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      Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

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          Abstract

          Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.

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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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            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

                Journal
                Proc Biol Sci
                Proc. Biol. Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                29 March 2017
                22 March 2017
                : 284
                : 1851
                : 20161976
                Affiliations
                [1 ] Faculty of Biological Sciences, University of Leeds , Leeds LS2 9JT, UK
                [2 ] Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto , Porto 4200-135, Portugal
                [3 ] Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP) , Porto 4200-465, Portugal
                [4 ] Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal
                [5 ] ICVS/3Bs-PT Government Associate Laboratory , Braga/Guimarães, Portugal
                [6 ] Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho , Braga, Portugal
                [7 ] Department of Biological Sciences, School of Applied Sciences, University of Huddersfield , Queensgate, Huddersfield HD1 3DH, UK
                [8 ] Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali , El Jadida 24000, Morocco
                [9 ] Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar , Tunis 2092, Tunisia
                [10 ] Tunis and High Institute of Biotechnology, University of Monastir , 5000 Monastir, Tunisia
                [11 ] General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters , Dubai 1493, United Arab Emirates
                [12 ] Medical Faculty in Pilsen, Institute of Biology, Charles University , Pilsen, Czech Republic
                [13 ] Vavilov Institute of General Genetics , Moscow, Russia
                [14 ] Institutul de Cercetari Biologice , Iasi, Romania
                [15 ] Department of Genetics, University of Leicester , Adrian Building, University Road, Leicester LE1 7RH, UK
                [16 ] Dipartimento di Biologia e Biotecnologie ‘L. Spallanzani’, Università di Pavia , Pavia, Italy
                [17 ] Faculdade de Medicina da Universidade do Porto , Porto 4200-319, Portugal
                Author notes
                [†]

                These authors contributed equally to this study.

                Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3703558.

                Author information
                http://orcid.org/0000-0002-4409-514X
                http://orcid.org/0000-0003-3118-0967
                Article
                PMC5378072 PMC5378072 5378072 rspb20161976
                10.1098/rspb.2016.1976
                5378072
                28330913
                c882b4a8-0fca-4cbe-bc41-e3d4b2b5e7e3
                © 2017 The Author(s)

                Published by the Royal Society. All rights reserved.

                History
                : 7 September 2016
                : 14 February 2017
                Funding
                Funded by: Leverhulme Trust, http://dx.doi.org/10.13039/501100000275;
                Award ID: F/10 105/D
                Funded by: Università degli Studi di Pavia, http://dx.doi.org/10.13039/501100004769;
                Award ID: MIGRAT.IN.G
                Funded by: Fundação para a Ciência e a Tecnologia, http://dx.doi.org/10.13039/501100001871;
                Award ID: COMPETE2020 - POCI
                Award ID: IF/01641/2013
                Award ID: POCI-01-0145-FEDER-007274
                Award ID: POCI-01-0145-FEDER-007569
                Award ID: PTDC/CS-ANT/113832/2009
                Award ID: SFRH/BD/45657/2008
                Award ID: SFRH/BD/48372/2008
                Categories
                1001
                70
                198
                Genetics and Genomics
                Research Article
                Custom metadata
                March 29, 2017

                phylogeography,Neolithic,Late Glacial,European origins,mitogenomes,haplogroups

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