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Performance of wild (W) and hatchery (H) spring Chinook salmon (Oncorhynchus tshawytscha) was evaluated for a sixth generation hatchery program. Management techniques to minimize genetic divergence from the wild stock included regular use of wild broodstock and volitional releases of juveniles. Performance of HH, WW, and HW (hatchery female spawned with wild male) crosses was compared in hatchery and stream environments. The WW juveniles emigrated from the hatchery at two to three times the rate of HH fish in the fall (HW intermediate) and 35% more HH than WW adults returned (27% more HW than WW adults). Performance in the stream did not differ statistically between HH and WW fish, but outmigrants (38% WW, 30% HW, and 32% HH fish) during the first 39 days of the 16-month sampling period composed 74% of total outmigrants. Differences among hatchery-reared crosses were partially due to additive genetic effects, were consistent with domestication (increased fitness for the hatchery population in the hatchery program), and suggested that selection against fall emigration from the hatchery was a possible mechanism of domestication.

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics and quantitative genetics.

We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analyses for the characterization of polymerase chain reaction products, in the identification of 11 novel single-nucleotide polymorphisms (SNPs) for distinguishing between rainbow trout Oncorhynchus mykiss and cutthroat trout O. clarkii. Single-nucleotide polymorphisms provide an important tool for species identification in studies of hybridization and introgression between these two species, but until now the time-consuming and costly nature of DNA sequencing has limited identification of new markers. The ability of HRM to accurately discern nucleotide changes in a DNA sequence make it a cost- and time-effective alternative to traditional sequencing for the detection of novel SNPs.

First-generation hatchery and wild spring Chinook salmon Oncorhynchus tshawytscha from the upper Yakima River, Washington, were placed into an artificial stream and allowed to spawn. Seven independent test groups were placed into the stream from 2001 through 2005. No differences were detected in the egg deposition rates of wild and hatchery females. Pedigree assignments based on microsatellite DNA, however, showed that the eggs deposited by wild females survived to the fry stage at a 5.6% higher rate than those spawned by hatchery females. Subtle differences between hatchery and wild females in redd abandonment, egg burial, and redd location choice may have been responsible for the difference observed. Body size did not affect the ability of females to spawn or the survival of their deposited eggs. How long a female lived was positively related to her breeding success, but female origin did not affect longevity. The density of females spawning in portions of the stream affected both egg depositio...

In all, 472 lingcod Ophiodon elongatus from six areas of Puget Sound, the Strait of Juan de Fuca, and the outer coast of Washington were assayed for 44 allozyme and 9 microsatellite DNA loci to investigate possible population subdivision. Levels of genetic variation at many of the allozyme loci and all of the microsatellite DNA loci were reasonably high, and there was no evidence of significant Hardy–Weinberg or linkage disequilibrium. Pairwise genotypic tests of population differentiation showed no evidence of genetic structuring among the 23 variable allozyme loci, the 9 microsatellite loci, or all 32 variable loci combined. The results of this investigation are consistent with the existence of a single genetic stock of lingcod throughout the greater Puget Sound region, including the Strait of Juan de Fuca and San Juan Islands. Despite the fact that most of the collections we analyzed did not consist of spawning fish from the spawning grounds, we believe that the combined absence of significant...

International audience; In 1997 the Cle Elum Supplementation Research Facility was established to enhance spring Chinook salmon returning to the upper Yakima River, Washington State. This effort increased spring Chinook abundance, yet conditions at the hatchery also significantly elevated the occurrence of jacks and yearling precocious males. The potential genetic effect that a large influx of early maturing males might have on the upper Yakima River spring Chinook population was examined in an artificial stream. Seven independent groups of fish were placed into the stream from 2001 through 2005. Males with four different life history strategies, large anadromous, jacks, yearling precocious, and sub-yearling precocious were used. Their breeding success or ability to produce offspring was estimated by performing DNA-based pedigree assessments. Large anadromous males spawned with the most females and produced the greatest number of offspring per mate. Jacks and yearling precocious males spawned with more females than sub-yearling precocious males. However, jacks, yearling and sub-yearling precocious males obtained similar numbers of fry per mate. In the test groups, large anadromous males produced 89%, jacks 3%, yearling precocious 7%, and sub-yearling precocious 1% of the fry. These percentages remained stable even though the proportion of large anadromous males in the test groups ranged from 48% to 88% and tertiary sex ratios varied from 1.4 to 2.4 males per female. Our data suggest that large anadromous males generate most of the fry in natural settings when half or more of the males present on a spawning ground use this life history strategy

