Genetic diversity and introgression in the Yaqui catfish (Ictalurus pricei) population from Arroyo Cajón Bonito, Mexico

Authors: Alexsandre Gutiérrez-Barragán, Alejandro Varela-Romero, Francisco León, Mariana Mateos, José Grijalva-Chon, John Garza, José Romo-León

Year: 2024

Abstract

The endangered Yaqui catfish Ictalurus pricei, a native species to northwestern Mexico and southwestern United States (USA), has been threatened by hybridization with the exotic Channel catfish I. punctatus. The Arroyo Cajón Bonito (ACB) in Yaqui river basin, México, harbors one of the few Yaqui catfish remnant populations. Unfortunately, Channel catfish was cultured next to the stream for several years, and eventual escapes occurred enabling hybridization with Yaqui catfish. In this study, 23 catfish from ACB previously analyzed with mitochondrial and nuclear genes, were sequenced using low-coverage Whole Genome Sequencing (lcWGS) to assess introgression between both species. Among the 23 individuals, 20 were pure Yaqui catfish, and one was a pure channel catfish. Admixture was detected in two individuals, one with 50% ancestry from both species (an F1 hybrid), and the other with 70% Yaqui and 30% Channel catfish ancestries, indicating a backcross. Local ancestry inference in the backcross revealed long tracts of admixture, which are expected under recent hybridization events. These findings confirm that hybrids are fertile, posing a major threat to the genetic integrity of Yaqui catfish. Furthermore, genetic diversity analyses revealed low nucleotide diversity, reduced heterozygosity, and medium-sized runs of homozygosity among pure Yaqui catfish individuals, suggesting early inbreeding in the ACB population. Further lcWGS analysis and sampling throughout the entire Yaqui catfish distribution are needed to better understand the negative impact of introgression, and guide informed conservation strategies between Mexico and USA.