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      Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia

      research-article
      1 , 2 , 3 , 1 , 4 , 5 , 6 , 7 , 8 , 9 , 3 , 10 , 11 , 12 , 13 , 14 , 13 , 15 , 16 , 1 , 17 , 2 , 2 , 18 , 19 , 8 , 8 , 8 , 20 , 21 , 8 , 22 , 8 , 22 , 23 , 24 , 25 , 26 , 25 , 25 , 18 , 27 , 2 , 28 , 29 , 30 , 31 , 32 , 7 , 8 , , 2 , 3 , 31 , , 1 , 33 ,
      Nature Communications
      Nature Publishing Group UK
      Archaeology, Evolutionary genetics, Genomics, Population genetics

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          Abstract

          The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia’s genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

          Abstract

          Ancient DNA analysis of early European farmers has found a high level of genetic affinity with present-day Sardinians. Here, the authors generate genome-wide capture data for 70 individuals from Sardinia spanning the Middle Neolithic to Medieval period to reveal relationships with mainland European populations shifting over time.

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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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              Genomic insights into the origin of farming in the ancient Near East

              We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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                Author and article information

                Contributors
                fcucca@uniss.it
                krause@shh.mpg.de
                jnovembre@uchicago.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                24 February 2020
                24 February 2020
                2020
                : 11
                : 939
                Affiliations
                [1 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Department of Human Genetics, , University of Chicago, ; Chicago, IL USA
                [2 ]ISNI 0000 0004 4914 1197, GRID grid.469873.7, Max Planck Institute for the Science of Human History, ; Jena, Germany
                [3 ]ISNI 0000 0001 2190 1447, GRID grid.10392.39, Institute for Archaeological Sciences, , University of Tübingen, ; Tübingen, Germany
                [4 ]ISNI 0000 0001 2353 285X, GRID grid.170693.a, Department of Anthropology, , University of South Florida, ; Tampa, FL USA
                [5 ]ISNI 0000 0000 8598 2218, GRID grid.266859.6, Department of Anthropology, , University of North Carolina at Charlotte, ; Charlotte, NC USA
                [6 ]ISNI 0000 0000 8700 0572, GRID grid.8250.f, Department of Archaeology, , Durham University, ; Durham, UK
                [7 ]ISNI 0000 0004 1789 9390, GRID grid.428485.7, Istituto di Ricerca Genetica e Biomedica - CNR, ; Cagliari, Italy
                [8 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Dipartimento di Scienze Biomediche, , Università di Sassari, ; Sassari, Italy
                [9 ]Private contractor, Cagliari, Sardinia Italy
                [10 ]ISNI 0000 0004 1762 5736, GRID grid.8982.b, Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, , Università di Pavia, ; Pavia, Italy
                [11 ]ISNI 0000 0001 2156 6853, GRID grid.42505.36, Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, , University of Southern California, ; Los Angeles, CA USA
                [12 ]ISNI 0000 0001 2156 6853, GRID grid.42505.36, Quantitative and Computational Biology Section, Department of Biological Sciences, , University of Southern California, ; Los Angeles, CA USA
                [13 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Department of Statistics, , University of Chicago, ; Chicago, IL USA
                [14 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Committee on Evolutionary Biology, , University of Chicago, ; Chicago, IL USA
                [15 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Epidemiology, , Harvard School of Public Health, ; Boston, MA 02115 USA
                [16 ]ISNI 0000000419368729, GRID grid.21729.3f, Department of Computer Science, , Columbia University, ; New York, NY USA
                [17 ]ISNI 0000 0001 2353 1689, GRID grid.11417.32, Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, , Université de Toulouse 3, ; Toulouse, France
                [18 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Human Evolutionary Biology, , Harvard University, ; Cambridge, MA 02138 USA
                [19 ]ISNI 0000 0004 1936 8411, GRID grid.9918.9, School of Archaeology and Ancient History, , University of Leicester, ; Leicester, UK
                [20 ]Soprintendenza Archeologia, belle arti e paesaggio delle province di Sassari e Nuoro, Sassari, Italy
                [21 ]ISNI 0000000101969356, GRID grid.28020.38, Departamento de Geografía, , Historia y Humanidades Escuela Internacional de Doctorado de la Universidad de Almería, ; Almería, Spain
                [22 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, , University of Sassari, ; Sassari, Italy
                [23 ]ISNI 0000000121663741, GRID grid.16563.37, Department of Sciences and Technological Innovation, , University of Eastern Piedmont, ; 15121 Alessandria, Italy
                [24 ]ISNI 0000 0001 2336 6580, GRID grid.7605.4, Legal Medicine Section, Department of Public Health and Paediatric Sciences, , University of Turin, ; 10126 Turin, Italy
                [25 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Department of History, Human Sciences and Education, , University of Sassari, ; 07100 Sassari, Italy
                [26 ]GRID grid.7080.f, Universitat Autònoma de Barcelona, Departament de Biologia Animal, Biologia Vegetal i Ecologia, ; 08193 Barcelona, Spain
                [27 ]ISNI 0000 0004 1936 9094, GRID grid.40263.33, Joukowsky Institute for Archaeology and the Ancient World, , Brown University, ; Providence, RI 02912 USA
                [28 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Genetics, , Harvard Medical School, ; Boston, MA 02115 USA
                [29 ]GRID grid.66859.34, Broad Institute of Harvard and MIT, ; Cambridge, MA USA
                [30 ]ISNI 000000041936754X, GRID grid.38142.3c, Howard Hughes Medical Institute, Harvard Medical School, ; Boston, MA USA
                [31 ]ISNI 0000 0001 2105 1091, GRID grid.4372.2, Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, ; Munich, Germany
                [32 ]ISNI 0000 0000 9372 4913, GRID grid.419475.a, Laboratory of Genetics, , NIA, NIH, ; Baltimore, MD USA
                [33 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Department of Ecology and Evolution, , University of Chicago, ; Chicago, IL USA
                Author information
                http://orcid.org/0000-0002-0923-9881
                http://orcid.org/0000-0002-8206-3907
                http://orcid.org/0000-0002-4884-9682
                http://orcid.org/0000-0001-7504-7477
                http://orcid.org/0000-0002-3941-8098
                http://orcid.org/0000-0002-0668-7865
                http://orcid.org/0000-0002-0589-4539
                http://orcid.org/0000-0001-9222-5124
                http://orcid.org/0000-0002-6448-015X
                http://orcid.org/0000-0002-3080-4005
                http://orcid.org/0000-0003-0970-6651
                http://orcid.org/0000-0003-2475-2007
                http://orcid.org/0000-0002-7037-5292
                http://orcid.org/0000-0001-9144-3920
                http://orcid.org/0000-0001-5345-0214
                Article
                14523
                10.1038/s41467-020-14523-6
                7039977
                32094358
                048cab22-a717-43d3-b8ca-4ec571e3652e
                © The Author(s) 2020

                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
                : 21 March 2019
                : 8 January 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100002803, Fondazione Cariplo (Cariplo Foundation);
                Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);
                Award ID: BCS-1032255
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000011, Howard Hughes Medical Institute (HHMI);
                Categories
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                © The Author(s) 2020

                Uncategorized
                archaeology,evolutionary genetics,genomics,population genetics
                Uncategorized
                archaeology, evolutionary genetics, genomics, population genetics

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