Phylogenomic assessment of the role of hybridization and introgression in trait evolution

Trait evolution in a set of species---a central theme in evolutionary biology---has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, rather than the species tree (hemiplasy). Recent work by Guerrero and Hahn (PNAS 115:12787-12792, 2018) provided a significant step towards teasing apart the roles of homoplasy and hemiplasy in trait evolution by analyzing it with respect to the species tree and the gene trees within its branches. Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is hybridization between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of bi-allelic traits, including polymorphic ones. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a trait9s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis when hybridization had occurred could provide misleading hypotheses about trait evolution.