Rapid Radiation and Rampant Reticulation: Phylogenomics of South American Liolaemus Lizards

ESQUERRÉ, DAMIEN; KEOGH, J SCOTT; DEMANGEL, DIEGO; MORANDO, MARIANA; AVILA, LUCIANO J; SITES, JACK W; FERRI-YÁÑEZ, FRANCISCO; LEACHÉ, ADAM D

SYSTEMATIC BIOLOGY

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2022 vol. 71 p. 286 - 300

1063-5157

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, whichin turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal withILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption thatrelationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of SouthAmerican lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrialDNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred atime-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordancebetween mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data alsoreveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogeneticdiscordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, andcontracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of themost studied lizard groups in the New World.[Andes; ddRADSeq; introgression; lizards; mtDNA; reptiles; SNPs.]