ArticleGenetics2017
Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model.
Article in Genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The effect of habitat loss and fragmentation on isolation by distance and divergence.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Efficient Bayesian inference under the multispecies coalescent with migration.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Inference of Gene Flow between Species under Misspecified Models.Molecular biology and evolution · 2022Article
- Article
- Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.National science review · 2021Article
- mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow.Genome biology and evolution · 2020Article
- ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.Genome biology · 2018Article
- Whole-genome data reveal the complex history of a diverse ecological community.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Ancestral polymorphisms explain the role of chromosomal inversions in speciation.PLoS genetics · 2018Article
- Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation.Molecular ecology · 2018Article
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2 authors.
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Abstract
The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, it has been reported that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions-including the assumption of constant gene flow until the present. This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used, by means of likelihood-ratio tests, to distinguish between alternative models representing the following divergence scenarios: (a) divergence with potentially asymmetric gene flow until the present, (b) divergence with potentially asymmetric gene flow until some point in the past and in isolation since then, and (c) divergence in complete isolation. We illustrate the procedure on pairs of
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