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

Citation

Nice, Chris et al. (2021), Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis, Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4hd

Abstract

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 quantify patterns of population differentiation in the northern most species, Eurycea chisholmensis, the Salado salamander, which is listed as a federally threatened species. Several thousand single nucleotide markers (SNPs) were used to quantify within- and among-population genetic variation. We used approximate Bayesian computation and a method based on linkage disequilibrium to estimate effective population size, Ne. Levels of differentiation were low, but revealed a primary division between northern and southern populations with no evidence of gene exchange between them. Pairwise differentiation, estimated as Gst, ranged from 0.0042 within regions to 0.0244 between regions. Genetic diversity was similar across all sampling locations and estimates of Ne were largely congruent across two methods and indicate population sizes large enough to maintain genetic variation, at least over the short term. These results can inform ongoing conservation efforts for this threatened species.

Methods

Matrix of posterior genotype probabilities for 175 salamanders at 8,731 SNP loci generated by genotyping-by-sequencing methods (similar to ddRAD.seq methods). The hierarchical Bayesian clustering algorithm ENTROPY was used to generate these genotype probabilities.

Usage Notes

This genotype matrix contains no missing data and can be used as is. Two additional files conatining individual identifiers in order and another with a key to locality codes accompany the genotype data dile.

Funding

Clearwater Underground Water District

Clearwater Underground Water District