Conservation Genomic Assessment of the Imperiled Leon Springs Pupfish, Cyprinodon bovinus, Across Temporal and Spatial Scales

The Leon Springs pupfish, Cyprinodon bovinus, is federally listed as endangered and currently confined to spring fed pools on the Diamond Y Spring Preserve in Pecos County, Texas, USA. A refuge population is maintained by U.S. Fish and Wildlife Service in Dexter, New Mexico, USA. The species is imperiled by the presence of an invasive congener, the sheepshead minnow, C. variegatus. To inform continued conservation and management planning for this species, a comprehensive conservation genomics study using double digest restriction-site associated DNA sequencing was performed. No evidence of contemporary hybridization or historical introgression between C. bovinus and C. variegatus was found. A refuge population maintained by the US Fish and Wildlife Service was significantly differentiated from wild samples collected at two locations, and the two wild locations (less than 1 km from each other) also exhibited significant heterogeneity. Estimates of within populations diversity and contemporary effective size were smaller for wild locations than the refuge population, with the point estimates for effective size below 200 for both wild locations. Temporal analyses, involving genetic data collected from samples obtained in 2013, suggest an increased magnitude of drift acting on the wild populations relative to the reserve population. Based on the results of this study, it appears that steps taken to remove C. variegatus and prevent hybridization between the species have been largely successful, but evidence of population fragmentation at very small spatial scales and low levels of diversity in the wild may jeopardize the long-term persistence of this species.