Category: Fraser River

Sockeye Salmon SNP Panel Genetic Baseline for the Fraser River

The accurate identification of population of origin of mixed-stock samples, and clear delimitations of stock structure, e.g., to the Conservation Unit level, are key components of fisheries management, including for Fraser River sockeye. Currently, genetic stock identification for sockeye salmon is conducted both in-season and post-season using a microsatellite panel. The Molecular Genetics Lab (MGL) at PBS is transitioning all salmonid genetic baselines from traditional microsatellite panels to medium density amplicon panels (i.e., ~500 SNP markers), although legacy microsatellite panels will also remain in operation for most species. The 500-marker SNP panels in operation at MGL have thus far yielded superior resolution to the microsatellite panels for stock identification work. Chinook, coho, and chum salmon all have SNP panels within MGL, and plans are in place to develop such panels for both sockeye and pink salmon as well.

Improving in-season pink salmon assessment through the collection of Fraser River pink salmon DNA baseline data

Historical data indicate that upper Fraser River pink salmon stocks return to the Fraser River earlier than lower Fraser River pink stocks. Given the differential migration timing between upper and lower Fraser River pink salmon, stock proportion estimates could provide in-season indications of timing for the total pink salmon run. This would improve the in-season assessment of pink salmon run size early in the season, when it is notoriously difficult to differentiate  between a run that is early and small or late and large.
Current pink salmon genetic stock identification (GSI) has focused on estimating the proportion of Fraser River versus non-Fraser pink salmon. Further differentiation between early/upper and late/lower Fraser River pink salmon stocks will require additional baseline samples from the spawning grounds. To obtain these data, we intend to hire temporary staff
to visit spawning sites for pink salmon in the Fraser River and collect new tissues for DNA analysis, targeting particular spawning areas that are represented poorly in the current DNA baseline by old samples of questionable quality. DNA will be extracted from these tissues and genotypes will be collected at 16 microsatellite loci to augment and/or replace (as appropriate) the current baseline.

Marking Maria Slough Chinook to evaluate representativeness of the exploitation rate indicator stock for the Fraser Summer Run age-0.3 stock group

The indicator stock for Fraser River summer run age-0.3 stock group of Chinook Salmon is the Lower Shuswap population in the interior of BC. However, Maria Slough is the only population in this stock group in the Lower Fraser River and its population is at a much higher conservation concern than the rest of the summer run age-0.3 stock. The CDFO Salmon Enhancement Program has re-initiated hatchery production as a conservation measure for supplementing Maria Slough Chinook since abundance has declined to less than 20% of its historic average. Additionally, the escapement estimate has low precision and moderate accuracy. This project will implement an innovative application of passive integrated transponder (PIT) technology to increase the accuracy and precision of the escapement, and pair it with applying coded wire tags (CWT) to Maria Slough Chinook to collect fisheries and other biological data.

Alternative estimation methods for salmon passage on fisheries opening days at Mission hydroacoustics site

The PSC Mission hydroacoustics (HA) program uses stratified counting method to estimate daily salmon passage across the river. Passages in nearshore areas (60m from the left-bank and 30m from the right-bank) are monitored by the 2 shore-based sonar systems which also simultaneously monitor fish’s swim speed and direction of travel. Passage beyond the nearshore monitoring areas is sampled by a mobile transecting vessel with a downward looking transducer. The  mobile system can estimate density of the offshore fish, but not swim speed or direction. Offshore fish are assumed to have a similar swim behaviour to the nearshore fish for the derivation of offshore fish passage rate through a mobile flux model 1.
In recent years, Food, Social and Ceremonial (FSC) fisheries have operated a driftnet fishery in the vicinity of the HA site. During fisheries openings, driftnets often cross the transect line of the mobile transecting vessel and severely impact the migration behaviour of salmon. When trying to evade the net, the salmon in offshore area deviate from their normal upstream migration behaviour by holding or milling thereby violating the assumption of uniform behaviour between nearshore and offshore fish used in the current estimation method. During the recent hydroacoustic review process and in responding to a memorandum of understanding between DFO, PSC and Sumas First Nation, PSC Hydroscoustics staff identified such evasive milling behaviour during fisheries as a source of likely bias. Therefore, alternative estimation methods should be investigated and developed for fishing days or opening hours to minimize bias due to fishing impacts.
For this project, we intend to explore the impact of replacing the data collected during fishing hours with an alternative dataset to derive the salmon passage during fishing hours. The method constructs the alternative dataset from the data outside the fishery opening hours (the non-fishing hours) using a projected ratio of fishing hour to non-fishing hour passages from the previous non-fishing day(s).

