Diagnostic Single-Nucleotide Polymorphisms Identify Pacific Ocean Perch and Delineate Blackspotted and Rougheye Rockfish

Diagnostic single-nucleotide polymorphisms (SNPs) that delineate Pacific ocean perch Sebastes alutus from other rockfish species and distinguish rougheye rockfish S. aleutianus and blackspotted rockfish S. melanostictus were developed from restriction endonuclease site differences in mitochondrial DNA sequences. The SNP developed for Pacific ocean perch was specific to that species in a panel of adult rockfishes common in Alaskan waters and positively recognized all of 994 adult specimens for reactions in which polymerase chain reaction product was obtained. Species-specific microsatellite alleles (Sma6) and SNPs were concordant in 113 blackspotted and 26 rougheye rockfish. Five additional individuals were heterozygous for the microsatellite alleles and are presumably hybrids. These SNP markers, which are substantially faster to assay and much less labor-intensive than restriction site analyses, can be used to identify individuals of any life stage during abundance surveys and provide necessary species identification in ecological and life history studies.