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Stephanie Peacock

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PhD candidate in Biological Sciences, co-supervised by Mark Lewis and Marty Krkosek (University of Toronto).

Stephanie Peacock

Biological Sciences - Ecology
CCIS 1-092
Curriculum Vitae

  • Mathematical biology
  • Host-parasite ecology
  • Pacific salmon

  • NSERC Vanier Scholar

Subject areas and related deposits

  • Adaptive management

    • Cessation of a salmon decline with control of parasites

      The resilience of coastal social-ecological systems may depend on adaptive responses to aquaculture disease outbreaks that can threaten wild and farm fish. A nine-year study of parasitic sea lice (Lepeophtheirus salmonis) and pink salmon (Oncorhynchus gorbuscha) from Pacific Canada indicates that adaptive changes in parasite management on salmon farms have yielded positive conservation outcomes. After four years of sea lice epizootics and wild salmon population decline, parasiticide application on salmon farms was adapted to the timing of wild salmon migrations. Winter treatment of farm fish with parasiticides, prior to the outmigration of wild juvenile salmon, has reduced epizootics of wild salmon without significantly increasing the annual number of treatments. Levels of parasites on wild juvenile salmon significantly influence the growth rate of affected salmon populations, suggesting that these changes in management have had positive outcomes for wild salmon populations. These adaptive changes have not occurred through formal adaptive management, but rather, through multi-stakeholder processes arising from a contentious scientific and public debate. Despite the apparent success of parasite control on salmon farms in the study region, there remain concerns about the long-term sustainability of this approach because of the unknown ecological effects of parasticides and the potential for parasite resistance to chemical treatments.

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  • Aquaculture

    • Fish farms, parasites, and predators: implications for salmon population dynamics

      For some salmon populations, the individual and population effects of sea lice (Lepeophtheirus salmonis) transmission from sea cage salmon farms is probably mediated by predation, which is a primary natural source of mortality of juvenile salmon. We examined how sea lice infestation affects predation risk and mortality of juvenile pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon, and developed a mathematical model to assess the implications for population dynamics and conservation. A risk-taking experiment indicated that infected juvenile pink salmon accept a higher predation risk in order to obtain foraging opportunities. In a schooling experiment with juvenile chum salmon, infected individuals had increased nearest-neighbor distances and occupied peripheral positions in the school. Prey selection experiments with cutthroat trout (O. clarkii ) predators indicated that infection reduces the ability of juvenile pink salmon to evade a predatory strike. Group predation experiments with coho salmon (O. kisutch) feeding on juvenile pink or chum salmon indicated that predators selectively consume infected prey. The experimental results indicate that lice may increase the rate of prey capture but not the handling time of a predator. Based on this result, we developed a mathematical model of sea lice and salmon population dynamics in which parasitism affects the attack rate in a type II functional response. Analysis of the model indicates that: (1) the estimated mortality of wild juvenile salmon due to sea lice infestation is probably higher than previously thought; (2) predation can cause a simultaneous decline in sea louse abundance on wild fish and salmon productivity that could mislead managers and regulators; and (3) compensatory mortality occurs in the saturation region of the type II functional response where prey are abundant because predators increase mortality of parasites but not overall predation rates. These findings indicate that predation is an important component of salmon–louse dynamics and has implications for estimating mortality, reducing infection, and developing conservation policy.

  • Model

    • Electronic Supplementary Material: Can reduced predation offset negative effects of sea louse parasites on chum salmon?

      This .zip file contains R code and data that accompanies the paper "Can reduced predation offset negative effects of sea louse parasites on chum salmon?". The R code includes three main files: (1) code to compile chum salmon spawner-recruit data from escapement, catch and age -at-return, (2) code to fit a Ricker population model testing for an effect of sea louse abundance on farmed or wild salmon on chum salmon productivity, and (3) code to solve a host-macroparasite model that includes the effect of predation in a multi-host system. Supporting data include escapement, catch and age-at-return data made publicly available by Fisheries and Oceans Canada. Details of the files within are given in the README.txt file.

