Long-term temporal sampling reveals upstream-downstream differences in genetic variation and effective population size in Rio Grande silvery minnow

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

Year: 2024

Abstract

Asymmetric flow of rivers, reproductive ecology and anthropogenic impacts affect abundance patterns between up and downstream localities and in turn, can influence effective population size (Ne) and how genetic diversity is distributed across the riverscape. We used genotyping-by-sequencing in thousands to evaluate temporal and spatial patterns of effective population size and diversity metrics in the endangered Rio Grande silvery minnow (Hybognathus amarus). Using archived Rio Grande silvery minnow DNA, we identified a significant reduction in allelic diversity and heterozygosity and a shift in allele frequencies for the period following a multi-year population bottleneck. We found that in almost all cases the wild population did not differ significantly from a 1:1 sex ratio. More recently, there was an ~80% reduction in Ne between 2022 and 2024, and in 2024 there was a significant excess of heterozygotes, very small estimates of NEB and an increase in values of g ̂2 consistent with a population bottleneck. Rio Grande silvery minnow is a pelagic broadcast spawner whereby eggs are released into the water column where they drift with river flow. Across the 25-year time-series, we found that contemporary Ne is reduced in the upstream-most population, and that departures from Hardy-Weinberg expectations and differences in the inbreeding metrics were also explained by river reach. Contrary to predictions, allelic diversity was not significantly different between reaches but was positively impacted by augmentation of the population with captive reared fishes.