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Research Team

Current Graduate Students, Research Associates, and Post-doctoral Fellows

Andres Araujo, Master’s Student

B.Sc. (Marine Science), University Escuela Naval, Colombia

Master’s research topic: Extreme sedimentation events caused by forestry-related activities and their impact on salmon production in the Lower Fraser Timber Supply Area

The lower Fraser timber supply area (Fraser TSA) is located on the delta of the Fraser River, which is known as an important spawning area for populations of Pacific salmon. While being ecologically significant, the Fraser TSA also represents an important area for commercial timber harvesting. However, forestry-related activities such as logging and road construction may alter salmon production by increasing sediment input to the Fraser River tributaries, thus perturbing fish habitat. The main objective of this project is to determine the probability of observing extreme sedimentation events caused by logging, road construction, and road use. Using this probability, I will quantify the effect of fine sediments on fish production in the Chilliwack River and Norrish Creek, two of the main watersheds of the Fraser TSA. To achieve this objective, I will address the following questions. (i) What is the probability of experiencing extreme sedimentation events given the natural sediment and discharge regime? (ii) What portion of the total sediment budget is derived from forestry activities? (iii) Taking into account the probability of extreme sedimentation events and the sediment input from forestry activities, what will be the effect on salmon production according to existing dose-response models? My methods in this study involve time series analyses and simulation in combination with minor field and lab components. Improved knowledge of sediment impacts on fish production in the Fraser TSA will help managers develop an ecosystem-based management approach to forestry practices. Supervisor: Andy Cooper


Adam Batty, Master’s Student

B.Env.Sci. Honours, University of Manitoba

Master’s research topic: Examination of speckled dace (Rhinichthys osculus) life history, habitat use, abundance, and population density in Canada

Canada's Species at Risk Act (SARA) maintains biodiversity by protecting a wide variety of species that are endangered or at risk of extinction. One example is the speckled dace, a minnow species living in western North America. The northernmost tip of the speckled dace distribution extends into south-central British Columbia in the Kettle and Granby rivers, and is isolated from downstream by Cascade Falls. The speckled dace is considered endangered by both COSEWIC and the British Columbia Ministry of Environment due to the limited extent of the species within Canada. Biological information about the species in Canada is limited to the results of one study by Peden and Hughes (1981). The federal SARA requires that decisions to list a species for protection are based on the best available science, however, no quantitative assessment of the speckled dace population size within Canada has been done. In order to properly manage the risk of extinction more information is required about speckled dace in Canada. I aim to improve knowledge of this population, specifically examining abundance, population density and habitat use. To determine abundance and population density, I quantitatively sampled within and outside of the known distribution of speckled dace using backpack electrofishing. I also collected habitat-use information in order to develop habitat models. When completed, the results of this research will be useful to decision makers considering the listing of speckled dace for protection under the SARA. Supervisors: Randall Peterman and Mike Bradford


Ashleen Benson, Ph.D. Student

B.Sc. (Biology), University of Saskatchewan
M.Sc. (Oceanography), University of British Columbia

Ph.D. research topic: Evaluating the ecological value of fishery survey data

The components, objectives, and means of implementation of Integrated Management (IM) have been the focus of recent initiatives at Fisheries and Oceans Canada, as both scientists and policy makers attempt to address uncertainties in its definition. Discourse on the topic appears to operate under the assumption that fishery survey data can be used to achieve the ecological objectives of IM. The goal of my analysis is to evaluate the assumption that fishery monitoring programs generate untapped ecological information that creates an opportunity for fishery science to move beyond biomass-based evaluations of fish populations. My focus is on the quality of spatial information in survey data. By providing insight into both stock status and stock structure, spatial information can reduce some key uncertainties in stock assessment and management, and advance the ecological objectives of IM. However, spatial patterns that are evident in historical data can be biased by past stock structure assumptions and the attendant survey designs, and may reflect changes in management more than the spatial dynamics of the fish population. Potential implications include undetected loss of spatial components of the population and an entrenched management structure that is not equipped to address emerging issues under IM and other ecosystem-based initiatives. I adopt a simulation modeling approach to explore the behaviour of a management system that ignores population substructure and spatial dynamics in the survey, the stock assessment, and ultimately, the spatial allocation of fishing effort. The rationale and simulation model structure are the focus of my talk. Supervisor: Sean Cox


Alston Bonamis, Master’s Student

B.Sc. (Biology), University of British Columbia
Dipl. Tech. (Renewable Resource Management), B.C. Inst. of Technology

Master’s research topic: Assessing baseline abundance and habitat use of the endangered Nooksack dace (Rhinichthys cataractae sp.)

Steep declines in biodiversity on a global scale have become an issue of significant concern in recent years. In Canada alone, over 500 species of flora and fauna are considered to be at risk. The Canadian Species at Risk Act (SARA), which came into force in 2003, provides legislated protection for these species. The Nooksack dace, a small freshwater minnow, is one such species designated as endangered under SARA. The federal government, fulfilling its obligations under SARA, has developed a Recovery Strategy for the Nooksack dace and is now required to complete an Action Plan that meets the objectives set out in the Recovery Strategy. However, there is a great deal of uncertainty hindering the development of an Action Plan and slowing the recovery of the Nooksack dace. Critical knowledge gaps exist in population abundance estimates, capture efficiency of sampling gear, and habitat use of the Nooksack dace in their native streams. The objectives of my research specifically address these knowledge gaps by: (1) Establishing accurate baseline abundance estimates of dace populations; (2) Developing a reliable, accurate and repeatable sampling method for assessing dace abundance; (3) Establishing long-term index sites for monitoring dace abundance in critical habitats; and (4) Developing long-term monitoring protocols for assessing effectiveness of recovery efforts. The overarching goal of my project is to enable recovery of the Nooksack dace throughout its range in BC by filling in critical knowledge gaps and providing managers with the tools necessary to develop an Action Plan and meet the deliverables set out in the Nooksack dace Recovery Strategy. Supervisors: Randall Peterman and Mike Bradford


Elysia Brunet, Master’s Student

B.Sc. (Integrated Science), Carleton University

Master’s research topic: Eliciting expert knowledge on the relative importance of metrics to be used in assessing the biological status of salmon Conservation Units in British Columbia.

