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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.
Afiliación
  • Nielsen SV; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
  • Vaughn AH; Center for Computational Biology, University of California Berkeley, Berkeley, California, United States of America.
  • Leppälä K; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
  • Landis MJ; Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.
  • Mailund T; Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.
  • Nielsen R; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
PLoS Genet ; 19(2): e1010410, 2023 02.
Article en En | MEDLINE | ID: mdl-36780565
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Indio Americano o Nativo de Alaska / Genética de Población Límite: Humans Idioma: En Revista: PLoS Genet Asunto de la revista: GENETICA Año: 2023 Tipo del documento: Article País de afiliación: Dinamarca Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Indio Americano o Nativo de Alaska / Genética de Población Límite: Humans Idioma: En Revista: PLoS Genet Asunto de la revista: GENETICA Año: 2023 Tipo del documento: Article País de afiliación: Dinamarca Pais de publicación: Estados Unidos