James T Thorson

James T Thorson
Alaska Fisheries Science Center · Habitat and Ecological Processes Research

PhD

About

230
Publications
75,763
Reads
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6,351
Citations
Introduction
I'm a statistical ecologist who focuses on theoretical and applied questions for marine fish ecology and management. My interests include spatio-temporal methods and applications, life-history theory, meta-analysis, population and community-dynamics models, and global fishery status
Additional affiliations
August 2018 - December 2021
Alaska Fisheries Science Center
Position
  • Program Lead
June 2012 - August 2018
National Marine Fisheries Service
Position
  • Statistical Ecologist
Education
September 2009 - December 2011
University of Washington Seattle
Field of study
  • Aquatic and Fisheries Sciences
January 2006 - August 2009
Virginia Polytechnic Institute and State University
Field of study
  • Fisheries and Wildlife Sciences

Publications

Publications (230)
Article
Full-text available
A robust assessment of the American eel (Anguilla rostrata) stock, required to guide conservation efforts, is challenged by the species' vast range, high variability in demographic parameters and data inadequacies. Novel ideas and underutilised resources that may assist both analytic assessments and spatially oriented modelling include (1) species...
Article
An abundance of studies in marine systems have documented species range shifts in response to climate change, and many more have used species distribution models to project species ranges under future conditions. However, there is increasing interest in moving beyond a single‐species focus to understand how species redistribution alters ecosystem d...
Article
Full-text available
Developing Species Distribution Models (SDM) for marine exploited species is a major challenge in fisheries ecology. Classical modelling approaches typically rely on fish research survey data. They benefit from a standardized sampling design and a controlled catchability, but they usually occur once or twice a year and they may sample a relatively...
Article
Data-limited species are often grouped into a species complex to simplify management. Commonalities between species that may indicate if species can be adequately managed as a complex include the following: shared habitat utilization (e.g., overlapping fine-scale spatial distribution), synchrony in abundance trends, consistent fishing pressure or g...
Article
Many marine fish species are widely distributed over large areas. Failing to acknowledge that such species may be composed of distinct populations may result in overestimation of the stock's true harvest potential. To avoid overexploitation, ways to identify population structuring are therefore needed. In this study, we developed and applied a stat...
Article
Full-text available
Abundance indices derived from fisheries-dependent data (catch-per-unit-effort or CPUE) are known to have potential for bias, in part because of the usual non-random nature of fisheries spatial distributions. However, given the cost and lack of availability of fisheries-independent surveys, fisheries-dependent CPUE remains a common and informative...
Article
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Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species' abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co-occur with others has been overlooked. Here, we tested whether the abundance of resident titmice can act as a gen...
Article
Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of...
Article
Density dependence is included in many population–dynamics models, but few options exist within species distribution models (SDMs). One option for density-dependence in SDMs proceeds by including an independent time-series of population abundance as covariate using a spatially varying coefficient (SVC). We extend this via three alternative approach...
Technical Report
Full-text available
The American eel (Anguilla rostrata) occupies a vast range in the West Atlantic Ocean and inflowing waters. Despite its presumed panmictic status, management of this species is geographically fragmented. There have been widespread calls for internationally coordinated efforts towards a range-wide stock assessment, but such an objective faces obstac...
Article
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Marine mammals have been proposed as ecosystem sentinels due to their conspicuous nature, wide ranging distribution, and capacity to respond to changes in ecosystem structure and functioning. In southern European Atlantic waters, their response to climate variability has been little explored, partly because of the inherent difficulty of investigati...
Article
Fisheries scientists and managers must track rapid shifts in fish spatial distribution to mitigate stakeholder conflict and optimize survey designs, and these spatial shifts result in part from animal movement. Information regarding animal movement can be obtained from selection experiments, tagging studies, flux through movement gates (e.g. acoust...
Article
Implementation of the United Nations Sustainable Development Goals requires assessments of the global state of fish populations. While we have reliable estimates of stock status for fish populations accounting for approximately half of recent global catch, our knowledge of the state of the majority of the world's “unassessed” fish stocks remains hi...
