Costa, RJ;
Wilkinson-Herbots, H;
(2017)
Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model.
Genetics
, 205
(4)
pp. 1597-1618.
10.1534/genetics.116.188060.
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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, Becquet and Przeworski (2009) report 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 paper 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; c) divergence in complete isolation. We illustrate the procedure on pairs of Drosophila sequences from approximately 30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this paper.
| Type: | Article |
|---|---|
| Title: | Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model. |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1534/genetics.116.188060 |
| Publisher version: | http://dx.doi.org/10.1534/genetics.116.188060 |
| Language: | English |
| Additional information: | Copyright © 2017 Costa and Wilkinson-Herbots Available freely online through the author-supported open access option.This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | Coalescent, gene flow, isolation, maximum-likelihood, speciation |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Statistical Science |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1542906 |
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