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

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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

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.
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.
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.

"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.

Copyright

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.