Online appendix for: Hybridization and transgressive evolution as drivers of adaptive radiations: Reticulate evolution generates diversity in the Puerto Rican Anolis lizards

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 reconst..., 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. ,