Identification of rockfish (Sebastes spp.) by restriction site analysis of the mitochondrial ND-3/ND-4 and 12S/16S rRNA gene region


Gharrett, Anthony J., Andrew K. Gray, and Jonathan Heifetz
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Species-specific restriction site variation in the 12S/16S rRNA and ND-3/ND-4 mtDNA regions was used to distinguish among 15 rockfish species of the genus Sebastes common to the waters of Alaska. Intraspecific variation exhibited by eight of the species (based on five individuals of each species) did not obscure the interspecific variation, except possibly between S. zacentrus and S. variegatus. Intraspecific nucleotide diversity averaged 0.0024 substitutions per nucleotide, whereas interspecific nucleotide divergence averaged 0.0249. In contrast, the average nucleotide divergences between Sebastes and two other scorpaenid species, Helicolenus hilgendorfi and Sebastolobus alascanus, were 0.0805 and 0.1073, respectively. Cladistic and phenetic analyses supported some, but not all, of the subgenera assignments of Sebastes. A scheme for distinguishing among the species studied was presented. Restriction sites of 10 restriction endonucleases were mapped in the two PCR-amplified mtDNA regions by using double digests. In all, we detected 153 sites corresponding to 640 (13.5%) of the 4815 nucleotides in the two regions combined. The ND-3/ND-4 region exhibited substantially more intraspecific, interspecific, and intergeneric variation than the 12S/16S rRNA region.