Restriction digest of PCR-amplified mtDNA from fin clips is an assay for sequence genetic "tags" among hundreds of fish in wild populations.

We tested the feasibility of recovering from wild populations mitochondrial DNA genetic "tags" that might result from release of hatchery-reared fingerlings for marine stock enhancement. A practical, nondestructive method of genetic "tag" recovery would allow quantitative assessment of the efficacy of such programs. A rare mtDNA variant with two sites each instead of one for TaqI and RsaI in the control region was used as a mock genetic "tag" in snook (Centropomus undecimalis). We assayed for the variant among nearly 900 fish by restriction digests of DNA amplified by polymerase chain reaction (PCR) obtained from fin-clip extracts, finding only a single second example of the variant. Thus, mtDNA "tags" can be nondestructively assayed for with specificity among hundreds of individuals.