Genomic Data Do Not Support the Species Status of the San Luis Valley Short-Horned Lizard (Phrynosoma diminutum)

Genomic data are increasingly used to understand the nature of species boundaries, which provides critical information about biodiversity and phylogeography. One example is the Greater Short-horned Lizard (Phrynosoma hernandesi), a wide-ranging species with substantial morphological and genomic variation throughout its range. Within the range of P. hernandesi, a miniaturized lizard was recently described as P. diminutum. Phrynosoma diminutum inhabits a distinct ecological region of Colorado in the San Luis Valley, but the unique location and size difference between P. diminutum and surrounding populations of P. hernandesi does not necessarily imply that P. diminutum is an independent evolutionary lineage. To determine whether genomic data support P. diminutum as an independent evolutionary lineage, we compared P. diminutum to surrounding populations of P. hernandesi using over 3,000 markers distributed throughout the genome. A phylogenetic analysis shows that P. diminutum is only weakly differentiated from nearby populations of P. hernandesi. Comparisons of genetic differentiation (fixation index, F_ST; genetic distance, D_XY) among five other closely related species of horned lizards provides further evidence that the low levels of genetic divergence observed in P. diminutum are reflective of population-level and not species-level divergence. Therefore, we propose that P. diminutum be placed in the synonymy of P. hernandesi rather than be recognized as a distinct species. Furthermore, we show how genomic data can be used to more accurately test species boundaries and avoid artificially inflating biodiversity estimates.