Deep genomic divergence among regional populations of Pecos Gambusia, Gambusia nobilis.

Authors: Kevin Conway, Robert Bretzing-Tungate, Andrew Fields, Megan Bean, Ryan Smith, Elizabeth Dolan, Rose Blanchard, David Portnoy

Year: 2025

Abstract

Gambusia nobilis is a federally Endangered species found across a fragmented distribution within the Pecos River Drainage of Texas and New Mexico. Drought, human water usage, and potential hybridization with the introduced congeneric G. affinis and G geiseri threaten species persistence. Therefore, a conservation genomics study was conducted to provide information about levels of standing variation and to characterize levels of hybridization and admixture. A total of 12 admixed individuals were found across 12 distinct geographic samples, with nearly half of those collected at Phantom Spring, which had receded into the cave mouth. Unsupervised clustering suggested hierarchical structure, with a primary K =3 and deep divergences were detected among samples grouped into the Leon Creek watershed, the Toyah Creek watershed, and water bodies within the Bitter Lake National Wildlife Refuge (F’ST = 0.55-0.76). Phylogenetic analyses showed three distinct clades corresponding to the identified groups, with split times estimated to be in the last 50,000 years. Subsequent analyses detected a number of phenotypic differences among the three groups, including male color pattern in life and number of caudal-fin rays in both sexes. Taken as a whole, the data indicated that there are three distinct evolutionary units (species) present that likely require individualized conservation planning.