James T. Thorson - Academia.edu (original) (raw)

Papers by James T. Thorson

Ices Journal of Marine Science, Mar 7, 2022

Developing Species Distribution Models (SDM) for marine exploited species is a major challenge in... more 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 small number of spatial locations. Spatial monitoring of commercial data (based on logbooks crossed with Vessel Monitoring Systems) can provide an additional extensive data source to inform fish spatial distribution. We propose a spatial hierarchical framework integrating both data sources while accounting for preferential sampling (PS) of commercial data. From simulations, we demonstrate that PS should be accounted for in estimation when PS is actually strong. When commercial data far exceed scientific data, the later bring little information to spatial predictions in the areas sampled by commercial data, but bring information in areas with low fishing intensity and provide a validation dataset to assess the integrated model consistency. We applied the framework to three demersal species (hake, sole, and squids) in the Bay of Biscay that emphasize contrasted PS intensity and we demonstrate that the framework can account for several fleets with varying catchabilities and PS behaviours.

Canadian Journal of Fisheries and Aquatic Sciences, Nov 1, 2017

abundance index, delta-generalized linear mixed model, Gaussian random field, spatial modeling, s... more abundance index, delta-generalized linear mixed model, Gaussian random field, spatial modeling, size-structured assessment model https://mc06.manuscriptcentral.com/cjfas-pubs Canadian Journal of Fisheries and Aquatic Sciences Spatio-temporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine

Ices Journal of Marine Science, Feb 21, 2021

Diet-based annual biomass indices can potentially use predator stomach contents to provide inform... more 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 predators and prey, such as predator functional responses and changes in overlap in space and time. To evaluate these factors, we fit spatio-temporal models to stomach contents of five Atlantic herring (Clupea harengus) predators and survey catch data for predators and Atlantic herring. We identified drivers of variation in stomach contents, evaluated spatial patterns in stomach content data, and produced predator-specific indices of seasonal Atlantic herring biomass. After controlling for spatio-temporal processes and predator length, diet-based indices of biomass shared similar decadal trends but varied substantially between predators and seasons on shorter time scales. Diet-based indices reflected prey biomass more than prey availability, but weak correlations indicated that not all biological processes were controlled for. Results provide potential guidance for developing diet-based biomass indices and contribute to a body of evidence demonstrating the utility of predator diet data to provide information about relative prey biomass.

Frontiers in Marine Science

Species-distribution shifts are becoming commonplace due to climate-driven change. Difficult deci... more 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 unbalanced sampling data when estimating abundance indices used for stock assessment, but their performance in these contexts has received little research attention. We therefore seek to answer two questions: (1) how well can a spatio-temporal model estimate the proportion of abundance in a new “climate-adaptive” spatial stratum? and (2) when sampling must be reduced, does annual sampling at reduced density or biennial sampling result in better model-based abundance indices? We develop a spatially varying coefficient model in the R package VAST using the eastern Bering Sea (EBS) bottom trawl survey and its northern Bering Sea (NBS) extens...

The spatial distribution of marine fishes can change for many reasons including density-dependent... more The spatial distribution of marine fishes can change for many reasons including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model, PDM (no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model, BM (positive abundance–area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes. We fit a spatio-temporal model and estimate changes in effective area occupied and abundance, and combine results to estimate the average abundance–area relationship as well as variability among taxa and regions. The average relationship is weak but significant (0.6% increase in are...

Fish and Fisheries, 2021

Implementation of the United Nations Sustainable Development Goals requires assessments of the gl... more 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 highly uncertain. Numerous publications have produced estimates of the global status of these unassessed fisheries, but limited quantity and quality of data along with methodological differences have produced counterintuitive and conflicting results. Here, we show that despite numerous efforts, our understanding of the status of global fish stocks remains incomplete, even when new sources of broadly available data are added. Estimates of fish populations based primarily on catch histories on average performed 25% better than a random guess. But, on average, these methods assigned fisheries to the wrong FAO status category 57% of the time...

