Microsatellite evidence for short-term stability in a hybrid zone between spring-run and fall-run Chinook salmon

Genetically distinct populations of spring-run and fall-run Chinook salmon (Oncorhynchus tshawytscha) inhabit the Trinity River, California and these two run types extensively hybridize. Levels of hybridization between these two runs are likely influenced by such anthropogenic factors as a dam and a hatchery, which were built in 1964. This study investigated whether levels of hybridization between the spring- and fall-runs over 12 years (3-4 generations) increased, decreased or remained stable. To evaluate levels of hybridization between these two populations, weekly samples of Chinook salmon returning to Trinity River Hatchery, were collected in 1992, 1994, and 2004, and genotyped at 11 microsatellite loci (N = 1001). Estimates of individual levels of admixture using STRUCTURE 2.0 were used to assess hybridization between the runs. Estimates of genetic differentiation in each sample year were weak (FST=0.004 for 1992, FST=0.011 for 1994, FST=0.004 for 2004), but significant (P0.05). Pairwise linkage disequilibrium events between loci were greatest during the presumed transition between runs, and occurred in a different week for each year. Consistency of trends in overall genetic differentiation (FST) and number of linkage disequilibrium events, combined with clinal similarities offered evidence for a stable hybrid zone over the last 12 years. A marked increase in linkage disequilibrium was associated with a decrease in water discharge coming from the dam, as well as an annual hatchery spawning hiatus aimed at avoiding matings between spring and fall runs, suggesting the possibility that levels of hybridization are influenced, to some degree, by the combination of hatchery practices, and the use of changes in flow by the salmon as a cue for upstream migration.