of-function phenotypes. We tested the performance of our method by assembling anatomical profiles of the Neanderthal and the chimpanzee, and comparing them to their known morphology. We demonstrate that this method reaches ~87% precision in identifying divergent traits, and ~89% in predicting their direction of change. We then reconstruct a putative anatomical profile of the Denisovan, offering 56 traits in which the Denisovan is expected to be different from modern humans or Neanderthals. We suggest that Denisovans likely shared many traits with Neanderthals, including a projecting face, robust jaws, low forehead and wide pelvis. We also identify additional changes along the Denisovan lineage, such as increased length of the dental arch, and expanded biparietal width. We find that the vast majority of morphologies identified in the late Pleistocene Xuchang crania from China, which were hypothesized to belong to Denisovans, are included in our reconstruction of the Denisovan anatomical profile, providing first genetic support to the classification of these individuals as Denisovans. We conclude that DNA methylation maps provide means to predict morphology, and can be used to uncover anatomical features that do not survive in the paleontological record.

    SY09: Gene flow detection and dating methods (July 9, 13:30−15:30)

    O-01-GF05

    Native American Genetic History Through Admixed Brazilians

    Alex Mas-Sandoval 1, 2, Lara R Arauna 2, Eduardo Tarazona-Santos 3, Maria Catira Bortolini 1, David Comas 2

    1 Universidade Federal do Rio Grande do Sul (Brazil),
    2 Universitat Pompeu Fabra (Spain),
    3 Universidade Federal de Minas Gerais (Brazil)

    Brazilian urban admixed populations are composed of three main genetic components: Native American, European and African. Although their proportions between and within populations are different, Native American component is usually the one found in lowest proportions (6-8%). We take advantage of 6487 urban admixed Brazilians genotyped at 2,5M SNPs in three locations of eastern Brazil (North-East, South-East and South regions) to extract the Native American haplotypes and rearrange them in Assembled Individuals with full Native American ancestry, emulating a historical landscape where Native Americans had not admixed with Europeans and Africans. This method allows us to analyze the Native Americans population structure in a region where most of Native American populations disappeared after European colonization. We find that population structure of Native American Assembled Individuals is driven by the geography of the sampling location while the populations structure of urban admixed Brazilians is modulated by the European or the African ancestry. Finally, in order to explore in depth the origin and the demographic history of the Brazilian Native American component we analyze how admixture with non-admixed Native-American populations have shaped these populations.

    SY18: Looking beyond the genome: cultural and behavioral drivers of biological evolution (July 11, 9:30−11:30)

    O-03-LB03

    Ancient Genomic Diversity Reveals Differences in Cultural Practices and Cultural Barriers between Prehistoric Farmers and Hunter-gatherers in Europe

    Zuzana Hofmanova 1, 2, Vivian Link 1, 2, Ilektra Schulz 1, 2, Jens Bloecher 3, Laura Winkelbach 3, Sofija Stefanovic 4, 5, Joachim Burger 3, Daniel Wegmann 1, 2

    1 University of Fribourg (Switzerland),
    2 Fribourg (Switzerland),
    3 Johannes Gutenberg University Mainz (Germany),
    4 University of Belgrade (Serbia),
    5 University of Novi Sad (Serbia)

    Humans differ from most other species in that we create our own ecological niche. Culture has thus shaped human genetic variation over millennia. While surprisingly little is known about prehistoric cultural practices, there is vested hope that patterns of ancient genetic diversity will elucidate how past societies were organized and interacted with each other. Yet such inferences remain challenging due to generally low numbers of individuals and especially the lack of population-level samples. Here we present novel samples from the region of the Danube Gorges (Balkans), located in the heart of the migration corridor through which farming was brought from Anatolia to Central Europe. Our archaeologically well-defined samples (~10000-5500 calBC) represent multiple closeby-settlements of a sedentary society before and during Neolithisation. Contrasting population-genomic and cultural affinities of our samples revealed that settlements differed strikingly in their interaction with immigrating farmers: while some exhibited strong barriers to gene flow, others incorporated multiple individuals of genetic ancestry common to Aegean farmers. To elucidate important aspects of social practices before, during and after this demographic shift, we accurately inferred within and between individual genetic diversity of our population sample by sequencing either whole genomes or many putatively neutral regions, and by using novel methods that account for post-mortem damage and the heterochronous nature of our reference panel. Notably, we found a lower within-individual diversity as well as a lower X to autosomes diversity in hunter-gatherers than farmers prior to their contact, consistent with an elevated population size and stronger patrilocality in farmers.