The primary goal of Fisheries and Oceans CanadaĻs (DFO) Wild Salmon Policy (2005) is to restore and maintain healthy and diverse salmon populations. To achieve this goal, the policy requires the annual assessment of the biological status of Conservation Units (CUs) by combining the status (red, amber or green) of a suite of indicators or metrics. Currently, various methods for combining metrics are being considered by the DFO. My research proposes to elicit expert knowledge on the relative importance of various metrics through a best-worst scaling (BWS) survey. Survey results, in the form of metric weight and scale, will be applied to existing ecological data to determine whether including the relative importance of metrics and status provides the same assessment of CU status as other methods. Since CU status is a factor in determining the extent of management intervention, differences in assessment status caused by using different methods could have important ecological and socio-economic implications. Supervisor: Randall Peterman

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Chantelle Caron, Master’s Student

B.Sc. (Environmental Biology), University of Alberta

Master’s research topic: Rockfish larval dispersal and recruitment in Indian Arm and Howe Sound, British Columbia

On February 1, 2007, 164 Rockfish Conservation Areas (RCAs) came into effect in British Columbia.  The goal of these areas is to mitigate the effects of direct and indirect fisheries on inshore rockfish populations, which have been declining in recent decades.  Marine protected areas such as these often provide the necessary habitat and reduced fishing pressure that may allow rockfish populations to achieve maximum reproductive rates.  This may in turn help population recovery and could sustain harvests in adjacent areas due to larval dispersal.  My academic research interests broadly encompass these issues.  I aim to research inshore rockfish larval dispersal and recruitment to determine time frames for the re-establishment of rockfish populations throughout Indian Arm and Howe Sound.  A better understanding of these processes will help determine long-term recovery and management plans for these species and may determine the effectiveness of RCAs.  There are 12 RCAs throughout Indian Arm and Howe Sound that, along with their adjacent unprotected areas, will provide ideal comparative study areas for this research.  I also hope to evaluate the ecological and political processes involved in marine protected area planning using the 12 RCAs in Indian Arm and Howe Sound, B.C. as examples. Supervisor: Sean Cox

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Brendan Connors, Postdoctoral Fellow

B.Sc. (Biology), University of Victoria
Ph.D. (Ecology), Simon Fraser University

Research topic: Epidemiological approaches to indicators of population and ecosystem health, quantifying the misclassification of threat status, and quantifying the support for hypothesized drivers of salmon dynamics. My current research in REM centers around three questions: (1) How do we decide which indicators of the status of populations and ecosystems are the most reliable? (2) How does variability in abundance influence the misclassification of the chance of extinction? (3) What makes sockeye salmon populations go up and down? We are tackling these problems by (1) adapting and applying tools from human epidemiology (e.g., receiver operating characteristic curves) to assess the reliability of indicators of population and ecosystem health, (2) quantifying how threat classification based on trends in abundance (i.e., chance of extinction) is influenced by autocorrelated stochastic variability in abundance, and (3) using multi-population models of stock-recruit dynamics to quantify the combined support for hypothesized drivers of declines in sockeye salmon productivity. Supervisor: Andrew Cooper and Randall Peterman


Jonathan Cummings, Master’s Student

B.A. (Biology and Environmental Studies), Oberlin College

Master’s research topic: Effects of water temperature and flow on management adjustments for Fraser River sockeye salmon

A major factor that negatively impacts both Fraser river sockeye salmon conservation (i.e. spawning escapement) and harvest is large in-river loss of fish (estimates have exceeded half a million fish in 8 of past 16 years), commonly associated with extreme migration conditions. Given that fisheries management entails a trade-off between harvest and conservation goals, better predictions of in-river losses will help avoid underestimates that can result in conservation concerns and overestimates that can result in foregone catch. Therefore, efficient management of the Fraser River sockeye fishery depends, in part, on precise and unbiased predictions of in-river loss. Biologists currently use environmental covariate models (Management Adjustment (MA) models) to predict discrepancies between lower river and spawning ground escapement estimates based on forecasts of river environmental conditions. These predictions of in-river loss are used to provide management advice on appropriate harvest adjustments. While a number of MA models have been proposed and historically applied, no formal assessment of past model performance has occurred. I conducted a retrospective analysis to rank a suite of potential MA model structures and predictor variables (i.e. Fraser River temperature and flow conditions, river entrance date, and historical discrepancies) using a variety of performance measures (i.e. mean absolute error, root mean square error, mean raw error, AIC, R2). Rank order of models depended upon the performance measures chosen, indicating that selecting management objectives is an important component of model selection. Therefore, in conjunction with clearly specified management objectives, the results of this study can provide a standardised process for selecting MA models that will increase the probability of achieving spawning escapement targets while balancing the trade-offs between harvest and conservation. Supervisor: Randall Peterman


Faye d'Eon-Eggertson, Master’s Student

B.Sc. (Biology), McGill University

Master’s research topic: Evaluating threat criteria for use in fisheries management There are many different criteria that fisheries management agencies and conservation organizations can use to determine whether fish populations are a conservation concern. My research objective is to determine which criteria are the most likely to correctly categorize the true conservation status of a population. I will be using a stochastic population dynamics model to simulate time series of sockeye salmon spawner abundance. I will then quantify the probability of each criterion correctly distinguishing between declining and non-declining time series. The results of this research may provide insight for management and conservation purposes as to which criteria are the most reliable as indicators of declining populations. Supervisor: Randall Peterman


Danielle Edwards, Master’s Student

B.Sc. (Biology), University of Victoria

An evaluation of the effects of management strategies on discarding in British Columbia's groundfish fisheries. Supervisor: Murray Rutherford


Jessica Finney, Master’s Student

B.Sc.Hons (Marine Biology), Dalhousie University

Master’s research topic: Predicting suitable habitat for deep-sea coral in British Columbia