Fisheries Research, 2021

Abstract Survival is an important population process in fisheries stock assessment models and is ... more Abstract 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 survival deviations are generally treated as independent by age and year, despite our understanding that many population processes can be autocorrelated and that not accounting for autocorrelation can result in notable bias. We address these concerns, as well as the strong retrospective pattern found in the last assessment of Southern New England yellowtail flounder (Limanda ferruginea), by incorporating two-dimensional (2D, age and year) first-order autocorrelation in survival and M. We found that deviations were autocorrelated among both years (0.53 ± 0.09, 0.63 ± 0.16) and ages (0.33 ± 0.12, 0.40 ± 0.16) when estimated for survival or M, respectively. Models with 2D autocorrelation on survival or M fit the data better and had reduced retrospective pattern than models without autocorrelation. The best fit model included 2D autocorrelated deviations in survival as well as independent deviations in M and altered estimates of spawning stock biomass by 18 % and F by 21 % in model years. In short-term projections with F = 0, including 2D autocorrelation in survival or M reduced spawning stock biomass by 48 %. We conclude that incorporating 2D autocorrelated variation in survival or M could improve the assessment of Southern New England yellowtail flounder in terms of model fit and consistency of biomass projections.

Journal of Geophysical Research: Oceans, 2018

We used univariate and multivariate spatiotemporal delta models to quantify changes in the distri... more We used univariate and multivariate spatiotemporal delta models to quantify changes in the distribution of ichthyoplankton in the southern California Current System from 1951 to 2016. We focus on mesopelagic species, because they are most abundant, and on northern anchovy (Engraulis mordax), Pacific sardine (Sardinops sagax), and Pacific hake (Merluccius productus), because they are important commercial and forage fish species. Univariate models indicated that changes in the relative abundance, area occupied, center of gravity, and spatiotemporal variability of numerically dominant warm‐water and cool‐water‐associated mesopelagic ichthyoplankton show strong species‐specific differences. Multivariate models revealed that the warm‐water‐associated mesopelagic assemblage exhibits an increasing, nonmonotonic, secular trend of increasing relative abundance underlying interannual variability, suggesting a tropicalization of the southern California Current System. In contrast, the cool‐wat...

Science, 2019

Accounting for a warming oceanFisheries provide food and support livelihoods across the world. Th... more Accounting for a warming oceanFisheries provide food and support livelihoods across the world. They are also under extreme pressure, with many stocks overfished and poorly managed. Climate change will add to the burden fish stocks bear, but such impacts remain largely unknown. Freeet al.used temperature-specific models and hindcasting across fish stocks to determine the degree to which warming has, and will, affect fish species (see the Perspective by Plagányi). They found that an overall reduction in yield has occurred over the past 80 years. Furthermore, although some species are predicted to respond positively to warming waters, the majority will experience a negative impact on growth. As our world warms, responsible and active management of fisheries harvests will become even more important.Science, this issue p.979; see also p.930

Fisheries Research, 2017

Theoretical considerations and applied examples suggest that stock assessments are highly sensiti... more Theoretical considerations and applied examples suggest that stock assessments are highly sensitive to the weighting of different data sources whenever data sources conflict regarding parameter estimates. Previous iterative reweighting approaches to weighting compositional data are generally ad hoc, do not propagate uncertainty about data-weighting when calculating uncertainty intervals, and often are not readjusted when conducting sensitivity or retrospective analyses. We therefore incorporate the Dirichlet-multinomial distribution into Stock Synthesis, and propose it as a model-based method for estimating effective sample size. This distribution incorporates one additional parameter per fleet (with the option of mirroring its value among fleets), and we show that this parameter governs the ratio of nominal ("input") and effective ("output") sample size. We demonstrate this approach using data for Pacific hake, where the Dirichlet-multinomial distribution and an iterative reweighting approach previously developed by McAllister and Ianelli (1997) give similar results. We also use simulation testing to explore the estimation properties of this new estimator, and show that it provides approximately unbiased estimates of variance inflation when compositional samples capture clusters of individuals with similar ages/lengths. We conclude by recommending further research to develop computationally efficient estimators of effective sample size that are based on alternative, a priori consideration of sampling theory and population biology.

