Terry D. Beacham

Managing fisheries using genetic data: case studies from four species of Pacific salmon

Abstract Pacific salmon exhibit complex patterns of population subdivision and undergo substantial marine migrations that result in stock intermixing. Stock assessment, fishery management, and conservation of salmon are all complicated by stock multiplicity and intermingling in fishing areas. Genetic data have been successfully used by several agencies in the Pacific Northwest for over a decade to address assessment, management, and conservation needs. Four case studies are described to document the design, implementation, results, and benefits of genetic analysis. These consist of: (1) the chinook salmon winter gill-net fishery in the lower Columbia River (allozymes), (2) commercial pink salmon fisheries in British Columbia (allozymes), (3) chum salmon fisheries in Alaska (allozymes, mtDNA, and microsatellites) and, (4) the recreational coho salmon fishery off Vancouver Island (microsatellite and MHC genes). Estimates of stock group and/or individual stock contributions to harvests are obtained using maximum likelihood methods. Simulations indicate that estimates are often within 5–10% of the true contributions and are quite precise (±2–10%) with sample sizes of 100–400. Genetic results have been used both in-season and post-season to determine fishery openings and closures to provide harvest benefits or meet conservation needs, to address catch allocation and equity issues among user groups and between countries, to provide data for in-season run-size updates, and to investigate migration patterns and timing.

Patterns of homing and straying in southern British Columbia coded-wire tagged chinook salmon (Oncorhynchus tshawytscha) populations

Abstract Chinook salmon ( Oncorhynchus tshawytscha ) reared in a hatchery can originate from the same river on which a hatchery is located (natal river) or from a foreign river. Non-displacement rearing occurs if juveniles originating from the same drainage as the hatchery are released back into the natal stream. Displacement rearing occurs if part of the rearing and release strategy occurs at a foreign drainage or includes the marine environment. We compared straying between non-displacement and three types of displacement releases where: (1) juveniles are transported, reared in a central hatchery and released back into natal drainage (satellite); (2) or transported, reared in a central or recipient hatchery and released in a foreign drainage (transplant); (3) or reared and released directly into the marine environment away from the home drainage (out-estuary). Compared with non-displacement rearing, displacement-reared fish were between two and five times more likely to stray (2.1–5.3% vs 1.2%). Out-estuary releases had the highest stray rates of the displacement rearing types and were suspected of being least successful at imprinting on the home stream. Analysis of hybrid and transplanted stocks suggested that there was a genetic component to homing. A hybrid stock was three times more likely to stray than the natal stock released at the same time and location (6.2% vs 2.4%). Transplanted fish without exposure to their ancestral drainage were more likely to stray back to the ancestral drainage than non-transplanted fish released at the same time and location (2.9% vs 0.1%). Approximately 50% of the stray migrants were recovered within 30xa0km of the release site, indicating that the highest risk of straying may occur during the transition from bi-coordinate navigation to imprinted natal stream clues.

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.

Seasonal Stock-Specific Migrations of Juvenile Sockeye Salmon along the West Coast of North America: Implications for Growth

Abstract Knowledge of the migratory habits of juvenile Pacific salmon Oncorhynchus spp. is required to test the hypothesis that ocean food resources are a limiting factor in their production. Using DNA stock identification techniques, we reconstructed the regional and seasonal changes in the stock composition of juvenile sockeye salmon O. nerka (n = 4,062) collected from coastal Washington to the Alaska Peninsula in coastal trawl surveys from May to February 1996–2007. Individuals were allocated to 14 regional populations. The majority were allocated to stocks from the Fraser River system (42%), while west coast Vancouver Island stocks accounted for 15% of the total catch; Nass and Skeena River sockeye salmon constituted 14% and Rivers Inlet 6% of the total. The remainder of the stocks identified individually contributed less than 5% of the sockeye salmon analyzed. These proportions generally reflected the abundance of those populations. In spring and summer, the majority of fish were caught in close prox...

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

We gathered mitochondrial DNA sequences (557u2003bp from the control region in 935 specimens and 668u2003bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species’ extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make‐up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.

