Thomas Carruthers

Thomas Carruthers
University of British Columbia | UBC · Institute for the Oceans and Fisheries

Doctor of Philosophy

About

65
Publications
15,440
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1,236
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Introduction
Tom is the CEO of Blue Matter Science, a quantitative fishery consultancy based in Vancouver, and an Adjunct Professor at the UBC Institute for the Oceans and Fisheries. Tom works on assessment and Management Strategy Evaluation frameworks for both data-rich and data-limited fisheries. He is a developer of R packages such as DLMtool and MSEtool and Apps such as MERA, Slick, SSES and the Atlantic bluefin MSE framework.

Publications

Publications (65)
Article
The age‐structured assessment model available in the MSEtool R package assesses stock status and exploitation for varying data availability, from limited to rich datasets. We investigated model accuracy in relation to data availability, population exploitation levels, initial population assumption and fishery selectivity misspecification. Estimates...
Technical Report
Full-text available
A multi-species, multi-fleet operating model was developed for the North Atlantic longline fishery including two primary species (swordfish and bigeye tuna) and four secondary species (blue shark, shortfin mako shark, white marlin, blue marlin). The operating model was used to generate a wide range of future exploitation scenarios for the various s...
Article
Full-text available
An individual tagging model was implemented within the spatial, seasonal, multi-stock, multi-fleet operating models of the peer-reviewed Management Strategy Evaluation (MSE) framework for Atlantic bluefin tuna to evaluate the benefits of a harvest strategy that utilizes conventional gene tagging. A multi-year Brownie estimator was developed to test...
Article
Full-text available
Fisheries managers are in need of quantitative tools to inform decisions regarding selection of robust management practices, prioritising research gaps and stocks to focus on, particularly where there are limited resources or data. To support these decisions, the use of Management Strategy Evaluation (MSE), that is, closed loop simulation‐testing o...
Article
Full-text available
There is a need for rigorous science to inform decision makers for Ecosystem Based FisheriesManagement (EBFM). It is important to establish challenging and plausible scenarios forecosystem dynamics and then test whether current and potential indicators can reflect stockstatus. Without the validation of indicators and the testing of relevant policy...
Article
A retrospective pattern within a stock assessment occurs when historical estimates systematically increase or decrease as data are removed and has been cited as a cause of persistent overfishing. For two case studies, Gulf of Maine cod and New England pollock, we demonstrated how closed-loop simulation can be used to evaluate the impacts of retrosp...
Article
Full-text available
Mitigating bycatch of non-target fish species is a common objective in fisheries management that may be supported by the gathering of data from fishery observer programs and quantitative analysis of bycatch risk factors. We build three GLM models based on Chinese tuna longline fishery observer data in terms of analysis of total bycatch rate (TB rat...
Article
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Fisheries researchers have focused on the value of information (VOI) in fisheries management and trade-offs since scientists and managers realized that information from different resources has different contribution in the management process. We picked seven indicators, which are log-normal annual catch observation error (Cobs), annual catch observ...
Technical Report
Full-text available
This workshop is the third in a series of workshops on guidelines for developing Management Strategy Evaluations (MSEs) within ICES, and was intended to explore some of the issues that arose out of workshops that actually developed MSEs for a range of ICES stocks since the second MSE guidelines workshop was held in early 2019. It is intended that r...
Technical Report
Full-text available
The three main robustness tests, senescence, growth curve for eastern stock, "Brazilian" catches, had already been coded in July 2020 (with 4 Operating Models (OMs) each), but the "Brazilian" catches test needed to be redone. Robustness tests on time-varying mixing and persistent change in mixing have now also been coded (with 2 OMs each) and will...
Article
Stock assessments are often used to provide management advice, such as a total allowable catch (TAC), to fishery managers. Many stocks are not assessed annually, and the TAC from the previous assessment is often maintained in years between assessments. We developed two interim management procedures (MPs) that update the estimate of current vulnerab...
Article
Full-text available
Common uncertainties in stock assessment relate to parameters or assumptions that strongly determine both the estimates of quantities of management interest (e.g. stock depletion) and related reference points (e.g. biomass at maximum sustainable yield). The risks associated with these uncertainties are often presented to managers in the form of dec...
Article
