Tag Archives: stock composition

Burman River Chinook Salmon Mark-Recapture

Concern for West Coast Vancouver Island (WCVI) natural Chinook currently limits PSC fisheries in Southeast Alaska, the Haida Gwaii recreational fishery and particularly the Area F troll fishery in northern British Columbia and troll fisheries and some recreational fisheries on the WCVI. Although the Burman River is enhanced, the population is of sufficient size to estimate the escapement with precision, and thermally marked otolith sampling provides an estimate of the naturally spawned fraction.
The program will estimate the escapement of adult Chinook salmon to the Burman River, a PSC Chinook escapement indicator, using both closed population and open population mark-recapture techniques refined between 2009-2014. The project will also quantify age, sex and origin compositions. Estimates of abundance of the thermally marked hatchery fraction combined with a precise escapement estimate will provide important information to verify and support the WCVI Aggregate ratio estimation project by providing an independent reference point (the Burman River Chinook hatchery fraction, independent of Robertson Creek Hatchery stock) in the northern WCVI area.



Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques

The Skeena River is host to the second largest aggregate of Chinook salmon in British Columbia. While the aggregate is a PSC escapement indicator stock, there are no biologically based escapement goals for this population. This project produces an annual escapement estimate for the Skeena River Chinook aggregate and provides information on the stock components that make up the Chinook return to the Skeena River. The project consists of genetic analyses of samples from Chinook salmon caught at the Tyee Test fishery in 2021. The project uses samples and data from two independent programs, the Tyee Test Fishery and the Kitsumkalum mark-recapture program. Chinook salmon scale samples will be collected from the Tyee Test Fishery and the DNA from the samples will be compared against genetic baselines from Skeena Chinook salmon populations. The proportion identified as Kitsumkalum Chinook will be expanded to generate escapement estimates for the Skeena River aggregate using the mark-recapture estimate of escapement for the Kitsumkalum population.



Calibration of Assessment Methods for Fraser Sockeye Enumeration

Since 2007, with support from the Southern Boundary Restoration and Enhancement Fund, calibration work has been conducted on twenty-five Sockeye populations of various stream types in the Fraser and has led to the development of indices for aerially surveyed Sockeye populations on the following three stream types: i) medium sized, clear streams, ii) medium sized, partially turbid/tannic streams and iii) large sized, clear streams. Although this represents substantial progress, significant gaps still exist on the remaining stream types and lake spawning populations. Calibration work involves the comparison between estimates generated using high precision enumeration techniques (enumeration fences, sonar, and/or mark-recapture programs) and those generated using standard low precision visual techniques. As annual calibration opportunities on target populations are limited, calibration work over the long term will be required to satisfy the data requirements for all stream types.  The actual populations to be calibrated will be determined based on in-season estimates of abundance.


Northern Boundary Area Sockeye Salmon Genetic Stock Identification

Provisions of the Pacific Salmon Treaty specify harvest sharing arrangements of Nass and Skeena River sockeye salmon returns for the U.S. and Canada. The United States is allowed to harvest a fixed percentage of the Annual Allowable Harvest of Nass and Skeena sockeye stocks in Alaska’s District 101 gillnet and District 104 purse seine fisheries. Accurate estimates of the stock-specific catch in commercial fisheries of each nation are required to estimate the total return of these stocks and the percentage of each stock caught in treaty-limited fisheries. Annual catches over or under the agreed percentage are made up for in subsequent years.

Until recently, the Alaska Department of Fish and Game (ADF&G) used scale pattern analysis successfully to estimate contributions of Nass, Skeena and Southeast Alaska sockeye stocks to fisheries in southern Southeast Alaska. Since  2006, the Auke Bay Laboratories has used genetic analysis for the Northern Boundary sockeye fisheries. Results from comparisons between stock composition using scales and genetic analysis show both methods provide accurate estimates of stock composition, although DNA analysis is able to discriminate stocks at a finer resolution than scales. An additional advantage of the DNA technique is that it does not require annual sampling to re-establish the escapement baseline.

The purpose of this project is to continue the genetic stock identification of the commercial sockeye catch in ADF&G District 101 gillnet fishery and District 104 seine fishery using the baselines developed by the ADF&G.

Development of a High Resolution SNP Baseline for Stock Identification of Coho Salmon

Genotyping by sequencing, or GBS, is a new type of DNA sequencing technology that allows the genotype of an individual to be determined by direct DNA sequencing. This new direct method of genotyping individuals will radically change stock identification, as several hundred markers per individual can be routinely screened for genotyping at a cost equivalent to or lower than that currently prevailing in stock identification applications. Screening more markers also provides increased resolution for stock identification.
The Molecular Genetics Laboratory (MGL) at the Pacific Biological Station in Nanaimo, BC, has assembled a panel of primers far in excess of any previous or current stock identification application in Coho Salmon by any agency. Application of this panel to a limited number of populations in southern British Columbia has indicated substantial differentiation among populations. GBS will clearly be the method of choice for Coho Salmon stock identification in the near future, as very high resolution estimates of stock composition will be available from this technique.
This project proposes to survey 40 populations of Coho Salmon in northern and central British Columbia with the aforementioned panel of primers, and evaluate the utility of the method for applied stock identification. This information will be merged with data from southern British Columbia populations that will be collected under a $10 million, 4-year Genome Canada project supported in part by Fisheries and Oceans Canada and in which the MGL is participating. A high-resolution stock identification baseline should thus be available for populations throughout British Columbia, and the GBS technology will allow new applications in stock identification, as it may be possible to identify individual Coho Salmon to specific populations (either hatchery or wild) if the baseline is adequate for the problem.

Mixed Stock Analysis of Districts 106, 108 and 111 Sockeye

Sockeye runs from the Stikine and Taku rivers in Southeast Alaska are harvested in Canadian aboriginal, recreational, and commercial gillnet fisheries, and in US subsistence, personal use, and commercial gillnet fisheries. In the US, commercial gillnet fisheries in Districts 106 and 108 harvest wild stocks of sockeye salmon bound for Southeast Alaska island and mainland lakes, and for lakes and tributaries in the Stikine, Nass, and Skeena River drainages, while fisheries in District 111 harvest wild stocks of sockeye primarily bound for systems in the Taku River or to Crescent and Speel lakes in Alaska. Significant numbers of enhanced sockeye salmon bound for release sites in the Stikine and Taku rivers or to Snettisham Hatchery are also caught in these fisheries. Catches of Stikine and Taku river sockeye salmon stocks in Districts 106, 108 and 111 gillnet fisheries and the U.S. Stikine subsistence fishery are subject to a harvest sharing agreement outlined in Annex IV of the Pacific Salmon Treaty, in which the US is allowed 50% of the Total Allowable Catch of Stikine River and a variable proportion of Taku River sockeye salmon depending on the return of enhanced fish. Stock contribution estimates are critical to document compliance with the harvest sharing agreements, reconstruct runs of wild stocks, estimate the return of enhanced fish, forecast upcoming returns, and support sustainable management.
Genetic stock identification (GSI) is the preferred method for estimating stock contributions in fisheries in and near the Stikine and Taku rivers, and has been in use for transboundary management since 2011. GSI has improved estimates compared to past methods (scale pattern analysis), and is less logistically complex, less labor intensive, less expensive, more accurate, and delivers more timely results at a finer resolution.
This project has been conducting GSI analysis on sockeye salmon tissue samples collected from commercial gillnet fisheries in areas in and near the Stikine and Taku rivers in Southeast Alaska since 2012. The analysis will be focused on tissue samples collected in Districts 106, 108, and 111.

Mixed stock analysis of districts 108 and 111 chinook fisheries

The Stikine and Taku rivers in Southeast Alaska (SEAK) support Chinook salmon runs important for various commercial, aboriginal, and recreational fisheries in both the United States (U.S.) and Canada. Included in these are U.S. commercial gillnet fisheries in Alaskan Districts 108 and 111, as well as sport fisheries near Wrangell, Petersburg, and Juneau. U.S. fisheries in these areas harvest stocks of Chinook salmon bound for SEAK and for tributaries in the transboundary Stikine and Taku rivers. Catches of Stikine and Taku river Chinook salmon stocks are subject to a harvest sharing agreement, in which the U.S. and Canada are each given an Allowable Catch specified by the Pacific Salmon Commission, and this relies on catch, escapement, recruitment information, and stock composition estimates to forecast indices of abundance. Until recently, stock composition of harvests was estimated primarily using coded-wire tags, which provided good estimates for marked stocks. However, expansions of these estimates could be uncertain due to a lack of coded-wire tags on all stocks contributing to the fishery, incomplete tagging of index stocks, and in some instances poor estimates of escapement or terminal run size. Genetic stock identification (GSI) provides a complementary set of accurate and reliable stock composition estimates necessary to meet the directives of abundance-based management of Chinook salmon, and is currently used to recalculate actual contributions of above-border Stikine and Taku Chinook salmon to the Districts 108 and 111 sport and commercial fisheries.

Terminal Abundance of WCVI Chinook Salmon

Chinook salmon stocks originating from the West Coast of Vancouver Island (WCVI) contribute significantly to the ocean harvests in fisheries in Southeast Alaska and northern British Columbia, as well as being of prime importance to near-shore fisheries along the WCVI itself. Consequently, commercial and sport fishermen, as well as First Nations up and down the coast have a vested interest in the status of WCVI Chinook salmon. Management agencies and organizations responsible for fisheries in Southeast Alaska, northern British Columbia, and along the WCVI have need of stock status information concerning WCVI Chinook salmon.
The overall goal of this project is to estimate the aggregate terminal returns of WCVI hatchery and natural origin Chinook salmon, including catch plus escapement inside the surf line such that the estimates are asymptotically accurate and have a CV of 15% or less. This will be achieved through 1) the first comprehensive assessment of catch plus escapement along the WCVI, and 2) refinement of the ‘driver stock’ approach for estimating aggregate terminal return from a distant fishery.
The “driver stock” approach was first developed through the Sentinel Stock Program, and is based on the assumption that an indicator stock (or stock group) experiences the same exploitation and maturation rates as the aggregate. If the assumption holds, the incidence of this indicator stock group in an ocean fishery (using information such as CWT, otolith, DNA) and in its terminal area would have the same ratio as the catch of the indicator stock group in the same ocean fishery to its terminal run size. When using a single CWT stock, estimating terminal run size is simple. However, given the complexity of the WCVI stock aggregate and terminal WCVI fisheries, the key assumptions of the method – i.e. that maturation rates and exploitation rates are constant across the WCVI aggregate, were not met.
The purpose of this project is to 1) improve the precision of the terminal return estimates of natural and hatchery origin chinook salmon along the WCVI, 2) quantify the variation in maturation, exploitation rates, abundance across the WCVI aggregate, and 3) use the additional information to refine the application of the driver stock approach to the WCVI aggregate through development of a Bayes method. These results will benefit existing stock reconstructions and forecasts in the assessment of the WCVI Chinook salmon stock complex.