Canadian Journal of Fisheries and Aquatic Sciences, 2019

Selectivity is a key parameter in stock assessments that describes how fisheries interact with di... more Selectivity is a key parameter in stock assessments that describes how fisheries interact with different ages and sizes of fish. It is usually confounded with other processes (e.g., natural mortality and recruitment) in stock assessments and the assumption of selectivity can strongly affect stock assessment outcome. Here, we introduce a new semi-parametric selectivity method, which we implement and test in Stock Synthesis. This selectivity method includes a parametric component and an autocorrelated nonparametric component consisting of deviations from the parametric component. We explore the new selectivity method using two simulation experiments, which show that the two autocorrelation parameters for selectivity deviations of data-rich fisheries are estimable using either mixed-effect or simpler sample-based algorithms. When selectivity deviations of a data-rich fishery are highly autocorrelated, using the new method to estimate the two autocorrelation parameters leads to more pre...

Conservation Letters, 2017

The exploitation status of marine fisheries stocks worldwide is of critical importance for food s... more The exploitation status of marine fisheries stocks worldwide is of critical importance for food security, ecosystem conservation, and fishery sustainability. Applying a suite of data-limited methods to global catch data, combined through an ensemble modeling approach, we provide quantitative estimates of exploitation status for 785 fish stocks. Fifty-three percent (414 stocks) are below B MSY and of these, 265 are estimated to be below 80% of the B MSY level. While the 149 stocks above 80% of B MSY are conventionally considered "fully exploited," stocks staying at this level for many years, forego substantial yield. Our results enable managers to consider more detailed information than simply a categorization of stocks as "fully" or "over" exploited. Our approach is reproducible, allows consistent application to a broad range of stocks, and can be easily updated as new data become available. Applied on an ongoing basis, this approach can provide critical, more detailed information for resource management for more exploited fish stocks than currently available.

ICES Journal of Marine Science, 2017

Several approaches have been developed over the last decade to simultaneously estimate distributi... more Several approaches have been developed over the last decade to simultaneously estimate distribution or density for multiple species (e.g. “joint species distribution” or “multispecies occupancy” models). However, there has been little research comparing estimates of abundance trends or distribution shifts from these multispecies models with similar single-species estimates. We seek to determine whether a model including correlations among species (and particularly species that may affect habitat quality, termed “biogenic habitat”) improves predictive performance or decreases standard errors for estimates of total biomass and distribution shift relative to similar single-species models. To accomplish this objective, we apply a vector-autoregressive spatio-temporal (VAST) model that simultaneously estimates spatio-temporal variation in density for multiple species, and present an application of this model using data for eight US Pacific Coast rockfishes (Sebastes spp.), thornyheads (S...

Environmental Development, 2016

Global consumption of aquatic food products has increased steadily in recent years, but regional ... more Global consumption of aquatic food products has increased steadily in recent years, but regional differences in availability and utilization of marine resources between developed and developing countries signal an important issue in global food security. Understanding the prospects for sustainable production potential from the seas is particularly important, given the likelihood of increasing demands for animal protein to meet the needs of a burgeoning human population. In this chapter, updated estimates of global fishery production potential from marine fisheries are provided to place the prospects for meeting human needs for protein and essential micronutrients into context. Satellite-based estimates of primary productivity by plankton size classes, and a more complete food web than in earlier approaches, were used to estimate marine ecosystem productivity. LMEs were designated as strata for the analyses. Inland seas and high-latitude LMEs were excluded from the study. Production estimates for the major functional groups that are important for current or potential fisheries are provided for each LME. Results showed an overall fishery production potential of 180 million tonnes per year and an additional 50 million tonnes per year of benthos for the LMEs included in the analysis. This prototype analysis is illustrative and further work is needed to refine these figures.

ICES Journal of Marine Science, 2014

Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary ... more Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary over time, but it is challenging to estimate the magnitude of time-variation of demographic parameters in population dynamics models, particularly when using penalized-likelihood estimation approaches. Random-effect approaches can estimate the variance, but are computationally infeasible or not implemented for many models and software packages. We show that existing models and software based on penalized-likelihood can be used to calculate the Laplace approximation to the marginal likelihood of parameters representing variability over time, and specifically demonstrate this approach via application to Stock Synthesis. Using North Sea cod and Pacific hake models as case studies, we show that this method has little bias in estimating variances for simulated data. It also provides a similar estimate of variability in hake recruitment (log-SD = 1.43) to that obtained from Markov chain Monte ...

Ices Journal of Marine Science, Apr 17, 2019

In the United States, implementation of strong legislative mandates and investments in scientific... more 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 fisheries. To better prepare for and respond to these Published by International Council for the Exploration of the Sea 2019. This work is written by US Government employees and is in the public domain in the US.

