Bayesian inference of admixture graphs on Native American and Arctic populations
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 propo...
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Online Access: | http://dx.doi.org/10.1371/journal.pgen.1010410 https://dx.plos.org/10.1371/journal.pgen.1010410 |
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crplos:10.1371/journal.pgen.1010410 2024-06-23T07:49:56+00:00 Bayesian inference of admixture graphs on Native American and Arctic populations Nielsen, Svend V. Vaughn, Andrew H. Leppälä, Kalle Landis, Michael J. Mailund, Thomas Nielsen, Rasmus Browning, Sharon R. National Institutes of Health National Science Foundation Graduate Research Fellowship 2023 http://dx.doi.org/10.1371/journal.pgen.1010410 https://dx.plos.org/10.1371/journal.pgen.1010410 en eng Public Library of Science (PLoS) http://creativecommons.org/licenses/by/4.0/ PLOS Genetics volume 19, issue 2, page e1010410 ISSN 1553-7404 journal-article 2023 crplos https://doi.org/10.1371/journal.pgen.1010410 2024-06-04T06:19:37Z 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. Article in Journal/Newspaper Arctic inuit Koryaks Saqqaq PLOS Arctic PLOS Genetics 19 2 e1010410 |
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English |
description |
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. |
author2 |
Browning, Sharon R. National Institutes of Health National Science Foundation Graduate Research Fellowship |
format |
Article in Journal/Newspaper |
author |
Nielsen, Svend V. Vaughn, Andrew H. Leppälä, Kalle Landis, Michael J. Mailund, Thomas Nielsen, Rasmus |
spellingShingle |
Nielsen, Svend V. Vaughn, Andrew H. Leppälä, Kalle Landis, Michael J. Mailund, Thomas Nielsen, Rasmus Bayesian inference of admixture graphs on Native American and Arctic populations |
author_facet |
Nielsen, Svend V. Vaughn, Andrew H. Leppälä, Kalle Landis, Michael J. Mailund, Thomas Nielsen, Rasmus |
author_sort |
Nielsen, Svend V. |
title |
Bayesian inference of admixture graphs on Native American and Arctic populations |
title_short |
Bayesian inference of admixture graphs on Native American and Arctic populations |
title_full |
Bayesian inference of admixture graphs on Native American and Arctic populations |
title_fullStr |
Bayesian inference of admixture graphs on Native American and Arctic populations |
title_full_unstemmed |
Bayesian inference of admixture graphs on Native American and Arctic populations |
title_sort |
bayesian inference of admixture graphs on native american and arctic populations |
publisher |
Public Library of Science (PLoS) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1371/journal.pgen.1010410 https://dx.plos.org/10.1371/journal.pgen.1010410 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic inuit Koryaks Saqqaq |
genre_facet |
Arctic inuit Koryaks Saqqaq |
op_source |
PLOS Genetics volume 19, issue 2, page e1010410 ISSN 1553-7404 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1371/journal.pgen.1010410 |
container_title |
PLOS Genetics |
container_volume |
19 |
container_issue |
2 |
container_start_page |
e1010410 |
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1802640663734386688 |