Population genomics of the imperiled Peppered Chub (Macrhybopsis tetranema): new nuclear & mitochondrial data & prospects for long-term monitoring

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

Year: 2023

Abstract

Peppered Chub (Macrhybopsis tetranema) is part of the Macrhybopsis aestivalis complex, which comprises nine recognized species. Peppered Chub is extirpated from more than 94% of its historic range and is now restricted to a 218-kilometer reach of the South Canadian River between Ute Lake (New Mexico) and Lake Meredith (Texas). This species is a pelagic broadcast spawner, and survival and reproductive success are linked to river discharge and connectivity. We sequenced whole nuclear and mitochondrial genomes and these were used as references to map nextRAD (Nextera-tagmented reductively-amplified DNA) sequencing data. We identified SNP-containing loci (microhaplotypes) from 190 individuals sampled across six temporal collections and several localities in the South Canadian River. The nuclear microhaplotype dataset was used to re-assess genomic diversity, geographical and temporal differentiation, and genetic effective population size (Ne) between 2015 and 2020. Genome-wide diversity was moderate and virtually identical across the time-series. There was little genetic differentiation between years and between samples collected in New Mexico and Texas. Recent collections (2018 – 2020) show an order-of-magnitude reduction in Ne that coincides with an exceptional drought in 2019. Using the mitochondrial genome as a reference we were able to identify a 12S gene fragment of 573 base pairs in length in 78 individuals. We found moderate levels of mitochondrial diversity, including a unique haplotype in a single individual from Texas that was not detected in New Mexico samples. A single haplotype detected in three samples was more similar to Shoal Chub (M. hyostoma) mtDNA, denoting mitochondrial introgression from that species into Peppered Chub. Future work includes the assessment of whether mitochondrial introgression from Shoal Chub was accompanied by introgression of nuclear loci. Additional sampling has been completed and future work also includes the development of a GTseq panel for long-term genetic monitoring.