While Fraser River Sockeye Salmon survival has declined over the past decade it has also exhibited high inter-annual variability. The processes responsible for this trend and the variability are not understood and require continued investigation. Partitioning mortality among important life history stanzas (e.g. freshwater rearing, downstream migration, ocean entry) is required to understand when and where production limitation occurs so that it can be incorporated into production forecasting models. The early marine period has been identified as a period of high mortality and a critical stage in determining brood year strength for this species. However, the mechanisms associated with this mortality, as well as the role the annual abundance of juvenile Fraser Sockeye entering the Strait of Georgia (SoG) plays, are unknown. Freshwater survival (from egg deposition to lake out-migration) is estimated for only two Fraser River Sockeye Salmon stocks annually. Currently, marine survival combines mortality across many important life history stanzas (downstream migration, ocean entry, marine rearing), providing little ability to identify or resolve important production limiting processes. Data collected from a juvenile trapping program in the lower Fraser River from 2012 through 2018 provided the first opportunities to identify when specific Sockeye stocks (CU’s) make their entry into the SoG. This information will assist in identifying production processes across many important life history stanzas and help explain observed survival trends.
This project will allow the hiring of a biologist to further the analysis already performed annually on data collected with operational funding provided by the PSC Southern Fund (2012-2016) and DFO (2017-18), and in-kind support from the DFO (2012-2016). These data have shown there are significant stock differences in downstream migration timing and relative abundance among Fraser Sockeye juveniles, both within and among years. This work will allow the development of new juvenile based models. Juvenile based models have shown to be the higher performing models for forecasting Sockeye Salmon returns where we have long juvenile time series (Chilko and Cultus Sockeye Salmon).
We propose that a combination of the variable ocean conditions between years and the variability in rearing duration in the Strait of Georgia will impact the growth and condition of juvenile Sockeye salmon as they leave the Strait of Georgia, and will influence survival during the first and second marine winters and subsequently total marine survival. This project will utilize sockeye samples collected during both the Mission downstream trapping and nearshore marine sampling in 2017 and 2018 to examine variability in stock specific condition (energy density and prevalence of pathogens). An association study (L. Godbout) will examine early marine growth (otoliths) in these two years. We will work collaboratively with Dr. J. King to include juvenile samples collected in 2018 in QCS in our analysis. In addition we will work with the NPAFC (Riddell and Beamish) winter survey in the North Pacific in February and March 2019 to compare these juveniles with sub-adults captured during their first and second marine winters. Samples of adult returns from dominant stocks will also be collected in 2019 and 2020. This will be the first work examining individual stocks across their entire life history from downstream migration, to early marine growth, high seas residence and spawning return. The results of this work will be used to test the critical size and period hypothesis and to identify indicators of salmon survival that can be measured during the early marine period. These results can immediately be incorporated in qualitative information that is compiled annually in DFO reports on observations across all life-history stages of Fraser River Sockeye to provide an indication of survival for these stocks in an upcoming return year. The goal long-term of this process and these results will be to improve quantitative forecasts of Fraser River Sockeye.
Abundance of Fraser River Sockeye salmon peaked in the early 1990s, and began declining from 1995 onward, hitting an all time, and highly unpredicted low in 2009 (Grant et al. 2017). The ongoing decline in productivity and abundance, and the unpredictable nature of the variation along that decline, prompted the call for a judicial inquiry. Science presented at the Cohen Commission of Inquiry, and generated since that time, all point to the early marine environment as a critical temporal period influencing variations in year-class strength (Rensel et al. 2010; Beamish et al. 2012; Peterman and Dorner 2012; Thomas et al. 2012). Studies undertaken to better understand the drivers of variation in early marine survival coalesce into four main themes: food limitation (e.g. Chittenden et al. 2010; Irvine and Akenhead 2013; Beamish et al. 2012), predation (Thomas et al. 2016), environmental stress (Hare et al. 1996; Duffy et al. 2011 Rensel et al. 2010; Healey 2011), and disease (Price et al. 2011; Miller et al. 2011; Miller et al. 2014; Tucker et al. 2018). Our genomics research focuses in on two of these themes: environmental stress and disease.
While environmental monitoring can provide information on seasonal and annual variations in temperature, salinity, oxygen, and harmful algal bloom events, salmon may be able to behaviorally avoid exposure to stressors, especially in the ocean, and it is unclear how much such variation may affect them. However, we now have the ability to detect variability in stressor impacts on the salmon themselves. We have developed biomarker panels to specifically identify the presence of different classes of stressors (e.g. thermal, hypoxic, and osmotic stress), physiological states indicative of poor health (e.g. inflammation, viral disease response, and state of immune stimulation), signatures repeatedly associated with imminent mortality, and the presence of harmful algal bloom species and key pathogens, all based on gill biopsy samples. We can run these biomarker panels simultaneously on a microfluidics qPCR “salmon Fit-Chip”.