Deep-sea coral provide valuable habitat for fish and other organisms but they are highly susceptible to anthropogenic threats. The most serious threats are posed by benthic fisheries, most notably bottom trawling, and other human activities that disturb the seafloor. Recent surveys of deep-sea coral suggest that they have been damaged or destroyed in virtually all parts of the world. To date, most deep-sea coral in Canada are unprotected. There is a particularly pressing need to develop a conservation strategy for deep-sea coral in BC, but it is not a simple task. Relatively little coral research has been conducted in BC, and the distribution of deep-sea coral remains largely unknown. The vast majority of sightings are derived from bycatch data from the trawl fishery and only provide information on the locations of previously damaged corals. Determining the distribution of deep-sea coral and identifying pristine coral aggregations is a crucial first step in establishing effective ocean management strategies to protect these rare and valuable habitats. This study makes a significant contribution toward addressing these information gaps. All known locations of corals were compiled from museum and other scientific collections. Environmental data on depth, slope, salinity, temperature, bottom current speed, and surface chlorophyll a concentrations were modeled to a 500m by 500m grid for the entire study area. Maximum entropy (Maxent) analysis was then used to predict potentially suitable habitat for several orders and families of coral in BC waters. Future research priorities include ground-truthing the predictions of this study and providing advice for developing a conservation strategy for deep-sea coral in BC. Supervisor: Randall Peterman


Lise Galand, Master’s Student

B.Sc. (Conservation Biology, Minor in Commerce), University of British Columbia

Master’s research topic: Assessing the impacts of bottom-fishing on benthic marine ecosystems off the coast of British Columbia

The groundfish and invertebrate fisheries in British Columbia (BC) use fishing gear such as trawls, long lines, and traps which come in contact with the ocean floor and have the potential to affect benthic marine ecosystems. Sustainable fishing practices are becoming increasingly recognized by organizations such as the Marine Stewardship Council (MSC), which assesses the management and ecosystem impacts of fisheries and rewards a fishery by providing it with MSC certification. It is therefore important that the bottom fisheries of BC use sustainable practices in order to facilitate certification, which would allow the fisheries access to sustainable seafood markets all over the world. Currently, there are no procedures for measuring the spatial scale impacts of these fisheries on benthic ecosystems off the coast of BC; thus there is a need for developing a framework to measure these impacts. My objective is to quantitatively assess the potential impacts of bottom fishing by collecting data on the density of benthic epifauna in selected areas off the coast of BC that experience different levels of fishing disturbance. I will then develop exposure-response models with those data. These models will look at the relationship between the degree of fishing disturbance at a particular area (exposure) and some characteristic of ecosystem function (response). The results of this research will hopefully provide managers with a better understanding of how benthic marine ecosystems respond to fishing disturbance. As a result, managers will be able to make changes to current fishing operations in order to reduce or remove the impacts on these ecosystems. Furthermore, this project will help to provide information to support the eco-certification of the bottom fisheries of British Columbia. Supervisor: Andy Cooper


Sabrina Garcia, Master’s Student

B.Sc. (Marine Science/Biology), University of Miami

Master’s research topic: Stock assessment of the big skate (Raja binoculata)

The big skate (Raja binoculata) fishery off the coast of British Columbia began in 1996 with two targeted fisheries in Northern Hecate Strait and Queen Charlotte Sound. The fishery uses trawl and longline fishing gear and currently has a 597-tonne cap on fishing in Hecate Strait and no cap on fishing in the Queen Charlotte Sound. The preferred market size for big skate is between the sizes of 65-90 cm, during which the animals are still immature. If populations are fished while too young, many big skate may not reach the age of maturation and thus will not be able to reproduce. Fishing of the big skate, like other fisheries for elasmobranchs, is of particular concern because of the specific life history traits: longevity, low fecundity, and late maturation. Additionally, caps on fisheries do not take discard mortality (bycatch that are thrown back into the water that do not survive) into account and it would be beneficial to determine the discard mortality rate for big skate in these two stocks. Information on population structure and biological parameters of the two stocks of big skate in British Columbia is limited. Using information from trawl surveys, a three-year tagging study on the big skate conducted by DFO’s Pacific Biological Station, and also fishery catch data, my objective is to use prior estimated life history parameters to build a biomass dynamics model for the big skate. This research will hopefully give managers a reference point for the two stocks and aid in determining whether these two stocks are in danger of becoming overfished. My research may also provide information to justify the use of slot limits, which would allow smaller individuals to escape trawls, and thus shift fishing away from immature individuals. Supervisor: Andy Cooper


Felice Griffiths, Master’s Student

B.Sc. (Biology), University of Victoria

Master’s research topic: Modeling Population Dynamics of the Itcha-Ilgachuz Caribou Herd in West-Central British Columbia

My research will apply population assessment methods commonly used in fisheries management to model population dynamics of the Itcha-Ilgachuz caribou herd, located in west-central British Columbia. This herd is of particular interest because it has shown growth over the past two decades where as most other woodland caribou in BC have been declining. My research will use Bayesian analysis to model population dynamics of this herd and provide information for future management decisions. Supervisor: Andy Cooper


Matthew Grinnell, Master’s Student

B.Sc. (Biology), University of Victoria

Master’s research topic: Reliability of at-sea observer release estimates in B.C. groundfish trawl fisheries

