Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers

Abstract

Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant units (ESUs) and compare the performance of allozyme, microsatellite, and intron markers for use in GSI mixture analyses. As expected, microsatellites and introns had high total heterozygosity (HT) values; but there was little difference among marker classes in the magnitude of population differentiation as estimated by Wright's fixation index (FST), which ranged from 0.041 (microsatellite loci) to 0.047 (allozyme loci) and 0.050 (intron loci). For allozyme and microsatellite loci, the relationships among populations followed the patterns of geographic proximity. In computer‐simulated mixture analyses, GSI estimates were more than 85% correct to the reporting group, the exact percentage depending on the marker data set and target group. Microsatellite loci provided the most accurate estimate (83%) in the 100% upper Columbia River ESU simulation, whereas simulation estimates for the 32‐locus allozyme baseline were 93–94% for the 100% middle Columbia River ESU and two Snake River management groups. The simulations also showed that the estimates improved substantially up to a sample size of 50 fish per population. Technical advances will concomitantly increase the number of useful microsatellite loci and the rate of laboratory throughput, making this class of molecular marker more valuable for GSI mixture analyses in the near future. In the meantime, we recommend that steelhead management in the Columbia River rely on both allozyme and microsatellite data for GSI procedures.

Monitoring the Reproductive Success of Naturally Spawning Hatchery and Natural Spring Chinook Salmon in the Wenatchee River, 2008-2009 Progress Report.

“…All individuals were genotyped at 11 microsatellite loci: Ots3 (Banks et al 1999), Ots104 (Nelson & Beacham 1999), Ots201b, 211 and 213 (Greig et al 2003, Ots2M and10M (Greig & Banks 1999)), Ots519NWFSC (Naish and Park 2002), Oke4 (Olsen et al 1998), Ogo4 (Olsen et al 1998), and Ssa408 (Cairney et al 2000. Microsatellite loci were amplified by Polymerase Chain Reaction (PCR), allele sizes were electrophoreticly resolved and scored according to the method of Winans et al (2004 Ogo4,Ots2M,201b,and 211,Ssa408).…”

An improved method for predicting the accuracy of genetic stock identification

“…Highly polymorphic microsatellite loci have been shown to provide considerable power for GSI (Kalinowski 2004;Winans et al 2004). Declining costs of genotyping and the recent completion of a cross-laboratory, standardized, microsatellite DNA baseline for over 150 populations throughout the range of Chinook salmon ) have led to microsatellites replacing allozymes for many GSI applications.…”

Population genetics of steelhead (Oncorhynchus mykiss) in the Klamath River

“…1). However, in comparison with the Columbia River to the north (Kostow 2003, Brannon et al 2004, Winans et al 2004, relatively little is known about the relationships among steelhead populations within the Klamath River system (Israel et al 2003, Papa et al in press), or between them and other populations in the KMP-ESU (Riesenbichler et al 1992, Busby et al 1994). In addition, non-native stocks of O. mykiss have been widely planted in the basin, and large hatcheries exist on both the Klamath (Iron Gate Hatchery) and Trinity (Trinity River Hatchery) rivers.…”