Abstract
Author(s): Pearse, Devon E.; Garza, John Carlos | Abstract: Steelhead/rainbow trout (Oncorhynchus mykiss) are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and enter the ocean through San Francisco Bay and the Golden Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon and trout hatchery propagation has been occurring for over 100 years. We collected genotype data for 18 highly variable microsatellite loci and 95 single nucleotide polymorphisms (SNPs) from more than 1,900 fish from Central Valley drainages to analyze genetic diversity, population structure, differentiation between populations above and below dams, and the relationship of Central Valley O. mykiss populations to coastal California steelhead. In addition, we evaluate introgression by both hatchery rainbow trout strains, which have primarily native Central Valley ancestry, and imported coastal steelhead stocks. In contrast to patterns typical of coastal steelhead, Central Valley O. mykiss above and below dams within the same tributary were not found to be each others’ closest relatives, and we found no relationship between genetic and geographic distance among below-barrier populations. While introgression by hatchery rainbow trout strains does not appear to be widespread among above-barrier populations, steelhead in the American River and some neighboring tributaries have been introgressed by coastal steelhead. Together, these results demonstrate that the ancestral population genetic structure that existed among Central Valley tributaries has been significantly altered in contemporary populations. Future conservation, restoration, and mitigation efforts should take this into account when working to meet recovery planning goals.
Highlights
IntroductionThe Central Valley of California supports both Chinook salmon (Oncorhynchus tshawytscha) and fish from the species O. mykiss, commonly knownSAN FRANCISCO ESTUARY & WATERSHED SCIENCE as steelhead (anadromous life history) or rainbow trout (resident life history)
The Central Valley of California supports both Chinook salmon (Oncorhynchus tshawytscha) and fish from the species O. mykiss, commonly knownSAN FRANCISCO ESTUARY & WATERSHED SCIENCE as steelhead or rainbow trout
These Distinct Population Segments (DPSs) include only anadromous life-history fish that spawn below impassable barriers to migration; O. mykiss isolated above natural or artificial barriers to fish passage are excluded from the DPS and, from protection under the U.S Endangered Species Act (ESA; Federal Register 2006)
Summary
The Central Valley of California supports both Chinook salmon (Oncorhynchus tshawytscha) and fish from the species O. mykiss, commonly knownSAN FRANCISCO ESTUARY & WATERSHED SCIENCE as steelhead (anadromous life history) or rainbow trout (resident life history). Much of the flow in the system is diverted for agricultural and domestic uses through an extensive system of levees and aqueducts Together, these effects have severely modified and reduced the habitat available to anadromous fishes (Lindley et al 2006). Populations of steelhead in California are divided into six Distinct Population Segments (DPSs) for management purposes; five on the coast and one in the Central Valley (Busby et al 1996) These DPSs include only anadromous life-history fish that spawn below impassable barriers to migration; O. mykiss isolated above natural or artificial barriers to fish passage are excluded from the DPS and, from protection under the U.S Endangered Species Act (ESA; Federal Register 2006). This DPS was listed as “Threatened” under the ESA in 1998 and this status was reaffirmed in 2006 (Federal Register 2006)
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