It is essential to evaluate at-sea observer monitoring programs (ASOP) periodically to ensure their accuracy and reliability, especially with respect to contentious issues that could undermine the credibility of the data collected. The BC trawl fishery has provided 100 % on-board observer coverage to monitor fishing activity since 1997. Managers use the ASOP data to determine total extraction from the fishery, including dead marketable-sized fish that are released at sea. An important assumption is that reports of marketable releases (MR) are accurate. However, the nature of the ASOP workplace may be conducive to certain types of pressures on the observer to under-report financially damaging fishing activity in some circumstances. Lennert-Cody and Berk (2007) recently investigated the reliability of monitoring data in a tuna fishery using the "random forest analysis." I assessed the reliability of the ASOP data using a similar technique; the analysis predicts the proportion of MR fish for each fishing event, based on the set of predictors available. Managers may be most interested in fishing events for which the analysis predicts a high proportion of MR fish, yet for which only a small proportion was recorded by the observer. Considering that observers have multiple fishing events, I will use mixed-effects models to determine the effect of each observer. Finally, I will simulate several types of unreliable observers to verify that the analysis is able to detect observers of interest. If we accept the assumption that the ASOP data represent a true account of fishing activity, this project will improve the perceived accuracy of the data gathered by the ASOP, as well as the stock assessments and the individual transferable quota management system that depend on the ASOP data. If this is not the case, then an important follow-up step is to determine the extent to which stock assessments and the ITQ management model are affected. Supervisor: Sean Cox

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Jessica Harris, Master’s Student

B.Sc. (Ecology), University of Toronto

Master’s research topic: Evaluation of adaptive cluster sampling for remotely operated vehicle surveys of inshore rockfish (Sebastes spp.)

Inshore rockfish (Sebastes spp.) are species of conservation concern in British Columbia. Detecting biologically important changes in rockfish population abundance is crucial to management of rockfish fisheries and fisheries in which rockfish are caught incidentally. Small remotely operated vehicles (ROV) are being considered as a low-cost and non-lethal method of conducting population surveys of rockfish; however population estimates from these surveys typically have low precision and low power to detect changes in rockfish density. In populations where the distribution of organisms is rare and clustered, previous studies have found that adaptive cluster sampling (ACS) may result in more precise abundance estimates than simple random sampling (SRS). The objective of this study is to determine if ROV surveys of rockfish using ACS result in more precise abundance estimates than ROV surveys using SRS, taking into account survey cost. I created a model of small-scale rockfish spatial distribution using data from submersible surveys of inshore and nearshore rockfish in Washington, British Columbia, and Alaska and used this model to simulate data with which to compare ACS and SRS. In the majority of simulations, ACS was less precise than SRS in ROV surveys of equivalent cost. ACS was only more precise than SRS when the adaptively sampled units were assumed to cost 50% or less of randomly sampled units, the population was highly clustered, the number of initial samples was large and network size was small. One explanation for this finding is that previous studies which found ACS was more precise than SRS excluded empty units from the final sample size in ACS and therefore compared unequal numbers of units sampled in ACS and SRS, potentially underestimating the total survey cost of ACS. Supervisor: Sean Cox


Kendra Holt, Research Associate

B.Sc. (Biology and Geography), University of Victoria
MRM (Master of Resource Management), Simon Fraser University

Research topic: Monitoring regional and stream-specific trends in salmon escapement in the presence of missing data

Salmon monitoring plans for regional stock groups often aim to estimate the average rate of change in escapement over time for an entire region, as well as estimate variation in such rates among individual streams (or sites) within the region. Unfortunately, large-scale monitoring programs in which multiple streams within a region are individually surveyed rarely have complete coverage through space and time. To deal with such incomplete data, two approaches have been proposed at the design and analysis phases, respectively: (i) "rotating panel" designs that allocate survey effort through space and time, and (ii) hierarchical statistical models (HMs) that use estimates from information-rich sites to make inferences about information-poor sites. While the benefits of these approaches have been demonstrated at the regional level, their reliability at estimating parameters at individual sites has not been formally examined. We used an operating model approach to evaluate how well rotating panel designs and HMs summarize regional- and site-level information about rates of change in salmon escapement over a 10-year period. We used historical escapement data from 22 coho streams in the Skeena River watershed, British Columbia, to generate realistic escapement time series at multiple streams. Our results show that both tools increase the precision of estimates of rates of population change at the regional level, but that gains are greatest for HMs. All estimates were unbiased at the regional level; however, at the individual level, the HM often produced biased estimates for sites with extreme rates of change. These results suggest that when unbiased estimates of the variation in escapement trends within a region is a key monitoring objective, rotating panel designs may be a better strategy for dealing with incomplete survey coverage than HMs. Supervisor: Randall Peterman


Ann-Marie Huang, Master’s Student

B.Sc. (Marine Biology), University of British Columbia

Master’s research topic: Re-evaluating long term escapement strategies for Fraser River sockeye salmon (Oncorhynchus nerka)

I am currently a full-time employee with Fisheries and Oceans Canada (DFO) and am taking the Master’s program part-time. I received a B.Sc. from the University of British Columbia with a specialization in marine biology, where I never took a vertebrate fish course because I thought they were boring. I have since learned the error of my ways.

Long term escapement goals for Fraser sockeye have undergone a fundamental change in the past few years. Escapement goals used to be based on a fixed escapement policy as per DFO’s 1987 Rebuilding Plan, but are now based on a fixed exploitation rate policy that was a result of the Fraser Sockeye Spawning Initiative. The objective of my research project is to re-evaluate the stock-recruitment assumptions that aided in the development of the long term escapement strategies for Fraser sockeye through the spawning initiative process. Specifically, I plan to examine the management implications of incorporating cycle-line interactions into long term escapement goals for Fraser sockeye at both the aggregate run timing level as well as the individual forecasted stock level. Supervisor: Sean Cox


Erica Johnson, Master’s Student

B.Sc.H. (Environmental Biology), Queen's University

Master’s research topic: A quantitative risk-assessment model for the management of invasive yellow perch in Shuswap Lake, British Columbia

