What can population genomics tell us about conservation of the imperiled Peppered Chub (Macrhybopsis tetranema)?

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

Year: 2022

Abstract

Peppered Chub (Macrhybopsis tetranema) is part of the Macrhybopsis aestivalis complex, which comprises nine recognized species, and belongs to the pelagic-broadcast spawning guild of fishes. This guild is adversely affected by fragmentation, altered flow regimes, habitat degradation of rivers of the North American Great Plains. Survival and reproductive success are positively linked to river discharge and connectivity. Peppered Chub is extirpated from more than 94% of its historic range and only occurs in a 218-kilometer reach of the South Canadian River between Ute Lake (New Mexico) and Lake Meredith (Texas). We assessed genomic diversity across this remnant population, evaluated genetic differentiation between several geographical and temporal samples, and estimated genetic effective population size (Ne) from Peppered Chub collected between 2015 and 2020. We identified 1627 SNP-containing loci (microhaplotypes), obtained from 189 individuals sampled across six temporal collections from several localities across the South Canadian River. Genome-wide diversity metrics were virtually identical across localities and across the time-series. Recent collections (2018 – 2020) show an order-of-magnitude reduction in Ne in 2019 that coincides with an exceptional drought. There was little genetic differentiation across sites or between sampled years in New Mexico. Likewise, we did not observe differentiation between New Mexico sampling localities and a single site upstream of Lake Meredith, Texas. Additional sampling and genetic analyses of samples collected from the border of New Mexico and to Lake Meredith is warranted to assess our findings more robustly. Based on our microhaplotype markers, future work should include the development of a panel of SNP-based markers to continue genetic monitoring and inform management decisions including establishment of a refuge population.