Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

We have modified the evolutionary model of Meng and Kubatko (2009) to incorporate intraspecific sampling of multiple individuals for estimation of speciation times and times of hybridization events for testing for hybridization in the presence of incomplete lineage sorting. We have also utilized a more efficient algorithm for obtaining our estimates. Using simulations, we demonstrate that our approach performs well under conditions motivated by an empirical data set for Sistrurus rattlesnakes where putative hybridization has occurred. We further demonstrate that the method is able to accurately detect the signature of hybridization in the data, while this signal may be obscured when other species-tree inference methods that ignore hybridization are used.Our approach is shown to be powerful in detecting hybridization when it is present. When applied to the Sistrurus data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure S. catenatus tergeminus in origin, which has significant conservation implications.In multi-gene phylogenetic analyses, gene phylogenies, which represent the evolutionary histories of particular genes, commonly differ from the overall species phylogeny, which represents the evolutionary relationships of the organisms as a whole. Multiple biological phenomena have been proposed to explain such incongruence, including hybridization [1], deep coalescence (also called incomplete lineage sorting (ILS)), recombination [2], horizontal gene transfer [3], and gene extinction and duplication [4]. Clearly, the possibility that such processes contribute to observed incongruence in gene trees complicates the inference of species phylogenies from multilocus data [5]. Most of the currently used methods for species tree estimation focus on modeling only one source of incongruence. For example, several software packages have been developed to estimate species phylogenies under the assumption that IL