All posts by Christina

Initiation and improvement of escapement studies for select Fraser River Coho & Chinook populations using electronic augmentation

The goals of this project are to utilize reliable, cost effective resistivity or sonar counting methods on select tributaries of the Fraser River to estimate escapements of Coho and/or Chinook salmon to a) improve estimate accuracy and b) determine precision of escapement estimates.

The project objectives are to:

1/ obtain a Middle Fraser Spring 1.3 Chinook tributary escapement estimate using a resistivity counter purchased through support of this proposal.  This program will improve upon existing aerial escapement estimation and will evaluate the potential to develop an indicator stock and calibrate historic escapement estimates in a stream supporting a Spring 1.3 Chinook population;

2/ at the conclusion of the Spring 1.3 Chinook portion, relocate the resistivity counter to Barriere River to estimate Coho returns.  This complex system of lakes and small tributaries is currently enumerated through visual methods however, estimate quality would benefit greatly from counts derived electronically as reliable visual counts can be difficult to obtain in this system;

3/ use PIT tagging methods to validate Bonaparte River Chinook and Coho fishway estimates. Currently the Bonaparte Chinook escapement trend does not track the escapement of other Fraser Spring Chinook 1.2 populations. There is concern that fish are able to move through the fishway and be counted then fall back undetected over the falls, and subsequently move back up river, and be counted again. A PIT tagging exercise will be conducted to investigate whether this is occurring and influencing escapement estimates for both Chinook and Coho;

4/ employ video technology to investigate co-migration of Chinook and Coho salmon with Pink salmon and other resident fish species through Bonaparte, Deadman, and Barriere rivers resistivity counters, as well as the selected Middle Fraser 1.3 Chinook system. Video validation will also be employed to determine counter efficiency and derive confidence limits around the resistivity estimates for each of our proposed systems; as well as,

5/ use SONAR (DIDSON/ARIS) to enumerate returns of Coho salmon to Spius Creek.  Spius is thought to be a significant contributor to the Lower Thompson IFC CU, however it is a very difficult system to enumerate visually.

A Pilot Study on the Application of Hydroacoustic Surveys to Assess the Abundance of Delaying Sockeye in Southern Georgia Strait

During their return migration from the Pacific Ocean, some stocks of Fraser River sockeye spend several weeks holding in southern Georgia Strait prior to commencing their migration up the Fraser River. The run size of these delaying stocks is challenging to accurately assess in-season because in-river hydroacoustics at Mission cannot provide estimates of daily abundances. Instead, more variable catch-per-unit-effort (CPUE) data from marine test fisheries must be relied upon exclusively. In years where a high proportion of sockeye are expected to delay, a troll test fishery has also been operated in southern Georgia Strait to inform run size assessments of delaying stocks. However, CPUE indices from this troll test fishery are highly variable and the resulting CPUE-based estimates of the abundance of delaying stocks are often uncertain, impeding fisheries management decisions.

We propose a pilot program using fisheries hydroacoustic surveys to estimate the abundance of delaying sockeye stocks in southern Georgia Strait. The project would be carried out over 5 weeks from the middle of August to September 2018, the same period that the Gulf Troll test fishery has traditionally operated and when Late-run sockeye abundance is expected to peak in Georgia Strait. A vessel will be chartered to tow a split-beam transducer along pre-determined transect lines within the Strait. The split-beam transducer will collect high resolution acoustic data on fish abundance along the transects, providing a weekly index of abundance within the Strait.

An Investigation of Cowichan Coho Run Timing and Marine Survival

Cowichan River Coho have received little attention in recent times despite significant historical abundances and focused stock assessment work on Chinook. Chum returns have been strong enough to support commercial fisheries in terminal areas over the last decade. Interception of adult Coho in Chum fisheries is a growing concern yet little information exists on run timing. We propose to apply PIT tags to Cowichan River Coho smolts in order to take advantage of the permanent in-river detection system installed in 2016 for Chinook research. It is anticipated that detection of tags inside of jacks and adults will allow run timing curves to be established. Similarly, marine survival estimates can be derived provided tag detection efficiency is known. Objectives in years’ three to five include investigating methods to enumerate adults using the same technology in a system where reliable escapement estimates are difficult to produce.

Modifications to the Chum Genetic and Environmental Management Model (ChumGEM), a run reconstruction computer model

A ChumGEM beta version was developed utilizing a growing genetic data set, historic catch data, escapement estimates and migration assumptions for boundary area Chum stocks. That project was funded in 2013 and completed in 2015. This proposal would support the required improvements and modifications to that beta version identified in our model evaluations over the last year.

Objectives of this work will be:

– Change model structure so that swim speed, diversion rate, and proportions of fish designated to each migration route are not fixed outside the model.

