Attachment 5.1.2.3 Pacilic Salmon Foundation l.604.664.7664 www.psf.ca 300 - I 682 West 7th Avenue l. 604.6647665 Vancouver. N2 Canada V6J 456 PACIFIC SALMON FOUNDATION

October 23,20'J,8

Stephanie Snider, MBA Trans Mountain Expansion Project

Dear Ms. Snider,

Enclosed you will find the 2017-2018 progress report for the Canadian component of the Marine Survival Project.

2017 marked the end of field programs and while some discreet projects are continuing the majority of the project has now moved into the analysis stage. Several working groups have been convened to lead the analysis and meetings have taken place over the summer and fall.

Ongoing projects for 20L8 include;

o Citizen Science program o Satellite imagery program . Synchronicity between phytoplankton and zooplankton phenology program r Strategic Salmon Health lnitiative (SSHt) o HarmfulAlgal Bloom monitoring o Modeling programs o Predation studies

The SSMSP has resulted in 23 accepted (21 published) manuscripts and many technical reports and affiliated publications.

Later this fall PSF will report out on key findings to communities around the and discussions of potential priority legacy projects is underway.

lf you have any questions or concerns please feel free to contact me at the coordinates below.

Rega

Tim Sucic VP Operations Pacific Salmon Foundation 300 - 1-682 West 7th Avenue Vancouver, BC V6J 456

Attachment 5.1.2.3 2017-2018 Activity Summary October 2018

THE SALISH SEA MARINE SURVIVAL PROJECT: 2017-2018 ACTIVITIES.

Overview

In 2017, the Canadian Salish Sea Marine Survival Project (SSMSP) teams continued their field programs including measurements of physical water properties, zooplankton, forage fish and juvenile fish sample collections, acoustic tracking studies and seal predation programs. The program involved academic and federal Principal Investigators for field studies as well community-based, citizen science sampling programs, such as the SSMSP Citizen Science Oceanography program which utilized volunteers to sample water quality and zooplankton data throughout the Strait of Georgia.

2017 made up the third and final year of the complete program of field studies in the Strait. Work continued to focus on the Cowichan, Big Qualicum and Fraser watersheds. A number of modeling initiatives were funded on the Canadian side for 2017-2018, and GIS and analytical capacity was increased. Work continued with the Strait of Georgia Data Centre (SGDC) to collate datasets gathered under SSMSP, and time series for use by the modelers. The Pacific Salmon Foundation (PSF) established a number of focused workgroups for the following: Biological Oceanography & Environmental Parameters: Zooplankton, Ichthyoplankton & Forage Fish: Juvenile Salmon: Predation, Parasitism & Disease; Nearshore Habitat; and Analysis & Modeling. Workgroup leaders were assigned, and meetings occurred during the summer and fall to assess progress to date with respect to the key SSMSP hypotheses.

Focus for Canadian SSMSP activities for 2018 was on sample processing and analyses, publications, and on synthesis activities. The vast majority of field projects are now complete, and several final reports have been submitted. Sample analysis and data analysis is ongoing at several major labs at the University of Victoria, University of British Columbia (UBC) and Fisheries and Ocean Canada (DFO) (e.g. the Strait of Georgia Zooplankton and Juvenile Salmon Programs). Ongoing Canadian projects for 2018 include the following: PSF Citizen Science program, Maycira Costa’s satellite imagery programs, Karyn Suchy’s Synchronicity between phytoplankton and zooplankton phenology program, EPIC 4, the Strategic Salmon Health Initiative (SSHI), PSF’s Harmful Algal Bloom monitoring, Brian Hunt’s project to examine the trophic structure of the Salish Sea plankton food web, the UBC Modeling programs, UBC Predation studies (seals and herons), and DFO-led Wild-Hatchery Interaction Studies (delayed release trials).

Modeling initiatives also are ongoing, and Villy Christensen is working with his counterparts, Carl Walters and post docs to continue development of a full Strait of Georgia model. Progress continues at UBC and the food web modelling component began September 2018.

