Estimates Of Stock Composition Research Articles

Microsatellite Variation in Yukon River Coho Salmon: Population Structure and Application to Mixed‐Stock Analysis

AbstractKnowledge of population structure facilitates the effective management of species that are harvested in mixed‐stock fisheries. In this study, we analyzed genetic variation at 19 microsatellite loci for 14 populations of Coho Salmon Oncorhynchus kisutch in the Yukon River. We then used this data to estimate the stock composition of adults that were harvested in a lower river test fishery. The Coho Salmon populations in the Yukon River exhibited a high degree of geographically based genetic structure (GST = 0.078), with a strong genetic disjunction between the lower and upper river populations. Further substructure was observed among the upper river populations, which allowed for the estimation of stock composition to areas within this region. Analyses involving simulated and real mixtures indicated that this level of divergence can be used to apportion Coho Salmon to regions and areas accurately (95–100%). The stock composition estimates for the test fishery revealed that the spawning migration was evenly divided (50:50) between the lower and upper river populations. The upper river populations generally had earlier migration timing, comprising 66% of the mixture in the beginning and 33% at the end. The largest component of the upper river region was Tanana at 44%, followed by Nenana at 5%, and Porcupine at 1%. While escapement monitoring is essential for the management of Coho Salmon, it is limited by funding shortfalls. However, mixed‐stock analysis in conjunction with sonar enumeration can provide information on stock‐specific proportions, abundances, and migration timings that can increase our knowledge and ability to manage Coho Salmon populations in the Yukon River.

Estimation of conservation unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125 198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based on variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 conservation units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon.

Parentage-based tagging combined with genetic stock identification is a cost-effective and viable replacement for coded-wire tagging in large-scale assessments of marine Chinook salmon fisheries in British Columbia, Canada.

Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage‐based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2–4 years, with a 105,722–individual, 380–population baseline available for assignment. Application of a GSI‐PBT system of identification to individuals in 2019 fisheries provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian‐origin Chinook salmon relative to CWTs, and an opportunity for a genetics‐based system to replace the current CWT system for salmon assessment.

Accurate estimation of conservation unit contribution to coho salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

Determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For coho salmon (Oncorhynchus kisutch), a stock identification baseline composed of some 57 982 individuals from 332 populations ranging from southeast Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 480 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 37 conservation units (CU) in British Columbia, 13 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian coho salmon.

Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada.

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage‐based tagging (PBT) may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded‐wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774—individual, 267—population baseline available for assignment. Coho salmon from un‐CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT‐GSI system of identification to individuals in 2017 fisheries and escapements provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian‐origin coho salmon relative to CWTs, and an opportunity for a genetic‐based system to replace the current CWT system for coho salmon assessment.

Genetic Mixture Analysis Supports Recalibration of the Fishery Regulation Assessment Model

Management of the commercially important Washington coastal Chinook Salmon Oncorhynchus tshawytscha troll fishery depends on the Chinook Salmon Fishery Regulation Assessment Model (FRAM). The Chinook Salmon FRAM uses historical and contemporary coded wire tag recoveries to estimate abundance and exploitation rates for particular indicator stocks. Those estimates are used to set limits on overall harvest and protect sensitive stocks. Current efforts are underway to implement a newer “base period” (time period on which exploitation rates are based). Our collaboration of science, management, and industry used genetic mixture modeling to provide independent stock composition estimates supporting FRAM recalibration. Genetic modeling suggested that total catch includes a much smaller proportion of a limiting Columbia River stock, a larger fraction of Canadian stocks, and an abundant Oregon coastal stock not previously included in the FRAM. Our results focus attention on particular stocks that will benefit from refinements in the Chinook Salmon FRAM.

Genetic mixed-stock analysis disentangles spatial and temporal variation in composition of the West Greenland Atlantic Salmon fishery

