Mitochondrial DNA Mixed-Stock Analysis of American Shad: Coastal Harvests Are Dynamic and Variable

Populations of American shad Alosa sapidissima are generally declining in size along the U.S. East Coast. Coastal harvest of migrating mixed-stock assemblages has been proposed as a possible cause of the decline, but the extent of fishing pressure on any particular stock has not been evaluated. To assess origin of shad harvested in the coastal fishery, we applied genetic mixed-stock analysis by using mitochondrial DNA (mtDNA) variation. We examined American shad from the coastal mixed fisheries off both Virginia and Maryland in 1992 and off Virginia alone in 1993 (N = 250 and 270, respectively), comparing mtDNA restriction fragment patterns for the coastal individuals with an archival database containing mtDNA genotypes of 1,734 individuals from 16 North American river stocks distributed from Florida to Canada. We used two different maximum-likelihood approaches to estimate the contributing-stock composition of oceanic mixtures, one yielding conditional estimates of stock composition, given observed haplotype frequencies, and the other yielding unconditional estimates and adjusted haplotype frequencies. The unconditional approach performed slightly better, but both statistical approaches indicated that composition of the coastal harvests was dynamic and variable from year to year and from location to location. For stocks contributing substantially to the fisheries, composition estimates derived through genetic analysis were roughly concordant with estimates based on returns from a concurrent tagging study.