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Abstract:
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Deep coalescence and hybridization are two well-known evolutionary mechanisms that can lead to incongruence among different gene trees. However, few studies have been dedicated to exploring the joint effect of the two processes and developing techniques to quantify their relative roles. Here we propose a model that allows incongruence in single-gene phylogenies to be due to both hybridization and incomplete lineage sorting, with the goal of determining the contribution of hybridization to observed gene tree incongruence in the presence of incomplete lineage sorting. A Bayesian method is developed for simultaneous estimation of the extent of hybrid speciation, species divergence times, and ancestral population sizes using DNA sequence data from multiple genes. The performance of our method is examined by using both simulated and empirical DNA sequence data.
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