    SY18: Looking beyond the genome: cultural and behavioral drivers of biological evolution (July 11, 9:30−11:30)

    O-03-LB05

    The Genomics of Megaliths: An Irish case study into the reconstruction of prehistoric societal landscapes through ancient DNA analysis

    Lara M Cassidy 1

    1 Trinity College Dublin (Ireland)

    The Irish Neolithic (circa 3,800-2,500) marks the emergence of complex civilization on the island, alongside the establishment of continued contacts with other Atlantic regions, which intensify in the succeeding Copper and Bronze Ages. In addition to these cultural upheavals, the Neolithic period has been demonstrated to both begin and end with mass migration into the island, potentially from multiple external sources. However, the variable interplay between geography and culture in the catalyzation of these population movements has remained an open question. Indeed, the archaeological record would suggest regional heterogeneity in the uptake of British and continental traditions at both transition points.

    Here, the potential social and cultural implications of such events are explored through the prism of ancient genomics. Imputed diploid genotypes for over 50 individuals sampled from the Mesolithic to Bronze Age periods, encompassing a diversity of megalithic structures, are presented and dissected through the use of haplotypic-sharing methods, as well as estimations of kinship and inbreeding. Combined with Y chromosome analysis these provide the first evidence of genetic structure on the island during specific prehistoric time intervals, which can be interpreted along both geographical and cultural lines. Furthermore, candidate refugiums that may recurrently act as reservoirs for older traditions and genetic ancestries are identified, as well as hub regions, which appear more susceptible to demographic disturbances on the continent, highlighting the immovable constraints of geography on both cultural and genomic evolution.

  10. The Following 15 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  epoch (07-06-2018),  Helen (07-08-2018),  Judith (07-06-2018),  Menchaca (07-06-2018),  MikkaK (07-06-2018),  Net Down G5L (07-07-2018),  Onur Dincer (07-06-2018),  parasar (07-08-2018),  Pribislav (07-06-2018),  RCO (07-06-2018),  rms2 (07-06-2018),  Ruderico (07-06-2018),  Silesian (07-06-2018),  Varun R (07-06-2018)

  11. #1506
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    This is part of paper published today: http://science.sciencemag.org/content/361/6397/88

    The prehistoric peopling of Southeast Asia

    SY23: Open Symposium (July 11, 9:30−17:00)

    O-03-OS02

    Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations

    Takashi Gakuhari 1, 3, Martin Sikora 2, Simon Rasmussen 2, Morten Allentoft 2, Takehiro Sato 1, Thorfinn Korneliussen 2, Minoru Yoneda 4, Hajime Ishida 5, Yasuhiro Yamada 6, Hiroki Shibata 7, Shigeki Nakagome 8, Eske Willerslev 2, 9, 10, Hiroki Oota 3

    1 Kanazawa University (Japan),
    2 University of Copenhagen (Denmark),
    3 Kitasato University (Japan),
    4 The University of Tokyo (Japan),
    5 University of the Ryukyus (Japan),
    6 National Museum of Japanese Histories (Japan),
    7 Kyushu University (Japan),
    8 the University of Dublin (Ireland),
    9 University of Cambridge (United Kingdom),
    10 Wellcome Trust Sanger Institute (United Kingdom)

    Post late-Paleolithic hunter-gatherers lived throughout the Japanese archipelago, Jomonese, are thought to be a key to understanding the peopling history in East Asia. Here, we report a whole genome sequence (x1.85) of 2,500-year old female excavated from the Ikawazu shell-mound, unearthed typical remains of Jomon culture. The whole genome data places the Jomon as a lineage basal to contemporary and ancient populations of the eastern part of Eurasian continent, and supports the closest relationship with the modern Hokkaido Ainu. The results of ADMIXTURE show the Jomon ancestry is prevalent in present-day Nivkh, Ulchi, and people in the main-island Japan. By including the Jomon genome into phylogenetic trees, ancient lineages of the Kusunda and the Sherpa/Tibetan, early splitting from the rest of East Asian populations, is emerged. Thus, the Jomon genome gives a new insight in East Asian expansion. The Ikawazu shell-mound site locates on 34,38,43 north latitude, and 137,8, 52 east longitude in the central main-island of the Japanese archipelago, corresponding to a warm and humid monsoon region, which has been thought to be almost impossible to maintain sufficient ancient DNA for genome analysis. Our achievement opens up new possibilities for such geographical regions.

