Genetic Stock Composition of Subyearling Chinook Salmon in Seasonal Floodplain Wetlands of the Lower Willamette River, Oregon

Abstract We used genetic identification methods to examine the stock composition of subyearling Chinook salmon Oncorhynchus tshawytscha in floodplain wetland and main-stem habitats of the lower Willamette River, Oregon. Using a microsatellite DNA baseline of 13 standardized loci and 30 Columbia River basin populations, we analyzed 280 subyearlings collected in winter and spring 2005-2006 from wetland and main-stem river sites. Genetic stock identification analysis indicated that spring Chinook salmon originating from the Willamette River made up a substantial proportion of the samples and contributed 16-71% to sample mixtures representing the wetland habitat sites. Fall Chinook salmon from lower Columbia River sources were also present and contributed 58% of winter samples. Spring Chinook salmon from lower Columbia River populations were present in both wetland (17%) and river (16%) samples in spring 2005, and subyearlings from summer-fall-run populations in the middle and upper Columbia River contributed...