Lisa W. Seeb

Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large‐scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus‐only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing ∼89 kb we observed a frequency of 4.30 × 10−3 SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high‐throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.

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.

Hatchery Reform in Washington State

Abstract Hatcheries support nearly all major fisheries for Pacific salmon (Oncorhynchus spp.) and steel-head (anadromous O. mykiss) in the Pacific Northwest. However, hatcheries have been a major source of controversy for over 30 years. The Hatchery Scientific Review Group (HSRG) was tasked by Congress to identify solutions to well-known problems so hatcheries could better meet their goals of supporting sustainable fisheries and assisting with the conservation of natural populations. We reviewed over 100 facilities and 200 programs and identified three principles of hatchery reform: (1) goals for each program must be explicitly stated in terms of desired benefits and purposes; (2) programs must be scientifically defensible; and (3) hatchery programs must respond adaptively to new information. We also identified several emerging issues critical to the success of hatcheries. We concluded that hatcheries must operate in new modes with increased scientific oversight and that they cannot meet their goals witho...

Genetic population structure of chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ2 tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.

Single Nucleotide Polymorphisms Provide Rapid and Accurate Estimates of the Proportions of U.S. and Canadian Chinook Salmon Caught in Yukon River Fisheries

Abstract As anadromous Chinook salmon Oncorhynchus tshawytscha bound for U.S. and Canadian spawning grounds migrate through the U.S. portion of the Yukon River, they are targeted by several fisheries. To fulfill treaty obligations between the two countries, fishery managers need to know what portion of fish caught in the United States are of Canadian origin. Allozyme markers have been used to assign individuals in mixed fishery samples to U.S. and Canadian portions of the Yukon River; however, these markers are limited by sampling difficulties and by the number of available loci. Microsatellite DNA markers have been considered as an alternative; however, microsatellite data are not readily transportable among laboratories or countries. Here we present the use of single nucleotide polymorphism (SNP) markers that combine the ease of sampling and large potential number of loci of other DNA markers with universally transportable data. Simulations and analyses of known fish suggest that the SNP baseline can be...

Allozymes and Mitochondrial DNA Discriminate Asian and North American Populations of Chum Salmon in Mixed-Stock Fisheries along the South Coast of the Alaska Peninsula

Abstract A representative baseline of allozyme allele frequencies of 69 stock groupings covering the entire range of chum salmon Oncorhynchus keta was evaluated for its ability to estimate stock of origin of Asian and North American chum salmon in complex mixtures. We estimated the origin of 2,000 chum salmon harvested incidentally in fisheries for sockeye salmon O. nerka along the south side of the Alaska Peninsula in the northern Pacific Ocean in 1993 and 1994 using a maximum likelihood algorithm. Of eight major regions (Japan, Russia, northwest Alaska summer run, Yukon River fall run, Alaska Peninsula–Kodiak Island, southeast Alaska, British Columbia, and Washington) reported, northwest Alaska summer-run populations predominated in the fishery with estimates ranging from 0.52 to 0.72. A mitochondrial DNA (mtDNA) marker capable of distinguishing the Japanese component from the rest of the Pacific Rim stocks was assayed in 400 of the 1994 samples. Estimates from the allozyme and mtDNA data were similar. ...

High Genetic Heterogeneity in Chum Salmon in Western Alaska, the Contact Zone between Northern and Southern Lineages

Abstract Genetic relationships among 64 spawning populations of chum salmon Oncorhynchus keta in western Alaska were studied using allele frequency data from 40 protein-encoding loci. Two major lineages of chum salmon inhabiting Alaska were detected using clustering and multidimensional scaling analyses of Cavalli-Sforza and Edwards chord distances. Populations of the northwest Alaska lineage occur in the largely unglaciated areas of Alaska north of the Alaska Peninsula (Beringia, the Beringian Refugium), and the Alaska Peninsula–Gulf of Alaska lineage occurs in the glaciated and unglaciated areas of the Alaska Peninsula, Kodiak Island, and southcentral Alaska. The two lineages come into contact in the 150-km area separating Herendeen Bay and Port Heiden on the northern Alaska Peninsula; this area may represent a major zoogeographic contact zone. Genetic data also suggest the lineages come in contact in upper Cook Inlet; the population representing the Susitna River drainage, which drains into Cook Inlet...

