Genetic monitoring in Rio Grande Silvery Minnow using genotyping-in-thousands by sequencing

Authors: Megan Osborne, Guilherme Caeiro-Dias, Thomas Turner

Year: 2023

Abstract

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States. Reductions in snowmelt runoff and increased extent of drying collectively threaten the endangered Rio Grande Silvery Minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Monitoring genetic effective population size has been widely advocated in conservation programs because it is an important predictor of adaptive potential. Until 2022 the trajectory of genetic diversity (including allelic richness, heterozygosity, and effective population size) in Rio Grande Silvery Minnow was measured annually using nine microsatellite loci and a mtDNA gene. In 2023, microsatellite markers were replaced by a Genotyping-in-Thousands by sequencing (Gt-seq) panel containing 285 loci distributed throughout the genome. We used the GT-seq panel to genotype samples from 1987, 1999-2012, 2015-2023; encompassing a period of almost four decades. The panel also includes a sex-specific marker, allowing us to track changes in the sex ratio in the wild population across the time-series. Population declines associated with drought resulted in increases in inbreeding metrics, reduced heterozygosity and smaller estimates of contemporary effective population size. We also recovered mitochondrial DNA sequences from NextRad data which revealed reductions in mitochondrial diversity associated with a multiyear population bottleneck that occurred from 2012-2014.