Gary A. Winans

Genetic Approaches to the Management of Pacific Salmon

Abstract The complex problems involved in managing Pacific salmon (Oncorhynchus spp.) are largely a consequence of the unusual life history features of these species. The strong homing instinct leads to the formation of discrete, locally-adapted spawning populations, each of which has the potential to evolve as an independent evolutionary unit. It is important, therefore, that the genetic consequences of different management policies be carefully evaluated. If current management goals (e.g., doubling the abundance of anadromous salmonids in the Columbia River basin through increased hatchery production and supplementation of natural populations) are realized, genetic issues will assume even greater importance in the future. To date, however, genetic concerns have not been adequately incorporated into the management process. We identify three genetic approaches, primarily based on easily obtained electrophoretic data, that can provide valuable information on which to base management decisions: (1) Using th...

Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers

Abstract Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant units (ESUs) and compare the performance of allozyme, microsatellite, and intron markers for use in GSI mixture analyses. As expected, microsatellites and introns had high total heterozygosity (H T) values; but there was little difference among marker classes in the magnitude of population differentiation as estimated by Wrights fixation index (F ST), which ranged from 0.041 (microsatellite loci) to 0.047 (allozyme loci) and 0.050 (intron loci). For allozyme and microsatellite loci, the relationships among populations followed the patterns of geographic proximity. In computer-simulated mixture analyses,...

Genetic Population Structure and Origin of Life History Types in Chinook Salmon in British Columbia, Canada

Abstract We used protein electrophoresis to examine genetic population structure and origin of life history types of chinook salmon Oncorhynchus tshawytscha in British Columbia, Canada. Among 31 allozyme loci resolved in 91 samples from 63 populations of chinook salmon in rivers and hatcheries throughout British Columbia, population heterozygosities averaged 0.084 (range 0.048–0.108) and were typical of values for populations in other regions. A hierarchical gene diversity analysis indicated that 91.3% of the total allele-frequency diversity was attributable to within-population variability; the remaining 8.7% was attributable to geographic variability among populations, which was partitioned into among-river (3.3%), among-area (3.5%), and among-region (1.9%) components. Two major groups of populations appeared in the principal components analysis and in cluster analysis of genetic distances. A coastal group included populations in four subgroups: Central coast, Georgia Strait, lower Fraser River, and wes...

Allozyme Variability of Oncorhynchus nerka in the Pacific Northwest, with Special Consideration to Populations of Redfish Lake, Idaho

Abstract We resolved allozyme variation among 28 enzymes encoded by 58 protein loci in 27 samples of sockeye salmon and kokanee Oncorhynchus nerka in the Pacific Northwest. Of 32 polymorphic loci, 16 were polymorphic at the P 0.95 level (frequency of the common allele ≤0.95). We found substantial variation at mAAT-1* and mAH-1,2*, loci not previously described in O. nerka in this portion of its distribution. Mean heterozygosity per sample ranged from 0.010 to 0.036 and averaged 0.028 over all samples. Wrights fixation index (F ST) averaged 0.153 over 16 P 0.95 loci, indicating considerable allele frequency variation among samples. The pattern of population differentiation of sockeye salmon, as revealed through genetic distance and principal component analyses, resembled a mosaic in that nearest geographic neighbors were not necessarily similar genetically. Allele frequencies at two to five loci differed significantly between sympatric sockeye salmon and kokanee in three separate localities, indicating ge...

An Update of Genetic Stock Identification of Chinook Salmon in the Pacific Northwest: Test Fisheries in California

Analyzing the stock composition of mixed-stock fisheries using genetic stock identification (GSI) procedures was developed for chinook salmon in the early 1980s when an incipient baseline was focused in the Columbia River basin. The current coastwide baseline of allozyme (protein) genetic loci includes approximately 75% of the major contributing populations from California to western Alaska for over 30 polymorphic loci. We review the 2-decade history of GSI studies of chinook salmon in fishery applications in the Pacific Northwest. By summarizing GSI results for four test fisheries in California, we demonstrate the use of a regional segment of the current baseline to monitor critically depleted stocks. Average FST is 0.099, with 12 loci FST > 0.05, in a 28 locus/53 population dataset from southern Oregon to southern California. Seven stock groups are recognized based on a multilocus pattern of differentiation that coincides with watersheds and coastal affiliations. Simulated mixture analyses indicate that stock groups are well resolved: percent correct assignment is 83% for Central Valley spring-run, but >92% for all other groups. Simulated mixture analyses also indicated that it is difficult to distinguish between mixtures with low levels (<1%) of Central Valley winter- or spring-run stocks given the present dataset. GSI estimates for four test fisheries indicate that Central Valley fall- and late fall-run chinook salmon comprised the majority of each mixture (89 to 95%). Critical or endangered stock groups were detected in test fisheries in the 1997 Point Conception fishery (3% Sacramento River winter-run) and in the 1999 Bodega Bay fishery (2.8% Upper Klamath-Trinity rivers). Preliminary regional baselines for intron and microsatellite loci show promise for added stock discrimination among chinook salmon populations. GSI projects are increasingly involving multiple agencies and using multicharacter procedures. Continued GSI

