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

Abstract

Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern 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. This species experiences ‘boom‐and‐bust’ population dynamics where 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 leveraged demographic and genetic data from wild and hatchery individuals to understand 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 remains low despite hatchery stocking and brief wild population recovery. Across the time series, single‐sample estimates of effective population size (NeD) were positively associated (r = 0.53) with wild/total abundance, but as the proportion of hatchery‐origin spawners increased, NeD was reduced (r = ‐0.55). Megadrought limits wild spawner abundance and precludes 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.Article Impact statement: Long‐term supportive breeding prevents extinction but genetic impacts accumulate in the face of repeated population collapse.This article is protected by copyright. All rights reserved

Fishes move to transient local refuges, not persistent landscape refuges during river drying experiment

“…For rare and imperilled species there may be only limited sources of colonisers. Rio Grande silvery minnow is capable of recovery from small populations, yet population supplementation with >3 million hatchery-reared fish has maintained species persistence through extreme drought, albeit with declining genetic diversity (Archdeacon, Dudley, et al, 2023;Osborne et al, 2024). Species with higher abundance were quicker to recolonise and recover after disturbances, whereas rare species took longer to recover in Virginia streams (Albanese et al, 2009).…”

“…Restoration actions to improve resilience may focus on implementing designer environmental flows to enhance spawning or survival of specific life-stages, or in extreme situations supplementing imperilled wild populations with hatchery fish to improve spawning stock and maintain genetic diversity of imperilled species (Osborne et al, 2024).…”