Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California

Abstract

Genetic analyses of coastal Oncorhynchus mykiss, commonly known as steelhead/rainbow trout, at the southern extreme of their geographic range in California are used to evaluate ancestry and genetic relationships of populations both above and below large dams. Juvenile fish from 20 locations and strains of rainbow trout commonly planted in reservoirs in the five study basins were evaluated at 24 microsatellite loci. Phylogeographic trees and analysis of molecular variance demonstrated that populations within a basin, both above and below dams, were generally each other's closest relatives. Absence of hatchery fish or their progeny in the tributaries above dams indicates that they are not commonly spawning and that above-barrier fish are descended from coastal steelhead trapped at dam construction. Finally, no genetic basis was found for the division of populations from this region into two distinct biological groups, contrary to current classification under the US and California Endangered Species Acts.

Disruption of historical patterns of isolation by distance in coastal steelhead

“…In the case of coastal California steelhead, data from 18 microsatellite loci in 60 modern populations documented moderate IBD (R 2 = 0.193, P \ 0.01; R 2 = 0.191, n.s. when only the eight populations studied here are considered; Garza et al 2004;Clemento et al 2009). While these nuclear data suggest a slightly stronger correlation between geographic and genetic distance than do our modern mtDNA sequences, they are consistent with the hypothesis that the historically-strong IBD we document here has been greatly reduced over the past hundred years.…”

“…Dams on the San Antonio and Nacimiento Rivers further disrupt migration to these tributary streams, and dams and other diversion structures also affect migration on Coyote Creek and the Pajaro River tributaries (Uvas and Llagas Creeks). Microsatellite data indicate that southern California O. mykiss populations above dams are primarily descended from steelhead trapped at construction and not from the hatchery rainbow trout subsequently released into the dam reservoirs, although some introgression has occurred (Clemento et al 2009). However, other studies that have compared pre-and poststocking genetic composition of salmonid populations have shown a range of genetic changes following stocking (e.g.…”

Rangewide microsatellite phylogeography of the endangered tidewater goby, Eucyclogobius newberryi (Teleostei: Gobiidae), a genetically subdivided coastal fish with limited marine dispersal

“…The southernmost Southern California Steelhead Unit south of the Santa Maria River is federally listed as endangered. However, this unit is gradationally distinguished in terms of F ST values and proportional differences in the alleles present, for both mitochondrial control region and microsatellites (Nielsen et al 1994;Clemento et al 2008). Examination of any single genetic locus does not appear to permit the diagnosis of individual southern steelhead.…”

“…The steelhead ESUs were also partly defined by their migratory (anadromous) habit, and freshwater populations had been excluded. However, recent genetic evidence does not distinguish freshwater resident populations from the migratory stocks (Clemento et al 2008). Thus, the migratory portions are now defined as Distinct Population Segments (DPS) rather than ESUs since they lack a distinct evolutionary trajectory from the freshwater forms (National Marine Fisheries Service 2007).…”

Texture Quality Analysis of Rainbow Trout Using Hyperspectral Imaging Method

“…Rainbow trout (Oncorhynchus mykiss, formerly named Salmo gairdneri) is one of the salmonid species which is native to tributaries of the Pacific Ocean in Asia and North America range from Alaska to Mexico (1,2). The Rainbow trout flesh is tender with a tasty and nutty flavor which made this fish very popular in chain food in all over the world (3).…”