University of Oulu

Nielsen SV, Vaughn AH, Leppälä K, Landis MJ, Mailund T, Nielsen R (2023) Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genet 19(2): e1010410.

Bayesian inference of admixture graphs on Native American and Arctic populations

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Author: Nielsen, Svend V.1; Vaughn, Andrew H.2; Leppälä, Kalle1,3;
Organizations: 1Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
2Center for Computational Biology, University of California Berkeley, Berkeley, California, United States of America
3Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
4Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
5Departments of Integrative Biology and Statistics, University of California Berkeley, Berkeley, California, United States of America
6Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1 MB)
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Language: English
Published: Public Library of Science, 2023
Publish Date: 2023-05-09


Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.

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Series: PLoS genetics
ISSN: 1553-7390
ISSN-E: 1553-7404
ISSN-L: 1553-7390
Volume: 19
Issue: 2
Article number: e1010410
DOI: 10.1371/journal.pgen.1010410
Type of Publication: A1 Journal article – refereed
Field of Science: 1184 Genetics, developmental biology, physiology
Funding: RN received grant R01GM138634, National Institutes of Health AHV received grant 2146752, National Science Foundation Graduate Research Fellowship Program The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Copyright information: © 2023 Nielsen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.