Application of next generation DNA sequencing markers for genetic monitoring of the endangered razorback sucker, Xyrauchen texanus

Authors: Abby Wicks, Trevor Krabbenhoft, Joel Corush, Thomas Turner, Megan Osborne, Thomas Dowling

Year: 2022

Abstract

Next-generation DNA sequencing methods have become a fixture in population studies, providing many simple, easily scored DNA markers (single nucleotide polymorphisms – SNPs) that are useful for fine-scaled studies of important population parameters. We developed and applied a panel of SNPs for studies of endangered razorback sucker (Xyrauchen texanus) and are using them to estimate key demographic and population genetic parameters linked to adaptive management. Characterization of stocked adults and progeny in off-channel refugia shows that SNP markers perform as well as, or better, than microsatellites for parentage assessment and for estimation of population genetic and demographic parameters. Characterization of SNPs from annual samples from Lower Colorado River populations provided estimates of population genetic parameters necessary for the long-term genetic monitoring program. SNPs are also useful for assessment of levels of introgressive hybridization between razorback and flannelmouth sucker (Catostomus latipinnis) in the Grand Canyon, where a sample of >1000 larvae in 2018 yielded only 14 razorback sucker. Of these, 635 flannelmouth sucker and eight razorback sucker remained after filtering of individuals with > 25% missing data. All eight razorback sucker exhibited signs of shared ancestry with flannelmouth sucker while approximately 2% of the 635 flannelmouth sucker larvae exhibited genetic variants from razorback sucker, consistent with past hybridization between species. Results validate the utility of SNP markers for conservation and management of endangered razorback sucker and other fishes.