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      The Genomic History of Southeastern Europe

      1 , 1 , 2 , 3 , 4 , 1 , 1 , 5 , 1 , 1 , 5 , 6 , 6 , 7 , 6 , 8 , 1 , 5 , 6 , 9 , 2 , 10 , 1 , 5 , 11 , 12 , 6 , 2 , 3 , 1 , 5 , 2 , 3 , 2 , 13 , 1 , 5 , 14 , 3 , 15 , 1 , 5 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 6 , 23 , 17 , 4 , 24 , 25 , 26 , 27 , 17 , 28 , 29 , 30 , 31 , 25 , 32 , 33 , 34 , 35 , 25 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 37 , 25 , 43 , 44 , 13 , 45 , 46 , 45 , 47 , 33 , 48 , 49 , 16 , 50 , 51 , 52 , 42 , 53 , 54 , 29 , 42 , 26 , 53 , 54 , 55 , 20 , 56 , 57 , 58 , 42 , 59 , 60 , 61 , 62 , 63 , 36 , 64 , 41 , 65 , 66 , 7 , 67 , 42 , 68 , 69 , 70 , 71 , 69 , 72 , 73 , 74 , 75 , 76 , 52 , 2 , 61 , 77 , 16 , 78 , 79 , 80 , 81 , 48 , 82 , 83 , 55 , 2 , 3 , 6 , 7 , 1 , 14 , 5

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          Abstract

          Farming was first introduced to Europe in the mid-7 th millennium BCE–associated with migrants from Anatolia who settled in the Southeast before spreading throughout Europe. To understand the dynamics of this process, we analyzed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document a West-East cline of ancestry in indigenous hunter-gatherers and–in far-eastern Europe–early stages in the formation of Bronze Age Steppe ancestry. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer admixture, but that some groups that remained mixed extensively, without the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe up to 2000 years before the migrations that replaced much of northern Europe’s population.

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          Most cited references 43

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

           Iosif Lazaridis,  Krause Johannes (corresponding) ,  Nick Patterson (2014)
          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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            Is Open Access

            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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              New method of collagen extraction for radiocarbon dating.