We are now at a total of 23 accepted (21 published) manuscripts from the SSMSP. There are also many technical reports and affiliated publications associated with SSMSP. Materials are available online on our publication tracker: SSMSP Publications1

1 Salish Sea Marine Survival Project Publication Tracker: https://docs.google.com/spreadsheets/d/14GrVYD0jUYFkUtCBOJ0TwUbWNFJMYqCb2yJLgMwbYcU/edit?usp=sharing

Page 1 of 7 Attachment 5.1.2.3 Next steps for PSF include a number of meetings for the fall of 2018 to report out our key findings to date to communities around the Strait of Georgia. PSF (Drs. Brian Riddell and Isobel Pearsall) are working on a series of recommendations for priority legacy projects based upon the key findings identified during SSMSP, and Isobel is working on a number of technical summaries, short videos and online story maps to provide project information to the interested public.

Highlights

Citizen Science Program

The Citizen Science Oceanography program was designed to sample and monitor the Strait of Georgia at a spatial scale not possible before. Collections are made of water quality (temperature, salinity, dissolved oxygen, chlorophyll content, nutrients), turbidity, phytoplankton, and zooplankton. The examination of phytoplankton also allows for an analysis of harmful algal species.

The program was begun in February 2015, with all vessel operators fully trained to carry out the program on the first “shakedown” cruises. During 2015, the program had vessels outfitted and actively sampling the Strait of Georgia from Campbell River, Deep Bay, Qualicum, Cowichan Bay, Victoria, Lund, Powell River, Sechelt and Steveston. There was also some sampling done in Ladysmith, partnering with the Snuneymuxw First Nations. Ocean Networks Canada provided a smart phone application for sample data transfer so that data can be transmitted directly to ONC, undergo QA/QC, archived and made freely available over the internet. In 2016 some changes were made to the program: the Victoria vessel was not continued as this area showed little seasonal variation oceanographically; instead it was replaced by a new vessel sampling out of Galiano Island. Thus, in total, there have been 10 groups actively monitoring the Strait for each year 2015-present. During 2016, PSF partnered with Hakai to examine ocean acidity on the and Powell River vessels. The program was continued through 2017 using the same format.

The complete tally of samples collected for 2015-2017 is as follows:

Sampling Vessel Nutrients Phytoplankton Chlorophyll Secchi Zooplankton Years Trips CTD casts Collected Collected Collected Recordings Collected Total Samples 2015 150 2,264 1,809 1,381 193 2,088 146 7,881 2016 199 1,445 1,587 2,064 349 2,825 60 8,330 2017 197 1,420 1,529 1,934 340 2,814 54 8,091

3 years 546 5,129 4,925 5,379 882 7,727 260 24,302 PSF was able to secure funding to run the Citizen Science Program for one additional year in 2018.

Several SSMSP scientists are utilizing the citizen science data for model validation, and to address other questions as part of their programs. Examples of these programs and applications include the following: o Strategic Salmon Health Initiative: is there a relationship between level of stress (fish from areas temps O > 17 C temp & <6ppm O2) and expression of disease states? o Harmful algal blooms: How does water temperature/ salinity/ DO/ nutrients affect prevalence of HABS? o Migration Pathways of Pacific Salmon: Is there are relationship between water quality/hotspots of plankton & migration pathways? o Kelp and Eelgrass Restoration: Characterizing turbidity and water properties in a number of estuaries around the Strait

Page 2 of 7 Attachment 5.1.2.3 o Juvenile Salmon Studies: Relating the distribution, diet and fish size for key juvenile salmon stocks to temperature, salinity and dissolved oxygen. o Modeling Studies and Satellite Data: Data collected by the citizen science program is being used to validate 3D biological models of the Salish Sea, and to ground-truth satellite imagery with on-ground data. All data are available from the Strait of Georgia Data Centre.2

