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Efficient Bayesian inference under the multispecies coalescent with migration

Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy c...

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Autores principales: Flouri, Tomáš, Jiao, Xiyun, Huang, Jun, Rannala, Bruce, Yang, Ziheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10622872/
https://www.ncbi.nlm.nih.gov/pubmed/37871206
http://dx.doi.org/10.1073/pnas.2310708120
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author Flouri, Tomáš
Jiao, Xiyun
Huang, Jun
Rannala, Bruce
Yang, Ziheng
author_facet Flouri, Tomáš
Jiao, Xiyun
Huang, Jun
Rannala, Bruce
Yang, Ziheng
author_sort Flouri, Tomáš
collection PubMed
description Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.
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spelling pubmed-106228722023-11-04 Efficient Bayesian inference under the multispecies coalescent with migration Flouri, Tomáš Jiao, Xiyun Huang, Jun Rannala, Bruce Yang, Ziheng Proc Natl Acad Sci U S A Biological Sciences Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow. National Academy of Sciences 2023-10-23 2023-10-31 /pmc/articles/PMC10622872/ /pubmed/37871206 http://dx.doi.org/10.1073/pnas.2310708120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Flouri, Tomáš
Jiao, Xiyun
Huang, Jun
Rannala, Bruce
Yang, Ziheng
Efficient Bayesian inference under the multispecies coalescent with migration
title Efficient Bayesian inference under the multispecies coalescent with migration
title_full Efficient Bayesian inference under the multispecies coalescent with migration
title_fullStr Efficient Bayesian inference under the multispecies coalescent with migration
title_full_unstemmed Efficient Bayesian inference under the multispecies coalescent with migration
title_short Efficient Bayesian inference under the multispecies coalescent with migration
title_sort efficient bayesian inference under the multispecies coalescent with migration
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10622872/
https://www.ncbi.nlm.nih.gov/pubmed/37871206
http://dx.doi.org/10.1073/pnas.2310708120
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