Abstract The West Greenland Atlantic Salmon (Salmo salar) fishery represents the largest remaining mixed-stock fishery for Atlantic Salmon in the Northwest Atlantic and targets multi-sea-winter (MSW) salmon from throughout North America and Europe. We evaluated stock composition of salmon harvested in the waters off West Greenland (n = 5684 individuals) using genetic mixture analysis and individual assignment to inform conservation of North American populations, many of which are failing to meet management targets. Regional contributions to this fishery were estimated using 2169 individuals sampled throughout the fishery between 2011 and 2014. Of these, 22% were identified as European in origin. Major North American contributions were detected from Labrador (∼20%), the Southern Gulf/Cape Breton (29%), and the Gaspe Peninsula (29%). Minor contributions (∼5%) were detected from Newfoundland, Ungava, and Quebec regions. Region-specific catches were extrapolated using estimates of composition and fishery catch logs and harvests ranged from 300 to 600 and 2000 to 3000 individuals for minor and major constituents, respectively. To evaluate the temporal stability of the observed fishery composition, we extended the temporal coverage through the inclusion of previously published data (1995–2006, n = 3095) and data from archived scales (1968–1998, n = 420). Examination of the complete time-series (47 years) suggests relative stability in stock proportions since the late 1980s. Genetic estimates of stock composition were significantly associated with model-based estimates of returning MSW salmon (individual years r = 0.69, and overall mean r = 0.96). This work demonstrates that the analysis of both contemporary and archived samples in a mixed-stock context can disentangle levels of regional exploitation and directly inform assessment and conservation of Atlantic Salmon in the West Greenland interceptory Atlantic Salmon fishery.

Genetic mixed stock analysis of an interceptory Atlantic salmon fishery in the Northwest Atlantic

Interceptory fisheries represent an ongoing threat to migratory fish stocks particularly when managed in the absence of stock specific catch and exploitation information. Atlantic salmon from the southern portion of the North American range may be subject to exploitation in the commercial and recreational salmon fisheries occurring in the French territorial waters surrounding St. Pierre and Miquelon off southern Newfoundland. We evaluated stock composition of Atlantic salmon harvested in the St. Pierre and Miquelon Atlantic salmon fishery using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 12,409 individuals, 12 regional groups) encompassing the species western Atlantic range. Individual salmon were sampled from the St. Pierre and Miquelon fishery over four years (2004, 2011, 2013, and 2014). Biological characteristics indicate significant variation among years in the size and age distribution. Nonetheless, estimates of stock composition of the samples showed consistent dominance of three regions (i.e., Southern Gulf of St. Lawrence, Gaspe Peninsula, and Newfoundland). Together salmon from these regions accounted for more than 70% of annual harvest over the decade examined. Comparison of individual assignments and biological characteristics revealed a trend of declining fresh water age with latitude of assigned region. Moreover, locally harvested Newfoundland salmon were ten times more likely to be small or one sea winter individuals whereas Quebec and Gaspe Peninsula salmon were two-three times more likely to be harvested as large or two sea winter salmon. Estimates of region specific catch were highest for salmon from the southern Gulf of St. Lawrence region ranging from 242 to 887 individuals annually. This work illustrates how genetic analysis of interceptory marine fisheries can directly inform assessment and management efforts in highly migratory marine species.

Geo-Referenced, Abundance Calibrated Ocean Distribution of Chinook Salmon (Oncorhynchus tshawytscha) Stocks across the West Coast of North America

Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year fluctuations in migratory distributions and stock-specific survival. In this study, the ocean distribution and relative abundance of Chinook salmon (O. tshawytscha) stocks encountered in the California Current large marine ecosystem, U.S.A were inferred using catch-per-unit effort (CPUE) fisheries and genetic stock identification data. In contrast to stock distributions estimated through coded-wire-tag recoveries (typically limited to hatchery salmon), stock-specific CPUE provides information for both wild and hatchery fish. Furthermore, in contrast to stock composition results, the stock-specific CPUE metric is independent of other stocks and is easily interpreted over multiple temporal or spatial scales. Tests for correlations between stock-specific CPUE and stock composition estimates revealed these measures diverged once proportional contributions of locally rare stocks were excluded from data sets. A novel aspect of this study was collection of data both in areas closed to commercial fisheries and during normal, open commercial fisheries. Because fishing fleet efficiency influences catch rates, we tested whether CPUE differed between closed area (non-retention) and open area (retention) data sets. A weak effect was indicated for some, but not all, analyzed cases. Novel visualizations produced from stock-specific CPUE-based ocean abundance facilitates consideration of how highly refined, spatial and genetic information could be incorporated in ocean fisheries management systems and for investigations of biogeographic factors that influence migratory distributions of fish.

