Phylogenomics of the Mesoamerican alligator-lizard genera Abronia and Mesaspis (Anguidae: Gerrhonotinae) reveals multiple independent clades of arboreal and terrestrial species.

• A phylogenomic analysis of the lizard genera Abronia and Mesaspis was performed. • Abronia and Mesaspis are both non-monophyletic. • Abronia + Mesaspis species formed clades in several different biogeographic regions. • A single origin of arboreality in the clade (Abronia + Mesaspis) was not supported. Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa. [ABSTRACT FROM AUTHOR]