Genetic stock identification of steelhead in the Columbia River Basin: An evaluation of different molecular markers

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 (EST), 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.