Authorea (Authorea), Oct 21, 2020

Understanding range edges is key to addressing fundamental biogeographic questions about abiotic ... more Understanding range edges is key to addressing fundamental biogeographic questions about abiotic and biotic drivers of species distributions. Range edges are where colonization and extirpation happen, so their dynamics are also important for natural resource management and conservation. We quantified positions for 153 range edges of marine fishes and invertebrates from three US continental shelf regions using decades of survey data and a spatiotemporal model to account for changes in survey design. We analyzed whether range edges maintained their edge thermal niches-temperature extremes at the range edgeover time. Most range edges (86%) maintained either cold or warm temperature extremes; 73% maintained both. However, the substantial fraction of range edges that altered their thermal niche underscore the multiplicity of relevant drivers. This study suggests that temperate marine species largely maintained their edge thermal niches during rapid change and provides a blueprint for testing temperature tracking of species range edges.

ICES Journal of Marine Science

Multispecies models have existed in a fisheries context since at least the 1970s, but despite muc... more 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 ecosystem-based fisheries management, the lack of more regular operational use is both surprising and compelling. We identify impediments hampering the regular operational use of multispecies models and provide recommendations to address those impediments. These recommendations are: (1) engage stakeholders and managers early and often; (2) improve messaging and communication about the various uses of multispecies models; (3) move forward with multispecies management under current authorities while exploring more inclusive governance structures and flexible decision-making frameworks for handling tradeoffs; (4) evaluate when a multispecies model...

ICES Journal of Marine Science

Weighting data appropriately in stock assessment models is necessary to diagnose model mis-specif... more 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 alternative that estimates an additional parameter and thereby “self-weights” data. However, the DM likelihood requires specifying an input sample size (ninput), which is often unavailable and results are sensitive to ninput. We therefore introduce the multivariate-Tweedie (MVTW) as alternative with three benefits: (1) it can identify both overdispersion (downweighting) or underdispersion (upweighting) relative to the ninput; (2) proportional changes in ninput are exactly offset by parameters; and (3) it arises naturally when expanding data arising from a hierarchical sampling design. We use an age-structured simulation to show that the MVTW (1...

Ices Journal of Marine Science, Mar 7, 2022

Developing Species Distribution Models (SDM) for marine exploited species is a major challenge in... more 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 small number of spatial locations. Spatial monitoring of commercial data (based on logbooks crossed with Vessel Monitoring Systems) can provide an additional extensive data source to inform fish spatial distribution. We propose a spatial hierarchical framework integrating both data sources while accounting for preferential sampling (PS) of commercial data. From simulations, we demonstrate that PS should be accounted for in estimation when PS is actually strong. When commercial data far exceed scientific data, the later bring little information to spatial predictions in the areas sampled by commercial data, but bring information in areas with low fishing intensity and provide a validation dataset to assess the integrated model consistency. We applied the framework to three demersal species (hake, sole, and squids) in the Bay of Biscay that emphasize contrasted PS intensity and we demonstrate that the framework can account for several fleets with varying catchabilities and PS behaviours.

Canadian Journal of Fisheries and Aquatic Sciences, Nov 1, 2017

abundance index, delta-generalized linear mixed model, Gaussian random field, spatial modeling, s... more abundance index, delta-generalized linear mixed model, Gaussian random field, spatial modeling, size-structured assessment model https://mc06.manuscriptcentral.com/cjfas-pubs Canadian Journal of Fisheries and Aquatic Sciences Spatio-temporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine

Ices Journal of Marine Science, Feb 21, 2021

Diet-based annual biomass indices can potentially use predator stomach contents to provide inform... more 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 predators and prey, such as predator functional responses and changes in overlap in space and time. To evaluate these factors, we fit spatio-temporal models to stomach contents of five Atlantic herring (Clupea harengus) predators and survey catch data for predators and Atlantic herring. We identified drivers of variation in stomach contents, evaluated spatial patterns in stomach content data, and produced predator-specific indices of seasonal Atlantic herring biomass. After controlling for spatio-temporal processes and predator length, diet-based indices of biomass shared similar decadal trends but varied substantially between predators and seasons on shorter time scales. Diet-based indices reflected prey biomass more than prey availability, but weak correlations indicated that not all biological processes were controlled for. Results provide potential guidance for developing diet-based biomass indices and contribute to a body of evidence demonstrating the utility of predator diet data to provide information about relative prey biomass.

