Molecular analysis of population genetic structure and recolonization of rainbow trout following the Cantara Spill

Mitochondrial DNA (mtDNA) sequence and allelic frequency data for 12 micros atellite loci were used to analyze population genetic structure and recolon ization by rainbow trout, Oncorhynchus mykiss, following the 1991 Cantara s pill on the upper Sacramento River, California. Genetic analyses were perfo rmed on 1,016 wild rainbow trout collected between 1993 and 1996 from the m ainstem and in 8 tributaries. Wild trout genotypes were compared to genotyp es for 79 Mount Shasta Hatchery rainbow trout. No genetic heterogeneity was found 2 years after the spill (1993) between tributary populations and geo graphically proximate mainstem fish, suggesting recolonization of the upper mainstem directly from adjacent tributaries. Trout collections made in 199 6 showed significant year-class genetic variation for mtDNA and microsatell ites when compared to fish from the same locations in 1993. Five years afte r the spill, mainstem populations appeared genetically mixed with no signif icant allelic frequency differences between mainstem populations and geogra phically proximate tributary trout. In our 1996 samples, we found no signif icant genetic differences due to season of capture (summer or fall) or samp ling technique used to capture rainbow trout, with the exception of trout c ollected by electrofishing and hook and line near Prospect Avenue. Haplotyp e and allelic frequencies in wild rainbow trout populations captured in the upper Sacramento River and its tributaries were found to differ geneticall y from Mount Shasta Hatchery trout for both years, with the notable excepti on of trout collected in the lower mainstem river near Shasta Lake, where m tDNA and microsatellite data both suggested upstream colonization by hatche ry fish from the reservoir, These data suggest that the chemical spill in t he upper Sacramento River produced significant effects over time on the gen etic population structure of rainbow trout throughout the entire upper rive r basin.