PIT Tag Studies

One of the key questions addressed in our program has been, where and when is mortality occurring? To address this, we have carried out a large-scale PIT tagging program in the Cowichan River. Over 56,000 PIT tags have been applied from 2014-2017 to four different cohorts of wild and hatchery juvenile Chinook during the spring in freshwater (Cowichan River), early in their first summer of marine life (Cowichan Bay close to shore, and then as they move out to open waters of the bay) and later in the fall of their first year in . Since 2014, adult Chinook returning to the Cowichan River have been scanned for PIT tags using automated antennas and hand-held scanners. These data allow us to compare survival among the 4 different groups, and to compare survival between wild and hatchery fish, as well as the relationship between size, time of ocean entry, growth, residency and survival. Results to date suggest survival increases with distance from the estuary, and that wild fish have a consistently higher survival than hatchery conspecifics by a factor of approximately 3:1. An interesting finding was the still very low survival of fish caught in September-October of their first year at sea. These fish were captured and tagged by micro-trolling (using modified troll gear to capture small Chinook) around the Gulf Islands. This suggests that significant mortality occurs during the first winter and beyond. Thus, there is evidence that there may be two key critical periods, one at marine entry, and the second over the first winter at sea. PIT tag returns will be collected through to 2020, at which time results will be finalized. Seal Predation Studies

The goal of the SSMSP Seal Predation studies has been to 1) estimate the numbers of chinook and coho smolts consumed in the Strait of Georgia by harbour seals, 2) evaluate their impact on salmon recovery, and 3) propose ways to mitigate the impact of seals. The approach has been to 1) determine diets and quantities consumed by individual seals in estuaries using DNA barcoding of scats collected at haulouts; 2) model overall consumption and seal-caused mortality of smolts using the diet and seal distribution data; 3) directly measure predation of PIT tagged coho smolts using head-mounted satellite-linked PIT tag scanners; and 4) determine hot-spots of predation risk during juvenile salmon out-migrations from back-mounted GPS/Daily Diary tags. Since 2012, researchers have been assessing the impact of seals on salmonids in the Strait of Georgia by counting the number of predators, quantifying predation events from visual observations, and determining diets from morphological and genetic analysis of fecal samples. Initial studies were done at a few sites, including Cowichan Bay and a few estuaries, and the data collected 2012- 2014 were used in a model being developed by PhD student Ben Nelson to test the impact of pinnipeds on Pacific salmon in the Strait of Georgia. Preliminary results from estuary scat data indicated that 20% of harbour seals in the Strait of Georgia may be eating up to half of the Chinook and Coho smolts that enter the Strait of Georgia. Most predation appeared to occur when juvenile fish were between 115-145mm in length. Most coho mortality occurs in April and May as they enter the Strait at this size range: while most Chinook mortality occurs in July, likely when they have grown to the preferred size range.

2 Strait of Georgia Data Centre website: www.sogdatacentre.ca

Page 3 of 7 Attachment 5.1.2.3 Between 2016-2017, scat collections were expanded to a number of non-estuary haul-outs in the Strait, to provide a more realistic estimate of overall impacts of predation. One of the criticisms of the seal diet work was a general distrust of the DNA meta-barcoding RRA diet method used. Thus, 2016 estimates of diet derived from DNA meta- barcoding and hard-part frequency-of-occurrence were compared with a third method―biomass reconstruction during 2017-2018.

Results include the following: • Age-class specific salmon consumption inside versus outside estuaries in 2016 showed minor but important differences in diet percentages in spring with lower predation rates on salmon in non-estuary sites. Salmon contribution to diets was significantly higher in estuaries in the fall, consisting primarily of adult Chum in both habitats. Thus, estuaries should not be used as proxies for non-estuary sites when assessing consumption of specific prey by harbour seals in the Strait of Georgia. Additionally, there appears to be year to year variability in the proportion of juvenile salmon in the diets of Harbour seals. These factors will need to be included in a reanalysis of the seal consumption model. • Analysis of the DNA meta-barcoding method has shown that this method yields biomass estimates that are similar to the currently accepted gold standard of diet analysis (Hardparts biomass reconstruction – a quite laborious process) while also providing better taxonomic resolution (down to species) for the salmon portion of diet. • Behaviour observations have included seal usage of log booms as haul-outs, and the use of log booms as salmon refuges. Other SSMSP studies have identified that large pulses of large hatchery fish enter the Salish Sea during a short window of time, possibly enabling the specialized foraging by seals. • Long-term monitoring is critical for assessing impacts of predation, particularly for species with large degrees of natural variability in production such as salmonids.