      Abstract for the paper:
      The impact of parasites on hosts is invariably negative when considered in isolation, but may be complex and unexpected in nature. For example, if parasites make hosts less desirable to predators then gains from reduced predation may offset direct costs of being parasitized. We explore these ideas in the context of sea louse infestations on salmon. In Pacific Canada, sea lice can spread from farmed salmon to migrating juvenile wild salmon. Low numbers of sea lice can cause mortality of juvenile pink and chum salmon. For pink salmon, this has resulted in reduced productivity of river populations exposed to salmon farming.However, for chum salmon, we did not find an effect of sea louse infestations on productivity, despite high statistical power. Motivated by this unexpected result, we used a mathematical model to show how a parasite-induced shift in predation pressure from chum salmon to pink salmon could offset negative direct impacts of sea lice on chum salmon. This shift in predation is proposed to occur because predators show an innate preference for pink salmon prey. This preference could be more easily expressed when sea lice compromise juvenile salmon hosts, making them easier to catch. Our results indicate how the ecological context of host-parasite interactions may dampen, or even reverse, the expected impact of parasites on host populations.

  • Parasites

    • Distinguishing sources of parasites on wild juvenile salmon

      Ecological systems are complex. All too often, complex models are fit to ecological data without consideration of whether parameters are estimable. I present a recent example for a parasite transmission model tracking the diffusion of sea lice from salmon farms in coastal British Columbia, fit to data of sea lice abundances on migrating wild juvenile salmon. The estimability of parameters is not clear from published point estimates, but an effort to obtain standard errors on parameter estimates revealed either a lack of information in the data or non-identifiable parameters. I used data cloning techniques to verify an estimability issue, and subsequently revised the model. Results from the revised parasite transmission model support previous work, suggesting that salmon farms are a significant source of sea lice on wild juvenile salmon. But management interventions have altered parasite dynamics on salmon farms in recent years, and the temptation is great to account for these dynamics in the parasite transmission model. Can parameters be estimated if this additional complexity is introduced?

  • Salmon

    • Metrics and sampling designs for detecting trends in the distribution of spawning Pacific salmon (Oncorhynchus spp.)

      The distribution of individuals among populations and in space may contribute to their resilience under environmental variability. Changes in distribution may indicate the loss of genetically distinct subpopulations, the deterioration of habitat capacity, or both. The distribution of Pacific salmon (Oncorhynchus spp.) among spawning locations has recently been recognized as an important component of status assessment by USA and Canadian management agencies, but metrics of spawning distribution have not been rigorously evaluated. We evaluated three metrics of spawning distribution and four sampling designs for their ability to detect simulated contractions in the production of coho salmon (Oncorhynchus kisutch). We simulated population dynamics at 100 sites using a spawner–recruit model that incorporated natural variability in recruitment, age-at-maturity, dispersal, and measurement error in observations of abundance. Sensitivity analyses revealed that high observation error and straying of spawners from their natal streams may mask changes in distribution. Furthermore, monitoring only sites with high spawner abundance, as is often practiced, failed to capture the simulated contraction of production, emphasizing the importance of matching monitoring programs with assessment objectives.

    • A review of metrics of distribution with application to Conservation Units under Canada's Wild Salmon Policy

      Metrics describing the distribution of individuals among groups and across the landscape can provide information on the resilience of a population that may not be apparent from abundance information alone. The distribution of spawners has therefore been recommended as an indicator of the biological status of Conservation Units (CUs) under Canada’s Wild Pacific Salmon. The objectives of this report were to review metrics of distribution from the scientific and management and compare those to metrics previously proposed for assessing status of CUs. Only a subset of metrics were relevant for assessing status of CUs, but others may be useful for other biological and management settings.

  • Salmon, aquaculture

    • Nine years of sea lice and pink salmon population dynamics in the Broughton Archipelago

      The abundance of sea lice on farmed salmon and wild juvenile salmon in the Broughton Archipelago has fluctuated significantly both among and within years. Years when sea lice have reached epizootic levels are associated with increased mortality and depressed productivity of wild salmon populations. In contrast, years when the abundance of sea lice is relatively low are associated with improved productivity of wild populations to levels similar in unexposed populations. In this talk, we compare these trends in sea lice and salmon population dynamics with trends in management practices of salmon farms in the Broughton Archipelago. Of particular interest is the effect of co-ordinated area management, which utilizes parasiticide treatment as well as strategic harvest and stocking schedules, in order to protect wild juvenile salmon from sea lice.