Species delimitation in endangered groundwater salamanders: implications for aquifer management and biodiversity conservation

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders (Eurycea) endemic to the Edwards–Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and non-adaptive population divergence and speciation. Our results uncover new cryptic species diversity and refine the borders of several threa..., Structure input file for the northern clade.A Structure data file consisting of 131 individuals genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.Sept.strStructure input file for E. chisholmensis and E. naufragia populations.A Structure data file consisting of 53 E. chisholmensis and E. naufragia samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.chinau.strStructure input file for E. tonkawae.A Structure data file consisting of 78 E. tonkawae samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.tonk.strStructure input file for the southeastern clade.A Structure data file consisting of 73 individuals from the southeastern clade (excluding Typhlomolge) genotyped at 146 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.EBlep.strStructure input file for the southwestern clade.A Structure data file consisting of 82 individuals from the southwestern clade genotyped at 604 loci. See R..., ,