Improvements to Fraser River Pink Salmon Run Reconstruction Models and In-Season Assessments

Fraser River pink salmon returns have been notoriously difficult to assess in-season. Many of the assessment tools originally developed for sockeye salmon do not perform well for pink salmon due to slower and more variable migration speeds. Small and highly variable catchability coefficients add additional uncertainty to pink salmon run size estimates based on test fishery catch-per-unit-effort (CPUE) data. While there is potential to improve in-season estimates using commercial catch indices (e.g. Area 7) in a reconstruction framework, the current data structure does not easily support a thorough investigation of this type of analysis. In 2019, atypical migration behaviour resulted in significant assessment challenges. Due to an incorrect alignment of test fishery and commercial CPUE data, pink salmon run reconstruction models underestimated the true run size. Both the data integrity and underlying model assumptions were scrutinized post-season and a clear need for model upgrades was noted by the Fraser River Panel and Technical Committee. The result of this project will be a more robust, and accurate in-season assessment tool for Fraser River pink salmon and future improvements in meeting management targets.


Lower Fraser River Gillnet test fishery site evaluation

The primary objective of the project is to evaluate alternative locations for the Cottonwood test fishery in the lower Fraser River. The project would start with an exploratory analysis of historical data and a meeting to discuss the various location options in addition to considering alternative test fishing methods. This would include an assessment by PSC staff of the feasibility of implementing this test fishery in 2021 which would be operated in parallel with the traditional Cottonwood test fishery.

Estimation of offshore fish passage at Mission by imaging sonar

For this project, we propose to use an Adaptive Resolution Imaging Sonar (ARIS) mounted on a fin-shaped metal body towed by the vessel to acquire data of fish images. This would allow for more accurate survey of offshore fish passage than the current mobile survey system at Mission Hydroacoustics (HA) site. The application of ARIS system will address two challenges that are difficult to resolve with the mobile split-beam system. These are (1) recognition of fish targets and (2) determination of fish’s swim direction. By directly measuring these two variables with an imaging sonar ARIS, we will obtain an accurate estimate of offshore fish passage, which has been identified as a limitation with current systems when estimating abundances at Mission.

Evaluating the use of FSC and commercial fishery catch data to inform in-season management of Pacific salmon fisheries

The overall objective of the project is to assess the utility of data collected from commercial pink salmon and Indigenous Food, Social, and Ceremonial (FSC) sockeye salmon fisheries to support Test Fisheries data used to inform estimates of daily sockeye abundance. ESSA will work with partners from the Pacific Salmon Commission (PSC), Fisheries and Oceans Canada (DFO), commercial fishers (Canfisco, Area B Harvesters), and FSC fishers (A’Tlegay Fisheries Society) to determine the feasibility of using data from commercial and FSC fisheries to support in-season estimates of daily abundance. While previous work demonstrated that commercial sockeye fishery catch data was a promising source of information to supplement test fishery catch data (Cave 2017, Ma et al. 2019), commercial fisheries for sockeye in the last decade have only opened on dominant-cycle years (i.e., 2010, 2014, and 2018), limiting the utility of this information. This project seeks to extend these promising results to other fisheries – namely the FSC sockeye fishery, which occurs in most years, and to the pink salmon commercial fisheries (odd years), thereby improving the utility of information gained from fisheries for in-season planning.

Using Deep Image Segmentation Methods to Detect and Classify Salmon Species from ARIS Sonar Images

Improvement of species composition estimates in the Fraser River during sockeye salmon migration is a priority of the Fraser River Salmon Fisheries Management for the 2021 projects. Given the low returns of Fraser River sockeye salmon and poor catches from test fishing programs in recent years, species composition estimates based on the catch data have become increasingly unreliable for the in-season management of Fraser stocks. To address this challenge, alternatives methods must be developed to provide reliable species composition estimates for both the daily and the seasonal total sockeye abundance estimates.

For this proposed project, we will use image data from a newer generation of imaging sonar (ARIS), which offers a higher spatial resolution than the DIDSON sonar used in the previous projects. This project is aimed at delivering the following 1) improved accuracy and reliability in species classification; 2) automatic measurements of fish length and other feature variables with confidence rankings that can be used in the PSC mixture model for species composition estimation.


Investigating thermal windows of juvenile Sockeye Salmon populations in freshwater

The influence of climate warming on the growth of juvenile Fraser River Sockeye Salmon rearing in nursery lakes is poorly understood, particularly in the context of the multiple factors that regulate growth in these environments. This represents a key area where climate change and other forcings may be influencing stock outcomes (i.e. productivity), unbeknownst to fisheries managers.

We aim to fill this gap by reconstructing stock-specific long-term time series of annual growth rates of juvenile Sockeye Salmon in freshwater in relation to their thermal environments. The PSC Scale Laboratory plans to measure an additional 10,000 scales this fall and winter to extend the current existing data of scale growth (1990-present) to 1970 – present. Scales of major Fraser River Sockeye Salmon stocks have been consistently collected by the PSC since 1950s and can be paired with otolith samples since the 1970s. Matching freshwater growth of Sockeye Salmon with adult returns will show the relationships between the freshwater growth and overall survival. Linking freshwater growth with biological factors (e.g. number of spawners) and environmental factors, particularly a large range of temperatures, will quantitatively determine the stock-specific thermal windows and identify the thermal optima.