Murdoch McAllister

Associate Professor

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Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

The development of an agent-based depletion model of Dungeness crab for the evaluation of seasonal management options (2022)

Dungeness crab (Cancer magister) range from the Aleutian Islands to Central California andgrow by moulting in the springtime, entering soft-shell condition after they moult. Unmarketablesoft-shell crabs become marketable after a few weeks when their shells harden. Only male crabslarger than 165mm in hard shell can be harvested and sold.This dissertation focuses on the Dungeness crab fishery in the Hecate Strait, British Columbia,between Haida Gwaii and the mainland, and develops fishery models using vessel monitoring system data, within-season harvest control rules, multiple types of biological variation, and seasonalclosures.The questions in this dissertation were driven by the central trade-off; having a long fishingseason while avoiding setting traps on soft-shell crabs. Four overarching questions related to thecentral trade-off are as follows: Which factors could most accurately predict weekly crabbing effort when it is of interest to model crab fishery dynamics in the evaluation of in-season crab fisherypolicy options? What type of population modelling approach is suitable for evaluating in-seasonfishery policy options for crustaceans where moulting causes the product to be unmarketablefor several weeks each year? Which factors drive within season changes in the vulnerability ofcrustaceans to capture in fisheries, e.g., abiotic factors like sea surface temperature, biologicalfactors like moult condition, or temporal factors like season? Would a management approachwhich closed and reopened the fishery based on a soft-shell survey lead to better long-term yieldsand catch rates than fixed date seasonal closures or no seasonal closures?The four main chapters in this thesis examine the Hecate Strait Dungeness crab fishery as acase study. Chapter 2 analyzes fishing effort over the course of the fishing season. Chapters 3 and4 develop an agent-based depletion model to attempt to estimate various biological quantities.Chapter 5 simulates three alternative management control rules for setting opening and closingdates.This dissertation contributes new methods for evaluating fine timescale commercial catchand trap haul data from vessel monitoring systems and found that setting fishery openings andclosures based on a weekly soft shell survey outperformed alternative management control rules.

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Predator-prey interactions between harbour seals (Phoca vitulina) and Pacific salmon (Oncorhynchus spp.) in the Salish Sea (2021)

Populations of Chinook (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) haveexperienced significant declines in abundance and productivity over the last 50 years in theSalish Sea as harbour seals (Phoca vitulina) recovered from hunting and culling. Some havehypothesized that increased predation by seals may be responsible for the declines in salmonsurvival, and their failure to recover after reductions in fishing effort. However, it is not known ifthese correlations exist for every population of salmon in the Salish Sea, or how many youngChinook and coho salmon are consumed by seals each year. I developed mathematical andstatistical models to investigate the potential causal relationship between seal predation anddeclines in Chinook and coho salmon populations in the Salish Sea. I also used simulationmodeling to evaluate outcomes that may result if managers reduced British Columbia’s harbourseal population to promote the recovery of salmon populations. I found that harbour sealdensities were strongly negatively associated with productivity of most wild Chinook salmonpopulations in the Salish Sea and Washington Coast that were included in the study. Integratingrecently collected seal diet data with a novel predation model indicates that large numbers ofjuvenile Chinook and coho salmon are eaten by seals, and that predation-related mortality haslikely increased significantly over the last 50 years. The results of my simulation model suggestboth lethal removals and contraception could reduce the seal population, but that importanttradeoffs exist between the two approaches. Overall, my findings increase understanding of therole that marine mammal predation plays in the early marine life stage of juvenile salmon, andidentifies potential outcomes and tradeoffs of actively managing predator populations.

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Fisheries harvest management procedures under time-varying productivity (2020)

Fish stocks often show persistent changes in fish production with hypothesized causes including time-varying recruit parameters, natural mortality of mature fish, and somatic growth. Changes in fish productivity can affect biological reference points and the expected robustness of harvest strategies in meeting long-term conservation and economic objectives. Current assessment approaches commonly assume “stationarity” in stock-recruit parameters and implemented harvest strategies commonly lack consideration of changes in fish productivity. This dissertation covers three studies based on statistical analysis and simulation methods that aim to advance understanding of time-varying stock-recruit parameters and harvest control rules (HCRs) to cope with changes in fish production. Chapter 2 examined the performance of a Kalman filter algorithm that estimates dynamic state variables (e.g., changing stock-recruit parameters) from inaccurate observations obtained from stock assessment outputs. In Chapter 3, stochastic optimization in policy space (SOPS) was used to find an optimal HCR that is robust to changes in productivity under closed-loop simulation or management strategy evaluation (MSE). By using SOPS and a simple population dynamics model, this chapter examined optimal HCRs under different types of regime shifts (e.g., changes in carrying capacity and intrinsic growth rates). Chapter 4 examined empirical HCRs in an extreme situation of “non-stationarity” in stock-recruit parameters (i.e., a spasmodic recruitment pattern), using Atlantic redfish stocks as a case-study. The Kalman filter detected the overall trend in the stock-recruit parameters over time. Also, it was found that optimal HCRs depend on the timing of biomass estimates relative to harvest, observation error, intrinsic population growth, and regime shifts types. In the case of spasmodic stocks, it was found that simple HCRs that used data from well-designed fishery-independent resource surveys were capable of handling changes in productivity. The present dissertation shows the importance of well-designed fishery-independent surveys and simple HCRs for tackling changes in productivity and guidelines are provided for developing HCRs that are robust to the occurrence of such changes. The models and findings presented here can be applied to improve the management of other stocks that show persistent changes in fish productivity.

