Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13,000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2-3 Mya throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kya. We estimate that Devils Hole was colonized by pupfish between 105 – 830 years ago, followed by genetic assimilation of pelvic fin loss and re...