Sacramento splittail (Pogonichthys macrolepidotus ) is an endemic cyprinid of the San Francisco Estuary watershed and a federal and California Species of Special Concern. This population genetic study of splittail was conducted to enable more informed conservation management decisions for the species. The first stage of this project was development of molecular markers capable of elucidating individual and population-level genetic relationships (Chapter 1). Primers were designed for 105 loci and tested for levels of polymorphism in five cyprinid species native to California: Sacramento splittail, Sacramento pikeminnow, tui chub, hitch, and Sacramento blackfish. Fifty-one loci were polymorphic for at least one species and 31 loci were polymorphic for multiple species. The number of polymorphic loci per species ranged from 16 to 26.

To assess splittail population structure, 13 of the characterized microsatellite markers were used to genotype young-of-the-year splittail from five major rivers draining into the estuary: Cosumnes, Napa, Petaluma, Sacramento, and San Joaquin rivers (Chapter 2). Two genetically distinct populations were found to exist within our study region; one largely comprised of splittail collected from the Petaluma and Napa rivers and the second comprised of splittail collected from tributaries in California's Central Valley: Cosumnes, Sacramento, and San Joaquin rivers. The microsatellite markers were also used to obtain an overview of foraging distribution patterns for splittail during the non-spawning season (Chapter 3). Individual foraging adults were genetically assigned to their population of origin to determine if adults exhibit overlapping or segregated distribution patterns during the non-spawning season. Both populations were found to forage in the Suisun Bay while, almost exclusively, only the Central Valley population utilized the Suisun Marsh during the non-spawning season. These results will enable more effective conservation management for the splittail.