  12. The Following 8 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  Helen (07-08-2018),  MikkaK (07-06-2018),  Onur Dincer (07-06-2018),  Ruderico (07-06-2018),  Silesian (07-06-2018),  traject (07-06-2018),  Varun R (07-06-2018)

  13. #1507
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    POA-233 The Transition to Farming in Eneolithic (Copper Age) Ukraine was Largely Driven by Population Replacement

    Ryan William Schmidt 1, Daniel Fernandes 1, 2, 3, Jordan Karsten 4, Thomas Harper 5, Gwyn Madden 6, Sarah Ledogar 7, Mykhailo Sokhatsky 8, Hiroki Oota 9, Ron Pinhasi 1, 2

    1 University College, Dublin (Ireland),
    2 University of Vienna (Austria),
    3 University of Coimbra (Portugal),
    4 University of Wisconsin-Oshkosh (United States),
    5 The Pennsylvania State University (United States),
    6 Grand Valley State University (United States),
    7 University of New England, Armidale (Australia),
    8 Borschiv Regional Museum (Ukraine),
    9 Kitasato University (Japan)

    The transition to a farming-based economy during the Neolithic happened relatively late in southeastern Europe. Material changes occurred through pottery manufacture, but it wasn't until the sixth millennium BCE that farming was adopted by the Cucuteni-Trypillian archaeological complex (4800-3000 BCE). In many parts of Europe, early farmers who were descended from Anatolian migrants slowly admixed with local hunter-gatherers over the course of the Neolithic. In Eastern Europe and the Balkans, this process may have been more complex since early farmers would likely have admixed with local groups prior to spreading into continental Europe. Studies from the Baltic and Estonia suggest little genetic input from early farmers or continuous admixture with hunter-gatherers. Here, we investigate the impact of Trypillian migrations into Ukraine through the analyses of 19 ancient genomes (0.6 to 2.1X coverage) from the site of Verteba Cave. Ceramic typology and radiocarbon dating of the cave indicate continuous occupation from the Mesolithic to the Medieval Period, with peak occupation coinciding with the middle to late Tripolye. We show that the Trypillians replaced local Ukrainian Neolithic cultures. Also, hunter-gatherers contributed very little ancestry to the Trypillians, who are genetically indistinct from early Neolithic farmers. The one exception is a female that has mostly steppe-related ancestry. Direct radiocarbon dating of this individual places her in the the Middle Bronze Age (3545 years before present).
    Her lack of farmer ancestry suggests abrupt population replacement resulting perhaps from inter-group hostilities or plague that spread through Europe during the Late Neolithic.

    POA-234 Population Dynamics at Late Chalcolithic and Early Bronze Age Arslantepe, Anatolia

    Eirini Skourtanioti 1, Choongwon Jeong 1, Yilmaz Selim Erdal 2, Marcella Frangipane 3, Philipp Wolfgang Stockhammer 4, Johannes Krause 1, 6, Wolfgang Haak 1, 5

    1 Max Planck Institute for the Science of Human History (Germany),
    2 Hacettepe University (Turkey),
    3 Sapienza University of Rome (Italy),
    4 Ludwig-Maximilians-University of Munich (Germany),
    5 The University of Adelaide (Australia),
    6 University of Tubingen (Germany)

    While Anatolia was highlighted as the genetic origin of early Neolithic European farmers, the genetic substructure in Anatolia itself as well as the demographic and cultural changes remain unclear. In eastern Anatolia, the archaeological record reflects influences from North-Central Anatolia, the northeastern sectors of Fertile Crescent and the Caucasus, and suggests that some of these were brought along with the movement of people. Central to this question is the archaeological site of Arslantepe (6th-1st millennium BC), strategically located at the Upper Euphrates, the nexus of all three regions. Arslantepe also developed one of the first state societies of Anatolia along with advanced metal-technologies. Archaeological research suggests that conflicts with surrounding groups of pastoralists affiliated to the Caucasus might have contributed to the collapse of its palatial system at the end of the Chalcolithic period (4th millennium BC). To test if these developments were accompanied by genetic changes, we generated genome-wide data from 18 ancient individuals spanning from the Late Chalcolithic period to the Early Bronze Age of Arslantepe. Our results show no evidence for a major genetic shift between the two time periods. However, we observe that individuals from Arslantepe are very heterogeneous and differentiated from other ancient western and central Anatolians in that they have more Iran/Caucasus related ancestry. Our data also show evidence for an ongoing but also recent confluence of Anatolian/Levantine and Caucasus/Iranian ancestries, highlighting the complexity of the Chalcolithic and Bronze Age periods in this region.