Life History and Seasonal Stock-Specific Ocean Migration of Juvenile Chinook Salmon

Abstract The ocean feeding grounds of juvenile Pacific salmon Oncorhynchus spp. range over several thousand kilometers in which ocean conditions, prey quality and abundance, and predator assemblages vary greatly. Therefore, the fate of individual stocks may depend on where they migrate and how much time they spend in different regions. Juvenile (n = 6,266) and immature (n = 659) Chinook salmon Oncorhynchus tshawytscha were collected from coastal Washington to Southeast Alaska in coastal trawl surveys from February to November 1998–2008, which allowed us to reconstruct changes in stock composition for seasons and regions by means of DNA stock identification techniques. Individuals were allocated to 12 regional stocks. The genetic stock assignments were directly validated by showing that 96% of the 339 known-origin, coded-wire-tagged fish were accurately allocated to their region of origin. Overall, the analyses performed in this study support the main findings of previous work based on tagging. However, gi...

Wild chinook salmon survive better than hatchery salmon in a period of poor production

The population dynamics of chinook salmon (Oncorhynchus tshawytscha) from the Cowichan River on Vancouver Island, British Columbia, Canada are used by the Pacific Salmon Commission as an index of the general state of chinook salmon coast wide. In recent years the production declined to very low levels despite the use of a hatchery that was intended to increase production by improving the number of smolts entering the ocean. In 2008, we carried out an extensive study of the early marine survival of the hatchery and wild juvenile chinook salmon. We found that both rearing types mostly remained within the Gulf Islands study area during the period when most of the marine mortality occurred for the hatchery fish. By mid September, approximately 1.3% of all hatchery fish survived, compared to 7.8%–31.5% for wild fish. This six to 24 times difference in survival could negate an estimated increased egg-to-smolt survival of about 13% that is theorized to result through the use of a hatchery. Estimates of the early marine survival are approximate, but sufficient to show a dramatic difference in the response of the two rearing types to the marine nursery area. If the declining trend in production continues for both rearing types, modifications to the hatchery program are needed to improve survival or an emphasis on improving the abundances of wild stocks is necessary, or both. The discovery that the juvenile Cowichan River chinook salmon remain within a relatively confined area of the Gulf Islands within the Strait of Georgia offers an excellent opportunity to research the mechanisms that cause the early marine mortalities and hopefully contribute to a management that improves the production.

The Application of Microsatellites for Stock Identification of Yukon River Chinook Salmon

Abstract In a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (FST) values, but loci with lower FST values also tended to provide more-accurate estimates of stock composition. The observed number of alleles was related to the power of the locus for providing accurate estimates of stock composition of simulated single-population samples. Mean estimated stock compositions for these mixtures ranged from 38.9% for simulations of single loci with fewer than 10 alleles to 85.5% for simulated loci with more than 60 alleles. Reliable population-specific estimation of stock composition was obtained with a minimum of five loci. Comparison of microsatellite stock identification power with an existing nine-locus single-nucleotide polymorphism (SNP) ...

Age and Morphology of Chum Salmon in Southern British Columbia

Abstract Differences in sex ratios by age, age compositions, gill-raker frequencies, and morphometric characters were investigated for stocks of chum salmon Oncorhynchus keta spawning at different times and in different river sizes in southern British Columbia. For all stocks pooled, males were more abundant than females at 3 and 5 years of age, but less abundant at 4 years. Early-spawning stocks from tributaries of the Fraser River and from rivers on Vancouver Island had older age compositions (means, 4.03 and 3.92 years, respectively) than did later-spawning stocks (means, 3.64 and 3.73 years, respectively). Early-returning stocks from all rivers also had fewer gill rakers (21.9) than did late-returning stocks (22.3). Males had larger heads, thicker caudal peduncles, and larger dorsal fins than did females, but females had larger anal fins than males. Chum salmon from large rivers (regardless of when they spawned) had larger body parts (head, fins, caudal peduncle) than did chum salmon from small rivers...

Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt

Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction‐site‐associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single‐nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome‐wide neutral and adaptive genetic variation for the applications of conservation and management.