– Change the model structure so that multiple years are fit simultaneously. Sharing information across years could improve model fit significantly. Variables controlling timing of arrival, swim speed, diversion rates, and migration proportions are likely consistent across years.

– Review priors on arrival timing- are the current model inputs realistic?

– Data verification – this model takes a large diversity of data, further evaluation of this is required.

– Review infill procedures especially for escapement, catch and GSI data.

– Identify plausible chum Genetic Unit (GU) specific diversion rates.

– Identify GU-specific variances in observation errors on escapement.

– Incorporation of age specific data when available.

– Investigate why several small stocks are not showing up in GSI data. Are we not seeing these fish, or are they not being recognized separately from larger stocks? Do we need to include them?

– Investigate methods for filtering the GSI data.

Feasibility study of Imaging Sonar at Lillooet River to assess Coho Salmon escapement to the Lillooet Conservation Unit

Inconsistent, and sometimes absent, annual funding and a lack of resources to develop a Coho centric assessment program have resulted in DFO being unable to generate an estimate of Coho salmon escapement to the Lower Fraser River Management Unit (LFRMU) from observed data. The absence of reliable escapement estimates for Coho in the LFRMU and its three component Conservation Units (Lillooet, Boundary Bay and Lower Fraser) represents a critical information gap for Southern Boundary Coho salmon Management.

Funding from the PSC in 2017 enabled the development of a simulation-estimation procedure which found that an index-style approach is the best method for aggregate escapement estimation for the LFRMU. However, due to the poor data and its limited time series, appropriate factors for in-filling cannot be estimated, thus a focused, long-term and dedicated strategy is required.

From our work in 2017, we found that escapement to the Lillooet is more variable than either the Lower Fraser CU or the Boundary Bay CU, and is thus more difficult to estimate properly through traditional stream survey assessments. The high underlying variability in abundance, coupled with the fact that Coho returning to the Lillooet CU must transit through the Lower Lillooet River, provide the unique potential for a census-style assessment for the entire CU. A census method would negate the need to determine in-filling factors, would provide a consistent and repeatable escapement estimate, and would not require additional effort to account for the CUs natural variability. Imaging sonar would be the most applicable census method and as such we propose to assess the feasibility of deploying imaging sonar on the Lower Lillooet River for the purpose of estimating Coho salmon escapement to the Lillooet CU.

Improving real time acquisition of sockeye ‘catch per set’ information from commercial purse seine Individual Transferable Quota (ITQ) fisheries

This project would involve three components. First, it would include facilitated engagement of a small group of partners (e.g., harvesters, PSC, DFO, Fraser River Panel members) near the beginning and end of the project. At the beginning the intent of this engagement would be to identify the data flow process, clarify needs of different partners, and decide upon requirements for a technical solution that would be developed through this project. A second phase of work would involve the detailed design, development, and implementation of a technical solution (e.g., technology transfer / training of harvesters, data entry application, database, data output templates) that supports the feasible, accurate, timely, cost-effective, and user friendly data collection and reporting of ‘catch per set’ information from commercial purse seine ITQ fisheries during the 2018 fishing season. A last component would involve undertaking a retrospective evaluation of the real time data flow process and an assessment of the value of information if it had been used in-season. Since this project is a pilot, the final component would occur at the end of the season to avoid disruptions to the 2018 inseason assessment and decision making process (i.e., the intent would be to make data available in season while assessing its timeliness and accuracy, though defer its application in stock assessment models until the end of the season).

Enumeration of Quesnel Basin Interior Fraser Coho using Dual-frequency Identification SONAR

We propose to install two SONAR units on the right and left banks of the Quesnel River at a proven sockeye enumeration SONAR site in order to accurately and precisely enumerate Quesnel system Interior Fraser Coho (IFC).  The Coho SONAR enumeration program will run for three years, from 2018 to 2020, using SONAR and related equipment provided in-kind by the UFFCA and DFO. Overlap in timing between sockeye and IFC will allow the continuation of existing sockeye SONAR operations for Interior Fraser Coho enumeration.

Currently, escapements to the Quesnel system are estimated using a single enumeration fence at McKinley Creek, as well as boat, foot and aerial counting methods for Quesnel Lake and Horsefly River tributaries.  Visual counting of Coho is difficult due to extreme weather events, seasonal limitations (late fall, early winter), extended and multimodal migrations, the defensive/cryptic nature of the animal and its choice of small, complex tributaries for spawning.

Due to potential shortfalls  (funding/weather/accuracy) in the aerial enumeration program, the key objective of this research is to develop an index between a SONAR count on the Quesnel and the McKinley enumeration fence count in order to establish a system-wide escapement estimate (relationship) based on the McKinley fence.