    POA-236 Genetic transition in the Swiss Late Neolithic and Early Bronze Age

    Anja Furtwaengler 1, Ella Reiter 1, Gunnar U. Neumann 1, Inga Siebke 2, Noah Steuri 3, Joachim Wahl 4, 5, Juergen Hald 6, Verena J. Schuenemann 1, 7, 8, Philipp Stockhammer 9, Albert Hafner 3, 10, Sandra Loesch 2, Johannes Krause 1, 7, 11

    1 Eberhard Karls University of Tuebingen (Germany),
    2 University of Bern (Switzerland),
    3 University of Bern (Switzerland),
    4 Ctiy of Constance (Germany),
    5 Eberhard Karls University Tuebingen (Germany),
    6 Ctiy of Constance (Germany),
    7 Eberhard Karls University Tuebingen (Germany),
    8 University of Zurich (Switzerland),
    9 Ludwig Maximilians University Munich (Germany),
    10 University of Bern (Switzerland),
    11 Max Planck Institute Jena (Germany)

    Recent studies have shown that the beginning of the Neolithic period as well as final stages of the Neolithic were marked by major genetic turnovers in European populations.The transition from hunter-gatherers to agriculturalists and farmers/farming in the 6th millennium BP coincided with a human migration from the Near East. In the 3rd millennium BP a second migration into Central Europe occurred originating from the Pontic steppe linked to the spread of the Corded Ware Complex ranging as far southwest as modern day Switzerland. These genetic processes are well studied for example for the Middle-Elbe-Saale region in Eastern Germany, however, little is known from the regions that connect Central and Southern Europe.
    Here, we investigate genomic data from 69 individuals from the Swiss Plateau and Southern Germany that span the transition of the Neolithic to the Bronze Age (5500 to 4000 BP). Our results show a similar genetic process as reported for the Middle-Elbe-Saale region suggesting that the migration from the Pontic steppe reached all the way into the Swiss plateau. The high quality of the ancient genomic data also allowed an analysis of core families within multiple burials, the determination and qualification of different ancestry components and the determination of the migration route taken by the ancestors of the Late Neolithic populations in this region. This study presents the first comprehensive genome wide dataset from Holocene individuals from the Swiss plateau and provides the first glimpse into the genetic history of this genetically and linguistically diverse region.

    POA-238 Efficiently integrating ancient DNA into modern Y chromosome trees

    Rui Martiniano 1, 2, Lara Cassidy 3, Daniel Bradley 3, Richard Durbin 1, 2

    1 University of Cambridge (United Kingdom),
    2 Wellcome Trust Sanger Institute (United Kingdom),
    3 Trinity College Dublin (Ireland)

    During the last decade, a huge wealth of ancient Y chromosome data has been generated as part of whole-genome shotgun and target capture sequencing studies. However, given the highly degraded nature of ancient DNA (aDNA) data, post-mortem deamination and often low genomic coverage, combining ancient and modern samples for phylogenetic analyses remains challenging. Most analyses use limited markers and/or extensive manual curation.
    Current standard methods for the analysis of Y chromosome data focus on known, gold-standard markers, but these contain only a subset of the total Y chromosomal variation.
    Examining all polymorphic markers is particularly useful when dealing with low coverage aDNA data because it substantially increases the number of overlapping sites between present-day and ancient individuals and it may also help uncover relationships inaccessible via standard known variation.
    We provide an automated workflow for jointly analysing ancient and present-day sequence data using all uniquely mappable regions of the Y chromosome. From a given high-coverage dataset, a maximum likelihood phylogeny is estimated and variants are assigned to each branch of the tree. Next, for each low coverage aDNA sample, we count the number of ancestral and derived alleles at each branch and use this information to map ancient lineages to their most likely place in the phylogeny. We apply this method to a large dataset of novel and publicly available data from ancient Eurasians and characterize patterns of Y chromosomal diversity across time as well as the impact of past migrations on the landscape of present-day paternal lineage distribution.

  14. The Following 14 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  Bollox79 (07-06-2018),  epoch (07-06-2018),  JonikW (07-06-2018),  kingjohn (07-06-2018),  KSDA (07-06-2018),  Menchaca (07-06-2018),  MikkaK (07-06-2018),  Onur Dincer (07-06-2018),  razyn (07-06-2018),  RCO (07-06-2018),  Ruderico (07-06-2018),  Silesian (07-06-2018),  traject (07-06-2018)

  15. #1508
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    POA-239 People from Ibiza: an unexpected isolate in the Western Mediterranean

    Simone Andrea Biagini 1, Neus Sole-Morata 1, Pierre Zalloua 2, Lisa Matisoo-Smith 3, David Comas 1, Francesc Calafell 1

    1 Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra (Spain),
    2 The Lebanese American University (Lebanon),
    3 University of Otago (New Zealand)

