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
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.