Transactions of the American Fisheries Society 132:997–1013, 2003 q Copyright by the American Fisheries Society 2003 Genetic and Phenotypic Evidence of Reproductive Isolation

Abstract.—The effective conservation of salmonids requires the recognition and preservation of populations that are diverse in genetic composition and life history. The management of sockeye salmon Oncorhynchus nerka in Bear Lake, Alaska, is based on the presumption that there are two, genetically isolated seasonal runs that exhibit a bimodal escapement pattern. We investigated the genetic composition and life history of the putative early and late runs in two consecutive years. Significant allele frequency differences at six microsatellite loci demonstrate restricted gene flow between the early and late runs (FST 5 0.017). There were also significant, and presumably adaptive, differences between the runs with respect to body weight, somatic weight, ovary weight, and egg size among females after correction to equal body sizes. Further, scale pattern analysis revealed highly significant differences in the growth-at-age patterns of these runs. These results demonstrate that there are significant genetic differences between seasonal runs of sockeye salmon and provide support for the management strategy that has been employed for nearly 20 years to protect the genetic diversity of this species in Bear Lake. Precise natal homing in Pacific salmon Oncor-hynchus spp. has resulted in the development o