    According to history, Ibiza's ancestry finds its roots in the Middle East, North Africa and Europe: before the Catalans conquered the island in 1235, Ibiza already had experienced many different cultures. It was the Phoenician Iboshim, the Carthaginian Ibosium, the Islamic Yabisah, up to the Catalan Eivissa. How all these different civilizations affected the modern genetic structure of the islanders is still unexplored. In this genome-wide study, we dug into the genetic structure of a group made up of individuals coming from different autonomous communities of Spain. Our results pointed to a clear split in two major groups, clearly separating Ibiza from the rest of the samples.
    We aimed to find the historical reasons behind this result: is Ibiza separating because of recent historical events, or because of some more well-established historical reasons?
    We explored the possibility that the modern samples from Ibiza had something to share with the ancient culture from Phoenicia using a sample retrieved in a Phoenician necropolis on the island of Ibiza. Mostly, our analyses pointed out different aspects that seem to link the genetics of the modern samples with the history of the area they lived in, more than to any ancient genetic echo from the past. According to history, Ibiza experienced a series of dramatic demographic changes due to several moments of famine, wars, up to malaria and plague. Interestingly, the ROH analysis is showing a level of homozygosity that might reflect an event of a not so distant founder effect.

    POA-252 Genome-Wide Ancient DNA Portrays the Forming of the Finnish Population Along a 1400-Year Transect

    Kerttu Majander 1, 2, 3, Elina Salmela 3, 1, Kati Salo 4, Thiseas Christos Lamnidis 1, Stephan Schiffels 1, Paivi Onkamo 5, 3, Johannes Krause 1

    1 Max Planck Institute for the Science of Human History (Germany),
    2 University of Tuebingen (Germany),
    3 University of Helsinki (Finland),
    4 University of Helsinki (Finland),
    5 University of Turku (Finland)

    The Finnish population has long been a subject of interest for the fields of medical and population genetics, due to its isolation-affected genetic structure and the associated unique set of inherited diseases. Recent advances in ancient DNA techniques now enable the in-depth investigation of Finland's demographic past: the impact of migrations, trade and altering livelihood practices.
    Here we analyse genome-wide data from over 30 individuals, representing ten archaeological burial sites from southern Finland, that span from the 5th to 19th century. We find the historical individuals to differ genetically from Finns today. Comparing them with surrounding ancient and modern populations, we detect a transition from genotypes generally connected with prehistoric hunter-gatherers, and specifically resembling those of the contemporary Saami people, into a more East-Central European composition, associated with the established agricultural lifestyle. Starting from the Iron Age and continuing through the Early Medieval period, this transition dates remarkably late compared to the respective changes in most regions of Europe. Our results suggest a population shift, presumably related to Baltic and Slavic influences, also manifested in the archaeological record of the local artefacts from the late Iron Age. Our observations also agree with the archaeological models of relatively recent and gradual adoption of farming in Finland.

    POA-253 The first Epipaleolithic Genome from Anatolia suggests a limited role of demic diffusion in the Advent of Farming in Anatolia

    Michal Feldman 1, Eva Fernandez-Dominguez 4, Luke Reynolds 3, Raffaela Bianco 1, Cosimo Posth 1, Adrian Nigel Goring-Morris 7, Jessica Pearson 2, Hila May 5, 6, Israel Hershkovitz 5, 6, Douglas Baird 2, Choongwon Jeong 1, Johannes Krause 1

    1 The Max Planck Institute for the Science of Human History (Germany),
    2 University of Liverpool (United Kingdom),
    3 Liverpool John Moores University (United Kingdom),
    4 Durham University (United Kingdom),
    5 Tel Aviv University (Israel),
    6 Tel Aviv University (Israel),
    7 Hebrew University of Jerusalem (Israel)

    Anatolia was home to some of the earliest farming communities, which in the following millennia expanded into Europe and largely replaced local hunter-gatherers. The lack of genetic data from pre-farming Anatolians has so far limited demographic investigations of the Anatolian Neolithisation process. In particular, it has been unclear whether farming was adopted by indigenous hunter-gatherers in Central Anatolia or imported by settlers from earlier farming centers. Here we present the first genome-wide data from an Anatolian Epipaleolithic hunter-gatherer who lived ~15,000 years ago, as well as from Early Neolithic individuals from Anatolia and the Levant. By using a comparative dataset of modern and ancient genomes, we estimate that the earliest Anatolian farmers derive over 90 percent of their ancestry from the local Epipaleolithic population, indicating a high degree of genetic continuity throughout the Neolithic transition. In addition, we detect two distinct waves of gene flow during the Neolithic transition: an earlier one related to Iranian/Caucasus ancestry and a later one linked to the Levant. Finally, we observe a genetic link between Epipaleolithic Near-Easterners and post-glacial European hunter-gatherers that suggests a bidirectional genetic exchange between Europe and the Near East predating 15,000 years ago. Our results suggest that the Neolithisation model in Central Anatolia was demographically similar to the one previously observed in the southern Levant and in the southern Caucasus-Iran highlands, further supporting the limited role of demic diffusion during the early spread of agriculture in the Near East, in contrast to the later Neolithisation of Europe.