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies.

Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washington, were placed into an artificial stream to evaluate the effect of a single generation of hatchery culture on their spawning behavior and ability to produce offspring. From 2001 to 2005, seven independent test groups containing wild and hatchery fish were placed into the stream. The effects of body weight, spawning ground longevity, attack frequency, social dominance, courting frequency, and mate number on breeding success in hatchery and wild males were evaluated. Male breeding success increased with body weight, while spawning ground longevity was negatively associated with breeding success. Although important, body weight had a lesser effect on male breeding success than did social dominance or attack frequency. Males with high attack and courting frequencies produced the most progeny; of the traits examined, the number of female spawning partners explained the greatest amount of variation (average r 2 = ...

Five microsatellite DNA loci (Ots-101*,Ots-107*,Oki-10*, Ogo-3*, and FGT-3*) were screened to evaluate the genetic characteristics and population structure for cutthroat trout from eight tributaries of the Pend Oreille River in northeastern Washington and to compare these collections with two hatchery stocks of westslope cutthroat trout, Oncorhynchus clarki lewisi, Yellowstone cutthroat trout, Oncorhynchus clarki bouvieri andahatchery rainbow trout, Oncorhynchus mykiss, strain that have been stocked in northeastern Washington. Relatively high levels of variation (numbers of alleles and heterozygosity) were observed in all collections and allele frequencies were quite variable among collections. Evidence of limited introgression by rainbow and/or Yellowstone cutthroat was found at several locations. Both FST values and tests of genetic differentiation indicated the existence of numerous, reproductively isolated populations. The population in Slate Creek was very similar to the Kings Lake Hatchery strain, and we conclude that this similarity is the result of historical introductions of this hatchery strain into what was presumably a stream without a native cutthroat population. In one stream, differences in introgression and allele frequencies were found above and below a barrier falls. Because of the substantial level of population differentiation observed among thevarious collections,werecommend that management and conservation actionsbefocusedatthelevelofindividual streams in order to maintain the productivity and genetic character of the existing populations of cutthroat trout.

Large-scale introductions of resident and anadromous salmonids from exogenous sources and urbanization have led to major changes in, and concern for the fate of, indigenous fish populations of the Lake Sammamish/Lake Washington Basin. Specifically, introductions of kokanee (the resident form of Oncorhynchus nerka) from the Lake Whatcom Hatchery and sockeye (the anadromous form of O. nerka) from Baker Lake have caused uncertainty about the ancestry of the kokanee that currently spawn in the basin. We used nine microsatellite loci to investigate the inter-relationships of kokanee populations that spawn in streams in the Sammamish sub-basin, sockeye salmon populations that share spawning areas with the kokanee, Lake Whatcom Hatchery kokanee and Baker Lake sockeye, and an outgroup, Meadow Creek kokanee, from Lake Kootenay which drains into the upper Columbia River. We observed high levels of genetic variation (5–49 alleles per locus). Explicit tests of population sub-division revealed that collections from most spawning aggregations differed from each other. Observed allele frequency distributions strongly suggest that natural spawning kokanee in the basin are not descended from recent Lake Whatcom stock introductions. We found no compelling evidence to suggest that the kokanee sampled from spawning areas within the Lake Sammamish sub-basin have resulted from, or been altered substantially by, past introductions of non-native kokanee or sockeye.