Ruth E. Withler

Estimation of Stock Composition and Individual Identification of Sockeye Salmon on a Pacific Rim Basis Using Microsatellite and Major Histocompatibility Complex Variation

Abstract The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of kn...

Stock Identification of Fraser River Sockeye Salmon Using Microsatellites and Major Histocompatibility Complex Variation

Abstract The utility of DNA-based variation for stock identification was evaluated for Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was determined from approximately 13,000 fish from 47 populations in the drainage. Genetic differentiation among the populations was observed, the overall F ST value for the 14 microsatellite loci surveyed being 0.054 and that for the MHC locus being 0.215. The variation among regions and populations within regions was approximately 20 times as great as that of the annual variation within populations for the microsatellite loci and 28 times as great for the MHC locus. The power of a microsatellite locus for population-specific identification in simulated mixture samples was positively correlated with the number of observed alleles at the locus. Analysis of simulated mixtures indicated that the mean percentage error of estimated stock compositions was less than ...

Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon

Polymorphism of the nucleotide sequences encoding 149 amino acids of linked major histocompatibility complex (Mhc) class II 131 and 132 peptides, and of the intervening intron (548–773 base pairs), was examined within and among seven Pacific salmon (Oncorhynchus) species. Levels of nucleotide diversity were higher for theB1 sequence than forB2 or the intron in comparisons both within and between species. For the codons of the peptide binding region of the BI sequence, the level of nonsynonymous nucleotide substitution (dN) exceeded the level of synonymous substitution (dS) by a factor of ten for within-species comparisons, and by a factor of four for between-species comparisons. The excess of dN indicates that balancing selection maintains diversity at this salmonidMhc class II locus, as is common forMhc loci in other vertebrates. Levels of nucleotide diversity for both the exon and intron sequences were greater among than within species, and there were numerous species-specific nucleotides present in both the coding and noncoding regions. Thus, neighbor-joining analysis of both the intron and exon regions provided phylogenies in which the sequences clustered strongly by species. There was little evidence of shared ancestral (trans-species) polymorphism in the exon phylogeny, and the intron phylogeny depicted standard relationships among the Pacific salmon species. The lack of shared allelicB1 lineages in these closely related species may result from severe bottlenecks that occurred during speciation or during the ice ages that glaciated the rim of the north Pacific Ocean approximately every 100 000 years in the Pleistocene.

Variation in Body Size, Morphology, Egg Size, and Biochemical Genetics of Pink Salmon in British Columbia

Abstract Stocks of pink salmon Oncorhynchus gorbuscha in British Columbia that were spawning from August through October 1982–1985 in rivers of different size were surveyed for variation in size, morphology, egg weight, and biochemical genetics. Fish that spawned in large rivers were longer and had proportionately larger heads, thicker caudal peduncles, and larger fins than those that spawned in small rivers. Differences in gill raker counts between the broodlines (i.e., fish spawned in even-numbered years versus those spawned in odd-numbered years) were greater than among stocks within broodlines. Differences in morphometric characters were greater among stocks within broodlines than between broodlines; this indicated morphometric adaptation to local conditions in the natal river. As the spawning season progressed, mean lengths of males and females and weight of eggs increased. Electrophoretic analysis indicated that in the odd-year broodline, pink salmon could be generally distinguished as originating f...

Estimation of Stock Composition and Individual Identification of Chinook Salmon across the Pacific Rim by Use of Microsatellite Variation

Abstract Variation at 13 microsatellite loci was surveyed for over 52,000 Chinook salmon Oncorhynchus tshawytscha sampled from 325 localities ranging from Russia to California; the variation was applied to estimate stock composition in mixed-stock fishery samples. A rapid increase in the accuracy of estimated stock composition in simulated mixtures with respect to population sample size was observed for sample sizes of up to about 75 individuals, at which point a 90% accuracy of assignment to population was achieved. The number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of the stock composition of single-population mixtures. In analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 75% accuracy for the average population was achieved by employing approximately 55 alleles in the analysis. Increasing the accuracy of the estimated stock composition to 90% for the average population requir...

Evaluation and Application of Microsatellite and Major Histocompatibility Complex Variation for Stock Identification of Coho Salmon in British Columbia

Abstract Variation at eight microsatellite loci and two linked exons of a major histocompatibility complex (MHC) locus was surveyed in approximately 21,000 coho salmon Oncorhynchus kisutch sampled from 138 localities ranging from southeast Alaska to the Columbia River, the majority of the sites being in British Columbia. The observed regional population structure enabled evaluation of the utility of using microsatellite and MHC variation for estimating the stock composition of coho salmon in mixed-stock fisheries. Both MHC exons were more effective for stock identification than any of the eight microsatellite loci examined. The two MHC exons combined were nearly as effective, on average, as the eight microsatellite loci combined. Some loci were particularly effective at discriminating stocks from specific regions. Mixed-stock analysis provided accurate estimates of contributions from the threatened Thompson River and upper Skeena River stocks, even when they composed less than 5% of the sampled fish. From...