Genetic Mixed‐Stock Analysis of American Shad in Two Atlantic Coast Fisheries: Delaware Bay, USA, and Inner Bay of Fundy, Canada

AbstractAmerican Shad Alosa sapidissima in the Hudson River, New York, and coastwide have shown major long‐term declines. A possible contributing factor is commercial fisheries that harvest this population outside of the Hudson River estuary. Using previously published and new reference microsatellite data from 33 baseline populations, our goals were (1) to estimate the proportion of Hudson River American Shad contributing to the two remaining major mixed‐stock fisheries along the Atlantic coast in Delaware Bay and the Bay of Fundy and (2) to estimate the proportions of other American Shad stocks contributing to these two fisheries at the highest level of stock specificity. Stock composition estimates for 2009 and 2010 Delaware Bay collections were made using three models that ranged from the most simple question (Hudson River and Delaware Bay populations) to one with all 33 baseline populations included. In all cases, a Hudson River contribution nearly equal to that of the Delaware Bay contribution was observed, indicating a substantial take on the otherwise protected Hudson River population. When all baseline populations were included for the larger 2010 Delaware Bay collection, 19 showed nonzero contributions, largely drawn from mid‐Atlantic U.S. rivers. The 2009 Bay of Fundy collection showed contributions from across most of the species’ range but was dominated by northern populations. Mixed‐stock analyses of collections from the two sites together indicate that these estuarine fisheries harvested not only proximal populations but those originating from a wide latitudinal range.Received April 3, 2014; accepted August 5, 2014

Distribution, Stock Composition and Timing, and Tagging Response of Wild Chinook Salmon Returning to a Large, Free‐Flowing River Basin

AbstractChinook Salmon Oncorhynchus tshawytscha returns to the Yukon River basin have declined dramatically since the late 1990s, and detailed information on the spawning distribution, stock structure, and stock timing is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio‐tagged in the lower basin during 2002–2004 and tracked upriver. Fish traveled to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging site. Similar distribution patterns were observed across years, suggesting that the major components of the run were identified. Daily and seasonal composition estimates were calculated for the component stocks. The run was dominated by two regional components comprising over 70% of the return. Substantially fewer fish returned to other areas, ranging from 2% to 9% of the return, but their collective contribution was appreciable. Most regional components consisted of several principal stocks and a number of small, spatially isolated populations. Regional and stock composition estimates were similar across years even though differences in run abundance were reported, suggesting that the differences in abundance were not related to regional or stock‐specific variability. Run timing was relatively compressed compared with that in rivers in the southern portion of the species’ range. Most stocks passed through the lower river over a 6‐week period, ranging in duration from 16 to 38 d. Run timing was similar for middle‐ and upper‐basin stocks, limiting the use of timing information for management. The lower‐basin stocks were primarily later‐run fish. Although differences were observed, there was general agreement between our composition and timing estimates and those from other assessment projects within the basin, suggesting that the telemetry‐based estimates provided a plausible approximation of the return. However, the short duration of the run, complex stock structure, and similar stock timing complicate management of Yukon River returns.Received March 5, 2014; accepted August 27, 2014

Genetic stock composition of loggerhead turtles Caretta caretta bycaught in the pelagic waters of the North Atlantic

Sea turtle populations disperse widely across oceans and migrate between terrestrial nesting habitat and distant feeding and developmental habitats. Understanding population stock structure is important for accurately assessing threats such as mortality from fishery bycatch and for defining specific demographic units of conservation concern. We compared 775 bp mtDNA control region haplotypes from 389 juvenile loggerhead turtles sampled as bycatch in the US pelagic longline fishery in the western North Atlantic Northeast Distant (NED) region to haplo- type frequencies observed in 23 genetically distinct nesting stocks representing the 4 distinct pop- ulation segments (DPSs) that have been identified throughout the Atlantic Ocean and Mediterran- ean Sea. We used Bayesian mixed-stock analysis to produce stock composition estimates for juvenile loggerhead turtles that use pelagic habitat in the central North Atlantic. We found that nearly all of the loggerheads caught in NED waters belonged to the Northwest Atlantic DPS (mean = 99.2%), with the majority coming from the large eastern Florida rookeries (mean = 84.0%). We also detected contributions from the western Florida rookeries (mean = 11.7%) and Mexico (mean = 3.5%) but found little evidence of contributions from the rookeries of the South Atlantic, Northeast Atlantic, or Mediterranean DPSs. These results will help improve specific threat assessments and are relevant to ongoing development of conservation plans that are aligned to the recent DPS listings for loggerheads.

An analysis of genetic stock identification on a small geographical scale using microsatellite markers, and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed-stock fishery to an almost exclusively single-stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.