We have accumulated 10 years of collections of juvenile Sockeye salmon originating from the Fraser River, which covers a period of extreme climactic variability as well as a large range of variation in Sockeye salmon year-class strength (as indicated by ocean survival and productivity). These fish have already been identified to stock through GSI, potentially allowing characterization of stressor impacts by stock.
We will apply the salmon Fit-Chips on 2,395 juvenile Fraser River Sockeye salmon sampled as smolt outmigrants in freshwater and ocean migrants in the Strait of Georgia through the Queen Charlotte Strait from 2008-2015. Bayesian hierarchical models will be applied to Fit-Chip data to examine the explanatory power of genomic stress indicators on estimates of ocean survival (smolt to adult including downstream migration) and spawner-recuit analysis. PCA-derived models that include monitoring data on environmental parameters will also be explored to examine how closely stress indices in salmon match the environmental triggers of specific stressors present in the regions where salmon were caught. Inclusion of a substantial number of fish from the Chilko indicator stock will strongly benefit model exploration on smolt to adult survival.
Area-under-the-curve (AUC) methods are employed to estimate escapement at the majority of Chum Salmon spawning sites in the Fraser River where escapement is enumerated. The AUC methodology requires visual counts of Chum Salmon on the spawning grounds and an estimate of the time (in days) Chum Salmon are available to be visually counted during these surveys. This time is termed survey residence time or survey life (SL). Currently, there is very little SL information specific to Fraser River Chum Salmon populations (Grant el at. 2007; Wenman et al. 2014). As a result, an average literature value for the Region is used for AUC estimates of lower Fraser River Chum Salmon spawning populations. It is not known if using the average literature value biases these AUC generated estimates although limited work suggest the literature value currently used is biased high (Grant el at. 2007; Wenman et al. 2014). We propose to accurately and precisely estimate SL for select lower Fraser River Chum Salmon spawning populations in 2019 and to determine a more appropriate SL value to use for all Fraser Chum Salmon escapement estimates using the AUC methodology.
The objective of this proposed work is to test the feasibility of using upward facing SONAR technology to assess daily abundances of Chilko Lake Sockeye as they migrate through the Chilko River in the spring 2019. This technology has proven to be effective for enumerating migrating smolts in comparable rivers in Alaska. The reliably of the method will be evaluated based on how well the daily SONAR-derived abundance indices predict the daily migration totals observed at the weir. If proven effective, the SONAR method would provide an alternate assessment method for the Chilko watershed that could be quickly employed in years when high flows either prevent the installation of the weir at the beginning of the migration, or necessitate the removal of the weir before the smolt migration is largely complete.
Additionally, if proven successful at Chilko, the upward facing SONAR method could potentially be used to assess Sockeye smolt populations in other areas of the Fraser watershed where population assessments are not currently conducted. Both the Cohen Report and the Fraser River Panel identified upstream juvenile Fraser Sockeye Salmon monitoring as a priority to address major data gaps. Expanding on this methodology, if deemed successful, would represent an important step to help improve stock specific information related to Fraser Sockeye productivity and an understanding of the potential limiting factors in the freshwater environment.
Fraser River sockeye have experienced low returns in recent years due to declines in survival that began in the mid-1990s, with the exception of a brief period of average to above returns from 2010 to 2014. Total Fraser sockeye survival is affected by both marine and freshwater drivers that occur on local to regional scales. Habitat is a limiting factor for salmon production in some freshwater streams and lakes, and can be improved through restoration and habitat alteration activities. Variation in population growth rates and production capacity of salmon systems are related to habitat variables, including riparian vegetation, stream depth, temperatures, and gravel size. However, in the absence of data on such stream-level habitat characteristics, or even juvenile data for most Conservation Units, which would allow us to isolate trends in marine versus freshwater survival, how are habitat-based stressors identified and restoration activities planned to ensure that projects are correctly prioritized across the Fraser watershed?
To identify these stressors and prioritize restoration activities we propose to collaborate with consultants and various DFO scientists. This work will improve information sharing between individuals within and outside of DFO by standardizing data storage across species, and making data, and data quality, accessible. In enabling access and exploration of these data on a watershed level, habitat issues affecting the survival of Fraser sockeye may be identified and prioritized.