DNA in action: Rapid application of DNA variation to sockeye salmon fisheries management

Commitment to conservation-based management of exploited fish species imposes unprecedented requirements for adaptive, real-time management of biologically and socially complex mixed-stock fisheries such as those conducted for Pacific salmon. Stock identification is a key component of the management process, with population-specific timing and abundance information often incorporated into management decisions. By using both microsatellite and major histocompatibility complex genetic variation, we achieved highly accurate estimates of stock composition for Fraser River sockeye salmon. Over a 2-month period in 2002, we analyzed 9300 returning Fraser River sockeye salmon sampled in mixed-stock fisheries, and provided stock composition estimates to fishery managers within 9–30 h of sample delivery. Stock-specific exploitation targets governed by conservation concerns were achieved in this fishery.

Molecular evolution at Mhc genes in two populations of chinook salmon Oncorhynchus tshawytscha

The DNA sequences of four exons of the MHC (major histocompatibilty complex) were examined in chinook salmon (Oncorhynchus tshawytscha) from an interior (Nechako River) and a coastal (Harrison River) population in the Fraser River drainage of British Columbia. Mhc class I A1, A2 and A3 sequences and a class II B1 sequence were obtained by PCR from each of 16–20 salmon from each population. The class I A1 and a pair of linked A2–A3 exons were derived from two different classical salmonid class I genes, Sasa‐A and Onmy‐UA, respectively. Allelic variation for B1, A1 and A2 was characterized by the high levels of nonsynonymous substitution indicative of the effects of natural selection on Mhc domains that contain peptide binding regions. The number of alleles detected at each of the four exons ranged from three (B1) to 22 (A1), but levels of nucleotide sequence divergence at all four exons were low relative to classical mammalian Mhc genes. The nucleotide similarity among alleles ranged between 89 and 99% over all exons, and all four domains possessed only two major sequence motifs. Allelic distributions at B1, A1 and A3 confirmed the genetic distinctiveness of the Harrison and Nechako chinook salmon populations revealed in previous studies. The two major allelic motifs of B1 and A1 segregated strongly between the populations. In spite of evidence that allelic diversity at these chinook salmon Mhc exons has been generated by selection, the level and distribution of diversity in the two salmon populations strongly reflected the demographic history of the species, which has been characterized by repeated bottlenecks and isolation‐by‐distance in glacial refugia.

Growth and Behavioral Consequences of Introgression of a Domesticated Aquaculture Genotype into a Native Strain of Coho Salmon

Abstract Selective breeding for enhanced growth in Pacific salmon Oncorhynchus spp. and other fish typically involves use of the largest mature individuals to breed for future generations of aquaculture broodstock. Owing to an altered selection regime, faster-growing fish may not be as adapted to the natural environment as wild fish. To increase understanding of the genetic changes underlying selection for enhanced growth that results in phenotypic differentiation of farmed from wild Pacific salmon, multiple generations of pure and hybrid families were generated for coho salmon O. kisutch, including pure farm (D), pure native (Ch; a natural strain propagated by wild and hatchery production), F1 and F2 hybrids, and F1 × wild backcross (BCh) genotypes. The family groups were reared in the laboratory under controlled conditions as (1) individual genotypic groups, (2) mixed groups under culture conditions, and (3) mixed groups under enriched (seminatural) conditions. The growth of the fish was tracked until s...

Stock Identification of Sockeye Salmon by Means of Minisatellite DNA Variation

Abstract Geographic variation in nuclear DNA among 10 populations of sockeye salmon Oncorhynchus nerka was examined over the Pacific-wide distribution of the species. Nuclear DNA was restricted with the enzymes Alu I and Hae III and hybridized with three minisatellite probes. The greatest differences in allele or DNA fragment (band) frequencies with all three probes occurred between northern (Russia, western Alaska) and southern (British Columbia. Washington) populations. Variation in frequencies was also observed among the six river drainage systems examined and between populations within drainages. It was not possible to classify individual fish to specific populations with a high degree of accuracy. However, for lest samples consisting of a single population (true value. 100%), the estimated contribution of that population averaged about 89% for a 10-stock baseline. Estimates increased to about 92% when populations within drainages were pooled to determine contribution by drainage for the six drainages...