Genetic assignment of individuals to their population of origin has many management applications, such as forensic identification of protected species, estimation of migration rates, mixed-stock analysis, and assessment of hybridization. In this study, microsatellite markers were used to obtain an overview of population structure and foraging distribution patterns for a migratory cyprinid, the splittail Pogonichthys macrolepidotus. We (Baerwald et al. 2007) recently discovered that splittail inhabiting the San Francisco Estuary form two genetically distinct populations, the Petaluma-Napa and Central Valley populations, and individuals reassigned back to their respective populations with high accuracy (98%). In the present study, we genotyped 242 age-0 splittail from previously unexamined locations in Suisun Marsh and the Sacramento-San Joaquin Delta to determine whether they belonged to one of the two established populations or to a yet-unknown population; we also assigned foraging adults to their population of origin to determine whether they exhibited overlapping or segregated distribution patterns during the nonspawning season. We determined that these fish were members of the two established populations. Both populations foraged in Suisun Bay during the nonspawning season, whereas Suisun Marsh was almost exclusively used by the Central Valley population. The Petaluma-Napa population was considerably more abundant in the western portion of Suisun Bay and appeared to preferentially forage closer to its spawning grounds. The results indicate that the distributions of the two splittail populations do not entirely overlap during spawning and foraging; this finding has important implications for the conservation and management of the species.
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