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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2023
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Online Access: | https://pure.au.dk/portal/da/publications/bayesian-inference-of-admixture-graphs-on-native-american-and-arctic-populations(f985300e-44d4-4f1a-8e95-f0e30622fc3b).html https://doi.org/10.1371/journal.pgen.1010410 http://www.scopus.com/inward/record.url?scp=85148003685&partnerID=8YFLogxK |
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ftuniaarhuspubl:oai:pure.atira.dk:publications/f985300e-44d4-4f1a-8e95-f0e30622fc3b 2023-05-15T14:24:32+02:00 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 2023-02 https://pure.au.dk/portal/da/publications/bayesian-inference-of-admixture-graphs-on-native-american-and-arctic-populations(f985300e-44d4-4f1a-8e95-f0e30622fc3b).html https://doi.org/10.1371/journal.pgen.1010410 http://www.scopus.com/inward/record.url?scp=85148003685&partnerID=8YFLogxK eng eng info:eu-repo/semantics/openAccess Nielsen , S V , Vaughn , A H , Leppälä , K , Landis , M J , Mailund , T & Nielsen , R 2023 , ' Bayesian inference of admixture graphs on Native American and Arctic populations ' , PLOS Genetics , vol. 19 , no. 2 , e1010410 . https://doi.org/10.1371/journal.pgen.1010410 article 2023 ftuniaarhuspubl https://doi.org/10.1371/journal.pgen.1010410 2023-03-22T23:56:46Z 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 Arctic inuit Koryaks Saqqaq Aarhus University: Research Arctic PLOS Genetics 19 2 e1010410 |
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Aarhus University: Research |
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English |
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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. |
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 |
publishDate |
2023 |
url |
https://pure.au.dk/portal/da/publications/bayesian-inference-of-admixture-graphs-on-native-american-and-arctic-populations(f985300e-44d4-4f1a-8e95-f0e30622fc3b).html https://doi.org/10.1371/journal.pgen.1010410 http://www.scopus.com/inward/record.url?scp=85148003685&partnerID=8YFLogxK |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic inuit Koryaks Saqqaq |
genre_facet |
Arctic Arctic inuit Koryaks Saqqaq |
op_source |
Nielsen , S V , Vaughn , A H , Leppälä , K , Landis , M J , Mailund , T & Nielsen , R 2023 , ' Bayesian inference of admixture graphs on Native American and Arctic populations ' , PLOS Genetics , vol. 19 , no. 2 , e1010410 . https://doi.org/10.1371/journal.pgen.1010410 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1371/journal.pgen.1010410 |
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PLOS Genetics |
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19 |
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2 |
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e1010410 |
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1766296947040190464 |