Genetic erosion in an endangered desert fish during a megadrought despite long‐term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short‐lived, obligate aquatic species, including 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. Rates of diversity loss are also affected by additions of hatchery‐origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single‐sample estimates of effective population size based on linkage disequilibrium (LD Ne) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery‐origin spawners increased, LD Ne declined (r = −0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery‐origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought. Resumen El uso humano del agua, combinado con una megasequía reciente, ha reducido el flujo de los ríos y arroyos en el suroeste de los Estados Unidos y ha provocado la seca periódica de segmentos de ríos que antes eran perennes. Las reducciones en la escorrentía del deshielo y el aumento de la sequía amenazan colectivamente a especies obligatoriamente acuáticas de vida corta, incluyendo la amenazada carpa chamizal (Hybognathus amarus). Esta especie está sujeta a una dinámica poblacional de explosión y colapso, bajo la cual