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      Craniometrics Reveal “Two Layers” of Prehistoric Human Dispersal in Eastern Eurasia

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          Abstract

          This cranio-morphometric study emphasizes a “two-layer model” for eastern Eurasian anatomically modern human (AMH) populations, based on large datasets of 89 population samples including findings directly from ancient archaeological contexts. Results suggest that an initial “first layer” of AMH had related closely to ancestral Andaman, Australian, Papuan, and Jomon groups who likely entered this region via the Southeast Asian landmass, prior to 65–50 kya. A later “second layer” shared strong cranial affinities with Siberians, implying a Northeast Asian source, evidenced by 9 kya in central China and then followed by expansions of descendant groups into Southeast Asia after 4 kya. These two populations shared limited initial exchange, and the second layer grew at a faster rate and in greater numbers, linked with contexts of farming that may have supported increased population densities. Clear dichotomization between the two layers implies a temporally deep divergence of distinct migration routes for AMH through both southern and northern Eurasia.

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          Ancient human genomes suggest three ancestral populations for present-day Europeans

          We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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            An Aboriginal Australian genome reveals separate human dispersals into Asia.

            We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
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              DNA analysis of an early modern human from Tianyuan Cave, China.

              Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.
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                Author and article information

                Contributors
                hiromura@sapmed.ac.jp
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                5 February 2019
                5 February 2019
                2019
                : 9
                : 1451
                Affiliations
                [1 ]ISNI 0000 0001 0691 0855, GRID grid.263171.0, School of Health Science, , Sapporo Medical University, ; Sapporo, 060-8556 Japan
                [2 ]ISNI 0000 0001 2180 7477, GRID grid.1001.0, Department of Archaeology and Natural History, , Australian National University, ; Canberra, ACT 0200 Australia
                [3 ]ISNI 0000 0004 1936 7830, GRID grid.29980.3a, Department of Anthropology and Archaeology, , University of Otago, ; Dunedin, 9054 New Zealand
                [4 ]ISNI 0000 0001 2256 9319, GRID grid.11135.37, School of Archaeology and Museology, , Peking University, ; Beijing, 100871 China
                [5 ]ISNI 0000 0001 0672 2184, GRID grid.444568.f, Department of Management, , Okayama University of Science, ; Okayama, 700-0005 Japan
                [6 ]ISNI 0000 0001 2149 6242, GRID grid.473808.0, Institute of Archaeology, , Vietnam Academy of Social Science, ; Hanoi, 61 Phan Chu Trinh, Hanoi, Vietnam
                [7 ]Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning, 530003 China
                [8 ]Fujian Museum, Fuzhou, 350001 China
                [9 ]Center for Austronesian Study, Jakarta, 12510 Indonesia
                [10 ]The National Research Center for Archaeology, Jakarta, 12510 Indonesia
                [11 ]ISNI 0000 0001 2287 1366, GRID grid.28665.3f, Institute of History and Philology, , Academia Sinica, ; Taipei, 11529 Taiwan
                [12 ]Matzu Folk Culture Museum, Nangan, Lienchiang 20942 Taiwan
                [13 ]Institute of Cultural Relics and Archaeology of Hunan, Changsha, 410008 China
                [14 ]Institute of Cultural Relics and Archaeology of Zhejiang, Hangzhou, 310014 China
                [15 ]Hemudu Site Museum, Ningbo, 315414 China
                [16 ]ISNI 0000 0004 0368 8015, GRID grid.418560.e, Institute of Archaeology, , Chinese Academy of Social Science, ; Beijing, 100710 China
                [17 ]Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou, 450000 China
                [18 ]ISNI 0000 0004 0474 1797, GRID grid.1011.1, Division of Tropical Health and Medicine, , College of Medicine and Dentistry, James Cook University, ; Townsville, Queensland 4811 Australia
                [19 ]ISNI 0000 0004 1936 7830, GRID grid.29980.3a, Department of Anatomy, , University of Otago, ; Dunedin, 9054 New Zealand
                [20 ]Southern Institute of Social Sciences, Vietnam Academy of Social Science, 49 Nguyen Thi Minh Khai, Ho Chi Minh, Vietnam
                [21 ]Commission for the Archaeology of Noneuropean Cultures of the German Archaeological Institute, 53173 Bonn, Germany
                Author information
                http://orcid.org/0000-0001-5453-7987
                Article
                35426
                10.1038/s41598-018-35426-z
                6363732
                30723215
                8c4ccb8d-b405-4f6e-9024-92c20bfc50c8
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 August 2018
                : 31 October 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001691, Japan Society for the Promotion of Science (JSPS);
                Award ID: 16H02527
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000923, Australian Research Council (ARC);
                Award ID: DP 110101097
                Award ID: 150104458
                Award Recipient :
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