Recent introductions of yellow perch (Perca flavescens) in British Columbia are causing concern over the potential loss of productivity in several major salmon stocks. Yellow perch are known to be aggressive invaders, and although their effects on Pacific salmon are not well understood, it is believed that they will compete with (and possibly prey upon) juvenile salmon in the Fraser River system. Such large uncertainties, as well as the large potential biological and economic losses from important harvested salmon populations, create a need for a risk assessment. This project has been designed to complement work being done by both federal and provincial agencies on aquatic invasive species in BC. Fisheries and Oceans Canada, in coordination with the Centre of Expertise for Aquatic Risk Assessment, has conducted a qualitative, broad-scale risk assessment of six invasive fishes, including yellow perch. My objective is to provide more detailed, quantitative information for a specific water body and the impacts on a specific species by developing a quantitative-risk assessment model to help estimate risk to sockeye salmon populations associated with an invasion of yellow perch into Shuswap Lake. This simulation model will evaluate a range of management actions related to controlling yellow perch at different stages of invasion by estimating their effectiveness at reducing ecological consequences while keeping management costs to a minimum. The results of this project will hopefully assist with the allocation of funds and help managers choose the most appropriate control method. The model will be flexible and adaptable to other aquatic invasive species that can potentially affect salmon in other freshwater systems. Supervisor: Randall Peterman


Jim Johnson, Master’s Student

B.Sc (Math with specialization in stochastics), Carleton University

Master’s research topic: Using multiple metrics to assess population health

It is essential to fisheries science to determine whether a population or ecosystem is healthy in order to make proper management and conservation decisions. Currently, abundance and mortality rates are used as indicators when determining the overall health of a population. A variety of indicators such as food-web complexity, species-richness, and productivity could also potentially be used to determine ecosystem health. However, there is a general lack of guidance as to where the cut-offs between healthy and unhealthy are for each indicator or how to combine the results from different indicators. Historically, medical researchers have dealt with similar problems when developing indicators to determine if a patient is healthy or not in the presence of a new disease. My objective is to use the resulting methods and lessons learned from medical science and adapt them to the above management and conservation issues within fisheries and ecosystem science. I will attempt to develop indicators and reference points which can then be used with statistical methods such as latent-class models to better determine cut-offs between healthy and unhealthy states in populations and ecosystems. These methods will also take into consideration the probabilities and high costs of misdiagnoses. The results of this project will help us to make more informed decisions as to when action or increased monitoring is required and improve our understanding of population and ecosystem health. Supervisor: Andy Cooper


Nicole Koshure, Master’s Student

Hon. B.Sc. (Environmental Science), University of British Columbia

Master’s research topic: Estimating trends in cetacean abundance and distribution from data collected for an opportunistic sightings network (BCCSN)

British Columbia's coastline is home to 18 species of cetaceans and three species of sea turtles, nine of which are at risk of extinction. The B.C. Cetacean Sightings Network (BCCSN) was established to gather sightings of these species from a network of coastal citizens. The objective of my research project is to estimate trends in relative abundance and distribution of cetaceans commonly found in the waters off north-eastern Vancouver Island, using sightings collected by one group of the BCCSN observers -- Straitwatch. While similar work has been done (Williams and Thomas, 2007) off coastal BC, relative abundance estimates have been constrained by small sample size. Conversely, the data available for my work will include more than 5,000 sightings collected over 8 years. Information on distribution and abundance is needed for informing a variety of conservation and management issues, including assessment of the sustainability of observed levels of small cetacean by-catch in commercial fisheries (Hall et al., 2002), and incorporation of predator needs into ecosystem-based fisheries management (Larkin, 1996). The specific objectives for this research are to: (1) establish baseline estimates of trends in cetacean abundance to guide future management decisions; (2) determine whether the assumption that the probability of detecting a species of cetacean is density-dependant, i.e., that a functional response exists; (3) create spatial distribution models of cetacean species within the study area to identify areas associated with species-specific factors determining marine mammal habitat use; (4) provide a means to evaluate the effectiveness of future management actions; and (5) improve the usefulness of data already collected by the BCCSN by identifying how to collect monitoring effort information from a large network of volunteer observers. Supervisor: Randall Peterman

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Bronwyn MacDonald, Master’s Student

B.A. (Geography and Environmental Studies), University of Victoria

Master’s research topic: Dynamic components of the recreational fishery on Chinook salmon in Alberni Inlet

Failure to recognize the dynamics of angler effort and predation can impede the success of management actions that seek to regulate harvest in open access recreational systems. An earlier study by Peterman and Steer (1981) characterized the relationship between Chinook sportfishing catch rates and stock size as a Type II functional response, showing that catchability within the tested fisheries increased as stock size declined. Thus, anglers caught a larger proportion of the stock per unit effort at lower abundance. Additionally, angler effort can fluctuate in response to the attractiveness of the fishery. Previous studies in freshwater systems have identified this dynamic predator-prey relationship, whereby angler effort numerically responds to changes in the abundance of their prey, and the regulations of their fishery (Johnson and Carpenter, 1994; Cox et al., 2002; Post et al., 2003). I am examining the functional and numerical responses within the Alberni Inlet Chinook sport fishery. I am currently investigating the relationships between Chinook abundance, catch rates, and effort at variety of temporal scales ranging from daily to annual. I will characterize the effort response in this marine fishery. I plan to use the findings to examine the trade-offs between limiting effort in this fishery versus reducing catch in outside areas. My data set includes ten years of daily escapement, recreational effort and Alberni Inlet catch (commercial, first nations and recreational) for the Stamp River Chinook (courtesy of DFO). I expect to find that the percent fishing mortality follows a non-linear relationship with abundance such that a higher percentage of Chinook are harvested at lower abundance. This relationship suggests that in years of low abundance, more extreme regulations may be required to constrain the recreational impact on the stock. Supervisor: Randall Peterman


Cameron MacKenzie, Master’s Student

B.Sc. (Ecology), University of Calgary

Master’s research topic: An examination of fixed locality surveys for estimating total abundance in a Dungeness crab fishery

