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 to spring wetland samples in 2006 (26%). The results suggest that floodplain restoration projects intended to improve fish habitats during winter and spring periods in the lower Willamette River may benefit Chinook salmon populations from the upper Willamette River, lower Columbia River, and upper Columbia River summer-fall evolutionarily significant units.

Spatial and trophic overlap of marked and unmarked Columbia River Basin spring Chinook salmon during early marine residence with implications for competition between hatchery and naturally produced fish

“…Specifically, Chinook salmon were genotyped for 13 microsatellite loci that have been recently standardized among several Northeast Pacific genetics laboratories (Seeb et al 2007). A total of 4596 fin clip samples were genotyped using the protocols described by Teel et al (2009). The relative probability of stock origin was estimated for each sample using the likelihood model of Rannala and Mountain (1997), as implemented in the genetic stock identification software ONCOR (Kalinowski et al 2007).…”

Comparative Use of Shallow and Deepwater Habitats by Juvenile Pacific Salmon in the Columbia River Estuary Prior to Ocean Entry

“…Briefly, tissue storage and data collection followed the protocols of Teel et al (2009). Regional genetic stock groups were based on the standardized database of microsatellite DNA loci described by Seeb et al (2007) and on previous genetic studies of Chinook Salmon in the Columbia River basin (Waples et al 2004;Myers et al 2006).…”

“…Regional genetic stock groups were based on the standardized database of microsatellite DNA loci described by Seeb et al (2007) and on previous genetic studies of Chinook Salmon in the Columbia River basin (Waples et al 2004;Myers et al 2006). Baseline genetic data and stock groups were described in detail by Teel et al (2009Teel et al ( , 2014, Roegner et al (2010), and Johnson et al (2013). Proportional stock composition was estimated by using the likelihood model of Rannala and Mountain (1997) as implemented by the genetic stock identification program ONCOR (Kalinowski et al 2007).…”

Ecology of Juvenile Salmon in Shallow Tidal Freshwater Habitats of the Lower Columbia River, 2007?2010

“…Each fish was weighed and measured before tagging. Fin tissues from individual juvenile Chinook salmon were collected for genetic stock identification described by Teel et al (2009), which included genetic mixture analysis and the relative probability of stock origin of each sample as estimated using the genetic stock identification computer program ONCOR (Kalinowski et al 2007). During surgery, each fish was placed ventral side up and a gravity-fed anesthesia supply line was placed into its mouth.…”

“…We used standard methods of genetic stock identification and individual assignment (reviewed by Manel et al 2005). Chinook salmon were genotyped using the methods described by Teel et al (2009). Data were collected for 13 microsatellite loci that have recently been standardized among several West Coast genetics laboratories (Seeb et al 2007).…”