Category: Southern Fund

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.

 

BC Fish Passage Restoration Initiative (Canton Creek Culvert Replacement Project)

There are more than 172,000 road crossings over fish-bearing streams in BC, with an estimated 92,000 of these crossings being either partially or fully impassable to fish. The Canadian Wildlife Federation (CWF) is working with the province of British Columbia’s Fish Passage Technical Working Group (FPTWG), Fisheries and Oceans Canada (DFO), the Pacific Salmon Foundation (PSF), and the Pacific Streamkeepers Federation (PsKF) to develop a BC Fish Passage Restoration Initiative to remediate these crossings and other barriers to fish movement in a strategic way that provides the most benefit to salmon and federally listed fish species-at-risk.

Canton Creek wetland is a large (approximately 4,000 m2) salt marsh located west of Canton Creek on the west coast of Vancouver Island. The wetland connects to Canton Creek though only during high flows, and through a ditch that otherwise dries out and strands fish. There are two culverts under Head Bay Forest Service Road that connect the wetland to the ocean, and the wetland is used by rearing Coho Salmon. Chinook Salmon juveniles also rear in the wetland. Connection to the ocean is tidally influenced, and the culverts are perched at lower tides. We have retained a contractor to develop a remediation plan for the wetland, which entails upgrading the two culverts connecting to the ocean with fish passable structures. Culverts will likely be replaced with open-bottom structures, though designs will determine whether a full replacement or a retrofit is the most effective way of achieving fish passage at variable tide levels.

Tranquil Creek Restoration

The degradation of freshwater habitat from forestry operations is believed to be a leading factor in the decline of Chinook populations in Tranquil Creek, Clayoquot Sound. Chinook populations along the west coast of Vancouver Island are declining, yet the problem is particularly acute in Clayoquot Sound. Tranquil Chinook populations are believed to be at just 3% of their historic abundance. In-stream and riparian restoration works are proposed for the prime rearing and spawning habitat in Tranquil Creek. This project was designed to address specific high-risk limiting factors to production in the freshwater life stages. Historically, Tranquil was one of the largest Chinook runs in Clayoquot Sound. Habitat restoration in this watershed can significantly contribute to regional recovery strategies for Chinook in the WCVI conservation unit.

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.

Okanagan River Summer Chinook Survival Study

The Okanagan Nation Alliance (ONA) is proposing to conduct a juvenile Chinook survival and habitat use study of the Okanagan River. Survival of hatchery-reared tagged Chinook would be tracked through potential mortality hot spots of the Canadian Okanagan River system. The results of the survival study will be highly important to guide resource allocation for future habitat restoration projects. Further, the results will be critical in refining hatchery smolt release strategies (timing and locations) to maximize survival and achieve rebuilding goals.