Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards

Understanding the factors that cause heterogeneity among gene trees can
increase the accuracy of species trees. Discordant signals across
the genome are commonly produced by incomplete lineage sorting (ILS) and
introgression, which in turn can result in reticulate evolution.
Species tree inference using the multispecies coalescent is designed to
deal with ILS and is robust to low levels of introgression, but
extensive introgression violates the fundamental assumption
that relationships are strictly bifurcating. In this study, we
explore the phylogenomics of the iconic Liolaemus subgenus of
South American lizards, a group of over 100 species mostly
distributed in and around the Andes mountains. Using
mitochondrial DNA (mtDNA) and genome-wide restriction
site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred
a time-calibrated mtDNA gene tree, nDNA species trees, and
phylogenetic networks. We found high levels of
discordance between mtDNA and nDNA, which we attribute in part to
extensive ILS resulting from rapid diversification. These data
also reveal extensive and deep introgression, which combined with
rapid diversification, explain the high level of
phylogenetic discordance. We discuss these findings in the
context of Andean orogeny and glacial cycles that fragmented, expanded,
and contracted species distributions. Finally, we use the new
phylogeny to resolve long-standing taxonomic issues in one of
the most studied lizard groups in the New World.