    POA-259 Reliable Inference of Genetic Diversity within and between Ancient and Modern Genomes

    Vivian Link 1, 7, Zuzana Hofmanova 1, 7, Athanasios Kousathanas 6, 7, Jens Bloechler 2, Christoph Leuenberger 3, Thomas Terberger 4, Detlef Jantzen 5, Joachim Burger 2, Daniel Wegmann 1, 7

    1 University of Fribourg (Switzerland),
    2 Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz (Germany),
    3 University of Fribourg (Switzerland),
    4 Lower Saxony State Office for Cultural Heritage (Germany),
    5 Landesamt fuer Kultur und Denkmalpflege (Germany),
    6 University of Lausanne (Switzerland),
    7 Swiss Institute of Bioinformatics (Switzerland)

    Comparing ancient and modern genomes provides insights into many aspects of population history. However, such comparison are complicated by particularities of ancient DNA (aDNA) such as post-mortem damage (PMD) and low endogenous DNA content resulting in low sequencing depth. In addition, modern data may be a poor reference for ancient diversity, and the analyses of aDNA should thus not rely on modern data to avoid biases.

    Here we introduce a probabilistic framework that accounts for these biases to accurately infer within and between individual genetic diversity even from genomes with median depth <1x, as we show using simulations and by downsampling. We achieve this accuracy by explicitly modeling PMD, and by carefully recalibrating base quality scores with a new method that does not rely on modern data, but exploits homozygous regions in the genome. Importantly, our method also allows for an unbiased clustering of heterochronous individuals using Multi-Dimensional Scaling, rather than by projecting ancient individuals onto a PCA spanned by modern diversity. Finally, our framework also allows for genotype calling, which we found to be unbiased and more accurate for aDNA than GATK.

    To illustrate the power of our framework, we studied the diversity among soldiers from a colossal Bronze-age battlefield in norther Europe at the banks of the Tollense River in northern Germany. Our findings suggest that these soldiers, while from a large geographic area, likely represented a single ethnic group.

  16. The Following 14 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  Dewsloth (07-06-2018),  epoch (07-06-2018),  kingjohn (07-06-2018),  KSDA (07-06-2018),  Lauχum (07-06-2018),  Menchaca (07-06-2018),  MikkaK (07-06-2018),  Onur Dincer (07-06-2018),  Pribislav (07-06-2018),  RCO (07-06-2018),  Ruderico (07-06-2018),  Silesian (07-06-2018),  traject (07-06-2018)

  17. #1509
    Registered Users
    Posts
    1,462
    Sex
    Y-DNA (P)
    C-F5481
    mtDNA (M)
    M8a

    Kyrgyzstan
    POA-264 Demographic processes in Estonia from Bronze Age through Iron Age to Medieval times.

    Mait Metspalu 1, Lehti Saag 1, 2, Kristiina Tambets 1, Alena Kushniarevich 1, Liivi Varul 3, Jyri Parik 1, Martin Malve 4, Heiki Valk 4, Lauri Saag 1, Valter Lang 4, Aivar Kriiska 4, Richard Villems 1, 2, Toomas Kivisild 5, 1, Christiana Lyn Scheib 1, 5

    1 University of Tartu, Institute of Genomics (Estonia),
    2 University of Tartu, Institute of Cell and Molecular Biology (Estonia),
    3 Tallinn University (Estonia),
    4 Institute of History and Archaeology, University of Tartu (Estonia),
    5 University of Cambridge (United Kingdom)

    N3 and R1a are the two most common Y chromosome haplogroups among modern Estonians. R1a appears with Corded Ware culture but the arrival of hg N has not been determined. To this end we have extracted and studied aDNA from teeth of 18 individuals bracketing the changes in the material culture in the end of the Bronze and early Iron Age. We find N3 in Iron Age but not in Bronze Age. Due to the small sample size we cannot refute the existence of hg N in the latter. In genome-wide analyses the Bronze Age and especially Iron Age samples appear very similar to modern Estonians implying population continuity.

    Christianization (13 cc AD) established a new elite of West European origin, which presumably had an impact on the genetic structure of the local population. To investigate this we extracted DNA from teeth of 35 individuals, who have been uncovered from both rural (considered local Estonian population) and town (likely of West European origin) cemeteries of Estonia. We compared the low coverage genomes with each other and with relevant modern and ancient Estonian and other European populations. We find that there is a clear discontinuity between the elite and common people, where the former group genetically with modern German samples and the latter with modern Estonians. We do find three individuals of mixed genetic ancestry. But importantly we do not see a steady shift of either local population strata, which suggests limited contact between the elite and the common people.

