Genetic analysis of Missouri’s Topeka Shiners with implications for the propagation of understudied small-bodied freshwater fishes

Abstract Objective Best practices for conservation hatcheries to conserve genetic diversity and minimize adaptation to captivity have been established for decades, but how to apply them is not clear in every circumstance. As a growing number of aquatic species are propagated in captive settings, addressing the fit of these practices to each system will help managers operate optimally while conserving hatchery resources. Small-bodied freshwater fish present a unique set of traits compared with species that are typically considered for propagation (i.e., salmonids), including a patchy distribution within a watercourse. We examine the propagation and reintroduction program that supports the Topeka Shiner Miniellus topeka, an endangered minnow in the Midwestern USA. Methods We genotyped shiners from groups with different histories (two reintroduced, three captive, and two remnant populations) at 11 microsatellite loci and compared genetic diversity, genetic structure, effective population size, and evidence of population bottlenecks. We also looked at the breeding structure by genetically assigning hatchery-reared young (n = 148) to candidate parents. Results We documented high levels of genetic structure among the two natural populations in our study. We also noted lower diversity and evidence of bottlenecks in hatchery-reared groups. However, hatcheries may support sufficient (>50) effective population sizes with minimal space. Conclusions Hatcheries may avoid bottlenecks in other small-bodied freshwater fish by collecting wild fish from a broad area and frequently incorporating them into the captive population. Within the hatchery, we emphasize the need to reduce generational overlap by stocking all production fish and/or subdividing the captive populations.