The effect of gene flow on coalescent-based species-tree inference

Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. Several studies have examined the impact of gene flow (e.g., Eckert and Carstens (2008); Chung and Ane (2011); Leache et al. (2014); Solis-Lemus et al. (2016)) and of ancestral population structure (DeGeorgio and Rosenberg, 2016) on the performance of species-level phylogenetic inference, and analytic results have been proven for network models of gene flow (e.g., Solis-Lemus et al. (2016); Zhu et al. (2016)). However, there are few analytic results for a continuous model of gene flow following speciation, despite the development of mathematical tools that could facilitate such study (e.g., Hobolth et al. (2011); Andersen et al. (2014); Tian and Kubatko (2016)). In this paper, we consider a three-taxon isolation-with-migration model that allows gene flow between sister taxa for a brief period following speciation, as well as variation in the effec...