Acoustic Tracking Studies This research is aimed to assess how individual physiological states relate to migration rates, behaviour and survival of juvenile salmon travelling through the Strait of Georgia and areas of the Salish Sea. Using small acoustic transmitters, the behaviour and fate of Chilko sockeye (2016 and 2017) and Seymour steelhead (2015) smolts was tracked from release through the Salish Sea. The condition of these smolts was assessed prior to transmitter implantation and release through the use of biomarkers for pathogen presence and load, presence of immune- or stress-related responses, and growth potential, to better understand the links between body condition during initial outmigration may influence survival and behaviour in the early marine environment. In 2017 Kintama Research also conducted a small acoustic telemetry pilot study to examine fine-scale movements and residency of sockeye salmon smolts near Okisollo Channel salmon farms. Key Findings include the following: • Survival Rates and Routes Survival rates for both Seymour Steelhead and Chilko sockeye vary geographically and are both segment- and route-specific. There is relatively poor survival close to natal areas and different species / ages appear to respond similarly. This low survival is likely attributed to high levels of predation by Bull Trout in freshwater. It is apparent that the physiological state of smolts is important also, and these studies provide some of the first direct evidence that piscivores target physiologically compromised prey. Survival is higher in the turbid , but drops again when smolts enter the marine waters of the Strait of Georgia. There is some evidence that the routes taken through the region are important to survival, but smolts did not appear to spend much time around individual fallowed fish farms. These studies are being continued in 2018 when farms are fully stocked.

Page 4 of 7 Attachment 5.1.2.3 • Travel rates Smolts travel slowest in clear freshwater areas and fastest in the turbid mainstem of the Fraser River. This may be related to predator avoidance. They travel more slowly through the Strait, but their rate of travel increases through the Discovery Islands, likely due to the impact of currents and tides in this region. There are large differences among species with respect to travel rates: Chilko River Chinook smolts took more than a month to travel from freshwater to marine entry into the Strait of Georgia, whereas this trip takes only one week for Chilko sockeye. Meanwhile, steelhead smolts travel 2-3 times faster than sockeye smolts likely due to their larger size.

Ongoing work includes retrospective analyses on ~10 years of acoustic telemetry studies to determine how migratory behaviour and survival are influenced by oceanographic conditions in the Salish Sea. Lastly, individual- based models (IBM) are being developed to simulate smolt migrations to test what navigation and/or orientation behaviours smolts use in the early marine environment. Together these studies will help our understanding of salmon smolt migrations and the trends in productivity and survival.

Strategic Salmon Health Initiative

The SSHI project specifically addresses the hypothesis that infectious disease is impacting early marine survival of salmon in the Salish Sea. The project also addresses the potential that salmon aquaculture interactions may contribute to risk of disease in Pacific salmon smolts. Research studies under the project have been active during 2017 and 2018. Results include the following: • The project has identified a number of infectious agents that are showing strong pathogenic potential in the Salish sea environment, most notably parasites Pavicapsula minibicornis, Ceratonova shasta, Loma, Paranucleospora theridion, and Tetracapsuloides bryosalmonae, and viruses PRV and ENV. Moreover, two different strains of a novel arenavirus have been shown to infect Chinook and Sockeye salmon in the Salish sea, and their potential linkages with disease is currently under study. In total they have discovered 9 novel viruses to date. • After the discovery of HSMI (Heart and Skeletal Muscle Inflammation) on a salmon farm in BC, SSHI began conducting further analysis on Pacific salmon to determine if the virus, PRV, is associated with, and ultimately causative of, disease in Pacific salmon. Preliminary analysis of audit data suggests association between PRV and Jaundice/anemia in Chinook salmon, matching findings in Norway for Rainbow trout, and in Japan and Chile for Coho salmon. SSHI published a paper that provided strong evidence that the same strain of PRV is likely causing different expression of diseases in Atlantic and Chinook salmon in BC, increasing the evidence that PRV transmission from farmed salmon poses a risk to wild Chinook salmon. • Sockeye smolt tracking studies have identified linkages between IHNV and migratory survival in the river, but it appears that predators, specifically Bull Trout, largely consume infected fish before the reach the Salish Sea. Hence, this research is also demonstrating linkages between infection state and risk of predation, and the potential role that predators may play in removing infected individuals, thereby increasing the general health of the populations. Given the strong evidence that seals may be consuming large numbers of smolts, it would be highly useful to determine if infection status could pose an enhanced risk of predation by seals also. • Current studies focus on agents with highest pathogenic potential to examine their potential for impact. Smolt samples collected over a decade are being assessed to determine whether any agents, or combinations of agents are associated with year-class strength, stock-specific marine survival estimates, and life-history variation (subyearlings are faring better than yearling Chinook). They have already shown that the agents of most concern are found at higher prevalence and show stronger levels of seasonal truncation in yearling Chinook, potentially contributing to their poor performance.