               R Longin (1971)
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                12 July 2018
                21 February 2018
                08 March 2018
                21 August 2018
                : 555
                : 7695
                : 197-203
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, Boston 02115 MA USA
                [2 ]Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
                [3 ]Institute for Archaeological Sciences, University of Tuebingen, Germany
                [4 ]Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
                [5 ]Howard Hughes Medical Institute, Harvard Medical School, Boston 02115 MA USA
                [6 ]Earth Institute and School of Archaeology, University College Dublin, Belfield, Dublin 4, Republic of Ireland
                [7 ]Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
                [8 ]CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
                [9 ]Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46. Ferrara 44100 Italy
                [10 ]Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, Australia
                [11 ]Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
                [12 ]Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
                [13 ]Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia
                [14 ]Broad Institute of Harvard and MIT, Cambridge MA
                [15 ]Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA
                [16 ]Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
                [17 ]National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 2 Saborna Str., BG-1000 Sofia, Bulgaria
                [18 ]Danube Private University, A-3500 Krems, Austria
                [19 ]Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, CH-4123 Basel-Allschwil, Switzerland
                [20 ]State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
                [21 ]Romanian National History Museum, Bucharest, Romania
                [22 ]Institute of Archaeology, Belgrade, Serbia
                [23 ]Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
                [24 ]Department of Geosciences, Biogeology, Universität Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
                [25 ]Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, 72072 Tuebingen, Germany
                [26 ]Heidelberg Academy of Sciences and Humanities, Research Center “The Role of Culture in Early Expansions of Humans” at the University of Tuebingen, Rümelinstraße 23, 72070 Tuebingen, Germany
                [27 ]‘Vasile Pârvan’ Institute of Archaeology, Romanian Academy
                [28 ]Human Biology Department, Cardinal Stefan Wyszyński University, Warsaw, Poland
                [29 ]KADUCEJ d.o.o Papandopulova 27, 21000 Split, Croatia
                [30 ]St. Cyril and Methodius University, Veliko Turnovo, Bulgaria
                [31 ]Department of Early Prehistory and Quaternary Ecology, University of Tuebingen, Schloss Hohentübingen, 72070 Tuebingen, Germany
                [32 ]INRAP/UMR 8215 Trajectoires, 21 Alleé de l’Université, 92023 Nanterre, France
                [33 ]Archaeological Museum of Istria, Carrarina 3, 52100 Pula, Croatia
                [34 ]Service Régional de l’Archéologie de Bourgogne-Franche-Comté, 7 rue Charles Nodier, 25043 Besançon Cedex, France
                [35 ]Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 16 route de Gray, 25030 Besançon Cedex, France
                [36 ]Regional Museum of History Veliko Tarnovo, Veliko Tarnovo, Bulgaria
                [37 ]Institute for Archaeological Sciences, Paleoanthropology, University of Tuebingen, Rümelinstraße 23, 72070 Tuebingen, Germany
                [38 ]Laboratory for human bio-archaeology, Bulgaria, 1202 Sofia, 42, George Washington str
                [39 ]Regional Museum of History, Vratsa, Bulgaria
                [40 ]DRAC Auvergne - Rhône Alpes, Ministère de la Culture, Le Grenier d’abondance 6, quai Saint Vincent 69283 LYON cedex 01
                [41 ]Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Pázmány Péter sétány 1/c. Budapest, Hungary
                [42 ]Department of Archaeology, Sofia University St. Kliment Ohridski, Bulgaria
                [43 ]Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, OX1 3QY Oxford, UK
                [44 ]Regional Museum of History, Haskovo, Bulgaria
                [45 ]Department of Anthropology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071, USA
                [46 ]Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Ivana Lučića 3, 10000 Zagreb, Croatia
                [47 ]Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802
                [48 ]Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine
                [49 ]CHU Sainte-Justine Research Center, Pediatric Department, Université de Montréal, Montreal, PQ, Canada, H3T 1C5
                [50 ]National History Museum of Romania, Calea Victoriei, no. 12, 030026, Bucharest, Romania
                [51 ]University of Bucharest, Mihail Kogalniceanu 36-46, 50107, Bucharest, Romania
                [52 ]Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, Schellingstr. 12, 80799 Munich, Germany
                [53 ]Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy
                [54 ]Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy
                [55 ]School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
                [56 ]Conservation Department in Šibenik, Ministry of Culture of the Republic of Croatia, Jurja Čulinovića 1, 22000 Šibenik, Croatia
                [57 ]Teleorman County Museum, str. 1848, no. 1, 140033 Alexandria, Romania
                [58 ]Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
                [59 ]University of Wisconsin, Madison WI, USA
                [60 ]Olga Necrasov Centre for Anthropological Research, Romanian Academy – Iași Branch, Theodor Codrescu St. 2, P.C. 700481, Iași, Romania
                [61 ]Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, Italy
                [62 ]Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
                [63 ]Regional Historical Museum Varna, Maria Luiza Blvd. 41, BG-9000 Varna, Bulgaria
                [64 ]National Museum in Belgrade, 1a Republic sq., Belgrade, Serbia
                [65 ]Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
                [66 ]Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
                [67 ]INRAP/UMR 8215 Trajectoires, 21 Allée de l’Université, 92023 Nanterre, France
                [68 ]CNRS/UMR 7041 ArScAn MAE, 21 Allée de l’Université, 92023 Nanterre, France
                [69 ]Institute of Ethnology and Anthropology, Russian Academy of Sciences, Leninsky Pr., 32a, Moscow, 119991, Russia
                [70 ]Archaeological Museum of Macedonia, Skopje
                [71 ]Regional museum of history, Shumen, Bulgaria
                [72 ]Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada
                [73 ]Institute of Archaeology & Ethnography, Siberian Branch, Russian Academy of Sciences, Lavrentiev Pr. 17, Novosibirsk 630090, Russia
                [74 ]Satu Mare County Museum Archaeology Department,V. Lucaciu, nr.21, Satu Mare, Romania
                [75 ]Municipal Museum Drniš, Domovinskog rata 54, 22320 Drniš, Croatia
                [76 ]anthropol - Anthropologieservice, Schadenweilerstraße 80, 72379 Hechingen, Germany
                [77 ]Institute for Prehistory, Early History and Medieval Archaeology, University of Tuebingen, Germany
                [78 ]Institute of Latvian History, University of Latvia, Kalpaka Bulvāris 4, Rīga 1050, Latvia
                [79 ]Department of Archaeology, Durham University, UK
                [80 ]School of Environmental Sciences: Geography, University of Hull, Hull HU6 7RX, UK
                [81 ]Department of Biology, Grand Valley State University, Allendale, Michigan, USA
                [82 ]Ephorate of Paleoanthropology and Speleology, Athens, Greece
                [83 ]The Italian Academy for Advanced Studies in America, Columbia University, 1161 Amsterdam Avenue, New York, NY 10027, USA
                Author notes
                Correspondence and requests for materials should be addressed to DR ( reich@ 123456genetics.med.harvard.edu ) or RP ( ron.pinhasi@ 123456ucd.ie ) or IM ( mathi@ 123456pennmedicine.upenn.edu )
                [*]

                These authors contributed equally to the manuscript

                [†]

                Present address; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104.

                Article
                NIHMS937437
                10.1038/nature25778
                6091220
                29466330

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