Potential users of the model proposed by Froese et al. (2018) should be aware of several issues. First, the method to calculate equilibrium numbers-at-length is incomplete and leads to negatively biased estimates of fishing mortality. Second, inadequate simulation testing fails to reveal that the method is highly sensitive to assumptions of equilib...
Article
Full-text available
Specifying annual catch limits for artisanal fisheries, low economic value stocks, or bycatch species is problematic due to data limitations. Many empirical management procedures (MPs) have been developed that provide catch advice based on achieving a stable catch or a historical target (i.e., instead of maximum sustainable yield). However, a thoro...
Article
Full-text available
A simulation‐based approach known as management strategy evaluation ( MSE ) is increasingly used by resource managers to identify management procedures that are robust to uncertainties in system dynamics. The majority of global fish populations are data limited and there is large uncertainty over their population and exploitation dynamics. The Data...
Article
Full-text available
The first relatively complete landscape-scale social–ecological system (SES) model of a recreational fishery was developed and ground-truthed with independent angling effort data. Based on the British Columbia multistock recreational fishery for rainbow trout (Oncorynchus mykiss), the model includes hundreds of individual lake fisheries, hundreds o...
Article
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A new indicator is described that uses multivariate posterior predictive data arising from management strategy evaluation (MSE) to detect operating model misspecification (exceptional circumstances) due to changing system dynamics. The statistical power of the indicator was calculated for five case studies for which fishery stock assessments have e...
Article
Full-text available
Qualitative risk assessment frameworks, such as the Productivity Susceptibility Analysis (PSA), have been developed to rapidly evaluate the risks of fishing to marine populations and prioritize management and research among species. Despite being applied to over 1,000 fish populations, and an ongoing debate about the most appropriate method to conv...
Article
A simple approach is described that uses the ratio of catches among a reference and a target stock to estimate their relative depletion. The catch-ratio estimator was simulation tested to identify conditions under which it can be expected to provide precise and unbiased estimates of relative depletion. The catch-ratio estimator is strongly affected...
Article
Full-text available
Virtual population analysis (VPA) is used in many stock assessment settings and requires a total catch-at-age data set where an age is assigned to each fish that has been caught. These data sets are typically constructed using ad hoc methods that rely on numerous assumptions. Although approaches are available to account for observation error in the...
Article
Full-text available
A method is described that uses stock-specific movement to impute stock-of-origin for electronic tags. A simple example of the approach was tested using cross-validation of electronic tags of known stock-of-origin. The imputation model achieved a failure rate of 3% and a success rate of 88%. In 9% of cases the imputation model did not classify stoc...
Conference Paper
Full-text available
Spatial-temporal assessment methods capture alternative population dynamics of bluefin tunas but also expose new analytical and management challenges. We briefly review some current spatial assessment methods. We describe the motivation for the Multistock Age Structured Tag integrated assessment model (MAST) that was developed for Atlantic bluefin...
Article
Full-text available
Rebuilding depleted fish populations is a priority of modern fisheries management. In the U.S., strong statutory mandates extend to both the goals and process by which stocks are to be rebuilt. However, the National Standard Guidelines that govern the implementation of the Magnuson-Stevens Fishery Conservation and Management Act may change to incre...
Article
Full-text available
Using a management strategy evaluation approach, we compare a range of new and established anagement procedures (MPs) for setting catch-limits in fisheries. Performance is evaluated with respect to fish life history type, level of stock depletion, data quality, and autocorrelation in recruitment strength. We quantify the robustness of each MP with...
Article
Full-text available
We develop and test spatial population dynamics models that estimate age-dependent offshore movement of fish populations from spatial fishery data. Spatially aggregated population dynamics models produced biased estimates of maximum sustainable yield (MSY) reference points when spatial dynamics were simulated. Spatial population dynamics models pro...
Article
Full-text available
Estimates of tag reporting rates are necessary in order to estimate tag-recovery rates and interpret tagging data in terms of movement rates, exploitation rates and abundance. We describe a Bayesian framework for the estimation of reporting rates for multiple fleets using coincidental tagging and catch data disaggregated by fish size, species, loca...
Article
Full-text available