    POB-111 Population migration and dairy pastoralism on the Bronze Age Mongolian steppe

    Christina Warinner 1, 2, 3, Choongwon Jeong 1, Shevan Wilkin 4, Tsend Amgalantugs 5, Abigail Bouwman 3, William Taylor 4, Sabri Bromage 6, Soninkhishig Tsolmon 12, Christian Trachsel 7, Judith Littleton 8, Cheryl Makarewicz 9, Erdene Myagmar 10, Bruno Frohlich 11, Jessica Hendy 4

    1 Max Planck Institute for the Science of Human History (Germany),
    2 University of Oklahoma (United States),
    3 University of Zurich (Switzerland),
    4 Max Planck Institute for the Science of Human History (Germany),
    5 Mongolian Academy of Sciences (Mongolia),
    6 Harvard School of Public Health (United States),
    7 University of Zurich (Switzerland),
    8 University of Auckland (New Zealand),
    9 Christian Albrechts University, Kiel (Germany),
    10 National University of Mongolia (Mongolia),
    11 Smithsonian Institution (United States),
    12 Mongolian University of Science and Technology (Mongolia)

    The steppe belt that extends across Eurasia was the primary corridor of Eneolithic and Bronze Age migrations that reshaped the genetics of Europe and Asia and dispersed the Indo-European language family. Beginning in the Eneolithic, a new and highly mobile pastoralist society formed on the Western Steppe. These steppe herders expanded both westwards, contributing to the Corded Ware culture of Eastern and Central Europe, and eastwards, contributing to the mobile pastoralist Afanasevo, Sintashta, Andronovo, and Okunevo cultures in Central Asia. The eastern extent of this Western Steppe herder expansion is not well defined. Here we investigate genome-wide ancestry data obtained from 20 Late Bronze Age (16th-9th century BCE) khirigsuur burials from Khovsgol, Mongolia and further investigate evidence for dairy pastoralism by LC-MS/MS analysis of dental calculus. Overall, we observe limited Western Steppe gene flow into Late Bronze Age Mongolia, but adoption of Western ruminant dairying by ca. 1500 BCE.

    POB-116 Population history of Native Siberians

    Elena S. Gusareva 1, Hie Lim Kim 1, 2, Vladimir Kharkov N. 3, Vadim Stepanov A. 3, Stephan Schuster C. 1

    1 Nanyang Technological University (NTU) (Singapore),
    2 Nanyang Technological University (NTU) (Singapore),
    3 Tomsk National Medical Research Center, Russian Academy of Science, Siberian Branch, Tomsk (Russian Federation)

    Northern Eurasia, which spans from the Arctic Ocean down to Inner Asia, and from Eastern Europe to the Pacific Ocean, is a territory of a great historical interest. Over 40 culturally and linguistically diverse indigenous ethnic groups populate this area, while their genetic variation and histories of people migrations in this region and their further migrations to the New World are still poorly studied. We present deep whole-genome sequencing data (>30x) from 300 individuals belonging to 30 distinct indigenous populations living in the North Asia region. We analyzed these data sets with worldwide reference populations and found that West Siberian populations shared their ancestry with Northern Europeans, and also with the Finno-Ugric speakers (Veps and Karelians) and some portion of Southeast Asians. The Central and East Siberians shared much less with Europeans and the Finno-Ugric speakers, while the Northeast component becomes much more prevalent. Koryaks are most distinctive among Siberians. The closest groups to them are Chukchi and Eskimo that also share some ancestry with Native Americans. Our results provide new insights into population histories of Siberians and evidence of ancient gene flow between Siberia and Europe or the New World.

    POB-162 Phenotype and phylogeny of Neolithic Japanese hunter-gatherers, Jomon people, based on whole nuclear genome sequences

    Hideaki Kanzawa-Kiriyama 1 , Timothy Jinam 2, Yoshuke Kawai 3, Takehiro Sato 4, Kazuyoshi Hosomichi 4, Atsushi Tajima 4, Kryukov Kirill 5, Noboru Adachi 6, Naruya Saitou 2, 7, Ken-ichi Shinoda 1

    1 National Museum of Nature and Science (Japan),
    2 National Institute of Genetics (Japan),
    3 University of Tokyo (Japan),
    4 Kanzawa University (Japan),
    5 Tokai University (Japan),
    6 University of Yamanashi (Japan),
    7 Graduate University fo Advanced Studies (SOKENDAI) (Japan)