The Dungeness crab (Cancer magister) fishery in British Columbia does not rely on stock assessment for management, but rather is managed by restricting sex, size and seasonality of the harvest. Management options being considered to meet established objectives for a sustainable and viable crab fishery include establishing a total allowable catch and allocating quota among commercial vessels, First Nations users and recreational trappers, all of which require estimating abundance. Previous work has shown that the relationship between abundance and catch-per-unit effort (CPUE) data is species-specific and determined by fishing methods and vulnerability to gear. Therefore, knowledge of the relationship between trap survey data and total abundance of Dungeness crab stocks would help inform decision makers in allocating catch quotas. My research objective is to determine whether relative abundance indices from repeated trapping surveys at fixed locations are proportional to total abundance of crab in the Burrard Inlet. Crab density at each location was estimated by visual surveys with a remotely-operated underwater vehicle (concurrent with the trapping survey) to estimate total crab abundance at each site. That density was compared to CPUE data from a randomized trapping survey throughout the inlet. Initial results indicate high exploitation of legal-sized males in the fixed sites and for the random trap survey. In-season depletion trends are consistent for both the trap and the ROV surveys. Future analysis will include using collected habitat data and a stratified random trap survey to estimate overall abundance of crab in the Burrard Inlet study site. Supervisor: Sean Cox


Michael Malick, Ph.D. Student

B.Sc. Fisheries Biology, Mansfield University, Mansfield, PA, USA
M.Sc. Fisheries, University of Alaska Fairbanks, Fairbanks, AK, USA

Ph.D. research topic: Linking Climate Variability, Ocean Processes, and Pacific Salmon Population Dynamics

Pacific salmon (Oncorhynchus spp.) populations are a basic component of ecosystems, cultures, and economies throughout the North Pacific Rim. Maintaining viable and productive salmon populations requires the ability to anticipate how ecological perturbations will affect the productivity of salmon stocks. Despite more than fifty years of research, there are still large uncertainties about how perturbations in climate and ocean systems influence salmon populations. These uncertainties create risks for management agencies, fish stocks, and communities that rely on salmon for economic and cultural prosperity. My research aims to reduce these uncertainties by (1) developing and quantifying specific relationships within the ecological causal network that links climate variability, ocean processes, and salmon populations and (2) identifying how knowledge of these relationships can be incorporated into effective salmon management practices. Specifically, my research focuses on two basic oceanographic processes that represent key intermediate processes that link climate variability and salmon dynamics, the spring phytoplankton bloom and ocean circulation patterns. To achieve my objectives, I am using methods and approaches from multiple disciplines including fisheries science, oceanography, statistics, and public policy. The outcomes of this integrative research should increase our ability to implement effective strategies that will support healthy salmon populations for future generations, even in the presence of anthropogenic climate change. Supervisor: Randall Peterman


Jonathan Martin, Research Associate

B.Sc.Hons (Biology), Memorial University of Newfoundland
M.Sc. (Marine Science), University of South Alabama

My career, both academic and professional, has allowed me to conduct underwater research in a wide range of environments, using a number of methods. Starting with research diving in the cold waters of Newfoundland studying gelatinous zooplankton ecology, I continued studying the same organisms in the warmer waters of the Gulf of Mexico. My graduate research experience made use of traditional methods of plankton study as well as blue-water scuba techniques and a towed video profiling system. Taking this knowledge of video-based research back home to Canada, I spent three years working as a fisheries research biologist with the department of Fisheries and Oceans working on the video-based stock assessment of inshore rockfish species (Sebastes spp.). It was during this time that I first had the opportunity to conduct research using ROVs and manned submersibles. Following my tenure at SFO, I was able to gain more practical experience in ROV piloting/tending and seamanship of small vessels working in the private sector before coming to Simon Fraser. My duties with REM are centered around field research, including operation and maintenance of the research vessel C.J. Walters and piloting and maintenance of the new Phantom DHD2+2 ROV.


Annie Morgan, Master’s Student

B.Sc. (Marine Science and Biology), University of Miami

Master’s research topic: Catch Mean Trophic Level as a Tool for Monitoring Changes in the Marine Ecosystem

Currently, 53% of the world’s fish stocks are reported as “fully exploited” and another 32% are “overexploited” or “depleted”. In recent years, fisheries managers have begun to shift from species-based management to ecosystem-based management. However, monitoring entire marine ecosystems can be a laborious and expensive process. Thus, there is a demand for tools and indices that will enable fisheries managers to monitor the ecosystem and its response to various fishing pressures in an inexpensive and effective way. My research will evaluate the use of catch mean trophic level (MTL) from global fisheries catch data as a potential tool for detecting changes in marine ecosystems. Catch MTL was introduced in 1998 as a possible way to track trends in ecosystem MTL over time and thereby measure the ecological consequences of fishing mortality. Presently, scientists have failed to reach a consensus regarding the best application of MTL as a monitoring tool. Through my research, I will assess a novel employment of MTL information and its ability to detect fishing impacts on marine ecosystems by using a number of simulated ecosystems around the world. With the results from this study, fisheries managers will be able to use changes in catch MTL as a cue for policy action, thus allowing for sustainable use of fish stocks. Additionally, the Convention on Biological Diversity and other collaborative organizations will be able to use this information to avoid further loss of biodiversity and to maintain the productivity of fisheries around the globe. Supervisor: Andy Cooper


Cameron Noble, Master’s Student

B.Sc.H. (Environmental Biology), Queen's University
B.Ed., University of British Columbia

Master’s research topic: Quantifying complexity in the future management of Fraser River sockeye fisheries

My research will examine how new in-river fisheries obligations and finer-scale escapement objectives constrain management options and yield in ocean fisheries for Fraser River sockeye.