Frontiers in Marine Science

Species-distribution shifts are becoming commonplace due to climate-driven change. Difficult deci... more 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 unbalanced sampling data when estimating abundance indices used for stock assessment, but their performance in these contexts has received little research attention. We therefore seek to answer two questions: (1) how well can a spatio-temporal model estimate the proportion of abundance in a new “climate-adaptive” spatial stratum? and (2) when sampling must be reduced, does annual sampling at reduced density or biennial sampling result in better model-based abundance indices? We develop a spatially varying coefficient model in the R package VAST using the eastern Bering Sea (EBS) bottom trawl survey and its northern Bering Sea (NBS) extens...

The spatial distribution of marine fishes can change for many reasons including density-dependent... more The spatial distribution of marine fishes can change for many reasons including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model, PDM (no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model, BM (positive abundance–area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes. We fit a spatio-temporal model and estimate changes in effective area occupied and abundance, and combine results to estimate the average abundance–area relationship as well as variability among taxa and regions. The average relationship is weak but significant (0.6% increase in are...

Fish and Fisheries, 2021

Implementation of the United Nations Sustainable Development Goals requires assessments of the gl... more 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 highly uncertain. Numerous publications have produced estimates of the global status of these unassessed fisheries, but limited quantity and quality of data along with methodological differences have produced counterintuitive and conflicting results. Here, we show that despite numerous efforts, our understanding of the status of global fish stocks remains incomplete, even when new sources of broadly available data are added. Estimates of fish populations based primarily on catch histories on average performed 25% better than a random guess. But, on average, these methods assigned fisheries to the wrong FAO status category 57% of the time...

Fisheries Research, 2021

Abstract Survival is an important population process in fisheries stock assessment models and is ... more Abstract 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 survival deviations are generally treated as independent by age and year, despite our understanding that many population processes can be autocorrelated and that not accounting for autocorrelation can result in notable bias. We address these concerns, as well as the strong retrospective pattern found in the last assessment of Southern New England yellowtail flounder (Limanda ferruginea), by incorporating two-dimensional (2D, age and year) first-order autocorrelation in survival and M. We found that deviations were autocorrelated among both years (0.53 ± 0.09, 0.63 ± 0.16) and ages (0.33 ± 0.12, 0.40 ± 0.16) when estimated for survival or M, respectively. Models with 2D autocorrelation on survival or M fit the data better and had reduced retrospective pattern than models without autocorrelation. The best fit model included 2D autocorrelated deviations in survival as well as independent deviations in M and altered estimates of spawning stock biomass by 18 % and F by 21 % in model years. In short-term projections with F = 0, including 2D autocorrelation in survival or M reduced spawning stock biomass by 48 %. We conclude that incorporating 2D autocorrelated variation in survival or M could improve the assessment of Southern New England yellowtail flounder in terms of model fit and consistency of biomass projections.

Journal of Geophysical Research: Oceans, 2018

We used univariate and multivariate spatiotemporal delta models to quantify changes in the distri... more We used univariate and multivariate spatiotemporal delta models to quantify changes in the distribution of ichthyoplankton in the southern California Current System from 1951 to 2016. We focus on mesopelagic species, because they are most abundant, and on northern anchovy (Engraulis mordax), Pacific sardine (Sardinops sagax), and Pacific hake (Merluccius productus), because they are important commercial and forage fish species. Univariate models indicated that changes in the relative abundance, area occupied, center of gravity, and spatiotemporal variability of numerically dominant warm‐water and cool‐water‐associated mesopelagic ichthyoplankton show strong species‐specific differences. Multivariate models revealed that the warm‐water‐associated mesopelagic assemblage exhibits an increasing, nonmonotonic, secular trend of increasing relative abundance underlying interannual variability, suggesting a tropicalization of the southern California Current System. In contrast, the cool‐wat...

