Pervasive gene flow across critical habitat for four narrowly endemic, sympatric taxa

Summary We studied genetic variation in four endangered animal taxa in the largest freshwater spring complex in the southwestern U.S.A., Comal Springs (TX): Eurycea salamanders, Heterelmis riffle beetles, Stygobromus amphipods and Stygoparnus dryopid beetles. They inhabit a spring complex with nearly stable conditions, which is threatened by climate change and aquifer withdrawals. The four taxa vary in their habitat affinities and body sizes. We used genotyping‐by‐sequencing to obtain hundreds to thousands of genetic markers to accurately infer the demographic history of the taxa. We used approximate Bayesian computation to test models of gene flow and compare the results among taxa. We also looked for evidence that would suggest local adaptation within the spring complex. An island model (equal gene flow among all subpopulations) was the most probable of the five models tested, and all four taxa had high migration rate estimates. Small numbers of single nucleotide polymorphisms (SNPs) in each taxon tested were associated with environmental conditions and provide some evidence for potential local adaptation to slightly variable conditions across habitat patches within Comal Springs. We discuss how the results of this study can add to the habitat conservation plan for Comal Springs. If part of the spring system dries, migrants may recolonise from elsewhere within the spring complex. However, genetic variants affecting survival in particular habitat patches could be lost during such droughts.