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 US 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 Myr ago 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 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species.

Sequencing and characterization of the complete mitochondrial genome of the endangered Devils Hole pupfish Cyprinodon diabolis (Cyprinodontiformes: Cyprinodontidae).

The Devils Hole pupfish (Cyprinodon diabolis) is an imperiled cypinodontid fish endemic to Devils Hole, a single groundwater-fed pool in western North America characterized by temperature and oxygen conditions lethal to most fishes. In this study, we obtained the 16,499 base pair (bp) mitochondrial DNA sequence of C. diabolis. The mitogenome encodes 13 polypeptides, 22 tRNAs, 12S and 18S rRNAs, and an 832 bp D-loop region, and has a nucleotide composition of A, 25.69%; T, 27.32%; G, 17.49%; and C, 29.50% (GC content: 46.99%). The availability of this mitogenome will facilitate evaluations of C. diabolis genetic structure for management and conservation of this iconic endangered species.