The spatiotemporal patterns of major human admixture events during the European Holocene

  1. Manjusha Chintalapati  Is a corresponding author
  2. Nick Patterson  Is a corresponding author
  3. Priya Moorjani  Is a corresponding author
  1. University of California, Berkeley, United States
  2. Broad Institute, United States

Abstract

Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on ~1,100 ancient genomes, we reconstruct major gene flow events during European Holocene. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9,600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of steppe pastoralism. Using time transect samples across sixteen regions, we provide a fine-scale chronology of the Neolithization of Europe and the rapid spread of Steppe pastoralist ancestry across Europe. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.

Data availability

All data analyzed during this study is publicly available at: https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data

Article and author information

Author details

  1. Manjusha Chintalapati

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    m_chintalapati@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
  2. Nick Patterson

    Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
    For correspondence
    nickp@broadinstitute.org
    Competing interests
    The authors declare that no competing interests exist.
  3. Priya Moorjani

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    moorjani@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0947-5673

Funding

National Institutes of Health (R35GM142978)

  • Priya Moorjani

Burroughs Wellcome Fund (Career Award at the Scientific Interface)

  • Priya Moorjani

Alfred P. Sloan Foundation (Sloan Research Fellowship)

  • Priya Moorjani

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. George H Perry, Pennsylvania State University, United States

Publication history

  1. Preprint posted: January 20, 2022 (view preprint)
  2. Received: February 5, 2022
  3. Accepted: May 29, 2022
  4. Accepted Manuscript published: May 30, 2022 (version 1)
  5. Version of Record published: July 18, 2022 (version 2)

Copyright

© 2022, Chintalapati et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Manjusha Chintalapati
  2. Nick Patterson
  3. Priya Moorjani
(2022)
The spatiotemporal patterns of major human admixture events during the European Holocene
eLife 11:e77625.
https://doi.org/10.7554/eLife.77625

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