View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Small populations with limited geographic distributions are predicted to be threatened by inbreeding and lack of genetic diversity, both of which may negatively impact fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. This imperiled species has experienced severe declines in population size over the last thirty years and suffered major, repeated bottlenecks in 2007 and 2013, when the population sunk to 38 and 35 individuals, respectively. In our previous work, we found higher levels of inbreeding (F_ROH = 0.34 - 0.81) and increased deleterious genetic variation in the form of loss-of-function homozygous derived genotypes in the Devils Hole pupfish, relative to nearby populations of Cyprinodon nevadensis and Cyprinodon salinus. Moreover, we discovered predicted loss-of-function mutations and deletions associated with reproduction and hypoxia tolerance. This includes a fixed early stop codon in cfap43 (n = 8/8 samples), which is associated with sperm flagellum defects and causes infertility in humans and mice and a deletion in the promoter of redd1 (n = 7/7 samples), an inhibitor of mTOR signalling. Here, we present two de novo reference genomes of C. diabolis and C. nevadensis mionectes and an additional 150 resequenced genomes of Death Valley and Ash Meadows desert pupfish to improve our understanding of inbreeding and mutation load in desert pupfish and assess whether the captive bred population of C. diabolis has successfully maintained wild genetic variation. We thus document inbreeding and mutation load in the Devils Hole pupfish and in pupfish across Death Valley to inform management of this conservation icon and hopefully reduce extinction risk.

Severe Inbreeding and Mutation Load in the Critically Endangered Devils Hole Pupfish