Migration of Pacific Rim chum salmon on the high seas: insights from genetic data

Wild stocks of chum salmon, Oncorhynchus keta, have experienced recent declines in some areas of their range. Also, the release of hatchery chum salmon has escalated to nearly three billion fish annually. The decline of wild stocks and the unknown effects of hatchery fish combined with the uncertainty of future production caused by global climate change have renewed interest in the migratory patterns of chum salmon on the high seas. We studied the composition of high-seas mixtures of maturing and immature individuals using baseline data for 20 allozyme loci from 356 populations from throughout the Pacific Rim. Composition estimates were made from three time series. Two of these time series were from important coastal migratory corridors: the Shumagin Islands south of the Alaska Peninsula and the east coast of the Kamchatka Peninsula. The third was from chum salmon captured incidentally in the Bering Sea trawl fishery for walleye pollock. We also analyzed geographically dispersed collections of chum salmon captured in the month of July. The time series show dynamic changes in stock composition. The Shumagin Island corridor was used primarily by Northwest Alaskan and Asian populations in June; by the end of July stocks from the Alaska Peninsula and southern North America dominated the composition. The composition along the Kamchatka coast changed dramatically from primarily Russian stocks in May to primarily Japanese stocks in August; the previously undocumented presence of stocks from the Alaska Peninsula and Gulf of Alaska was also demonstrated. Immature chum salmon from throughout the Pacific Rim, including large proportions of southern North American stocks, contributed to the Bering Sea bycatch during the months of September and October. The migration routes of North American stocks is far more widespread than previously observed, and the Bering Sea is an important rearing area for maturing and immature chum salmon from throughout the species range.

Genetic Diversity of Sockeye Salmon of Cook Inlet, Alaska, and Its Application to Management of Populations Affected by the Exxon Valdez Oil Spill

Abstract Genetic data from sockeye salmon Oncorhynchus nerka were collected from all major systems in upper Cook Inlet, Alaska, that produce sockeye salmon, including the Kenai River drainage, a major system that was affected by the Exxon Valdez oil spill. The products of 29 enzymes encoded by 67 protein-encoding loci resolved by allozyme analysis revealed a substantial amount of genetic diversity among populations distributed both within and among major drainages. The data support a model of population structure based on the nursery lake. A gene diversity analysis estimated that 0.4% of the total variability was attributable to the effect of sampling at different sites within nursery lakes, compared with 7.5% among nursery lakes within regions and 2.9% among regions. This diversity probably arises from isolation and genetic drift within nursery lakes and the tendency of sockeye salmon to home with great fidelity. Sockeye salmon from these drainages are commercially harvested in mixed-stock aggregations i...

Complementary uses of ecological and biochemical genetic data in identifying and conserving salmon populations

Abstract This paper addresses the need to define distinct population segments within species of salmonid fishes. The paper focuses on identifying the smallest detectable population with unique sets of characters (i.e. a ‘species’ under the phylogenetic species concept); such units require identification before any subsequent groupings under which individual populations may ultimately be managed. Stream distance measurements between populations fail to identify ancestral discontinuities and are therefore excluded as a basis for estimating relationships. The requirement for genetic information in distinguishing populations has been met through characters reflecting ancestral lineages (including adequate biochemical genetic surveys and congruent meristic information), and those reflecting local adaptations (such as timings of migration and spawning, and distinct temperature tolerances). These different types of genetic information form complementary data sets for distinguishing populations because they reflect different evolutionary processes and time scales. Within distinct ancestral groupings defined by biochemical genetic data may exist adaptively distinct populations that cannot be distinguished in the absence of life history and ecological information. Examples are summarized in which a logical process has been applied for distinguishing populations; this includes an initial survey that focuses on identifying ancestral groupings followed by a systematic search for adaptive distinctions within these groupings.