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HomeSouthern California Trout Genetic Study
(2010) California Department of Fish and Wildlife grant awarded to Trout Unlimited Chapter 920 (San Diego) for genetic analysis of rainbow trout populations in Southern California rivers and streams extending from Ventura County to San Diego County.

The primary objective of this study was to document the location and genetic lineage of existing rainbow trout populations in the southernmost extent of their native range to support ongoing and future steelhead recovery efforts. It was the first large-scale population genetic analysis of O. mykiss in this southern region that used statistical analysis of data from high resolution microsatellite and SNP genotypes. Over 600 caudal fin clips were collected from trout residing in twenty seven creeks and rivers spanning ten watersheds extending south from Montecito Creek, through the Santa Clara River watershed, to the Sweetwater River watershed in San Diego County. Prior to this study there was little data on trout in this geographic area. About 75 exploratory and tissue collection trips between 2010 and 2013 were performed throughout the southern watersheds by volunteers from the Trout Unlimited -San Diego Chapter and colleagues, and CDFW fisheries biologists. The tissue samples were submitted to the NOAA Fisheries Service Southwest Fisheries Science Center in Santa Cruz, where samples were processed and analyzed by staff of the Molecular Ecology and Genetic Analysis Team. Genotypes from individual trout sampled from focal populations were combined with those from previously genotyped O. mykiss populations throughout California, including seven hatchery rainbow trout strains and O. m. nelsoni, a subspecies of trout from Baja California, Mexico, for a total of 2,180 fish analyzed. This analysis identified two major classes of existing trout in this region, native coastal steelhead lineage and hatchery rainbow trout. The majority of the populations sampled were of hatchery descent. Only three groups of populations in the southernmost rivers contained significant evidence of native coastal steelhead ancestry: the San Luis Rey River in San Diego County, Coldwater Canyon Creek in the Santa Ana River watershed in Riverside County, and populations from the San Gabriel River in Los Angeles County, with the exception of the Iron Fork and Devil’s Canyon Creek populations. This study provided evidence that habitat conditions are sufficient in southern watersheds of the Southern California Steelhead Distinct Population Segment to support survival of trout that are of native coastal steelhead lineage. Although these trout historically migrated between the ocean and fresh water, they have been locked into their headwaters for many generations due to dam building, habitat degradation and low water flow. This study has now demonstrated where these native populations are and will help focus efforts by fisheries managers, policy makers and restoration workers to protect these populations and increase their numbers.

Final Report from Trout Unlimited – San Diego Chapter (Jacobson, Marshall, Dalrymple, Kawasaki, Pearse, Abadia-Cardoso and Garza; 3-31-2014) submitted to California Department of Fish and Wildlife / Fisheries Restoration Grant Program for Grant P0950015: Genetic Analysis of Trout (Oncorhynchus mykiss) in Southern California Coastal Rivers and Streams.