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 nonadaptive population divergence and speciation. Our results uncover cryptic species diversity and refine the borders of several threatened and endangered species. The US Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards–Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards–Trinity salamanders and other codistributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.

Ring species, exemplified by salamanders of the Ensatina eschscholtzii complex, represent a special window into the speciation process because they allow the history of species formation to be traced back in time through the geographically differentiated forms connecting the two terminal forms of the ring. Of particular interest is the nature and extent of reproductive isolation between the geographically terminal forms, in this case E. e. eschscholtzii and E. e. klauberi. Previous studies have documented infrequent hybridization at the end of the ring. Here, we report the first fine-scale genetic analysis of a hybrid zone between the terminal forms in southern California using individual-based Bayesian analyses of multilocus genetic data to estimate levels and direction of hybridization and maximum-likelihood analysis of linkage disequilibrium and cline shape to make inferences about migration and selection in the hybrid zone.

Background: The subgenus Syrrhophus (genus Eleutherodactylus) contains >40 species of small, direct-developing frogs that occur at low to moderate elevations from Texas through Mexico and into Guatemala and Belize, with two species in western Cuba. Morphological conservatism and phenotypic convergence have made species delimitation challenging and resulted in a complicated taxonomic history. Since 2015, molecular systematic work has uncovered eleven new species from western Mexico and one from eastern Mexico, but current taxonomy still underestimates species level diversity and there is confusion surrounding the validity and boundary of several species. Methods: We used phylogenetic analysis of 16S ribosomal RNA (rRNA) sequences, multivariate statistical analysis of morphological data, and bioacoustic analysis of male advertisement calls to discover two additional unnamed species of Eleutherodactylus from Central and Western Mexico. We describe those species here. Results: Eleutherodactylus (Syrrhophus) humboldti sp. nov. is described from the Quaternary Valle de Bravo volcanic field of the Eje Neovolcánico in Central Mexico. This species is sister to E. maurus and is 3% divergent in 16S. Eleutherodactylus (Syrrhophus) jamesdixoni sp. nov. is described from the Sierra Madre Occidental of western Mexico. This species is sister to E. nitidus and is 3% divergent. We provide color photographs, advertisement call recordings, and molecular diagnoses of these new species and their sister species to aid future workers.