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Evaluating key assumptions of a hook-based relative abundance index derived from the catch of bottom longlines (2018)

Catches from bottom longline surveys are used to construct relative abundance indices for many demersal species. Due to their careful design, survey-based relative abundance indices are assumed to be proportional to the true species abundance. However, longlines catches may be affected by interspecific competition, gear saturation, and fine-scale gear and species interactions created by feeding behaviours and habitat preferences. A hook-based relative abundance index, the instantaneous rate of bait loss per species (λs), which accounts for hook competition and gear saturation, may resolve some of the problems with the common catch per unit effort (CPUE) index. I evaluated whether a linear or non-linear relationship exists between the λs index and abundance, and whether assumptions about bare hooks, species behaviours and fine-scale habitat affect the λs index. Using longlines targeting Yelloweye Rockfish (Sebastes ruberrimus) and Quillback Rockfish (S. maliger) in the inside waters of Vancouver Island, British Columbia, Canada, as a case study, I compared longline catches with underwater observations of the hooks and surrounding species from a Remotely Operated Vehicle in March (n = 13) and August (n = 12) of 2010. The results did not refute a linear model between the λs index and observed density, when compared to a non-linear model, except for the August Yelloweye index. The λs index did have a better fit with observed density than CPUE for Yelloweye, but not for Quillback. Adding hook-level habitat into the λs index improved the fit for Yelloweye, but not for Quillback. Additionally, observations showed that bare hooks were mainly due to non-target species, including large invertebrates. The annual λs index for the rockfish survey was estimated under different scenarios for bare hooks and species interactions, but the trends in the λs index were robust. Trends in the λs index differed from CPUE trends in some areas. My research results cast some doubt on the assumption that for a few inshore rockfish the λs index is consistently linearly related to abundance. Caution needs to be taken in extrapolating these results to other situations, as the experiments occurred in a small area and incorporated limited seasonal and temporal variation.

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Spatial and length-based models for management of migratory transboundary species : application to Pacific hake (Merluccius productus) (2018)

This dissertation develops new modeling tools to provide new scientific perspectives on migratory transboundary fish populations. I particularly focus on two main issues: (1) the interaction between age/size based migratory movement, spatial availability, and fisheries exploitation rates, and (2) time-varying fisheries selectivity caused by size based migration and cohort targeting. I use Pacific hake (Merluccius productus) as a case study. Pacific hake occurs off the Pacific coast of the U.S.A. and Canada and is characterized by ontogenetic migratory movement (older fish migrate further north), strong recruitment events, and time-varying selectivity due to targeting of strong cohorts. In this dissertation, I present two new modeling approaches, and explore the effects of spatial structure on management outcomes using a closed-loop evaluation. First, I use a Lagrangian approach to develop a migration model that describes the Pacific hake dynamics including seasonal migrations, fisheries dynamics, and cohort targeting. Second, I introduce a new stock assessment method that bypasses the requirement of estimating selectivity by using catch at length and growth parameters to produce estimates of exploitation rate at age. This method produces mixed results because of low precision in selectivity estimates. Third, I evaluate the impacts of harvest control rules on the outcomes experienced by Canada and the U.S.A while sharing the Pacific hake resource. I use the migration model described above in a closed-loop simulation to evaluate the long-term impact of 61 harvest control rules. The results indicate that there are differences in performance of harvest control rules between the two nations when maximizing potential long-term yield and log yields. This is a result of the reduced availability of the resource in Canadian waters as the overall harvest rate increases. Caps on allowable catch may help to avoid reduced availability issues. I believe that the results and conclusions presented in this dissertation can inform the future management and modeling of Pacific hake. In addition, the methods presented here could be used for management of other resources subject to time-varying selectivity and other transboundary stocks managed under agreements that do not consider spatial management explicitly.

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Evaluation of Restricted-Area Culling Strategies to Control Local Red Fox Density (2015)

Lethal control of red foxes is often implemented on restricted areas where immigration from neighbouring sources is expected to make it difficult to keep local fox density low. The justification of lethal wildlife control should include demonstrating its effectiveness. To this end, population dynamics modelling may help to assess the performance of different control strategies in a range of real-world circumstances. A Bayesian state-space model for within-year fox population dynamics was developed that could be fitted to data on daily culling effort and success obtained from gamekeepers on shooting estates in Britain. The estimation model included parameters for key population processes within the culling area: immigration, cub recruitment and non-culling mortality. A simulation-estimation study showed that given a minimum of three years’ data the estimation of fox density and demographic parameters was reliable. Informative priors for the key model parameters were constructed using empirical data and meta-analysis. Data from 22 estates were modelled on a two-weekly time-step. Most estates achieved some suppression of the fox population relative to estimated carrying capacity, but few maintained consistently low densities. The number of foxes killed was a poor indicator of culling effectiveness, highlighting the need for modelling. Estimated immigration rates onto estates were typically high, indicating rapid replacement of culled foxes. There was unexpectedly high spatial variation among estates in estimated carrying capacity and immigration rate. There was evidence from a limited subset of estates that the variable density of released game birds may explain this. The food requirement of the fox population during the nesting period was assumed to indicate predation pressure on wild birds. Alternative culling strategies to reduce this requirement were evaluated using posterior parameter estimates from some estates. Culling concentrated in spring and summer only was more effective than culling uniformly throughout the year. Autumn-only culling was not an effective strategy for wild birds. Open-loop strategies were most effective as culling effort was used all the time. However, closed-loop strategies, where culling effort was conditional on feedback from simulated field-sign searches, achieved similar effects on food requirements using less effort. This revealed trade-offs between effectiveness, cost and animal welfare.

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