Page 5 of 7 Attachment 5.1.2.3 This project will contribute to our understanding of the role of infectious disease in early marine survival of salmon, and is also contributing to ongoing risk assessments associated with the salmon aquaculture industry. Next steps will include an analysis of cumulative effects. An overarching question in the SSMSP syntheses will be better understanding cumulative impacts of stressors e.g. do harmful algal blooms and low dissolved oxygen act synergistically with disease development to ultimately cause mortality? Additionally, SSHI is preparing for challenge studies by attempting to culture viral and bacterial microbes, reaching out to experts on microbes likely to be highly ranked for follow up research, and working with VIU and UBC to set up challenge facilities.

2014-5 Studies

2014 funds were utilized towards the cost of a Seymour steelhead acoustic tagging study which was planned in 2014, and executed in 2015. 274 acoustic tags (around $400 each) were purchased for a study examining the behaviour and fate of Seymour steelhead smolts by tracking them from release through the Salish Sea.

Seymour steelhead salmon smolts share a migration route and have a similar coastal life history as Fraser sockeye smolts. In total, 274 Seymour steelhead smolts were tagged and released during the third week of May 2015. The release locales included: 30 tagged fish released in the Seymour River above the new rockslide, 84 tagged fish released in the lower Seymour near the estuary, and 160 tagged fish released at West Vancouver near Point Atkinson (Fig. 1). This release strategy was used because recent studies identified Burrard Inlet as having high risk of mortality for steelhead smolts (Balfry et al. 2011), and they wanted to ensure as many smolts as possible reached the OTN (Ocean Tracking Network) marine acoustic arrays to facilitate objectives of linking initial physiological state to travel rates and Figure 1. Locations of release of acoustic-tagged Seymour steelhead smolts. Yellow lines show the location of the fate. acoustic arrays, which pick up acoustically-tagged fish when the swim past.

Approximately 200 smolts were taken back to UBC (week of May 25) for a lab-holding study to assess any influences of tagging and saltwater exposure on survival and growth.

The 84 fish released in the lower Seymour experienced 79% survival through the estuary. Survival to the array was 27.3% for fish released at West Vancouver, and 9.1% for fish released in lower Seymour (Fig 2). Thus, transporting fish ~18 km resulted in a 3-fold increase in Figure 2. Relative survival of Seymour steelhead released in survival. Seymour River and Burrard Inlet were noted as Seymour River vs West Van.. regions of particularly low survival for migrating smolts. We are not sure why- but these areas may be predation hotspots. Other studies have shown that predation by herons is occurring in this area and Burrard may also be an area where there is significant seal predation. This remains to be investigated further.

The condition of the smolts was assessed prior to transmitter implantation and release through the use of biomarkers for pathogen presence and load, presence of immune- or stress-related responses, and growth potential, to better understand the links between condition during initial outmigration and survival and behaviour

Page 6 of 7 Attachment 5.1.2.3 in the early marine environment. They did find that gene expression profiles were predictive of fate: - two genes (IL-17D, RPL6) involved with an ‘inflammatory response’ were found to be upregulated in smolts that died in freshwater.

Figure 3. Travel rates of Seymour steelhead- note the particularly high travel rates through - likely related to the high currents and tides in this region.

Travel rates of were about 2-3 times faster through the same marine regions as they found with sockeye smolts – see below (e.g. 15-20 km per day in the Strait of Georgia, 40-50 km per day in the Discovery Islands, 30-40 km per day at northern ) (Fig. 3). Their faster speeds are probably due to their much large body sizes compared to sockeye smolts.

Figure 4. Route Specific Survival of Seymour Steelhead: Discovery Passage: 97.7%, Channel: 46.2%

New acoustic receivers around the Discovery Islands revealed that smolts primarily migrated (77%) through the westernmost route (Discovery Passage- red line in Fig. 4), and those that did benefitted from ~97% survival per 100 km compared to ~47% per 100 km for , to the east (blue line in Fig 4).

