Data from: 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 threatened and
endangered species. The U.S. 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 co-distributed
groundwater-dependent organisms are highly vulnerable to extinction within
the next century.