James T Thorson

Alaska Fisheries Science Center · Resource Ecology and Fisheries Management

Species’ ranges are shifting in response to increasing temperature and decreasing oxygen in coastal oceans. Forecasting these shifts is limited by information on physiological oxygen thresholds and how they depend on temperature. Here, we adopt an ecophysiological metric, the metabolic index, and estimate its parameters from data collected on marin...

Understanding how ecosystem change influences fishery resources through trophic pathways is a key tenet of ecosystem‐based fishery management. System models (SM), which use numerical modeling to describe physical and biological processes, can advance inclusion of ecosystem and prey information in fisheries management; however, incorporating SMs in...

Mass-balance ecosystem models including Ecopath with Ecosim (EwE) are widely used tools for analyzing aquatic ecosystems to support strategic ecosystem-based management. These models are typically developed by first tuning unknown parameters to achieve mass balance (termed “Ecopath”), then projecting dynamics over time (“Ecosim”) while sometimes tu...

Marine fishes are heterogeneously distributed across their ranges according to population dynamics governed by complex spatiotemporal relationships between ontogenetic habitat usage, species interactions, environmental variability, and harvest patterns. However, few stock assessments incorporate spatial population structure in the determination of...

Hierarchical models can express ecological dynamics using a combination of fixed and random effects, and measurement of their complexity (effective degrees of freedom, EDF) requires estimating how much random effects are shrunk toward a shared mean. Estimating EDF is helpful to (1) penalize complexity during model selection and (2) to improve under...

1. In the face of biodiversity loss worldwide, it is paramount to quantify species’ extinction risk to guide conservation efforts. The International Union for the Conservation of Nature (IUCN)’s Red List is considered the global standard for evaluating extinction risks. IUCN criteria also inform national extinction risk assessments. Bayesian models...

Ecological analyses typically involve many interacting variables. Ecologists often specify lagged interactions in community dynamics (i.e. vector‐autoregressive models) or simultaneous interactions (e.g. structural equation models), but there is less familiarity with dynamic structural equation models (DSEM) that can include any simultaneous or lag...

Scientific bottom-trawl surveys are ecological observation programs conducted along continental shelves and slopes of seas and oceans that sample marine communities associated with the seafloor. These surveys report taxa occurrence, abundance and/or weight in space and time, and contribute to fisheries management as well as population and biodivers...

Indices of abundance based on fishery catch-per-unit-effort (CPUE) are important components of many stock assessments, particularly when fishery-independent surveys are unavailable. Standardizing CPUE to develop indices that better reflect the relative abundance requires the analyst to make numerous decisions, which are influenced by factors that i...

Species distribution models (SDMs) are an important tool for conservation and resource management. However, managers are often interested in derived quantities such as range or area occupied, and how these are calculated can have a large impact. Ecosystem‐based management typically requires spatial information about species distributions, which is...

Accounting for marine stocks spatiotemporal complexity has become one of the most pressing improvements that should be added to the new generation of stock assessment. Disentangling persistent and dynamic population subcomponents and understanding their main drivers of variation are still stock-specific challenges. Here, we hypothesized that the sp...

Scientific bottom-trawl surveys are ecological observation programs conducted along continental shelves and slopes of seas and oceans that sample marine communities associated with the seafloor. These surveys report taxa occurrence, abundance and/or weight in space and time, and contribute to fisheries management as well as population and biodivers...

Designing effective spatial management strategies is challenging because marine ecosystems are highly dynamic and opaque, and extractive entities such as fishing fleets respond endogenously to ecosystem changes in ways that depend on ecological and policy context. We present a modelling framework, marlin , that can be used to efficiently simulate t...

Fisheries scientists compare processes among species to estimate species productivity, management reference points, and climate sensitivities. Ecologists have developed “phylogenetic comparative methods” (PCMs) to address these questions, but there is surprisingly little application of PCM within fisheries science. Here, I bridge this gap by introd...

Phylogenetic comparative methods (PCMs) can be used to study evolutionary relationships and trade-offs among species traits. Analysts using PCM may want to (1) include latent variables, (2) estimate complex trait interdependencies, (3) predict missing trait values, (4) condition predicted traits upon phylogenetic correlations and (5) estimate relat...

Changing distribution and abundance of small pelagic fishes may drive changes in predator distributions, affecting predator availability to fisheries and surveys. However, small pelagics are difficult to survey directly, so we developed a novel method of assessing the aggregate abundance of 21 small pelagic forage taxa via predator stomach contents...

Many demographic processes vary by age and over time, but are also hypothesized to exhibit cohort-specific patterns in variation; accounting for this variation within fisheries management remains a key challenge for contemporary stock assessments. Although there is evidence for time, age, and cohort-specific patterns in the variation of various com...

Marine heatwaves have been linked to negative ecological effects in recent decades1,2. If marine heatwaves regularly induce community reorganization and biomass collapses in fishes, the consequences could be catastrophic for ecosystems, fisheries and human communities3,4. However, the extent to which marine heatwaves have negative impacts on fish b...

State-space assessment models (SSMs) ha v e garnered attention recently because of their ability to estimate time variation in biological and fisheries processes such as recr uitment, nat ural mort alit y, catchabilit y, and selectivit y. Ho w e v er, current SSMs cannot model time-varying growth internally nor accept length data, limiting their us...

