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      The genetic prehistory of the Baltic Sea region

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          Abstract

          While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.

          Abstract

          The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

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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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            Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

            Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.
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              Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.

              The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.
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                Author and article information

                Contributors
                mittnik@shh.mpg.de
                krause@shh.mpg.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                30 January 2018
                30 January 2018
                2018
                : 9
                Affiliations
                [1 ]ISNI 0000 0004 4914 1197, GRID grid.469873.7, Department of Archaeogenetics, , Max Planck Institute for the Science of Human History, ; 07745 Jena, Germany
                [2 ]ISNI 0000 0001 2190 1447, GRID grid.10392.39, Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, , University of Tübingen, ; 72070 Tübingen, Germany
                [3 ]ISNI 0000 0001 2264 7233, GRID grid.12955.3a, Department of Anthropology and Ethnology, , Xiamen University, ; 361005 Xiamen, China
                [4 ]Department of Archaeology, Lithuanian Institute of History, 01108 Vilnius, Lithuania
                [5 ]ISNI 0000 0001 0775 3222, GRID grid.9845.0, Institute of Latvian History, , University of Latvia, ; Riga, LV-1050 Latvia
                [6 ]The Cultural Heritage Foundation, 72212 Västerås, Sweden
                [7 ]ISNI 0000 0000 9774 6466, GRID grid.8207.d, Archaeological Research Collection, , Tallinn University, ; 10130 Tallinn, Estonia
                [8 ]Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia 199034
                [9 ]ISNI 0000 0001 0943 7661, GRID grid.10939.32, Institute of History and Archaeology, , University of Tartu, ; 50090 Tartu, Estonia
                [10 ]ISNI 0000 0004 1936 9377, GRID grid.10548.38, Archaeological Research Laboratory, , Stockholm University, ; 11418 Stockholm, Sweden
                [11 ]ISNI 0000 0004 0410 2071, GRID grid.7737.4, Finnish Museum of Natural History - LUOMUS, , University of Helsinki, ; 00014 Helsinki, Finland
                [12 ]GRID grid.466123.4, Research Centre for Medical Genetics, ; Moscow, 115478 Russia
                [13 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Genetics, , Harvard Medical School, ; Boston, MA 02115 USA
                [14 ]GRID grid.66859.34, Broad Institute of Harvard and MIT, ; Cambridge, MA 02142 USA
                [15 ]ISNI 000000041936754X, GRID grid.38142.3c, Howard Hughes Medical Institute, Harvard Medical School, ; Boston, MA 02115 USA
                [16 ]ISNI 0000 0001 2243 2806, GRID grid.6441.7, Department of Anatomy, Histology and Anthropology, , Vilnius University, ; 03101 Vilnius, Lithuania
                [17 ]ISNI 0000 0004 1936 7304, GRID grid.1010.0, School of Biological Sciences, , The University of Adelaide, ; Adelaide, SA 5005 Australia
                Article
                2825
                10.1038/s41467-018-02825-9
                5789860
                2437a86e-a001-4370-871a-f993796fc42a
                © The Author(s) 2018

                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/.

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