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, FST; genetic distance, DXY) 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.
Phylogeography of the Greater Short-horned Lizard (Phrynosoma hernandesi) and the San Luis Valley Short-horned Lizard (P. diminutum). (A) Geographic distribution of P. hernandesi in Western North America with colors corresponding to population structure estimate assuming three populations (modified from Leaché et al., 2021). The range of P. diminutum in the San Luis Valley is shown in gray with an example of an adult female (UWBM:HERP:10231) from Zapata Ranch, Alamosa Co., Colorado. (B) A phylogenetic network estimated using the concatenated SNP data places P. diminutum (highlighted with asterisks) adjacent to samples from the South population of P. hernandesi. (C) Population structure analysis using the SNP data in ADMIXTURE supports a model with three populations of P. hernandesi with P. diminutum (highlighted with asterisks) inside the South population of P. hernandesi. (D) A phylogenetic analysis of the concatenated SNP data using BEAST places P. diminutum within P. hernandesi. Black dots on the phylogeny indicate posterior probabilities ≥ 0.95.
Minimum pairwise fixation index (FST) and genetic distance (DXY) for each group analyzed in the study. Species that are higher up on the graph (greater minimum pairwise FST) and farther right on the graph (greater minimum DXY) are more differentiated from at least one other group, while those groups lower down and farther left on the graph are less differentiated from at least one other group. The three populations of P. hernandesi are shown as squares, and P. diminutum is shown as a star.
EEMS plots showing migration (A) and diversity (B) across the geographic range of P. hernandesi (black dots) and P. diminutum (black stars). Scale bars represent relative distance from the isolation-by-distance model.
Contributor Notes
Associate Editor: B. L. Stuart.