Isolation and divergence of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) in western North America support multiple diversification processes and a complex demographic history

Authors

Christopher Robert Blair, CUNY New York City College of TechnologyFollow
Carlos Joaquín Pavón-Vázquez, CUNY New York City College of TechnologyFollow
Qaantah Rana, CUNY New York City College of Technology
Keaka Farleigh, Miami University - Oxford
Erika Crispo, Pace University
Thomas Panzera, Pace University
Felipe de Medeiros Magalhães, CUNY New York City College of Technology
Britt White, University of Texas at Austin
Uri Omar Garcia-Vazquez, Universidad Nacional Autónoma de México

Document Type

Article

Publication Date

8-15-2025

Abstract

The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (Cophosaurus texanus) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of C. texanus, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and multiple species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that C. texanus texanus is nested within lineages of C. texanus scitulus, supporting the hypothesis that this system may constitute a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.

Comments

This is the author's accepted manuscript of an article originally published in Molecular Phylogenetics and Evolution, available at https://doi.org/10.1016/j.ympev.2025.108442