Hybridization between delta smelt and two other species within the family Osmeridae in the San Francisco Bay-Delta

Hybridization among closely related species may pose a threat to species persistence, especially between native and introduced species. We analyzed nine microsatellite loci, mitochondrial sequences and 16 species-specific single nucleotide polymorphisms (SNPs) in two native species (delta smelt and longfin smelt) and one introduced species (wakasagi smelt) in the family Osmeridae to describe the extent of hybridization among these species in the San Francisco Bay-Delta, CA, USA. We identified 29 putative hybrids with a microsatellite-based Bayesian assignment method, and we further screened these putative hybrids with the SNP loci and mitochondrial DNA (mtDNA) sequencing. From the Yolo Bypass, 11 % of morphologically ambiguous individuals were F-1 hybrids and 0.1 % of positively identified delta smelt from throughout the San Francisco Bay-Delta were F-1 hybrids according to their SNP genotypes. mtDNA sequencing revealed wakasagi smelt as the maternal parent for all five delta smelt x wakasagi smelt hybrids and longfin smelt as the maternal parent for the single longfin smelt 9 delta smelt hybrid. Hybridization among these three species appears to occur at relatively low frequencies and may not be an immediate threat to the persistence of the imperiled native species; however, the presence of hybrid individuals warrants continued monitoring.