Conservation genomics of endangered Death Valley pupfishes

Authors: David Tian, Nicolas Alexandre, Sean Lema, Bruce Turner, Olin Feuerbacher, Kevin Wilson, Michael Schwemm, Jennifer Gumm, Christopher Martin

Year: 2023

Abstract

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. Following the receding of pluvial lakes during the late Pleistocene, desert pupfishes in the Death Valley region became isolated in springs and creeks, limiting population sizes and connectivity. One of the most extreme examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. Our previous research on this population found that levels of inbreeding were exceptionally high (FROH = 0.58) as a result of its demographic history. Over the past three decades, this endangered species has seen a significant decline in its population size, with two critical bottlenecks occurring in 2007 and 2013 when the population declined to 38 and 35 individuals, respectively. Our follow-up study assesses population structure, genetic diversity, structural variation, and past demographic history across desert pupfish species to understand how small, isolated populations cope with inbreeding. Here, we present two chromosome-scale de novo reference genomes of C. diabolis and C. nevadensis mionectes, and 150 resequenced genomes of Death Valley and Ash Meadows desert pupfishes. The development of these genetic resources will enable more accurate measurements of inbreeding and mutation load, comparisons of wild and captive populations of C. diabolis, and inference of genomic architecture for a lethal heart defect in some developing C. diabolis embryos.