Science, 2019

Accounting for a warming oceanFisheries provide food and support livelihoods across the world. Th... more Accounting for a warming oceanFisheries provide food and support livelihoods across the world. They are also under extreme pressure, with many stocks overfished and poorly managed. Climate change will add to the burden fish stocks bear, but such impacts remain largely unknown. Freeet al.used temperature-specific models and hindcasting across fish stocks to determine the degree to which warming has, and will, affect fish species (see the Perspective by Plagányi). They found that an overall reduction in yield has occurred over the past 80 years. Furthermore, although some species are predicted to respond positively to warming waters, the majority will experience a negative impact on growth. As our world warms, responsible and active management of fisheries harvests will become even more important.Science, this issue p.979; see also p.930

Fisheries Research, 2017

Theoretical considerations and applied examples suggest that stock assessments are highly sensiti... more Theoretical considerations and applied examples suggest that stock assessments are highly sensitive to the weighting of different data sources whenever data sources conflict regarding parameter estimates. Previous iterative reweighting approaches to weighting compositional data are generally ad hoc, do not propagate uncertainty about data-weighting when calculating uncertainty intervals, and often are not readjusted when conducting sensitivity or retrospective analyses. We therefore incorporate the Dirichlet-multinomial distribution into Stock Synthesis, and propose it as a model-based method for estimating effective sample size. This distribution incorporates one additional parameter per fleet (with the option of mirroring its value among fleets), and we show that this parameter governs the ratio of nominal ("input") and effective ("output") sample size. We demonstrate this approach using data for Pacific hake, where the Dirichlet-multinomial distribution and an iterative reweighting approach previously developed by McAllister and Ianelli (1997) give similar results. We also use simulation testing to explore the estimation properties of this new estimator, and show that it provides approximately unbiased estimates of variance inflation when compositional samples capture clusters of individuals with similar ages/lengths. We conclude by recommending further research to develop computationally efficient estimators of effective sample size that are based on alternative, a priori consideration of sampling theory and population biology.

Canadian Journal of Fisheries and Aquatic Sciences, 2019

Selectivity is a key parameter in stock assessments that describes how fisheries interact with di... more Selectivity is a key parameter in stock assessments that describes how fisheries interact with different ages and sizes of fish. It is usually confounded with other processes (e.g., natural mortality and recruitment) in stock assessments and the assumption of selectivity can strongly affect stock assessment outcome. Here, we introduce a new semi-parametric selectivity method, which we implement and test in Stock Synthesis. This selectivity method includes a parametric component and an autocorrelated nonparametric component consisting of deviations from the parametric component. We explore the new selectivity method using two simulation experiments, which show that the two autocorrelation parameters for selectivity deviations of data-rich fisheries are estimable using either mixed-effect or simpler sample-based algorithms. When selectivity deviations of a data-rich fishery are highly autocorrelated, using the new method to estimate the two autocorrelation parameters leads to more pre...

Conservation Letters, 2017

The exploitation status of marine fisheries stocks worldwide is of critical importance for food s... more The exploitation status of marine fisheries stocks worldwide is of critical importance for food security, ecosystem conservation, and fishery sustainability. Applying a suite of data-limited methods to global catch data, combined through an ensemble modeling approach, we provide quantitative estimates of exploitation status for 785 fish stocks. Fifty-three percent (414 stocks) are below B MSY and of these, 265 are estimated to be below 80% of the B MSY level. While the 149 stocks above 80% of B MSY are conventionally considered "fully exploited," stocks staying at this level for many years, forego substantial yield. Our results enable managers to consider more detailed information than simply a categorization of stocks as "fully" or "over" exploited. Our approach is reproducible, allows consistent application to a broad range of stocks, and can be easily updated as new data become available. Applied on an ongoing basis, this approach can provide critical, more detailed information for resource management for more exploited fish stocks than currently available.

ICES Journal of Marine Science, 2017

Several approaches have been developed over the last decade to simultaneously estimate distributi... more Several approaches have been developed over the last decade to simultaneously estimate distribution or density for multiple species (e.g. “joint species distribution” or “multispecies occupancy” models). However, there has been little research comparing estimates of abundance trends or distribution shifts from these multispecies models with similar single-species estimates. We seek to determine whether a model including correlations among species (and particularly species that may affect habitat quality, termed “biogenic habitat”) improves predictive performance or decreases standard errors for estimates of total biomass and distribution shift relative to similar single-species models. To accomplish this objective, we apply a vector-autoregressive spatio-temporal (VAST) model that simultaneously estimates spatio-temporal variation in density for multiple species, and present an application of this model using data for eight US Pacific Coast rockfishes (Sebastes spp.), thornyheads (S...