My academic and personal interests lie in the area of Pacific Salmon, and the continuing production of B.C.'s fisheries. To that end, I will specifically be working to quantify the increase in management complexity of Fraser River sockeye, as management moves towards implementing Canada's Wild Salmon Policy. Supervisor: Sean Cox


Athena Ogden, Master’s Student

B.A., Hons. (Philosophy), University of British Columbia
Ph.D. (Philosophy of Science), University of British Columbia

Master’s research topic: Evaluation of potential recovery strategies for Cowichan River Fall Chinook salmon

Cowichan River Fall Chinook salmon are one of the two largest remaining naturally-spawning Chinook populations in the Lower Strait of Georgia. Historically, total annual spawner returns were estimated at up to 25,000 adults and jacks, and the current target escapement is 6,500 adults. However, the abundance of annual natural spawners has been less than 2,000 since 2005. The decline has occurred in spite of recent decreases in harvest rates of commercial and recreational fisheries, and increases in hatchery supplementation. My research objective is to determine the potential for recovery of the Cowichan Chinook under different management and ocean-survival scenarios. My stochastic population dynamics model estimates the probability of recovery and long-term persistence of the stock under different rates of hatchery brood take and harvest, in the context of different possible future ocean survival rates. Quantification of the trade-offs inherent in different management actions can provide fisheries managers with another tool to help them to choose optimal management strategies. Supervisor: Randall Peterman

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Erin Porszt, Master’s Student

B.Sc. (Marine and Freshwater Biology), University of Guelph

Master’s research topic: An evaluation of threat criteria for Fraser River sockeye salmon conservation units

The implementation of Canada’s policy for the conservation of wild Pacific salmon requires Fisheries and Oceans Canada (DFO) to develop measurable indictors and benchmarks to assess the biological status of conservation units (CUs), yet there is considerable variation in both definitions of threat and the defensibility of assessment methods. My research objective is to determine which threat criteria best indicate when there is a substantial chance of quasi-extinction (extremely low abundance) for CUs. The threat criteria considered in the analysis were various forms of the Committee on the Status of Endangered Wildlife in Canada (COSEWIC)’s criterion A, "Declining Total Population", and another set that I developed which considers aspects such as the decline from historical abundance levels and a geographical shift and/or shrinkage in spatial distribution. For each criterion, a retrospective analysis examined the historical spawner escapement data to determine the number of triggering events (threat criterion met) that would have occurred in the past for several Fraser sockeye CUs. I determined whether a CU actually had a high (or low) chance of quasi-extinction based on its future trajectory (i.e. the ratio of spawner abundance in successive generations). Each criterion was evaluated based on the proportion of all years, across all CUs, which were "correct triggering events", "false positives", "false negatives", or "correct non-triggering events". The criteria can be ranked and used accordingly by decision makers based on their priorities (maximize correct triggering events/minimize false negatives), and may provide the DFO with a better categorization of threat status for sockeye salmon in the Fraser River. Supervisor: Randall Peterman


Rhonda Reidy, Master’s Student

B.Sc. (Biology), University of Victoria

Master’s research topic: The potential impact of sea otters on the British Columbia geoduck clam fishery

The reintroduction of sea otters (Enhydra lutris) in British Columbia in the early 1970s has been successful and the current BC population is expanding. Otter population growth potentially conflicts with the commercial geoduck fishery, which is forecasting extensive losses in annual yield due to competition with sea otters on the West Coast of Vancouver Island (WCVI). My objective is to assess whether sea otters significantly affect geoduck density and total mortality on the WCVI. I used existing bed-specific, repeated fishery data separated by at least three years, as a ≥control-impact≤ study at 15 study sites within 7 geoduck-fishing locations to estimate density and total mortality rates (Z /yr) of geoduck clams in the presence and absence of sea otters on WCVI. I used the Chapman and Robson (1960) estimator to estimate Z for each study site. Results suggest that geoduck age distribution is similar between years but varies across sites. Geoduck densities are lower where sea otters were reintroduced and where otters have recently expanded their range. However, the data had too low power (<60%) to conclude whether sea otters significantly impact geoduck density. Total geoduck mortality rates were significantly higher for two sites where otters are present. As one of the first quantitative examinations of the interaction between sea otters and the commercial geoduck fishery, my results will inform managers and harvesters of the likely impacts of this recovering top marine predator on biological and economic yields from the commercially important geoduck fishery. Supervisor: Sean Cox


Malissa Smith, Master’s Student

B.Sc. (Environmental Science), Simon Fraser University

Master’s research topic: Evaluation of the management strategy for the BC spot prawn fishery

Fisheries and Oceans Canada (DFO) recently adopted a decision-making framework incorporating the Precautionary Approach (PA). The main objectives of the framework are to ensure resource sustainability and to meet the requirements of various eco-certification programs by demonstrating the application of reference points, harvest rules and compliance with the PA. Treatment of uncertainty and risk are central to the framework, with explicit requirements to communicate the risk of resource decline associated with management actions. The fishing industry and DFO have identified a need to evaluate the management procedure for the British Columbia spot prawn (Pandalus platyceros) fishery. The objective of my research is to determine, through testing a series of candidate management strategies, which management strategy for the spot prawn fishery is most likely to meet PA objectives. I will achieve this goal by: (i) developing an operating model for operations and management; (ii) calibrating the operating model based on available data, effort, and survey data; and (iii) running a closed-loop simulation that combines the operating model with a model for annual survey observations and an in-season model of the fishery to simulate spot prawn population dynamics and response to harvesting. P. platyceros are protandric hermaphrodites, starting their lives as males, transitioning to females around age 3, and dying at age 4 after spawning. The development of a stage-based model for a protandric hermaphrodite is a novel aspect of my research because it is relatively rare in the literature. This research will enable the British Columbia prawn fishery to improve their consistency and production quality through the application of effective management decisions, and has the potential to create a stronger Canadian market for spot prawn products through eco-certification programs. Supervisor: Sean Cox


Aaron Springford, Research Associate

B.Sc.Hons (Environmental Science), Simon Fraser University
MRM (Master of Resource Management), Simon Fraser University

Research topic: (1) Testing in-season management strategies for Fraser River sockeye salmon fisheries. (2) An exposure-response methodology for assessing the impacts of bottom-fishing gear on benthic marine ecosystems. (3) Using spatial information to standardize relative abundance indices derived from fisheries data.