    Funadomari Jomon are 3,500-3,800 year-old northern Japanese hunter-gatherer. Here, we determined high depth and low depth nuclear genome sequences from Funadomari Jomon female (F23) and male (F5). F5 belongs to Y chromosome haplogroup D1b2b, which is rare haplogroup in modern Japanese. We genotyped the genome of F23, and HLA class-I type (homozygous for A*24:02:01, B*15:01:01, and C*03:03:01) and many phenotypic traits (e.g. non-shovel shape incisor and wet-type earwax) were determined. We observed high HBD similar to modern southern Native Americans, but long HBD tracts longer than 10cM is small, suggesting no close consanguineous mating but small population size in northern Jomon populations. MSMC analysis also suggested their small population size for more than 10,000 years. Phylogenetic relationship between F23 and modern/ancient Eurasians and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40,000-year-old Tianyuan. This indicates that Northern Jomon people are genetically isolated from continental East Eurasians for long time. Intriguingly, we found that not only modern three Japanese (Ainu, mainland Japanese, and Ryukyuan) but also Ulchi, Koreans, the aboriginal Taiwanese and the Philippines are genetically closer to F23 compared to Han Chinese at the significant level (Z>3). These informations are one of a key to reconstruct ancient population structure and history in East Eurasia.

  18. The Following 14 Users Say Thank You to rozenfeld For This Useful Post:

     Agamemnon (07-06-2018),  bmoney (07-06-2018),  cacarlos (07-06-2018),  kingjohn (07-06-2018),  KSDA (07-06-2018),  Menchaca (07-06-2018),  MikkaK (07-06-2018),  Onur Dincer (07-06-2018),  Pribislav (07-06-2018),  RCO (07-06-2018),  rms2 (07-06-2018),  Ruderico (07-06-2018),  Silesian (07-06-2018),  traject (07-06-2018)

  19. #1510
    Registered Users
    Posts
    1,370
    Sex
    Omitted

    Quote Originally Posted by rozenfeld View Post
    SY06: Evolutionary epigenomics, progress and prospects (July 12, 9:30−11:30)

    O-04-EE03

    Reconstructing Denisovan Anatomy Using DNA Methylation Maps

    David Gokhman 1, Nadav Mishol 1, Marc de Manuel Montero 2, David de Juan 2, Jonathan Shuqrun 1, Tomas Marques-Bonet 2, 3, Yoel Rak 4, Liran Carmel 1

    1 The Hebrew University of Jerusalem (Israel),
    2 UPF-CSIC (Spain),
    3 ICREA (Spain),
    4 Tel Aviv University (Israel)

    The Denisovan is a human group unique for having its DNA sequence and methylation mapped, but whose morphology remains almost completely unknown. Here, we present a method to reconstruct anatomical profiles from DNA methylation patterns, based on linking unidirectional promoter methylation changes to loss-of-function phenotypes. We tested the performance of our method by assembling anatomical profiles of the Neanderthal and the chimpanzee, and comparing them to their known morphology. We demonstrate that this method reaches ~87% precision in identifying divergent traits, and ~89% in predicting their direction of change. We then reconstruct a putative anatomical profile of the Denisovan, offering 56 traits in which the Denisovan is expected to be different from modern humans or Neanderthals. We suggest that Denisovans likely shared many traits with Neanderthals, including a projecting face, robust jaws, low forehead and wide pelvis. We also identify additional changes along the Denisovan lineage, such as increased length of the dental arch, and expanded biparietal width. We find that the vast majority of morphologies identified in the late Pleistocene Xuchang crania from China, which were hypothesized to belong to Denisovans, are included in our reconstruction of the Denisovan anatomical profile, providing first genetic support to the classification of these individuals as Denisovans. We conclude that DNA methylation maps provide means to predict morphology, and can be used to uncover anatomical features that do not survive in the paleontological record.
    This is really cool! BTW, Chris Stringer called it: https://www.sciencealert.com/ancient...-human-species

  20. The Following 2 Users Say Thank You to epoch For This Useful Post:

     ffoucart (07-06-2018),  parasar (07-08-2018)

Page 151 of 405 FirstFirst ... 51101141149150151152153161201251 ... LastLast

Similar Threads

  1. Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)
    By History-of-Things in forum Ancient (aDNA)
    Replies: 3027
    Last Post: Yesterday, 04:43 PM
  2. R2 - Ancient DNA Discussion
    By Tomasso29 in forum R2-M479
    Replies: 7
    Last Post: 06-05-2020, 02:06 PM
  3. Ancient Celtic Y dna discussion
    By Principe in forum Ancient (aDNA)
    Replies: 39
    Last Post: 10-15-2018, 01:27 PM
  4. Replies: 47
    Last Post: 09-15-2015, 09:09 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •