Category: 2018

Expanded Bilateral Chum Salmon SNP Genetic Baseline for Genetic Stock Identification

The amplicon sequencing chum salmon SNP panel, with 538 polymorphic highly discriminating markers has been developed as part of the first year of this project. A large proportion of the tissue archive was then genotyped using this panel to develop a coastwide baseline for chum salmon. This resulted in a high-resolution, Conservation Unit (CU)-focused genetic baseline for which initial results indicate higher resolution than the previous microsatellite baseline (Sutherland et al., in prep.). The markers included in this panel were bilaterally agreed upon, and calibration of laboratories in the US with Canada has begun. Transferability of mixed-stock analysis between countries will be possible with this panel. However, to date several southern regions within Canada remain difficult to resolve or for other reasons require additional genotyping effort to finalize the southern chum baseline. We propose to augment the SNP baseline in seven specific regions in order to improve genetic stock identification within the south coast, and therefore improve characterization of streams of origin of chum salmon intercepted in fisheries.

S18-SP22 Expanded Bilateral Chum Salmon SNP Genetic Baseline for Genetic Stock Identification (WDFW) 2018 Report


Automating In-Season Salmon Species Composition Estimation at Mission Using Imaging Sonar

In this project, we will make efforts on improving the accuracy and robustness of automatically measured fish length based on sonar images, since length data can be fitted to a mixture model to determine the species proportion, as currently implemented by Pacific Salmon Commission (PSC) with manually measured fish length data. The mixture model will be added to the existing software package (developed with support by the 2010-2011 Southern Fund). Species composition outputs from this automated software processor can replace PSC’s manual method to significantly reduce the processing time for in-season estimation.

The proposed project will deliver the following 1) automatically measured fish length from DIDSON image data. This measurement function is expected to be available to processing PSC’s ARIS image data providing the ARIS file format is available to ViTech; 2) a mixture model implemented in a stand-alone software program. 3) improved accuracy in species classification between salmon species and resident fish; 4) maximized automation of data processing and improved accuracy in species classification among salmon species.

S18-FRP19 Automating In-Season Salmon Species Composition Estimation at Mission using Imaging Sonar

DNA stock composition of Juan be Fuca chinook

This project will support DNA analysis of samples collected in the Victoria area fishery. The objective is to estimate stock composition of the catch of chinook salmon in the Victoria area sport fishery with a specific focus on estimating fishery related mortality in this fishery of spring and summer 52 chinook returning to the Fraser River as well as other chinook stocks of concern such as Nooksack.

This project consists of 1) additional sampling effort within the existing creel survey to increase probability of achieving a minimum 100 DNA samples per month from April-September, and 2) DNA lab analysis of the tissue sample, and 3) reporting to the Pacific Salmon Commission’s Southern Fund and fishery stakeholders.  A priority is placed on June and July sampling coinciding with peak migration timing of spring and summer 52 Fraser chinook – but sampling May to August will be addressed in this proposal.

Note there are no CWT indicators for the Fraser spring and summer 52 chinook.  Since exploitation is primarily in the Fraser and Juan de Fuca, the exploitation can be approximated using the run reconstruction of Fraser River chinook salmon, which provides estimates of total return to the mouth of the Fraser.  Information related to mortality of other stock groups may also be used in chinook FRAM and in Southern Resident Killer Whale conservation.

DNA stock composition of chinook catch in the Strait of Georgia recreational fishery

This project will support DNA analysis of chinook samples collected in the Strait of Georgia area recreational fishery. The objective is to estimate fishery related mortality and exploitation rate of spring and summer 52 chinook returning to the Fraser River as well as other stocks. Sampling in the existing creel survey and by a group of 30+ ‘Avid Anglers’ will ensure adequate sample sizes. This project is incremental to the DNA sampling proposed separately for the Victoria area / Juan de Fuca and will assess the level of harvest and so exploitation of this Fraser chinook stock group in the approach through the Strait of Georgia relative to the exploitation in the Strait of Juan de Fuca.

Historic CWT from Dome Creek (spring 5/2) suggest the majority of this stock group approaches through Juan de Fuca.  The last of the Dome Creek CWT was over 10 years ago and there is significant debate on the impact of approach fisheries on this and other stocks of concern. This project will provide more up to date information on relative fishery impacts.  If the exploitation is minor then estimation of the exploitation using the Fraser chinook run reconstruction (provides the abundance to the mouth of the Fraser) plus the Juan de Fuca fishery may be sufficient as an indicator stock (that is assume a constant small percentage from all other marine fisheries).   

The stock composition estimates from this project will also support conservation of chinook as critical habitat for southern resident killer whales.

S18-VHP16 Estimation of stock composition of Chinook fisheries in the Strait of Georgia and Juan de Fuca Strait


Bessette Creek Resistivity Counter

The installation of a temporary automated fish counting system (resistivity counter) is being proposed for the Bessette Creek watershed to provide accurate escapement information for Coho salmon. Escapements in this system are currently estimated via streamwalks and the Area-Under-the-Curve method. Migrations of returning Coho are multimodal and often extended over a long period. Their propensity to move during high water events, to occupy systems intermittently, and to behave cryptically/defensively once at their spawning grounds can make visual enumerations difficult. As a result, it is a real challenge to accurately enumerate Coho returns using ground surveys in complex habitat such as the Bessette Watershed. Visual counting conditions are frequently poor due to high flows, turbid and dark water conditions (tannins), which probably leads to an underestimate of the spawning escapement. One method that has proven effective in this situation is resistivity. It is able to remain in place during high water events if properly situated, can see past turbid conditions and can remain running for extended periods of time. An electronic counter, although initially expensive to install, can supply accurate escapement estimates of salmonids for many years to come at a fraction of the cost of existing labour intensive techniques. The information can be downloaded via telephone connection which accommodates remote monitoring of salmon escapement information into this system.

Operation over multiple years is necessary to calibrate the method with existing escapement estimates collected via streamwalk surveys. If the method proves successful, the plan is to replace traditional streamwalk surveys with resistivity counter monitoring on a long term basis. Long-term operation will be funded through existing Aboriginal Fisheries Strategy funding, providing a legacy of more accurate data and cost savings.

S19-SP36 Bessette Creek Resistivity Counter 2019 Report

S18-SP07 Bessette Creek Coho Enumeration Using a Resistivity Counter

S17-I33 Bessette Creek Coho Enumeration Using a Resistivity Counter (Year 1 of 3)


Size Selective Mortality and Early Marine Growth: Potential Mechanisms Regulating Salmon

Our goal is to address the Fraser River Panel Priority #2, the examination of mechanisms affecting early survival of Fraser River Sockeye Salmon, as early marine life is expected to set recruitment dynamic patterns of Pacific salmon. In this two-year project, we propose to examine the factors influencing the size of Fraser Sockeye during their first year at sea, a hypothesized critical time in determining their survival, given that fish must be large enough to avoid predators and have sufficient reserves to survive their first winter (Beamish and Mahnken 2001). Currently, there is no consensus on the importance of size-selective mortality and compensatory growth as mechanisms regulating the mortality and abundance of Fraser River Sockeye Salmon.

We propose retrospective and comparative analyses of growth characteristics derived from the scales of two Fraser River stocks demonstrating contrasting patterns of freshwater and marine residence and, importantly, opposite trends in adult returns. Over the last decade Harrison (sea type) has had a high number of adult returns contrary to Chilko (lake type) Sockeye Salmon returns, which have been low. These stocks differ in their life-history in that Harrison fry outmigrate to sea ~ 2 months after Chilko smolts (Beamish et al. 2016).

Our goals are to: (a) evaluate the extent of size-selective mortality, (b) determine the factors influencing juvenile length at the end of their first year at sea, and (c) determine the factors influencing the number of returning adults.

S17-I32 Size selective mortality and early marine growth in Fraser sockeye salmon 2017

Upriver Bright Density Dependence: Analyses of Existing Samples

The main objective of this study is to evaluate metrics of growth in otolith samples of natural origin recruits (NOR) to test the hypothesis that early freshwater growth of Hanford Reach Fall Chinook salmon is related to adult spawner and/or subsequent juvenile abundance (density dependent effects). The proposed project will determine whether the prior year adult escapement and/or pre-smolt abundance of juvenile fall Chinook salmon in the Hanford Reach is related to early freshwater growth in these fish.

N18-VHP17 Upriver Bright Density Dependence: Analyses of Existing Samples Report

Estimation of Fraser River – South Thompson Age 0.3 Chinook Aggregate Escapement

The goal of the project is to estimate the spawning escapement of the Fraser River – South Thompson age 0.3 aggregate (ST0.3A Chinook). The ST0.3A escapement will be estimated using Coded Wire Tags (CWT), Genetic Stock Identification (GSI), and CWT exploitation rate indicator stock data from escapement and Fraser River fisheries. To achieve this objective, we will increase recovery of CWTs from Chinook carcasses in the Lower Shuswap River; conduct a high-precision mark-recapture project and CWT sampling in the Middle Shuswap River; collect age samples across the South Thompson watershed; produce a CWT release group of Middle Shuswap River smolts (to augment the Lower Shuswap indicator stock); and analyze GSI and age data from the Albion Test Fishery.

N18-VHP16 Estimation of 2015 – 2018 Escapements of the South Thompson 0.3 Chinook Aggregate using a Bayesian Model that Combines Data on CWT Recoveries and GSI_Report Title Page


Lower Shuswap River Chinook Salmon Indicator Stock (Fraser River Summer-run Age 0.3 Stock)

A mark-recapture project would be conducted to estimate escapement and would involve capturing and marking live fish as they migrate to the spawning grounds and recovering carcasses. The Coded Wire Tag (CWT) smolt group is required to continue representation of Lower Shuswap River (and Fraser River Summer 0.3) Chinook in subsequent fisheries and escapement. This project includes capture of brood stock, rearing of like-timed and like-sized 0+ smolts, and purchase and application of 100,000 CWTs to those hatchery smolts, as part of the overall release group.

The data acquired from the application of CWT’s aids in the computation of the exploitation rate data that are used for several purposes, including estimation of maturation rates, reconstruction of production for stock-recruitment analysis, monitoring Individual Stock Based Management (ISBM) fishery obligations (specified in the 2009 Agreement), development of agency forecasts for the PSC Chinook model calibration, and providing an independent verification of the PSC Chinook model representation of fisheries, stock dynamics, and stock distribution among fisheries and escapement.

In particular, the Fraser River Summer-run Age 0.3 Chinook Stock (South Thompson aggregate including the Lower Shuswap) is one of the largest contributors to Southeast Alaska (SEAK) and Northern BC (NBC) fisheries, as well as recreational and First Nations harvests in the ocean and freshwater. Because of this fact, high quality, accurate escapement estimates are required to accurately forecast the NBC and SEAK AABM abundance indices. Recently, the CTC and PSC have expressed concerns about the performance of the Chinook Model, especially for northern fisheries, and this project will ensure availability of quality escapement and maturation rate data for one of the largest stocks.

Taku River Canadian Fishery Sampling & Stock Assessment

Data acquired through the Lower Taku River commercial and assessment fisheries are vital elements of the Taku River fishery management and stock assessment programs. Sampling involves the inspection for and recovery of coded-wire tag (CWT) information from Chinook and coho salmon which is used in the estimation of smolt production, the inspection for and recovery of spaghetti tags from Chinook, sockeye, and coho to support abundance metrics, the collection of otoliths from sockeye to estimate contributions of enhanced sockeye salmon, and the collection of age, sex, and length samples from Chinook, sockeye and coho salmon caught in the fisheries. These baseline stock assessment data are used for stock recruitment analyses, preseason forecasting programs for Chinook and sockeye salmon, and monitoring stock health.

N20-I25 Taku River Canadian Commercial Fishery Sampling & Stock Assessment 2020 Report

N19-I24 Taku River Canadian Commercial Fishery Sampling & Stock Assessment 2019 Report

N18-VHP07 Taku River CDN Comercial Fishery Sampling and Stock Assessment Report 2018

NF17-VHP11. Taku Fishery Sampling & Stock Assessment - Final