(1) The long-term goal of this project is to test in-river management strategies for Fraser River sockeye salmon using a simulation model that includes: (a) flexible sockeye migration dynamics that include key biological- and climate-driven effects on population-specific migration patterns; (b) fisheries managed under alternative harvest strategies; (c) in-season planning, assessment, and monitoring; and (d) measures of management performance. Identification of this goal was one outcome of an April 2007 workshop, and it therefore reflects the interests of SFU researchers, Fisheries and Oceans Canada, and participating stakeholders. Ultimately, our objective is to evaluate not only broad fishery management strategies (e.g., effort vs. quota limitation), but also how specific uncertainties (e.g., migration patterns, measurement errors, en-route mortality) may affect long-term performance of these strategies.

(2) Bottom-fishing has a demonstrated effect on some benthic ecosystems when examined at the scale of a fishing event. However, there are no existing procedures or methods for assessing these impacts on a larger spatial scale. We are developing an exposure-response approach to assess the potential impacts of bottom-fishing gear on seafloor habitat. The exposure-response models will combine spatial mapping of bottom-fishing effort intensity and habitat (the exposure) with submersible surveys of habitat-forming species density (the response). Our end goal is to improve our understanding of the sensitivity of different bottom habitats to fishing so that the industry can mitigate their impacts and ultimately improve long-term ecosystem and fishery sustainability.

(3) Although fisheries monitoring programs increasingly record precise measures of fishing location, this information is ignored in nearly all population assessments. I have developed a spatial hierarchical Bayesian method (SHBM) that incorporates this location information to reduce biases caused by fishery targeting and spatial autocorrelation. The approach has been shown to reduce biases in estimates of stock productivity by up to 80 percent, even if fishery targeting and population aggregation are occurring simultaneously (i.e. a worst-case scenario). The broad implication is that available spatial fishery information can significantly improve the chances of achieving management goals, including conservation of exploited fish populations. Software developed for the analysis is in the process of being packaged for use in the R statistical environment. Supervisor: Sean Cox


Kelli Stingle, Master’s Student

B.Sc. (Biology), University of Puget Sound, Tacoma, Washington

Master’s research topic: Predicting blue whale habitat distribution in the Santa Barbara Channel from photographic identification data.

In 2007 National Marine Fisheries Services (NMFS) declared an unusual mortality event in the Southern California Bight when four ship struck blue whales (Balaenoptera musculus) were found dead in waters surrounding the Santa Barbara Channel. Ship strike mitigation efforts depend upon predictions of where whales and ships occur, yet no model exists to accurately predict blue whale occurrence in the channel. Systematic line transect surveys show blue whales do not use the channel, yet photographic identification studies consistently document whales in the area. My objective is to use existing data, collected for mark-recapture studies, to predict blue whale habitat in the Santa Barbara Channel using a generalized additive model. Currently the Coast Guard is conducting an economic analysis of the existing traffic separation scheme into the Los-Angeles Long Beach Harbor, North America’s second busiest port, that does not consider blue whale habitat. Coast Guard actions must abide by the Marine Mammal Protection Act and the Endangered Species Act. Results from my model could alter their recommendations on the best traffic separation scheme. Supervisor: Andy Cooper


Dorian Turner, Master’s Student

B.Sc. (Ecology), University of Calgary

Research topic: Modeling the effects of Run-of-River hydroelectric projects on instream fish habitat

Run-of-river (ROR) hydroelectric projects use the natural flow and gradient of a river to produce electricity. A portion of the river’s flow is diverted out-of-channel and transported downhill to a powerhouse, where the water turns turbines, generating electricity. The river water is subsequently returned to the channel downstream from the powerhouse, restoring natural stream flow. As a result of this process, a portion of the river channel between the intake structure and the outlet from the powerhouse, often stretching several kilometers, experiences reduced flow levels. Assessing the impacts of reduced flow levels on fish habitat is a somewhat unresolved issue. With the emergence of ROR hydroelectric project development by Independent Power Producers (IPPs) as a major component of B.C.’s energy policy, there is a growing need for effective and efficient methods to assess the instream flow requirements for fish species. Conventional instream habitat models (e.g. PHABSIM, RHYHABSIM, EVAH, etc.) have been used for quantifying the impacts of flow changes by linking traditional hydraulic engineering models to habitat preference curves of different fish species for water depth, velocity, and bed particle size. However, the application of these conventional models can be limited by the cost and expertise associated with field data collection. My research objective is to determine whether or not generalized habitat models, which use simpler and more cost-effective stream descriptions, can be used to produce similar results to the conventional instream habitat models in streams on the Southwest coast of British Columbia. Supervisor: Randall Peterman


Pier van Dishoeck, Master’s Student

B.Sc. (Biology), University of British Columbia

Master’s research topic: Salmonid response to flow release in the Lower Bridge River, British Columbia

Regulation of rivers for hydropower generation can profoundly affect downstream fish, including anadromous salmonids. Regulation can demand management trade-offs between water release (to improve fish production) and water diversion (to increase power production). Although such research is rare, the most direct way to establish a relationship between discharge and fish production is to experimentally manipulate flow, and concurrently monitor ecological response.

Regulation of the Bridge River, near Lillooet BC, diverted all flows above the dam into an adjacent drainage. To inform the water use planning process, BC Hydro has undertaken an experimental flow release program, with two of four proposed flow release trials completed to date. Monitoring includes annual juvenile salmonid stock assessment, using depletion electrofishing at standardized sites. I apply these data to: 1) examine the performance of depletion estimators; and, 2) test hypotheses about the relationship between flow and fish production.

Biologists commonly use depletion estimators to derive population estimates. Despite extensive discussion of alternative mathematical treatments, performance is rarely compared, and a preferred method has not been established. I use simulation to compare alternatives; results suggest a Bayesian estimator (Mantyniemi et al 2005) with robust results and characterization of uncertainty. I use this to derive datasets for the two Bridge River release periods. I intend to compare the datasets using traditional repeated measures analyses and a hierarchical Bayesian model. The anticipated system-specific relationship between flow and fish production is required by BC Hydro and other stakeholders to meet fisheries objectives in the long term management of the project, as well as to inform trade-offs between fisheries, and other social, financial and environmental objectives. Supervisors: Sean Cox and Mike Bradford


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