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

Population genetics of the Salado salamander

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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 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.

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Data availability

Genotypic data are available on the Dryad Digital Repository at: https://datadryad.org/stash/share/lw_ECi_Rpm0hbwTPX91iUlKCFEgeTsQHbW1Zd7dyn54.

Code availability

Custom scripts available from the corresponding author.

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Acknowledgements

We thank C. Mier Y Teran for assistance in the lab, and Ashley Wall and Ryan Jones for assistance in the field. Jim Ott and the Martin/Nice/Ott lab group provided valuable comments and discussion. Three anonymous reviewers and the Associate Editor provided valuable criticism. We also thank Shane Flaherty and the Texas State University LEAP High Performance Computing Cluster. This research was funded by the Clearwater Underground Water District. The views expressed in this paper are the authors’ and do not necessarily reflect the view of the U.S. Fish and Wildlife Service.

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Authors and Affiliations

  1. Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX, 78666, USA

    Chris C. Nice

  2. Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA

    James A. Fordyce

  3. Department of Genetics, University of Georgia, Athens, GA, 30602, USA

    V. Alex Sotola

  4. United States Fish and Wildlife Service, Texas Fish and Wildlife Conservation Office, San Marcos, TX, 78666, USA

    Justin Crow & Peter H. Diaz

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  1. Chris C. Nice
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  2. James A. Fordyce
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  3. V. Alex Sotola
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  4. Justin Crow
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  5. Peter H. Diaz
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Contributions

All authors contributed to the study conception and design, material preparation, data collection and analysis. The first draft of the manuscript was written by Chris C. Nice and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Chris C. Nice.

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Nice, C.C., Fordyce, J.A., Sotola, V.A. et al. Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis. Conserv Genet 22, 811–821 (2021). https://doi.org/10.1007/s10592-021-01364-z

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