In many situations, species distribution models need to make use of multiple data sources to address their objectives. We developed a spatio-temporal modelling framework that integrates research survey data and data collected by observers onboard fishing vessels while accounting for physical barriers (islands, convoluted coastlines). We demonstrate...

Many economic sectors rely on marine ecosystem services, and holistic management is necessary to evaluate trade-offs between sectors and facilitate sustainable use. Integrated ecosystem assessments (IEA) integrate system components so that managers can evaluate pathways to achieve desired goals. Indicators are a central element of IEAs and capture...

Producers and users contributing to diverse scientific enterprises are often siloed. FISHGLOB is a sociotechnical infrastructure supporting collaboration and data sharing between experts in, and users of, fish bottom trawl surveys, a form of ocean monitoring.

Attached is a presentation to PICES 2022 of this work.

NOW AVAILABLE ONLINE @ https://www.int-res.com/abstracts/MEPS/SPF2/p_av2/: Trophic interactions are proximate drivers of ecosystem function, including predator-prey dynamics, and their spatio-temporal variability may reflect ecosystem shifts and changes in trophic transfer. We investigated biogeographic structuring of trophic interactions by anal...

Species-distribution shifts are becoming commonplace due to climate-driven change. Difficult decisions to modify survey extent and frequency are often made due to this change and constraining survey budgets. This often leads to spatially and temporally unbalanced survey coverage. Spatio-temporal models are increasingly used to account for spatially...

Spatio-temporal models are widely applied to standardise research survey data and are increasingly used to generate density maps and indices from other data sources. We developed a spatio-temporal modelling framework that integrates research survey data (treated as a “reference dataset”) and other data sources (“non-reference datasets”) while estim...

Many mobile marine taxa are changing their distributions in response to climate change. Such movements pose a challenge to fisheries monitoring and management, particularly in systems where climate‐adaptive and ecosystem‐based management objectives are emphasized. While shifts in species distributions can be discerned from long‐term fisheries‐indep...

Species distribution models (SDMs) are widely used to relate species occurrence and density to local environmental conditions, and often include a spatially correlated variable to account for spatial patterns in residuals. Ecologists have extended SDMs to include spatially varying coefficients (SVCs), where the response to a given covariate varies...

Traits underlie organismal responses to their environment and are essential to predict community responses to environmental conditions under global change. Species differ in life‐history traits, morphometrics, diet type, reproductive characteristics and habitat utilization. Trait associations are widely analysed using phylogenetic comparative metho...

Introduction Seabirds are abundant, conspicuous members of marine ecosystems worldwide. Synthesis of distribution data compiled over time is required to address regional management issues and understand ecosystem change. Major challenges when estimating seabird densities at sea arise from variability in dispersion of the birds, sampling effort over...

Multispecies models have existed in a fisheries context since at least the 1970s, but despite much exploration, advancement, and consideration of multispecies models, there remain limited examples of their operational use in fishery management. Given that species and fleet interactions are inherently multispecies problems and the push towards ecosy...

Environmental conditions can create spatial and temporal variability in growth and distribution processes, yet contemporary stock assessment methods often do not explicitly address the consequences of these patterns. For example, stock assessments often assume that body weight-at-age (i.e. size) is constant across the stocks’ range, and may thereby...

Spatio-temporal modelling frameworks are important tools for evaluating changes in the population structure of freshwater species, to inform population assessments. However, in the stream networks occupied by freshwater species, two data points in space are more related by physical connectivity than by straight-line, Euclidian distance. Therefore,...

Aim There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, evidence for whether the effects of within‐trophic‐level biotic interactions (e.g. competition and heterospecific attraction) are dis...

Generating accurate data for stock assessments is resource-demanding, necessitating periodic evaluation of survey sampling designs and potential impacts on stock assessments. We developed a framework for bootstrapped resampling of survey age data and calculation of input sample sizes as a function of among-bootstrap variance in age compositions. Da...

Weighting data appropriately in stock assessment models is necessary to diagnose model mis-specification, estimate uncertainty, and when combining data sets. Age- and length-composition data are often fitted using a multinomial distribution and then reweighted iteratively, and the Dirichlet-multinomial (“DM”) likelihood provides a model-based alter...

Marine population modeling, which underpins the scientific advice to support fisheries interventions, is an active research field with recent advancements to address modern challenges (e.g., climate change) and enduring issues (e.g., data limitations). Based on discussions during the ‘Land of Plenty’ session at the 2021 World Fisheries Congress, we...

Although species distribution models (SDMs) are commonly used to hindcast fine‐scale population metrics, there remains a paucity of information about how well these models predict future responses to climate. Many conventional SDMs rely on spatially‐explicit but time‐invariant conditions to quantify species distributions and densities. We compared...

The spatial distributions of marine fish populations are influenced by environmental conditions, intrinsic properties of the populations, and prior distribution. The influence of these factors may not be consistent across age classes. For this study, age composition estimates for walleye pollock (Gadus chalcogrammus) collected on bottom-trawl surve...

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...

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...

Shifts in the distribution of groundfish species as oceans warm can complicate management efforts if species distributions expand beyond the extent of existing scientific surveys, changing the proportion of groundfish available to any one survey each year. We developed the first-ever model-based biomass estimates for three Bering Sea groundfishes (...

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, for example, highly parameterized models or prior transforma...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...