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      The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers

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          Summary

          The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [ 1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300–4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [ 3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.

          Highlights

          • A degree of genetic continuity from the Mesolithic to the Neolithic in the Baltic

          • Steppe-related genetic influences found in the Baltic during the Neolithic

          • No Anatolian farmer-related genetic admixture in Neolithic Baltic samples

          • Steppe ancestry in Latvia at the time of the emergence of Balto-Slavic languages

          Abstract

          Jones et al. present genome-wide data spanning the Mesolithic-Neolithic transition in Latvia and Ukraine that show that massive migration of Anatolian farmers was not a universal driver for the spread of Neolithic lifeways and possibly Indo-European languages throughout Europe.

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          Most cited references29

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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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              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
                Journal
                Curr Biol
                Curr. Biol
                Current Biology
                Cell Press
                0960-9822
                1879-0445
                20 February 2017
                20 February 2017
                : 27
                : 4
                : 576-582
                Affiliations
                [1 ]Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
                [2 ]Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
                [3 ]Institute of Latvian History, University of Latvia, Kalpaka Bulvāris 4, Rīga 1050, Latvia
                [4 ]Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
                [5 ]McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
                [6 ]Division of Archaeology, Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
                [7 ]School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
                Author notes
                []Corresponding author erj35@ 123456cam.ac.uk
                [∗∗ ]Corresponding author am315@ 123456cam.ac.uk
                [∗∗∗ ]Corresponding author ron.pinhasi@ 123456ucd.ie
                [∗∗∗∗ ]Corresponding author dbradley@ 123456tcd.ie
                [8]

                Lead Contact

                Article
                S0960-9822(16)31542-1
                10.1016/j.cub.2016.12.060
                5321670
                28162894
                a672a0c0-1536-4329-a573-e1495cf60201
                © 2017 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 30 October 2016
                : 10 November 2016
                : 29 December 2016
                Categories
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                Life sciences
                ancient dna,neolithic transition,genomics,population genetics,baltic,ukraine
                Life sciences
                ancient dna, neolithic transition, genomics, population genetics, baltic, ukraine

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