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Data and code from: Aquifer geology drives speciation in cave-adapted fishes

Brownstein, Chase1; Watkins-Colwell, Gregory2; Policarpo, Maxime3; Harrington, Richard4; Hoffman, Eva5; Casane, Didier6; Near, Thomas1

Published Jun 02, 2026 on Dryad. https://doi.org/10.5061/dryad.bk3j9kdr4

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Abstract

Subterranean faunas often exhibit numerous adaptations to these harsh environments. Yet, owing to the remoteness of caves, underground speciation remains poorly understood, and whether subterranean ecosystems are evolutionary dead ends has been debated since the 1800s. We use comparative genomics and computed tomography to describe a new cavefish, Typhlichthys styx sp. nov., and show that speciation and secondary contact in Typhlichthys occur across aquifer boundaries. Although minimally distinct on the basis of morphology, different cavefish lineages have dispersed using widespread aquifers contained within Carboniferous-aged limestone formations across southeastern and central North America, facilitating secondary sympatry of cavefish species last sharing common ancestry eight million years ago. Our results establish a mechanism for allopatric speciation underground dependent on subterranean geology.