Discovery and validation of species–specific diagnostic SNP markers for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis) and the versatile fairy shrimp (Branchinecta lindahli)

Abstract

Because only 3–7% of historically present vernal pool habitat remains in coastal San Diego County, conservation efforts must prioritize both the maintenance of these pools and the genomic integrity of their inhabitants. Coastal vernal pools found in southern California are home to the federally endangered San Diego fairy shrimp Branchinecta sandiegonensis. Simovich et al. (J Crustac Biol 33:730–740, 2013) characterized hybridization between B. sandiegonensis and the versatile fairy shrimp (Branchinecta lindahli) using morphological characters, but these characters are only found in adult females. To detect adult female, male and juvenile hybrids in the wild, we developed a genomic hybrid index comprised of 20 SNP loci using 16 individuals with no morphological evidence of hybridization, collected from populations unlikely to facilitate introgression. These loci have alternatively fixed alleles between the two species. This genomic hybrid index was validated using 426 individuals from 27 localities using morphology and habitat information. Our data suggest that some artificial and disturbed pool basins harbor hybrids, and thus have the potential to be stepping-stones for the future spread of hybrids. This genomic hybrid index will be a useful tool for identifying putative Branchinecta hybrids from both mature and immature life history stages, and aid in the monitoring and recovery of non-admixed B. sandiegonensis.