S19-FRP12 Fraser salmon cross-species escapement and productivity database for investigating habitat stressors 2019 Report
The unpredictability and variation in adult recruits for Fraser sockeye both within and among major stocks cause challenges for harvest planning and rebuilding initiatives. This multi-year project will monitor and analyze variation in biological condition of juvenile sockeye in fresh water to understand variation in stock-specific survival. This project will apply and extend the results from a previous SEF juvenile sockeye research project that found stock-specific energetic condition of juveniles reflects variation in lake primary productivity and density of juveniles within a natal rearing lake. Moreover, mechanistic links to survival were developed, such as, interannual variability in fall-fry and smolt energetic condition are consistent with density-dependent growth and survival, critical minimal energy levels are associated with swim performance and potentially survival, and interannual and stock-specific variability in the portion of individuals at or near these critical energy levels. We propose to extend and apply these results by strategically assessing stock-specific variability in biological condition of juvenile salmon from key Fraser sockeye stocks.
S19-FRP06 Monitoring the biological condition of juvenile Fraser sockeye in relation to stock-specific survival 2019 Interim Report
The objective of the project is to assess the migration timing, size, age, and condition of specific stocks of upper Fraser juvenile Sockeye at the start of their seaward migration. In addition, new capture methods/sampling technologies may be examined as potential options for future juvenile assessments. This project represents a coordinated effort with existing DFO Science projects (Fraser Sockeye Adult Escapement Program, Environmental Watch Program, Mission Downstream Smolt Project in the lower Fraser River, juvenile salmon surveys in the Salish Sea, and ocean condition assessments) to provide better resolution and new information on the survival and productivity of Fraser Sockeye stocks, particularly during the freshwater residency period and the seaward juvenile migration.
S19-FRP17A Upstream Fraser River sockeye (Oncorhynchus nerka) smolt monitoring feasibility project 2019: Nautley River 2019 Report
Historical data generated from reconstructed estimates of daily marine abundances of Fraser River sockeye salmon form the basis for critical components of pre-season planning and in-season stock assessments. Pre-season, historical time-series of timing and diversion are used to parameterise forecast models and fisheries simulations. In-season, reconstructions are used to update estimates of run abundance, timing, diversion rate and test fishery catchability (expansion lines). For fisheries planning and assessment purposes, PSC Secretariat biologists assess these estimates at a refined stock resolution, often subset by cycle-line. Over time, the stock-resolution, file structure, and assumptions applied to inseason run reconstructions has evolved, leading to inconsistencies across the time series. In addition, post-season adjustments, including updated stock ID and corrected/updated catches, can lead to a disparity between the in-season run reconstruction files and postseason estimates.
We propose to update and standardize historical run reconstruction files using recently updated post-season catch and Mission passage information and currently adopted data standards. We also propose to build a new data warehouse to store post-season estimates of daily run reconstructions, from which time series of fish migration behaviour and fishery harvest parameters can easily be updated and queried at various stock resolutions and year-aggregations (e.g. by cycle line or dominant year). These improvements will bring the quality of the run reconstruction estimates in line with the recent improvements to the post-season catch, passage and escapement records, and help the Secretariat provide the Fraser River Panel with key inputs to both the preseason and in-season management processes. Updated stock-specific information on migration timing and diversion rate would also be shared with DFO to facilitate improvements to stock-specific forecasts for these important inputs in fisheries planning.
S19-FRP02 Improving pre-season planning and in-season estimates of Fraser River sockeye stocks through stock- and cycle line-specific estimates 2019 Report
Studies and analyses conducted from 2009-15 have demonstrated the spatially-stratified hydroacoustic counts can be combined with species composition data from the fishwheels and Whonnock test fisheries to produce scientifically defensible estimates of the number of sockeye and pink salmon that pass the Mission hydroacoustic site in odd-number years (Robichaud et al. 2010; English et al. 2016). In 2013 and 2015, fish length data derived from images acquired by imaging sonar DIDSON was used in mixture-model discrimination analysis to derive species composition estimates for the near-shore strata monitored by the DIDSON systems at the Mission hydroacoustic site (Grant et al. 2014). Substantial differences have been observed between the DIDSON length-based species composition estimates for near-shore strata and those derived from fishwheel samples (English et al. 2016). Both methods have their strengths and weaknesses. For the fishwheel, species should be identified accurately, but sockeye and pink salmon may not be equally vulnerable to the gear. For the imaging sonar systems, both species should be equally vulnerable to being observed in the image, but the measurement of lengths from the DIDSON images is less precise than manual measurements and the length distributions of sockeye and pink salmon are highly overlapped. To date, the PSC1 estimates of sockeye proportions derived from DIDSON length-based approach have tended to be higher than those derived from the fishwheel samples. Being a next generation of DIDSON, the adoptive resolution imaging sonar (ARIS) can provide a much higher down-range resolution than DIDSON for fish images. Through this project, we will assess the reliability of the ARIS length-based species composition estimates and further explore the potential causes of the discrepancies between ARIS and fishwheel based species proportions.
S19-FRP01 A fishwheel-Aris study to compare fish size and species ID 2019 Report
S17-I35 A Fishwheel-ARIS study to evaluate the ARIS length-based discrimination estimates of species composition for the Mission Hydroacoustic monitoring