Thus, it appeared that migration of smolts through areas of fish farms (Sutil Channel) may be related to lower survival.

Page 7 of 7 Attachment 5.1.2.3 SYNOPSIS OF SSMSP PROJECTS 2018

Program Description Key Findings Oceanography These studies look at spring bloom timing, and Changing oceanographic conditions directly alter productivity in the Strait of Georgia. Studies plankton community structure, abundance and also examine water quality – temperature, distribution, and the changes to the phytoplankton turbidity, oxygen levels, salinity, ocean acidity, community have direct effects on higher trophic nutrients and chlorophyll levels – and how levels with possible implications to overall salmon variations affect marine life from survival. phytoplankton up to fish. In terms of productivity, it appears that 2017 was a bit less productive than 2016 and both were less productive than 2015. The relationship between bloom timing and the Strait of Georgia food web is under analysis. Links between Phytoplankton- The overall goal of this research was to examine This study has informed us on the drivers of spring Zooplankton the level of synchrony between phytoplankton bloom in the Strait of Georgia. These data are now and zooplankton using long-term satellite- being paired with zooplankton species and timing to derived data. determine how prey availability to salmon is influenced by early vs. late spring blooms.

Citizen Science This involves volunteers using a “mosquito Temperatures below 17◦C are best for juvenile fleet” of their own fishing vessels to do salmon early rearing; given that surface waters were oceanographic surveys in nine overlapping warmer than this in July and August for 2015-2017, it areas. That makes it possible to be “everywhere appeared that waters as deep as 10 m in the summer at once” collecting oceanographic data at in most regions of the Strait were not good habitat for spatial and temporal scales not previously these fish. realized. However, there were regional variations, with favourable water temperatures in highly mixed areas of the Strait (e.g. Campbell River and the Gulf Islands). Juvenile Chinook appear to have very defined rearing areas within the Strait, so current work relates these regional conditions to growth and survival of the various stocks caught in the DFO trawl surveys. Zooplankton Zooplankton are the small invertebrates that Overall zooplankton biomass in the central Strait has are the main consumers of phytoplankton and been trending up since 2005, with 2017 having higher also the main prey item for larval and juvenile than average biomass. This should be good for forage fish. These studies look at how zooplankton fish and salmon, although this also included levels vary and how that impacts salmon. increasing abundances of gelatinous zooplankton (not good fish food). However, in the Northern Salish Sea, the zooplankton data series from 2015-2017 suggests low levels of poor-quality food for Coho, Chinook and Sockeye and higher levels of quality prey items for Pink and Chum. Work is ongoing to link the trends and patterns in the zooplankton to potential environmental drivers and potential impacts to higher trophic levels, including juvenile salmon survival. Herring The Strait of Georgia juvenile (age-0) Pacific The relative biomass of age-0 herring in the Strait was Herring survey was done to provide an index of lower and stable during 2013-2017, compared to the the relative biomass of age-0 herring and relate peaks within the time series. it to the abundance of age-3 herring. This index Age-0 herring were heavier for a given length in 2007- may represent trends in potential prey 2017 compared to herring sampled prior to 2007. This availability to Coho and Chinook Salmon. may have implications for juvenile Chinook and Coho, which are piscivorous. The increase in body condition of Young-of-Year (YOY) herring since the 2000 has likely resulted in only the largest juvenile Chinook able to prey on YOY herring due to mouth gape limitations.

Attachment 5.1.2.3 Program Description Key Findings Juvenile Salmon (in River) These studies assess and identify the range of Mainstem and large side channel edge habitats with potential factors that impact the survival of suitable velocities and intact over-stream and/or juvenile salmon in river. Work was carried out instream riparian vegetation cover were critically on Cowichan River to look at habitat important for Chinook fry rearing. preference, and in-river survival. Freshwater survival is low during low flow years and survival rates of hatchery fish are much lower than for wild fish. The high level of in-river losses appears to be related to predation, and are particularly exacerbated during low flow years. The high level of predation by herons was an unexpected finding. Juvenile Salmon- Marine PIT tag This program was designed to determine the There appear to be two key survival periods- early studies life history period which is the bottleneck to after entry to sea, and then during the first winter. survival in juvenile Chinook Salmon, and to Hatchery fish appear to survive about 50-60% as well compare survival of wild and hatchery fish. as wild fish, however, initial survival during the early marine period appears higher for hatchery fish.