Article
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Spatial management has been adopted worldwide to mitigate habitat impacts while achieving fisheries management objectives. However, there is little theory or practice for predicting the impact of spatial regulations on future fishery production; this would provide scientific basis for greater flexibility in fisheries management when balancing fishe...
Article
Abundance indices from scientific surveys are key stock assessment inputs, but when the availability of fish varies in space and time, the estimated indices and associated uncertainties do not accurately reflect changes in population abundance. For example, indices for many semi-pelagic species rely on acoustic and bottom trawl gear that differ in...
Article
Taxa can expand beyond historical scientific survey footprints and into new areas with different survey protocols as they move to track their preferred climate. In global groundfish fisheries, for example, scientists estimate population dynamics within the spatial extent of a fishery‐independent survey using an index known as a design‐based estimat...
Article
Survival is an important population process in fisheries stock assessment models and is typically treated as deterministic. Recently developed state-space assessment models can estimate stochastic deviations in survival, which represent variability in some ambiguous combination of natural mortality (M), fishing mortality (F), and migration. These s...
Article
Attributing variability in fish demographic processes to environmental conditions is helpful when assessing population status and forecasting changes in ecosystem function. Empirical orthogonal function (EOF) analysis has long been used to explore variability in physical processes, but has been only recently employed to study variability in biologi...
Article
Understanding the dynamics of species range edges in the modern era is key to addressing fundamental biogeographic questions about abiotic and biotic drivers of species distributions. Range edges are where colonization and extirpation processes unfold, and so these dynamics are also important to understand for effective natural resource management...
Article
Nearshore areas represent important habitats for many species, at least for part of their life cycle. Therefore, modeling and mapping nearshore habitats is essential for natural resource management and conservation, such as determining potential impacts to marine populations and their habitats from human activities and identifying conservation meas...
Article
Full-text available
Diet-based annual biomass indices can potentially use predator stomach contents to provide information about prey biomass and may be particularly useful for species that are otherwise poorly sampled, including ecologically important forage fishes. However, diet-based biomass indices may be sensitive to underlying ecological dynamics between predato...
Article
Full-text available
Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring d...
Article
Delta-models (a.k.a. hurdle models) are widely used to fit biomass samples that include zeros and a skewed response for positive catches, and spatio-temporal extensions of these models are increasingly used to quantify trends in abundance (i.e., estimate abundance indices). Previous research has shown estimated indices are proportional to changes i...
Article
Full-text available
Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of...
Article
Full-text available
Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of...
Article
Spatio-temporal models are increasingly used to develop indices of population abundance from fishery-dependent and –independent data. Developments in spatio-temporal index standardization were discussed at a workshop hosted by The Center for the Advancement of Population Assessment Methodology (CAPAM) titled “Development and application of spatio-t...
Article
Detecting and analyzing patterns of distribution shifts and range expansion/contraction is important to understand population dynamics and changes in stock status. Here, we develop a spatio‐temporal model for yellow croaker (Larimichthys polyactis), which was fitted to bottom trawl survey biomass data collected in the Yellow Sea in the winter of 20...
Article
Ocean management involves monitoring data that are used in biological models, where estimates inform policy choices. However, few science organizations publish results from a recurring, quantitative process to optimize effort spent measuring fish age. We propose that science organizations could predict the likely consequences of changing age-readin...
Article
The northern Bering Sea is transitioning from an Arctic to subarctic fish community as climate warms. Scientists and managers aim to understand how these changing conditions are influencing fish biomass and spatial distribution in this region, as both are used to inform stock assessments and fisheries management advice. Here, we use a spatio‐tempor...
Technical Report
Full-text available
The National Oceanic and Atmospheric Administration’s (NOAA) Deep Sea Coral Research and Technology Program convened a 4-day virtual science priorities workshop on May 12-15, 2020. The purpose of the workshop was to build partnerships and inform research priorities for the Program’s 4-year Alaska Deep-Sea Coral and Sponge Initiative (2020-2023). A...
Preprint
Full-text available
Marine biota is redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of d...
