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Inferring population histories for ancient genomes using genome-wide genealogies

View ORCID ProfileLeo Speidel, View ORCID ProfileLara Cassidy, View ORCID ProfileRobert W. Davies, View ORCID ProfileGarrett Hellenthal, View ORCID ProfilePontus Skoglund, Simon R. Myers
doi: https://doi.org/10.1101/2021.02.17.431573
Leo Speidel
1Francis Crick Institute, London, UK
2Genetics Institute, University College London, London, UK
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Lara Cassidy
3Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
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Robert W. Davies
4Department of Statistics, University of Oxford, Oxford, UK
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Garrett Hellenthal
2Genetics Institute, University College London, London, UK
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Pontus Skoglund
1Francis Crick Institute, London, UK
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Simon R. Myers
4Department of Statistics, University of Oxford, Oxford, UK
5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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  • For correspondence: myers@stats.ox.ac.uk
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Abstract

Ancient genomes anchor genealogies in directly observed historical genetic variation, and contextualise ancestral lineages with archaeological insights into their geography and lifestyles. We introduce an extension of the Relate algorithm to incorporate ancient genomes and reconstruct the joint genealogies of 14 previously published high-coverage ancients and 278 present-day individuals of the Simons Genome Diversity Project. As the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies, we additionally present a fast and scalable method, Colate, for inferring coalescence rates between low-coverage genomes without requiring phasing or imputation. Our method leverages sharing patterns of mutations dated using a genealogy to construct a likelihood, which is maximised using an expectation-maximisation algorithm. We apply Colate to 430 ancient human shotgun genomes of >0.5x mean coverage. Using Relate and Colate, we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 17, 2021.
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Inferring population histories for ancient genomes using genome-wide genealogies
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
bioRxiv 2021.02.17.431573; doi: https://doi.org/10.1101/2021.02.17.431573
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Inferring population histories for ancient genomes using genome-wide genealogies
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
bioRxiv 2021.02.17.431573; doi: https://doi.org/10.1101/2021.02.17.431573

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