Comparison of Radiotelemetry and Microsatellites for Determining the Origin of Yukon River Chinook Salmon

AbstractChinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment and stock composition derived from genetic and radiotelemetry data collected from the same Chinook salmon. Radiotelemetry and genetic individual assignments were highly concordant. Agreement between methods for individual assignment was 79% to region and 93% to country when using the most probable genetic criterion, improving to 94% for region and 98% for country when using the ≥95% probability genetic criterion; however, under the more stringent criterion, fewer individuals could be assigned. Further analysis showed that estimates of stock composition based on radiotelemetry and genetic methods were within 6% of each other and were not significantly different. The concordance between estimates of individual assignment and stock composition from the radiotelemetry and genetic methods indicates that both methods are credible tools for fishery assessment of Yukon River Chinook salmon.Received October 14, 2011; accepted April 17, 2012

Microsatellite Mixed‐Stock Identification of Coho Salmon in British Columbia

AbstractVariation at 17 microsatellite loci was analyzed for about 50,000 coho salmon Oncorhynchus kisutch sampled from 274 locations ranging from Russia to California (but largely from British Columbia), and the variation was applied to estimate stock composition in mixed‐stock fishery samples. High resolution of mixed‐stock samples was possible; accurate estimates of stock composition were available for coho salmon originating from 39 regions (Russia, 1 region; Yukon River, 1; southeast Alaska, 1; British Columbia, 28; Washington, 5; Columbia River, 1; Oregon, 1; California, 1). The power of a locus in providing accurate estimates of stock composition of simulated single‐population mixtures was related to the number of alleles observed at the locus. Approximately 800 alleles were observed across the 17 microsatellites. Analysis of known‐origin samples indicated that accurate regional estimates of stock composition were obtained; estimates from 37 of 39 regions had accuracy greater than 90%. Estimated stock compositions of five mixed‐fishery samples collected in British Columbia and the San Juan Islands (Washington) reflected the presence and timing of migration of the local populations. Microsatellites provided accurate estimates of stock composition from many locations in the British Columbia distribution of coho salmon.Received July 5, 2011; accepted October 22, 2011

A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

AbstractThe following questions were addressed in this study: (1) If a suite of 12–15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single‐nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12‐locus Fisheries and Oceans Canada (DFO) microsatellite suite range include adding either 4 microsatellites or 25 SNPs to the existing suite to achieve an overall population‐specific accuracy of 86% across 60 populations. For the 13‐locus Genetic Analysis of Pacific Salmon (GAPS) microsatellites, either 2 microsatellites or 20–25 SNPs can be added to the existing suite to achieve approximately 86% population‐specific accuracy in estimated stock composition. The enhanced DFO (16 loci) and GAPS (15 loci) microsatellite baselines were projected to require 179 and 166 SNPs, respectively, for equivalent precision of the population‐specific estimates. The level of regional accuracy of individual assignment available from the enhanced DFO and GAPS suites of microsatellites was projected to require 90 and 82 SNPs, respectively. The level of individual assignment to specific populations available from the enhanced DFO and GAPS suites of microsatellites was projected to require 137 and 121 SNPs, respectively.Received January 10, 2011; accepted August 22, 2011

Canadian‐Origin Chinook Salmon Rearing in Nonnatal U.S. Tributary Streams of the Yukon River, Alaska

AbstractYukon River Chinook salmon Oncorhynchus tshawytscha are described as having a “stream‐type” life history strategy. After emergence from river gravel, juveniles typically feed and grow in tributary streams of the Yukon River throughout their first summer, overwinter in freshwater, and usually leave their rearing areas for marine waters during the second spring or summer. Nonnatal rearing has been described in the upper Canadian portion of the drainage, but information is lacking for downstream U.S. waters. In 2006–2007, a study was conducted to document nonnatal rearing and the genetic origin of Chinook salmon in U.S. tributary streams of the Yukon River. Eight nonspawning streams were selected for study, seven located in a 260‐km segment between the U.S.–Canada border and Circle, Alaska, and one located 742 km downstream from the border. Age‐0 juveniles were captured in all eight streams. Genetic stock composition analyses using 13 standardized microsatellite loci assigned the fish to Canadian source populations. The Carmacks region (over 460 km upstream from the border) contributed 91% to the mixtures in 2006 and 82% in 2007. Canadian stocks nearest the border and from large river systems were underrepresented in the collections. Simulation and known‐origin mixture analyses demonstrated that stock composition and individual assignment estimates derived from the genetic baseline were accurate and precise. Some juveniles may have traveled over 1,200 km to reach rearing areas in U.S. waters. Future studies would help define the importance of this life history strategy to the overall health and productivity of Yukon River Chinook salmon.

