Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

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Abstract

Early Neolithic (~7700-year-old) genetic data from the Russian Far East implies a high level of genetic continuity in this region.

Abstract

Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.

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Most cited references 44

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

Iosif Lazaridis, Nick Patterson, Nick Patterson … (2015)

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

Wolfgang Haak, Iosif Lazaridis, Nick Patterson … (2015)

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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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.

Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf … (2014)

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

Journal ID (nlm-ta): Sci Adv

Journal ID (iso-abbrev): Sci Adv

Journal ID (publisher-id): SciAdv

Journal ID (hwp): advances

Title: Science Advances

Publisher: American Association for the Advancement of Science

ISSN (Electronic): 2375-2548

Publication date Collection: February 2017

Publication date (Electronic): 01 February 2017

Volume: 3

Issue: 2

Electronic Location Identifier: e1601877

Affiliations

[1 ]Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K.

[2 ]Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.

[3 ]The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.

[4 ]Geromics, Ulsan 44919, Republic of Korea.

[5 ]Clinomics Inc., Ulsan 4919, Republic of Korea.

[6 ]Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.

[7 ]Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.

[8 ]School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland.

Author notes

[* ]Corresponding author. Email: vs389@ 123456cam.ac.uk (V.S.); ron.pinhasi@ 123456ucd.ie (R.P.); jongbhak@ 123456genomics.org (J.B.); am315@ 123456cam.ac.uk (A.M.)

[†]

These authors contributed equally to this work.

[‡]

Adjunct professor at Seoul National University, Seoul, Republic of Korea.

Author information

Youngjune Bhak http://orcid.org/0000-0002-9273-6984

Marcos Gallego-Llorente http://orcid.org/0000-0003-3498-6018

Michael Hofreiter http://orcid.org/0000-0003-0441-4705

Daniel G. Bradley http://orcid.org/0000-0001-7335-7092

Anders Eriksson http://orcid.org/0000-0003-3436-3726

Ron Pinhasi http://orcid.org/0000-0003-1629-8131

Jong Bhak http://orcid.org/0000-0002-4228-1299

Andrea Manica http://orcid.org/0000-0003-1895-450X

Article

Publisher ID: 1601877

DOI: 10.1126/sciadv.1601877

PMC ID: 5287702

PubMed ID: 28164156

SO-VID: da415f8a-2603-4b72-899d-5ba6bd93c9a4

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

History

Date received : 10 August 2016

Date accepted : 21 December 2016

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100005370, Gates Cambridge Trust;

Award ID: ID0EDGAK13284

Award Recipient : Veronika Siska

Funded by: FundRef http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: ID0E1SAK13285

Award ID: ADNABIOARC (263441)

Award Recipient : Ron Pinhasi

Funded by: FundRef http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: ID0EU4AK13286

Award ID: GeneFlow (310763)

Award Recipient : Michael Hofreiter

Funded by: FundRef http://dx.doi.org/10.13039/501100002613, Ulsan National Institute of Science and Technology;

Award ID: ID0ECJBK13287

Award ID: Research Fund (1.140113.01)

Award Recipient : Jong Bhak

Funded by: Civil-Military Technology Cooperation Program;

Award ID: ID0EEWBK13288

Award ID: Research Fund (14-BR-SS-03)

Award Recipient : Jong Bhak

Funded by: Civil-Military Technology Cooperation Program;

Award ID: ID0ENBCK13289

Award ID: Research Fund (14-BR-SS-03)

Award Recipient : Yun Sung Cho

Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;

Award ID: ID0EGGCK13290

Award ID: DTP

Award Recipient : Marcos Gallego-Llorente

Funded by: FundRef http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: ID0E6NCK13845

Award ID: Consolidator Grant 647787 ‘LocalAdaptation’

Award Recipient : Andrea Manica

Funded by: FundRef http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: ID0EHTCK13846

Award ID: Consolidator Grant 647787 ‘LocalAdaptation’

Award Recipient : Anders Eriksson

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Copyeditor Nova Morabe

Keywords: ancient genetics,east asia,neolithic,russian far east,human population genetics

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Keywords: ancient genetics, east asia, neolithic, russian far east, human population genetics

Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

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Most cited references 44

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

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

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.

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