Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis: Population genetics of the Salado salamander

Aquatic, karst and spring endemic organisms have become a focus of conservation efforts as human population densities and demand for groundwater increase. This is especially true of Texas salamanders in the genus Eurycea that have been the subject of investigations of patterns of genetic differentiation in order to understand their systematics and to inform conservation planning. Here we generated data from several thousand single nucleotide polymorphisms (SNPs) to quantify within- and among-population genetic variation in the northernmost species, Eurycea chisholmensis, the Salado salamander, which is listed as a federally threatened species. We used approximate Bayesian computation and a method based on linkage disequilibrium to estimate effective population size, $$N_{e}$$ . Levels of differentiation were low, but revealed a primary division between northern and southern populations with no evidence of gene exchange between them. Genetic diversity was similar across all sampling locations and estimates of $$N_{e}$$ were largely congruent across the two methods and indicate population sizes large enough to maintain genetic variation, at least over the short term. These results suggest that two management units comprise the range of E. chisholmensis but that further sampling in intervening areas is required to precisely delineate, and determine the nature of, the boundary of these units.