Genetic Variability in Chinook Salmon Stocks from the Columbia River Basin

Abstract Levels of allozymic variability at 33 protein loci are reported for juvenile chinook salmon Oncorhynchus tshawytscha collected at 28 locations in the Columbia River basin. Fish were classified as spring, summer, or fall run types, depending on time adults reentered the river. Average heterozygosity per sample (H) ranged from 0.023 to 0.097; H over all samples was 0.070 (0.003 SE). On average, fall-run chinook salmon had significantly greater H values than the springor summer-run fish. Spring-run chinook salmon from the Snake River had the lowest values of H (mean, 0.044) in relation to other stocks of spring-run fish, i.e., almost 50% less allozymic variability than spring-run chinook salmon in the lower Columbia River. The probable cause for low levels of heterozygosity in these upriver populations is an increased frequency of natural and humanrelated population bottlenecks. Measures are recommended for hatcheries to maintain effective population sizes and thereby minimize the loss of genetic va...

Population Genetic Structure and Life History Variability in Oncorhynchus nerka from the Snake River Basin

Abstract We used the variation at 64 allozyme loci to examine genetic relationships among 32 samples of sockeye salmon Oncorhynchus nerka and kokanee (resident sockeye salmon) from the Snake River basin and other North American locations. The genetic differentiation among populations was pronounced: Wrights F ST was higher (0.244) than has been reported in any other study of Pacific salmon. A detailed examination of the O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve the relationships between the resident and anadromous forms. In Redfish Lake, adult sockeye salmon that returned in 1991–1993 were genetically distinct from local kokanee but similar to a small group of “residual” sockeye salmon discovered in the lake in 1992. This result is consistent with the hypothesis that the original sockeye salmon population was not extirpated by Sunbeam Dam early in this century. Populations of O. nerka t...

Allozyme Studies of Pacific Salmonids with Nonlethal Sampling of Fin Tissue

Abstract We evaluated the use of nonlethal sampling of bony fin tissue to obtain allozyme data for Pacific salmonids Oncorhynchus spp. Enzyme activity was detected for 53 loci, including many polymorphic loci, in caudal fin tissue sampled from chinook salmon O. tshawytscha, chum salmon O. keta, coho salmon O. kisutch, sockeye salmon O. nerka, and steelhead O. mykiss. This represents 61% of all the loci (N = 87) routinely analyzed using eye, heart, liver, and muscle tissue. Anal, dorsal, caudal, pelvic, and pectoral fin tissues all expressed the same loci with approximately the same strength of activity. Fin tissue sampled from adult salmonids yielded a slightly greater number of loci than did juvenile samples. Sufficient allozyme activity was observed for 9 mg of juvenile chinook salmon and steelhead fin tissue for some loci; however, the minimal amount of tissue needed to obtain all detectable loci was 54 mg. We performed computer simulations to test the feasibility of using allozyme data from fin tissue...

A Genetic and Phenetic Baseline before the Recolonization of Steelhead above Howard Hanson Dam, Green River, Washington

Abstract In 2011, steelhead Oncorhynchus mykiss (anadromous rainbow trout) will be systematically transported above Howard Hanson Dam, Green River, Washington. We are interested in providing data to help manage the stock of fish that are selected to recolonize the upper river and to track how resident rainbow trout above the dam respond genetically after 80 years of isolation. We characterized relevant gene pools in the upper Green River before fish transportation with 11 microsatellite loci to evaluate the genetic variability within and among collections. We also examined morphometric and coloration patterns as potential indicators of adaptive variation. Hatchery steelhead are clearly different from wild steelhead (F ST = 0.037); genetic assignment tests correctly distinguished 91% of the steelhead. While there was no reduction in the amount of genetic variability in the resident rainbow trout above Howard Hanson Dam compared with that of wild steelhead collections below the dam, the two groups had low b...

Allozyme variability of Oncorhynchus nerka in Japan

We examined allozymic variation in 65 protein-coding loci in three samples of sockeye salmon (Oncorhynchus nerka) from Hokkaide, and Honshu, Japan, Over-all, six variable loci were seen and each of the three samples was variable at 3–5 loci. Two loci,mAH-1,2* andALAT*, were variable at the P0,95 level. Average heterozygosity ranged from 0.012 to 0.013, representing some of the lowest recorded values for the species. Although frequencies ofALAT* alleles differed significantly among the three samples, the overallχ2 for six polymorphic loci was not statistically significant. New data for four Russian samples at 45–64 loci were also obtained. In comparison to the Japanese samples, three samples from the Kamchatka Peninsula had two to three times the level of variation; and a sample from Iturup Island (Kuril Island archipelago) was slightly more variable. Although the anadromous sockeye salmon were originally planted from Iturup Island to Lake Shikotsu, a close genetic affinity was not indicated. These seven samples ofO. nerka were compared with representative samples previously studied in North America using five polymorphic loci. Two large groups of samples were indicated in multilocus analyses: 1) a cluster of the seven Asian samples, one Alaskan sample, and one northern British Columbia sample; and 2) a group that included a southern British Columbia sample (Fraser River), and samples from the Columbia River and Washington. We discuss these findings in light of maintaining viable populations of both forms ofO. nerka.