Genome-wide Data Reinforces the Evolutionary Relationships of Previously Problematic Earless Lizards (Phyrnosomatidae: Holbrookia)

In the face of anthropogenic change and the potential loss of species, documenting biodiversity – including accurately delimiting species complexes – is of tantamount importance. Genome-wide data are powerful for investigating lineage divergence, though deciding if this divergence represents species-level differentiation remains challenging. Here, we use genome-wide data to investigate species limits in four currently recognized species of Earless Lizards (Phrynosomatidae: Holbrookia), with a focus on H. lacerata and H. subcaudalis, the latter having potentially imperiled populations. This group’s taxonomy has been repeatedly revised; most recently, H. lacerata and H. subcaudalis were elevated to species status using conserved morphological data and a few molecular markers. In this study, we used double-digest restriction-site associated DNA sequencing to delineate species limits for our focal taxa. We recovered five populations that corresponded to five well-supported lineages with very little gene flow among them. Our results support the recognition of H. lacerata and H. subcaudalis as two separate species, based on strong phylogenetic support for these lineages and genetic divergence measures that exceed those of currently recognized species within Holbrookia. Genomic methods for species delimitation offer a promising approach to assess biodiversity in taxonomically confounded taxa or organisms of conservation priority.