Use of Statistical Bootstrapping to Calculate Confidence Intervals for the Fall Chinook Salmon Run Reconstruction to Lower Granite Dam

AbstractMeeting escapement and recovery goals for Pacific salmon Oncorhynchus spp. is greatly facilitated by accurate and precise estimates of run size and stock composition. Although this is particularly important for endangered Pacific salmon runs like the Snake River fall Chinook salmon O. tshawytscha evolutionarily significant unit, few studies provide estimates with confidence intervals (CIs) and standard errors (SEs). We developed a run reconstruction method for fall Chinook salmon returning to Lower Granite Dam on the Snake River. We showed that composition estimates of fish returning to large river systems can be obtained through subsampling. The methods reported here yield CIs around those estimates. We used compound bootstrap methods to derive CIs and SEs on return numbers and composition. In general, if the number of fish returning for a group was 300 or more, we were 90% confident that our return estimate represented the true number within 10%. Estimates for smaller groups were generally imprecise. The analytical technique described here provides fishery managers with information necessary for assessing escapement and recovery goals and addressing conservation and harvest allocations of adult Snake River fall Chinook salmon.

Mixed‐Stock Analysis of Yukon River Chum Salmon: Application and Validation in a Complex Fishery

AbstractYukon River chum salmon Oncorhynchus keta are managed under the Pacific Salmon Treaty (PST), which requires conservation and equitable sharing of this fishery resource by the USA and Canada. Fall chum salmon are of special concern because they spawn in both the United States and Canada, and the focus of the PST is on Canadian‐origin salmon. Yukon River chum salmon were assayed for genetic variation at 22 microsatellite loci to establish a baseline for mixed‐stock analysis (MSA) applications to assist in addressing conservation and allocation issues. The baseline has been applied yearly to estimate the stock composition of Yukon River fall chum salmon from samples collected in the Pilot Station test fishery. Accuracies in MSA simulations for 12 of 14 management regions exceeded 90%, with a range of 80–98%, for the 12 most informative loci. Stock composition estimates were within 10% of the actual proportions in a known‐origin mixture analysis. Stock‐specific abundance estimates, which were derived from combining the estimates of genetic stock composition of Pilot Station test fishery harvests with sonar abundance estimates, were concordant with upriver escapement data. The combination of genetic MSA using the baseline developed in this study and sonar abundance provides a viable tool for assessing stock strength and assisting managers in regulating fisheries to maintain the productivity and evolutionary potential of Yukon River chum salmon.

Summer–Fall Distribution of Stocks of Immature Sockeye Salmon in the Bering Sea as Revealed by Single‐Nucleotide Polymorphisms

AbstractWe report stock composition estimates for immature (ocean‐age .1 and .2) sockeye salmon Oncorhynchus nerka distributed across the Bering Sea in late summer and fall. We establish a baseline data set composed of single‐nucleotide polymorphism markers that can achieve very high accuracies in identifying sockeye salmon stocks from throughout their range in Asia and North America. We demonstrate the capabilities of this data set to address high‐seas salmon issues by analyzing samples collected by researchers from Russia, Japan, and the United States during late summer and fall 2002–2004 as part of the Bering–Aleutian Salmon International Survey. According to our findings, (1) Gulf of Alaska (GOA) stocks formed a significant portion of the immature sockeye salmon migrating in the eastern and central Bering Sea in summer and fall, and western GOA stocks had a broader distribution in the Bering Sea than eastern GOA stocks; (2) Asian stocks migrated as far east as the western Aleutian Islands and the Donut Hole area (international waters in the center of the Bering Sea); and (3) Bristol Bay stocks were the most widely distributed, accounting for more than one‐half of the mixtures in all areas except the central and southern areas of the Russian Exclusive Economic Zone (REEZ) in the western Bering Sea and north of the western Aleutian Islands. These results provide a significant increase in our knowledge of the distribution of sockeye salmon, firmly establishing that the REEZ is a summer–fall feeding area for immature North American sockeye salmon, particularly stocks of southeastern Bristol Bay origin. Bristol Bay sockeye salmon appear to enter and exit the REEZ primarily along a migration route that extends across the Aleutian Basin.