Environmental Development, 2016

Global consumption of aquatic food products has increased steadily in recent years, but regional ... more Global consumption of aquatic food products has increased steadily in recent years, but regional differences in availability and utilization of marine resources between developed and developing countries signal an important issue in global food security. Understanding the prospects for sustainable production potential from the seas is particularly important, given the likelihood of increasing demands for animal protein to meet the needs of a burgeoning human population. In this chapter, updated estimates of global fishery production potential from marine fisheries are provided to place the prospects for meeting human needs for protein and essential micronutrients into context. Satellite-based estimates of primary productivity by plankton size classes, and a more complete food web than in earlier approaches, were used to estimate marine ecosystem productivity. LMEs were designated as strata for the analyses. Inland seas and high-latitude LMEs were excluded from the study. Production estimates for the major functional groups that are important for current or potential fisheries are provided for each LME. Results showed an overall fishery production potential of 180 million tonnes per year and an additional 50 million tonnes per year of benthos for the LMEs included in the analysis. This prototype analysis is illustrative and further work is needed to refine these figures.

ICES Journal of Marine Science, 2014

Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary ... more Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary over time, but it is challenging to estimate the magnitude of time-variation of demographic parameters in population dynamics models, particularly when using penalized-likelihood estimation approaches. Random-effect approaches can estimate the variance, but are computationally infeasible or not implemented for many models and software packages. We show that existing models and software based on penalized-likelihood can be used to calculate the Laplace approximation to the marginal likelihood of parameters representing variability over time, and specifically demonstrate this approach via application to Stock Synthesis. Using North Sea cod and Pacific hake models as case studies, we show that this method has little bias in estimating variances for simulated data. It also provides a similar estimate of variability in hake recruitment (log-SD = 1.43) to that obtained from Markov chain Monte ...

Ices Journal of Marine Science, Apr 17, 2019

In the United States, implementation of strong legislative mandates and investments in scientific... more 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 fisheries. To better prepare for and respond to these Published by International Council for the Exploration of the Sea 2019. This work is written by US Government employees and is in the public domain in the US.

Authorea (Authorea), Oct 21, 2020

Understanding range edges is key to addressing fundamental biogeographic questions about abiotic ... more Understanding range edges is key to addressing fundamental biogeographic questions about abiotic and biotic drivers of species distributions. Range edges are where colonization and extirpation happen, so their dynamics are also important for natural resource management and conservation. We quantified positions for 153 range edges of marine fishes and invertebrates from three US continental shelf regions using decades of survey data and a spatiotemporal model to account for changes in survey design. We analyzed whether range edges maintained their edge thermal niches-temperature extremes at the range edgeover time. Most range edges (86%) maintained either cold or warm temperature extremes; 73% maintained both. However, the substantial fraction of range edges that altered their thermal niche underscore the multiplicity of relevant drivers. This study suggests that temperate marine species largely maintained their edge thermal niches during rapid change and provides a blueprint for testing temperature tracking of species range edges.

ICES Journal of Marine Science

Multispecies models have existed in a fisheries context since at least the 1970s, but despite muc... more 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 ecosystem-based fisheries management, the lack of more regular operational use is both surprising and compelling. We identify impediments hampering the regular operational use of multispecies models and provide recommendations to address those impediments. These recommendations are: (1) engage stakeholders and managers early and often; (2) improve messaging and communication about the various uses of multispecies models; (3) move forward with multispecies management under current authorities while exploring more inclusive governance structures and flexible decision-making frameworks for handling tradeoffs; (4) evaluate when a multispecies model...

ICES Journal of Marine Science

Weighting data appropriately in stock assessment models is necessary to diagnose model mis-specif... more 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 alternative that estimates an additional parameter and thereby “self-weights” data. However, the DM likelihood requires specifying an input sample size (ninput), which is often unavailable and results are sensitive to ninput. We therefore introduce the multivariate-Tweedie (MVTW) as alternative with three benefits: (1) it can identify both overdispersion (downweighting) or underdispersion (upweighting) relative to the ninput; (2) proportional changes in ninput are exactly offset by parameters; and (3) it arises naturally when expanding data arising from a hierarchical sampling design. We use an age-structured simulation to show that the MVTW (1...