Article
Ecologists and oceanographers inform population and ecosystem management by identifying the physical drivers of ecological dynamics. However, different research communities use different analytical tools where, for example, physical oceanographers often apply rank‐reduction techniques (a.k.a. empirical orthogonal functions [EOF]) to identify indica...
Article
Full-text available
Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals, and sponges (DSCS). Related management decisions require information about...
Article
We describe and illustrate a spatio-temporal modelling approach for analyzing age-or size-specific catch-per-unit-effort (CPUE) data to develop indices of relative abundance and associated composition data. The approach is based on three concepts: 1) composition data that are used to determine the component of the population represented by the inde...
Article
Fisheries managers use biological reference points (BRPs) as targets or limits on fishing and biomass to maintain productive levels of fish stock biomass. There are multiple ways to calculate BRPs when biological parameters are time varying. Using summer flounder (Paralichthys dentatus) as a case study, we investigated time-varying approaches in co...
Article
Full-text available
Climate change is rapidly affecting the seasonal timing of spatial demographic processes. Consequently, resource managers require information from models that simultaneously measure seasonal, interannual, and spatial variation. We present a spatio-temporal model that includes annual, seasonal, and spatial variation in density and then highlight two...
Article
Accounting for variation in prey mortality and predator metabolic potential arising from spatial variation in consumption is an important task in ecology and resource management. However, there is no statistical method for processing stomach content data that accounts for fine‐scale spatio‐temporal structure while expanding individual stomach sampl...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Estimating fish condition, the relative weight of an individual fish given its body length, is a convenient way to relate the physiological health and energetic status of fishes to their productivity. Despite evidence of density-dependence effects on condition in some species, previous research has not jointly estimated synchronous changes in condi...
Article
Full-text available
Taiwan has a long history of fishery operations and contributes significantly to the global fishery harvest. The East and South China seas are important fishing grounds for which publicly available data are very limited. More efforts are needed to digitise and analyse historical catch rate data to illuminate species and community changes in this re...
Article
Fishing communities are increasingly required to adapt to environmentally driven changes in the availability of fish stocks. Here, we examined trends in the distribution and biomass of five commercial target species (dover sole, thornyheads, sablefish, lingcod, and petrale sole) on the US west coast to determine how their availability to fishing po...
Article
For stochastic growth processes, integrated mixed-effects (IME) models of capture-recapture data and size-at-age data from calcified structures such as otoliths can reduce bias in model parameters. Researchers have not fully explored the performance of IME models for simultaneously estimating the unknown ages, growth model parameters, and derived v...
Article
Multivariate data reduction techniques are widely used to describe modes of variability in atmospheric and oceanographic conditions for the world’s oceans. Dominant modes of variability such as the Pacific Decadal Oscillation (PDO) are typically defined as a statistical summary of physical measurements, and include both principle components represe...
Article
Characterizing population distribution and abundance over space and time is central to population ecology and conservation of natural populations. However, species distribution models and population dynamic models have rarely been integrated into a single modelling framework. Consequently, fine‐scale spatial heterogeneity is often ignored in resour...
Article
Fisheries scientists use biological models to determine sustainable fishing rates and forecast future dynamics. These models require both life‐history parameters (mortality, maturity, growth) and stock‐recruit parameters (juvenile production). However, there has been little research to simultaneously predict life‐history and stock‐recruit parameter...
Article
Full-text available
Species distribution models (SDMs) are a common approach to describing species’ space‐use and spatially‐explicit abundance. With a myriad of model types, methods and parameterization options available, it is challenging to make informed decisions about how to build robust SDMs appropriate for a given purpose. One key component of SDM development is...
Article
Determining how fish respond to variation in biotic and abiotic conditions is a crucial prerequisite to forecasting changes in productivity and spatial distribution of fish stocks and designing sustainable marine resource management strategies. In the present study, we investigated the physical and biological drivers of the spatio-temporal dynamics...
Article
Full-text available
Multispecies models are widely used to evaluate management trade‐offs arising from species interactions. However, identifying climate impacts and sensitive habitats requires integrating spatial heterogeneity and environmental impacts into multispecies models at fine spatial scales. We therefore develop a spatio‐temporal model of intermediate comple...
