Environmental DNA mitochondrial markers to assess potential occupancy of Endangered Yaqui catfish in the Yaqui River basin, Mexico

Abstract

Acquiring data on rare and threatened species can be challenging, particularly in remote areas. Environmental DNA (eDNA) offers a less effort-intensive method for detecting species compared to physical fish sampling methods. In our study, we focused on the Endangered Yaqui catfish Ictalurus pricei, a freshwater fish endemic to the Sonoran desert in Arizona, USA, and Sonora, Mexico, and the non-native channel catfish I. punctatus. We developed and employed mitochondrial eDNA markers to sample 35 locations in the Yaqui River basin in Mexico and employed a hierarchical Bayesian formulation of a co-occurrence model to investigate the interactions between the species while accounting for the effects of covariates on species occupancy and detection. Our best model included the influence of channel catfish mitochondrial eDNA on detecting Yaqui catfish mitochondrial eDNA, and we found that channel catfish mitochondrial eDNA detection was negatively related with water temperature and elevation but positively related to substrate size. Yaqui catfish occupancy, as determined with mitochondrial eDNA detection, was best explained by stream permanence and the presence of forested areas, while channel catfish mitochondrial eDNA occurrences were also associated with stream permanence, as well as conifer and shrub-dominated landscapes. Non-native channel catfish mitochondrial eDNA was found in all but 5 locations where Yaqui catfish mitochondrial eDNA was detected, indicating a high likelihood of interaction and hybridization. This potential for hybridization poses a significant threat to the already Endangered Yaqui catfish, emphasizing the need to protect and secure remaining populations for their long-term survival.