Information developed during recently completed evaluations of the status of seven species of anadromous Pacific salmonids (Oncorhynchus spp.) in the Pacific Northwest was used to characterize patterns of intraspecific diversity along three major axes: ecology, life history and biochemical genetics. Within the study area, the species' ranges, and therefore the number of distinct ecological regions inhabited differ considerably, with pink and chum salmon limited to the northern areas and chinook salmon and steelhead distributed over the widest geographic range. The species showed comparable differences in the patterns of life history and genetic diversity, with chinook and sockeye salmon and steelhead having the most major diversity groups and pink, chum and coho salmon having the least. Both life history and genetic diversity showed a strong, positive correlation with the extent of ecological diversity experienced by a species, and the correlation between the number of major genetic and life history groups within a species was even stronger (r=0·96; P<0·05). Departures from these general diversity relationships found in some species (especially sockeye and coho salmon and cutthroat trout) can be explained by different interactions with the freshwater environment and, for cutthroat trout, by the occurrence of substantial intrapopulational diversity in life history traits, a hierarchical level not considered in this study.

A computer oriented approach to the collection and analysis of morphometric characteristics in juvenile chinook salmon (Oncorhynchus tshawytscha) is described. A three-step data collection and storage method is used whereby X–Y coordinate data for relevant morphological features on a body form are collected with a digitizing pad and used to calculate morphometric characters. To test this method, I calculated two morphometric data sets, a conventional and a truss network, and compared them by multivariate analysis in a preliminary study of growth and development in one hatchery stock of fish, and in a survey of population differences in three naturally occurring populations of chinook salmon. Technical advantages of using a digitizing pad for collecting morphometric data are demonstrated. Hatchery-reared chinook salmon showed marked changes in body shape during the period of spring smoltification when marked changes in condition factor occurred. Multivariate differences were discerned among the three Oregon coastal stocks. Truss data provided more specific information concerning shape changes in the study of early development and produced greater between-group differences in the geographic survey. The results of these preliminary analyses can be applied to problems of identifying smolt status in hatchery fish and stock origin in mixed-stock fisheries.

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 P0.95 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. Wrightˈs fixation index (FST) averaged 0.153 over 16 P0.95 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 genetic and reproductive distinctiveness of the two sympatric forms. Sockeye salmon from Redfish Lake (Sawtooth Valley, Idaho) were of particular interest because of their extensive freshwater migration and extremely low abundance in recent years. We found no evidence that any of the recorded stock transfers of O. nerka into the Sawtooth Valley (Redfish and Alturas lakes) have had a genetic impact on populations surveyed here. The O. nerka from Sawtooth Valley presently occupy a distinctive position in multilocus space, particularly with respect to mAH‐1,2*, mAAT‐l *, and ALAT*. Continued studies of O. nerka in the Sawtooth Valley are focusing on juvenile outmigrants and “residual” sockeye salmon.

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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 west Vancouver Island. An inland group included six subgroups: Nass River, Skeena River, north Thompson River, upper and mid‐Fraser River, south Thompson River, and lower Thompson River. The geographic extents of the inland and coastal groups largely coincided with the geographic distributions of stream‐ and ocean‐type juvenile forms and may reflect postglacial colonization by two ancestral lineages that survived in Pleistocene refugia. The presence of genetically undifferentiated stream‐type fish in coastal streams populated by ocean‐type fish may reflect either postglacial life history differentiation from ancestral ocean‐type fish or life history flexibility of ocean‐type fish.

Abstract– In contrast to the well‐known "lake‐type" sockeye salmon, two additional anadromous life‐history types have been recognized within the species: ‘river‐type’ sockeye salmon whose juveniles spend 1 or 2 years in off‐channel river habitats prior to migrating to sea, and “sea‐type” sockeye salmon that initially rear in similar river habitats yet migrate to sea as underyearlings. Persistent populations of river‐/sea‐type sockeye salmon occur in small numbers throughout the species’range in North America but are usually associated with glacier‐fed rivers. We found published and unpublished records showing that riverine‐spawning sockeye salmon occur in 11 rivers in western Washington, USA, that don't have access to juvenile lake‐rearing habitat. Evidence of persistent spawning was strongest for the Nooksack and Skagit rivers in northern Puget Sound. We analyzed allozyme frequency differentiation in 26 laketype and 12 river‐/sea‐type populations of sockeye salmon in North America, ranging from northern Puget Sound, Washington (including 3 in the Nooksack and Skagit rivers) to northern Southeast Alaska. Across this 2000 km range, river‐/sea‐type sockeye salmon showed very little genetic differentiation between populations, much less than that displayed by the highly divergent lake‐type sockeye salmon. Genetic similarity among river‐/sea‐type sockeye salmon in this study is likely a result of common ancestry and a high level of historical gene flow among river‐/sea‐type sockeye salmon populations.

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 (HT) values; but there was little difference among marker classes in the magnitude of population differentiation as estimated by Wright's fixation index (FST), 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, GSI estimates were more than 85% correct to the reporting group, the exact percentage depending on the marker data set and target group. Microsatellite loci provided the most accurate estimate (83%) in the 100% upper Columbia River ESU simulation, whereas simulation estimates for the 32‐locus allozyme baseline were 93–94% for the 100% middle Columbia River ESU and two Snake River management groups. The simulations also showed that the estimates improved substantially up to a sample size of 50 fish per population. Technical advances will concomitantly increase the number of useful microsatellite loci and the rate of laboratory throughput, making this class of molecular marker more valuable for GSI mixture analyses in the near future. In the meantime, we recommend that steelhead management in the Columbia River rely on both allozyme and microsatellite data for GSI procedures.