Article
Full-text available
Szuwalski argues that varying age structure can affect surplus production and that recruitment is a better metric of productivity. We explain how our null model controlled for age structure and other processes as explanations for the temperature-production relationship. Surplus production includes growth, recruitment, and other processes and provid...
Article
Studies that attempt to measure shifts in species distributions often consider a single species in isolation. However, understanding changes in spatial overlap between predators and their prey might provide deeper insight into how species redistribution affects food web dynamics. Here, we review a suite of 10 metrics [range overlap, area overlap, t...
Article
There are many methods available for estimating the current abundance of fish species. Design-based estimators, which assume random sampling within the sampling domain, have conventionally been used to provide relative indices of abundance. More recently, the use of spatiotemporal models has increased because of their ability to explicitly account...
Article
Summer flounder (Paralichthys dentatus) are an economically and ecologically important fish on the Northeast U.S. shelf. There is evidence that their spatial distribution has shifted over time. However, there are conflicting reports on the importance of various potential drivers of the shift. Here, we investigate whether the stock has shifted and t...
Article
Analysing how fish populations and their ecological communities respond to perturbations such as fishing and environmental variation is crucial to fisheries science. Researchers often predict fish population dynamics using species‐level life‐history parameters that are treated as fixed over time, while ignoring the impact of intraspecific variation...
Article
Length measurements from fishery catch can be used in data-limited assessments to estimate important population parameters to guide management, but results are highly sensitive to assumptions about biological information. Ideally, local life history studies inform biological parameters. In the absence of reliable local estimates, scientists and man...
Article
Full-text available
How to properly weight composition data is an important ongoing research topic for fisheries stock assessments, and multiple methods for weighting composition data have been developed. Although several studies indicated that properly accounting for time-varying selectivity can reduce estimation biases in population biomass and management-related qu...
Article
Full-text available
Spatiotemporal predictions of bycatch (i.e., catch of nontargeted species) have shown promise as dynamic ocean management tools for reducing bycatch. However, which spatiotemporal model framework to use for generating these predictions is unclear. We evaluated a relatively new method, Gaussian Markov random fields (GMRFs), with two other frameworks...
Article
Bayesian inference is an appealing alternative to maximum likelihood estimation, but estimation can be prohibitively long for integrated fisheries stock assessments. Here, we investigated potential causes of long run times including high dimensionality, complex model structure, and inefficient Bayesian algorithms for four US assessments written in...
Article
Full-text available
Oceanographers have spent decades developing annual indices that summarize physical conditions in marine ecosystems. Examples include the Pacific Decadal Oscillation, summarizing annual variation in the location of warm waters in the North Pacific, and cold‐pool extent (CPE), summarizing the area with cold near‐bottom waters in the eastern Bering S...
Article
Spatio-temporal models have become key tools for evaluating population trends and habitat usage. We developed a spatio-temporal modelling framework employing a combination of encounter/non-encounter, count, and biomass data collected by different monitoring programs (“combined data”). The three data types are predicted using a computationally effic...
Article
Climate change and fishery impacts modify the spatial distribution of marine species. Understanding and predicting changes in distribution is important for adaptation by fishers and the management of fishery resources and biodiversity. However, identifying such trends is challenging given the variability inherent in trawl survey data. We apply a no...
Article
Full-text available
Climate change is altering habitats for marine fishes and invertebrates, but the net effect of these changes on potential food production is unknown. We used temperature-dependent population models to measure the influence of warming on the productivity of 235 populations of 124 species in 38 ecoregions. Some populations responded significantly pos...
Article
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In the United States, implementation of strong legislative mandates and investments in scientific programmes have supported sustainable fisheries management for seafood production, marine ecosystems, and maritime communities and economies. Changing climate and ocean conditions present new and growing challenges that affect the ability to manage fis...
Article
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Fisheries scientists provide stock, ecosystem, habitat, and climate assessments to support interdisplinary fisheries management in the US and worldwide. These assessment activities have evolved different models, using different review standards, and are communicated using different vocabulary. Recent research shows that spatio-temporal models can e...