The majority of global fish stocks lack adequate data to evaluate stock status using conventional stock assessment methods. This poses a challenge for the sustainable management of these stocks. Recent requirements to set scientifically based catch limits in several countries, and growing consumer demand for sustainably managed fish have spurred an...
Technical Report
Full-text available
In January 2014, the Natural Resources Defense Council (NRDC) convened a group of experts from NMFS, state agencies, academic institutions, and non-governmental organizations for a Workshop on the science and management of data-limited fisheries. The goal of the Data-Limited Methods (DLM) Workshop was to evaluate and seek to improve current methods...
Article
In 2007, an Individual Fishing Quota (IFQ) program was introduced to the valuable red snapper (Lutjanus campechanus) fishery in the US Gulf of Mexico. This study assessed the current perceived scale and causes of red snapper discarding in the Gulf in recent years within the commercial reef fish fishery, according to commercial fishermen. Data were...
Article
Full-text available
Methods that use only fisheries catch records to determine the status of exploited fish populations have been used to draw important conclusions regarding the world's fisheries. The reliability of two such approaches is evaluated by simulating a range of fisheries development and overfishing scenarios. The success rate and bias of stock status clas...
Data
Annual catches by longline (LL), purse-seine (PS), bait boat (BB), and other (Oth) gears in (A) the Gulf of Mexico, (B) the Gulf of St. Lawrence, (C) the western Atlantic, (D) the eastern Atlantic, and (E) the Mediterranean Sea. (TIF)
Data
Partial derivatives for the derivation of B0 from MSY and Fmsy (DOC)
Data
Archival tag observation probabilities for state-space likelihoods in the MAST model for Atlantic bluefin tuna (DOC)
Data
Description of symbols and indices used in MAST (DOC)
Data
Electronic tag data state-transition equations in the MAST model (DOC)
Data
Summary of key MAST model output at the posterior mode for Atlantic bluefin tuna (A) base-case with time-invariant gear selectivity and normal reporting-rate priors; (B) estimated time-invariant gear selectivity and β(3,3) reporting-rate priors; (C) estimated time-varying gear selectivity and N(0.1,0.065) reporting-rate priors; (D) base-case with e...
Data
Estimated tag reporting rates of the MAST model for Atlantic bluefin tuna by scenario (A) base-case with time-invariant gear selectivity and normal reporting-rate priors; (B) estimated time-invariant gear selectivity and β(3,3) reporting-rate priors; (C) estimated time-varying gear selectivity and N(0.1,0.065) reporting-rate priors; (D) base-case w...
Data
Initialization of age-structured model assuming selectivity at age, natural mortality, age-specific fecundity, and Beverton-Holt recruitment (DOC)
Data
State dynamics and observation model (DOC)
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Life-history parameters defining φ (DOC)
Data
Summary of conventional tag cohorts of Atlantic bluefin tuna in the MAST model (DOC)
Data
Summary of commercial CPUE data on relative abundance in the MAST model for Atlantic bluefin tuna (DOC)
Data
Map of MAST spatial areas and electronic tag geolocations. (TIF)
Data
Data, estimated parameters, and initial states (DOC)
Article
Full-text available
Atlantic bluefin tuna (Thunnus thynnus) is considered to be overfished, but the status of its populations has been debated, partly because of uncertainties regarding the effects of mixing on fishing grounds. A better understanding of spatial structure and mixing may help fisheries managers to successfully rebuild populations to sustainable levels w...
Article
Full-text available
We formulate and simulation-test a spatial surplus production model that provides a basis with which to undertake multispecies, multi-area, stock assessment. Movement between areas is parameterized using a simple gravity model that includes a "residency" parameter that determines the degree of stock mixing among areas. The model is deliberately sim...
Article
Full-text available
When deriving relative abundance indices on the basis of fishery catch-per-unit-effort (CPUE) data, biases may be introduced by systematic changes in the spatial distribution of fishing. We present and simulation test an integrated approach that combines the conventional generalized linear modelling (GLM) approach to CPUE standardization with data...
Article
Full-text available
Uncertainty about reporting rates of tags returned by fishermen has often prevented tagging data from being used in stock assessments. In this study we conduct a meta-analysis to estimate tag reporting rates of commercial tuna fleets by comparing their tag return data with those of the USA longline pelagic observer program. The longline fleets of V...
Article
Full-text available
Relative abundance indices derived from nominal catch-per-unit-effort (CPUE) data are a principle source of information for the majority of stock assessments. A particular problem with formulating such abundance indices for pelagic species such as tuna is the interpretation of CPUE data from fleets that have changed distribution over time. In this...

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