Genetic Identification of Chinook Salmon in the Columbia River Estuary: Stock-Specific Distributions of Juveniles in Shallow Tidal Freshwater Habitats

Abstract

Extensive efforts are underway to restore and conserve nearshore shallow water habitats in the Columbia River estuary with the intent of increasing the estuary's capacity to provide food, refuge, and other crucial ecosystem functions for juvenile salmon. Juvenile Chinook Salmon Oncorhynchus tshawytscha, including those from the five Evolutionarily Significant Units listed as threatened or endangered under the U.S. Endangered Species Act, are particularly expected to benefit from the habitat improvements. However, information on the temporal and spatial estuarine distributions of juveniles from specific populations or stocks is lacking and impedes restoration planning for at-risk salmon. We conducted a series of surveys to sample juvenile Chinook Salmon occupying shallow-water habitats with sandy beaches in six hydrogeomorphic reaches across the tidal freshwater portion of the estuary and also at one long-term reference site near the estuary mouth. Sites were sampled bimonthly over 26 months during 2010–2012 to capture seasonal patterns of stock-specific habitat use. Genetic stock identification analyses were conducted on the samples using microsatellite DNA loci and genotypic data representing spawning populations from throughout the Columbia River basin. We identified three tidal freshwater areas that could be distinguished by genetic stock composition. Lower tidal freshwater reaches were dominated by fall-run juveniles from West Cascade tributaries (>70%), upper reaches had a large proportion of fish from the upper Columbia River summer–fall stock (>60%), and middle reaches were characterized by greater stock diversity with no single stock contributing more than 30% in each reach. Stock-specific juvenile habitat use differed by season, life history type, and between natural and hatchery-produced fish. Data from this study provide improved descriptions of the near-shore estuary habitat use of several Columbia River genetic stocks of Chinook Salmon that can assist managers in the design and selection of estuary restoration projects.

Received November 11, 2013; accepted February 18, 2014

ACKNOWLEDGMENTS

We thank Andrew Claxton, Meegan Corcoran, Brian Kelly, Rick Nelson, Elizabeth Phillips, and Katrina VanRaay for assistance with field work and Mary Ramirez for help with graphics. We also thank Don Van Doornik and Laurie Weitkamp for constructive reviews of the manuscript. We appreciate the contribution of Cynthia Studebaker, technical lead for the U.S. Army Corps of Engineers, who along with NOAA Fisheries provided funding for this study.