Population genetics and conservation implications for the endangered delta smelt in the San Francisco Bay-Delta

Over the last two decades, the collapse of the endangered delta smelt (Hypomesus transpacificus) in the San Francisco Bay-Delta has resulted in politically charged conservation decisions, including the rationing of valuable Delta water for use in California agriculture and urban centers. A fundamental question remaining in delta smelt conservation is whether current management strategies have been appropriately designed to protect the remaining genetic variation in delta smelt populations, rather than merely mitigating the decline of the species. We used 15 microsatellite markers to characterize genetic variation within and among sampling regions on geographic and temporal scales, to estimate changes in effective population size over time, to determine if a genetic bottleneck exists and to define conservation management units for this species. A genetic bottleneck was detected in each of the four sampling years, and a significant decline in effective population size was observed between sampling years 2003 and 2007. We also detected a weak geographic signal in any given sampling year that was unsupported by temporal consistency of this signal. We assessed two strategies for defining conservation units, and concluded that continuing to manage the species as a single, panmictic population throughout its range is the most feasible management strategy. The results of this study will inform conservation decisions and provide an effective means for genetically monitoring this imperiled species.