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      Population genomics of Bronze Age Eurasia.

      1 , 1 , 2 , 3 , 1 , 1 , 1 , 4 , 5 , 1 , 1 , 1 , 6 , 6 , 7 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 8 , 8 , 15 , 16 , 17 , 18 , 19 , 15 , 20 , 21 , 22 , 23 , 8 , 24 , 17 , 25 , 26 , 27 , 28 , 15 , 29 , 30 , 2 , 31 , 32 , 27 , 33 , 34 , 35 , 36 , 21 , 37 , 36 , 23 , 38 , 39 , 40 , 1 , 3 ,   41 ,   42 , 2 ,   1
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          Abstract

          The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

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          Most cited references29

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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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            Massive migration from the steppe was a source for Indo-European languages in Europe

            We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.
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              Patterns of damage in genomic DNA sequences from a Neandertal.

              High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
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                Author and article information

                Journal
                Nature
                Nature
                1476-4687
                0028-0836
                Jun 11 2015
                : 522
                : 7555
                Affiliations
                [1 ] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
                [2 ] Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden.
                [3 ] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
                [4 ] 1] Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark [2] Faculty of Archaeology, Leiden University, 2300 Leiden, The Netherlands.
                [5 ] Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden.
                [6 ] Oxford Radiocarbon Accelerator Unit, University of Oxford, Oxford OX1 3QY, UK.
                [7 ] Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, 2100 Copenhagen, Denmark.
                [8 ] Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland.
                [9 ] Archaeological Institute, University of Zurich, CH-8006, Zurich, Switzerland.
                [10 ] Department of Anatomy, Wrocław Medical University, 50-368 Wrocław, Poland.
                [11 ] Department of Anthropology, University of Toronto, Toronto ONM5S 2S2, Canada.
                [12 ] Department of Archeology and General History, Gorno-Altaisk State University, 649000 Gorno-Altaisk, Russia.
                [13 ] Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia.
                [14 ] Environmental Research and Material Science and Centre for Textile Research, The National Museum of Denmark, 1471 Copenhagen K, Denmark.
                [15 ] Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St Petersburg, Russia.
                [16 ] Department of Anthropology, Polish Academy of Sciences, 50-449 Wrocław, Poland.
                [17 ] Biocentre of the Ludwig-Maximilian-University München, 82152 Munich, Germany.
                [18 ] 1] Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, H-1117 Budapest, Hungary [2] Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.
                [19 ] The Archaeological Museum of Wrocław, 50-077 Wrocław, Poland.
                [20 ] Samara State Academy of Social Science and Humanities, 443099 Samara, Russia.
                [21 ] Institute of Archaeology of the Hungarian Academy of Sciences, Research Center for the Humanities, H-1250 Budapest, Hungary.
                [22 ] 1] Institute of Archaeology and Museology, Faculty of Arts, Masaryk University, CZ-602 00 Brno, Czech Republic [2] Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, CZ-602 00 Brno, Czech Republic.
                [23 ] Department of Archaeology, University of Tartu, 51003 Tartu, Estonia.
                [24 ] Archaeological Superintendence of Lombardy, 20123 Milano, Italy.
                [25 ] Department of Archaeology, University of Vilnius, LT-01513 Vilnius, Lithuania.
                [26 ] The SAXO Institute, University of Copenhagen, 2300 Copenhagen S, Denmark.
                [27 ] Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia.
                [28 ] Department of History, Yerevan State University, 0025 Yerevan, Armenia.
                [29 ] 1] Hungarian National Museum, H-1083 Budapest, Hungary [2] Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary.
                [30 ] Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary.
                [31 ] Institute of Archaeology and Ethnology of the Polish Academy of Sciences, 61-612 Poznań, Poland.
                [32 ] Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
                [33 ] Zoological Institute of the Russian Academy of Sciences, 199034 St Petersburg, Russia.
                [34 ] Department of Archaeology, State Historical Museum, 109012 Moscow, Russia.
                [35 ] Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic.
                [36 ] Research Center for the History and Culture of the Turkic Peoples, Gorno-Altaisk State University, 649000 Gorno-Altaisk, Russia.
                [37 ] Department of Pre- and Early History, Institute of Archaeological Sciences, Faculty of Humanities, Eötvös Loránd University, H-1088 Budapest, Hungary.
                [38 ] Matrica Museum, 2440 Százhalombatta, Hungary.
                [39 ] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia.
                [40 ] Department of Archaeology, Faculty of History, Moscow State University, 119991 Moscow, Russia.
                [41 ] 1] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark [2] Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.
                [42 ] Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA.
                Article
                nature14507
                10.1038/nature14507
                26062507
                db4c6f56-9fb5-453b-bd6a-9266886dd4be
                History

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