Application of genetic markers to provide species identification and define stock structure: Analyses of selected marine fishes of the Mid -Atlantic Bight

Molecular markers and techniques were employed to develop a genetic key for the forensic identification of 16 species of Chesapeake Bay sportfishes and to investigate the stock structure of one of those species, the weakfish Cynoscion regalis. Regions within the ATP synthetase 6 (ATPase 6), Cytochrome b , cytochrome c oxidase I, NADH dehydrogenase 4 (ND4), and 12S/16S ribosomal RNA mitochondrial genes were amplified using the polymerase chain reaction (PCR) and digested with a bank of restriction endonucleases to find a genetic marker that exhibited complete interspecific differentiation and low intraspecific variation. Complete separation of all sixteen species was accomplished by restriction fragment length polymorphism (RFLP) analysis of an approximately 1495 bp region of the 12S/16S ribosomal RNA mitochondrial genes with the single endonuclease Rsa I. Ten species exhibiting a single digestion pattern and the remaining six were dimorphic. Analyses of four microsatellite loci and two nuclear intron regions were used to investigate the genetic basis of population structure of weakfish collected at five locations along the U.S. East Coast. Microsatellite mean expected heterozygosities ranged from a low of 8.5% for the SOCO14 marker to a high of 92.8% for the CNE612 locus. Mean expected heterozygosities for the CRESIA1 and RP2 intron regions were 5.1% and 24.0%, respectively. None of the sample genotype distributions differed significantly from Hardy-Weinberg expectations, and pairwise FST values were consistently low (0.000--0.087 for microsatellite loci, 0.000--0.050 for intron regions). Analyses of molecular variance (AMOVA) and exact F permutation tests of sample heterogeneity were nonsignificant for all loci. Evaluation of some individuals in the Georgia 1997 sample exhibiting unusually small allele sizes using the previously developed genetic key based on the 12S/16S rRNA marker revealed that two other species of Cynoscion , the sand seatrout C. arenarius and the silver seatrout C. nothus, had been inadvertently included in the sample of YOY weakfish. Based on data from the mitochondrial marker and the SOC050 microsatellite locus, a number of the Georgia 1997 fish were identified as hybrid offspring of weakfish and sand seatrout crosses