Cowichan Adult Chinook Enumeration methodology change

Adult Chinook returning to the Cowichan River have been enumerated using a counting fence since 1988 as a PSC indicator stock. The operation of the fence has been met with various technical/environmental challenges over the years resulting in site relocation as well as several re-builds. Cowichan Tribes has expressed concern regarding negative impacts to fish including migration delays and physical damage.  This proposal will investigate the use of PIT tags as an alternative method for estimating escapement.   Specifically, tags returning from juvenile deployments will be expanded based on a mark rate from a sub-sample of the population.  PSC funding will be used to both deploy tags in juveniles as well as to support an estimate of mark rate in the adult population.

The use of PIT tags will also allow additional information to be collected including downstream survival of juveniles, marine survival estimates, age class composition and migration time.  Additionally, predation investigations may also be supported as PIT tags have been detected inside other animals and in scat within the surrounding area.

Independent Evaluation of Wild Coho Marine Survival Rates in the Strait of Georgia (Black Creek)

Black Creek (fence) is DFO’s only wild coho indicator system for the Strait of Georgia (SOG). Since 1984 an uninterrupted data set has been compiled under the present program and is considered one of the longest time series of coho smolt and adult returns in the Pacific Region. Marine survivals are currently being evaluated using coded wire tags (CWT) on wild, non-adipose marked coho (~20% of smolts). Based on the lower than expected ratio of CWT fish returning with the current program, DFO would like to use PIT tags as an alternate method to evaluate marine survival, and investigate if there would be a difference in survivals based on CWT or PIT tag methodologies. The advantage of using PIT tags is that every returning fish to Black Creek would be automatically scanned at the enumeration fence for the presence of a PIT tag, while the CWT component relies on handling each fish and scanning by hand. Also, a PIT array will scan all adults, even if the fence is topped, while the current CWT program is unable to scan fish when the fence is topped, and fish bypass the trap box. As an end result, this project would improve our ability to evaluate wild coho marine survival rates in the SOG.

Since the early 2000’s DFO in partnership with the A-Tlegay Fisheries Society have continued to deliver the downstream and adult Black Creek program. The application of PIT tags on juveniles and monitoring of adults in the following year(s) at the fence would only be a slight augmentation to the current program, without any major labour or infrastructure costs, just tags, antenna arrays, application and reporting.

Understanding the mechanisms of population depression for endangered Cultus Lake Sockeye Salmon to inform fisheries management

The Fraser River watershed produces the most abundant bilateral (US and Canada) Sockeye Salmon (Oncorhynchus nerka) fisheries opportunities of any drainage in British Columbia, contributing significantly to commercial, recreational, and First Nations’ interests. Within the watershed, variations amongst populations in run-timing, abundance trends (i.e. cyclical dominance), and other life history traits, evoke a very complex fishery management framework. As Fraser River Sockeye Salmon harvests are managed in a mixed-stock fisheries context (common migration run-timings), less abundant conservation units (CU) can have disproportionate influences on aggregate fishery exploitation potentials.

The Cultus Lake Sockeye Salmon CU is a critically-endangered Fraser River population exhibiting extremely depressed abundances (COSEWIC 2003; DFO Stock Assessment data, unpublished). Cultus Lake Sockeye Salmon are part of the Fraser River Late Run timing group, co-migrating with abundant CU’s, such as the Shuswap Complex CU, which has experienced record escapements in recent years (dominant line). Determination of the ultimate mechanism(s) of influence on survival is critically important to engage informed habitat and fisheries management that succeeds in rebuilding this stock, and alleviating constraints on targeting other Late-Run CUs in the Fraser River mixed stock fishery.

A genomic tool called the ‘salmon FitChip’ has been recently developed by the DFO Molecular Genetics Laboratory to identify specific stressors (e.g. thermal, hypoxia, osmotic and general stress), and diseases (infectious agents, viral disease, inflammation, immune stimulation) in Pacific Salmon (Oncorhynchus spp.) that is based on targeted host response profiling of gill tissue. Gill is an ideal tissue to monitor environmental responses due to its direct contact with water. The chip is populated with biomarker panels that are predictive of the presence of specific stressors, which have been validated in a series of control challenge studies. To predict the presence of a specific stressor requires only 6-12 co-expressed biomarkers (Miller et al. 2017). Within our biomarker panel, we will also include previously validated assays to a range of freshwater infective agents (viruses, bacteria and fungal and protozoan parasites) (Miller et al. 2016) detected in Fraser River Sockeye Salmon in previous years. This is the first tool of its kind to enable the simultaneous assessment of multiple stressor and disease influences on salmonids, or any other species for that matter.

We propose to pair this new genomic tool with our habitat and fish condition information in Cultus Lake (and Chilliwack Lake as a reference) to assess fish stress responses to these potential drivers of poor freshwater survival. Identifying the underlying causes of this early life-stage mortality in nursery habitats will actively inform habitat and fisheries management on remedial actions to improve Cultus Sockeye survival, with the goal of alleviating future constraints on the broader Fraser late-run Sockeye fisheries.