Conservation and Genetic Stock Identification: A Study Investigating the Stock-Specific Distribution and Performance of Juvenile Chinook Salmon in the Columbia River Estuary

Research, management and conservation of salmon populations have primarily targeted the freshwater phase of the salmon lifecycle, however recent attention has focused on the importance of the estuarine and ocean phases in the abundance and distribution of Pacific salmon (Brodeur et al. 2000). One potentially critical and interesting life-history phase of Pacific salmon is early entry into salt water (Casillas 1999). Coded wire and PIT tag recoveries, scale analysis and length at age data have all provided insight into the use of estuarine and nearshore habitats by juvenile salmonids. Nevertheless, there are significant gaps in our understanding of how and when juveniles use these environments. The research presented here is the genetic component of a multidisciplinary, multiagency collaboration investigating the stock-specific temporal and spatial distribution of juvenile chinook salmon (Oncorhyncus tshawytscha) in the Columbia River estuary. The first goal of our study was to establish a Columbia River microsatellite genetic baseline to evaluate genetic structure and differentiation among populations and evolutionarily significant units (ESUs) of chinook salmon in the Columbia River basin. The second goal of the study was to use the genetic baseline and individual assignment tests to identify putative source populations and ESUs of juvenile chinook salmon mixtures sampled at different spatial and temporal scales in the Columbia River estuary. We collected genotypes at eight microsatellite loci for 3,04