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Inference of Gene Flow between Species under Misspecified Models.
Huang, Jun; Thawornwattana, Yuttapong; Flouri, Tomás; Mallet, James; Yang, Ziheng.
Afiliação
  • Huang J; School of Biomedical Engineering, Capital Medical University, Beijing 100069, P.R. China.
  • Thawornwattana Y; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
  • Flouri T; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom.
  • Mallet J; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
  • Yang Z; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom.
Mol Biol Evol ; 39(12)2022 12 05.
Article em En | MEDLINE | ID: mdl-36317198
Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genômica / Fluxo Gênico Tipo de estudo: Prognostic_studies Idioma: En Ano de publicação: 2022 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genômica / Fluxo Gênico Tipo de estudo: Prognostic_studies Idioma: En Ano de publicação: 2022 Tipo de documento: Article