Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

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Abstract

During the 1 ^st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.

Abstract

The Scythian culture was widespread throughout the Eurasian Steppe during the 1 ^st millennium BCE. This study provides genetic evidence for two independent origins for the Scythians in the eastern and western steppe with varying proportions of Yamnaya and East Asian ancestry, and gene flow among them.

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Most cited references 31

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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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Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Martin Kircher, Susanna Sawyer, Matthias Meyer (2011)

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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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): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Publishing Group

ISSN (Electronic): 2041-1723

Publication date (Electronic): 03 March 2017

Publication date Collection: 2017

Volume: 8

Electronic Location Identifier: 14615

Affiliations

[1 ]Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz , 55099 Mainz, Germany

[2 ]CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle , 75016 Paris, France

[3 ]Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, USA

[4 ]Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, USA

[5 ]Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science , Akademika Lavrentieva 10, Novosibirsk 630090, Russia

[6 ]Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science , Akademika Lavrentieva 17, Novosibirsk 630090, Russia

[7 ]Novosibirsk State University , Pirogova str. 2, Novosibirsk 630090, Russia

[8 ]Molecular Genetics and Genome Analysis Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz , 55099 Mainz, Germany

[9 ]Department of History and Cultural Studies, Freie Universität Berlin , 14195 Berlin, Germany

[10 ]Samara State University of Social Sciences and Education , Samara 443099, Russian Federation

[11 ]Max Planck Institute for the Science of Human History , Kahlaische Straße 10, 07745 Jena, Germany

[12 ]Dépt. de Génétique & Evolution, Unité d'anthropologie, Université de Genève , 1205 Genève, Suisse

[13 ]Howard Hughes Medical Institute, Harvard Medical School , Boston, Massachusetts 02115, USA

[14 ]Branch of Margulan Institute of Archaeology , Astana 010000, Kazakhstan

[15 ]Stiftung Preussischer Kulturbesitz , 10785 Berlin, Germany

Author notes

[a ] jburger@ 123456uni-mainz.de

[*]

These authors contributed equally to this work.

Article

Publisher Item ID: ncomms14615

DOI: 10.1038/ncomms14615

PMC ID: 5337992

PubMed ID: 28256537

SO-VID: 4078d2ee-8b8c-4b05-afe0-90e9d9bd8f1c

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This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

History

Date received : 19 August 2015

Date accepted : 13 January 2017

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Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

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Most cited references 31

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

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.

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