Juvenile Salmon- Acoustic Tracking These studies have been designed to determine Key findings include the following: Studies migration survival of Pacific salmon through -Survival rates vary geographically and are segment- freshwater and segments of the Strait of and route-specific Georgia, travel speeds and routes and the -Travel speeds vary among species causes of mortality enroute. Studies have also -Pathogens and immune function were important to examined the length of time that Pacific salmon migration success, with higher predation on “sick” spend around fish farms in the Discovery Island smolts in clear headwaters. region. -juvenile sockeye spent very little time around (unstocked) fish farms in Discovery Islands.

Juvenile Salmon- DFO Trawl These studies examine the factors affecting Chinook stocks appear to have defined distributions Surveys, Purse Seine and Beach salmon growth in the marine environment and throughout the first summer until September. These relate information on ocean entry time, size, juveniles will experience very different rearing growth, diet, competitors, and origin (stock, conditions, with likely impacts to relative survival. hatchery or wild) to survival. Coho stocks appear more mixed in the Strait. Spatial analysis of stock distribution, growth and condition, and the relationships between primary productivity through to juvenile salmon growth and survival are underway. Growth of Coho and Chinook in the Strait was high during the warm conditions of 2014-2016: Coho are again resident in the Strait over Seines the winter. Predation-Seals Salmon have a number of predators and these -Seals may be taking up to 40% juvenile Coho and studies have focused on the role of predation, Chinook in the Strait, BUT we need to re-assess these particularly from seals, on the survival of estimates given studies that show lower rates of juvenile salmon. Key questions include: predation on salmon in non-estuary sites and -How many Chinook and Coho smolts are significant year to year variability consumed in the Strait of Georgia by Harbour -Seal predation on smolts occurs primarily at dusk and seals? midnight. -What is the impact of seals on salmon -Seals show a variety of feeding strategies, and only recovery? some are specialised for feeding on smolts as they exit -How can we mitigate the impact of seals? rivers and enter salt water.

Attachment 5.1.2.3 Program Description Key Findings Harmful Algae These studies have examined prevalence of -Phytoplankton community composition is strikingly harmful algae blooms and how they affect different year to year and may have significant juvenile salmon. impacts on the resultant food web. -Harmful algal blooms (both toxic and mechanically harmful species) were common in the Strait and they impact wild juvenile salmon in the Strait, with similar impacts to those confirmed in BC salmon farms. Multi-year data on harmful algae species and their environmental preferences are currently being analyzed. Habitat Restoration and Research These studies look at salmon habitat – -Estuaries are vital for the smaller Chinook fry- rearing specifically eelgrass and kelp beds, how they life history component. Eelgrass and kelp provide vital have changed over time, and the progress of habitat for juvenile salmon, and are severely restoration efforts. impacted by anchorages and marine debris. -Forage fish need specific habitat to lay their egg, and these shoreline habitats need to be protected as many are under threat.

Ecosystem Modelling This project is to develop a coupled Project is in progress: The initial hydrodynamic hydrographic and biogeochemical model of the (GETM) and biogeochemical (FABM) models were Salish Sea, and link this to a spatial food web developed by Bolding & Bruggeman in 2017. Greig model to evaluate how the combination of Oldford (PhD student) has started work on the food changes in environmental productivity, food web model (spatial EwE) Sept 2018. web structure and human impacts has changed An initial version of an individual based model (IBM) in the Salish Sea over recent decades. to explore smolt survival as a function of predator abundance (initially with seals) has been developed by Carl Walters. He is continuing to refine this.

Strategic Salmon Health Initiative This project is studying the microbes present in -8 novel salmon viruses have been found salmon in British Columbia that may be in aquaculture & wild individuals undermining the productivity of Pacific salmon, -Studies of HSMI - analysis of audit data suggests as well as the role of potential exchanges association between PRV and jaundice/anemia in between wild and cultured salmon. Chinook salmon. If PRV transmission from farmed to wild salmon occurs, this poses a risk to wild Chinook salmon. -Their studies show linkages between infection status and risk of predation/mortality in sockeye salmon.

Attachment 5.1.2.3