Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between two species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may, then, play a key role in adaptive radiation by allowing lineages to diversify into new ecological space. Here, we test for signatures of historical hybridization in the Anolis lizards of Puerto Rico and evaluate two hypotheses for the role of hybridization in facilitating adaptive radiation – the hybrid swarm origins hypothesis and the syngameon hypothesis. Using whole genome sequences from all ten species of Puerto Rican anoles, we calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the radiation and employed multispecies network coalescent methods to reconstruct phylogenetic networks that allow for hybridization. We then analyzed morphological data for these species to test for patterns consistent with transgressive evolution, a phenomenon in which the trait of a hybrid lineage is found outside of the range of its two parents. Our analyses uncovered strong evidence for introgression at multiple stages of the radiation, including support for an ancient hybrid origin of a clade comprising half of the extant Puerto Rican anole species. Moreover, we detected significant signals of transgressive evolution for two ecologically-important traits, head length and toepad width, the latter of which has been described as a key innovation in Anolis. 

We collected whole genome sequences from species of Puerto Rican Anolis lizards. From the resulting data, we inferred gene trees using RAxML and a species tree using ASTRAL.  We then calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the Puerto Rican Anolis radiation and employed multispecies network coalescent methods (SNaQ, PhyloNet, and NANUQ) to reconstruct phylogenetic networks that allow for hybridization. We examined modes of speciation using likelihood ratio tests of speciation with gene flow. Finally, we reconstructed ancestral states for ecologically-important traits under a Brownian motion model on phylogenetic networks implemented in PhyloNetworks and then tested for transgressive evolution in these traits.