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Thorson, J. T.

Publications and source records attributed to Thorson, J. T..

7 recordsLinked to original sources

Diffusion-enhanced spatio-temporal models for estimating spatial expansion

Spatial expansion is a common feature of many ecological processes, including biological invasions, range shifts, population recovery, and the spread of pathogens and human activities. Although such expansion often arises from diffusive processes, there remain few general statistical methods to quantify these dynamics. Here, we present a diffusion-enhanced spatio-temporal model (DESTM) that approximates diffusive process using Gaussian Markov random fields (GMRF). The model works by incorporating the statistical interaction between spatial diffusion and temporal lags into a joint precision structure of the latent field. To demonstrate, we simulate data from a diffusion movement process using a continuous-time Markov chain (CTMC), and then approximate this mechanistic process using the DESTM. We show that separable spatio-temporal models can lead to large bias in estimates of the local density. In contrast, the DESTM did not appear to bias inferences, and reverts to the separable model when diffusion is not apparent. Finally, we apply the model to two large-scale examples of spatial expansion: (1) the historical spread of the Japanese distant-water longline fleet across the Pacific, representing anthropogenic spatial expansion in the ocean, and (2) the recovery and geographic expansion of Bald Eagle populations across North America. Estimates from both case studies, supported by model comparisons and ecological plausibility, suggest that the DESTM provides a better description of the underlying expansion dynamics, although improvements in forecast performance were more apparent for the Japanese longline fleet. We highlight that the model provides a fast and efficient framework for modeling spatial expansion dynamics, with the potential to represent increasingly complex ecological dynamics through future extensions. We propose that future research explore this framework as a quantitative tool to explain how spatial expansion occurs.

ecology↗

Dynamic structural equation models for ecosystem-based fisheries management: case studies and a practical guide

Once central challenge in adopting ecosystem-based fisheries management (EBFM) is understanding and predicting the interconnected processes, feedbacks, and temporal dependencies that characterize ecosystem dynamics. Structural equation models and structural causal models (SEM and SCM) quantify interconnected relationships and evaluate causality from observational data but cannot readily accommodate the incomplete and irregularly sampled data typical of complex systems. Dynamic structural equation models (DSEM) estimate SEMs but accommodate lagged effects, missing data, and non-linear and non-stationary effects. However, there is little guidance regarding how DSEM can be used to support EBFM, particularly within governance and decision-making contexts. Here, we present three case studies that highlight distinct inferential goals for understanding ecosystem processes in the context of EBFM. First, we quantify ecosystem-level indicators to support monitoring of climate-driven ecosystem changes. Second, we examine whether hypothesized direct and indirect ecosystem linkages improve predictions of recruitment. Finally, we compare support for hypotheses of causal drivers of fish productivity. To provide practical advice, we synthesize lessons learned into a workflow to for others navigating DSEM. We suggest that the first step is identifying the inferential objective, which establishes the foundation for the remainder of the workflow, guiding the development of graphical models, model specification, and the selection of statistical and scientific validation steps (e.g., testing conditional independencies) needed to evaluate hypothesized causal relationships. By integrating observational data, expert knowledge, and mechanistic hypotheses within a unified framework, DSEM is a powerful tool for advancing EBFM, and more broadly, understanding the processes that govern complex ecosystems.

ecology↗

AI for Fisheries Science: Neural Network Tools for Forecasting, Spatial Standardization, and Policy Optimization

The development of Artificial Intelligence (AI) presents novel opportunities for tackling complex marine resource management challenges. Among AI models, neural networks are a powerful class of tools capable of learning nonlocal and lagged patterns from fisheries data as well as approximating nonlinear relationships among multiple latent variables using estimation methods that automatically implement statistical shrinkage. This gives them potential to effectively handle data obtained from fisheries populations subject to dynamic environments. We highlight two flexible subclasses and one application of neural networks: Long Short-Term Memory (LSTM) and Convolutional Neural networks (CNNs) and policy discovery via Reinforcement Learning. LSTMs are designed to handle sequential data by allowing prediction from past values at both short and long time-lags. CNNs are not explicitly designed to handle temporal information, but can interpolate a spatial latent variable based on its value within a geographic neighborhood, and can be combined with LSTM models for this purpose. This "Food for Thought" paper introduces and applies these neural network approaches, both alone and in combination, to demonstrate their potential application for several foundational topics in fisheries science: 1) the forecasting of population weight-at-age, 2) the standardization of spatio-temporal indices of relative abundance, and 3) the discovery of harvest policies to optimize catches and maintain spawning biomass. Each section provides a simple, simulated example and describes the tradeoffs - particularly the lack of inferential capability - presented by using neural networks over traditional approaches for each topic. We then outline medium-term research questions that may clarify, facilitate or qualify the applicability of these tools to fisheries management science. Finally, we discuss how future combinations of these approaches could result in simplified ways to estimate and forecast stock biomass and provide harvest advice.

ecology↗

Changes in body size with age do not follow the temperature-size rule

The temperature size-rule is often described as a reduction in ectothermic body size with warming. This coincides with the expectation that faster growth under warming would lead to larger sizes early in life but smaller sizes later in life. Here, we use > 99,000 observations of weight-at-age of four commercially-important fishes over 25 years to ask whether changes in size and growth can be explained by temperature. We also examine whether oxygen, a key part of a proposed mechanism behind the temperature size-rule, explains patterns of weight-at-age better than temperature. Changes in weight-at-age over time were more related to temperature than oxygen but the effect of temperature on weight was small and did not vary by age, counter to the temperature size-rule. Importantly, these results were sensitive to how the relationship between weight-at-age and temperature was modeled. While the functional form (linear or polynomial) mattered little, how space was included in the model led to different conclusions regarding how temperature affects size and growth. Assuming that spatial and spatiotemporal random effects - those that account for the higher degree of similarity between observations collected closer in space and time - are shared across ages led to different results compared to allowing these effects to vary by age. Models with shared effects suggested weight for younger ages had positive relationships with temperature and negative relationships for older ages. However, these models provided spurious support for the temperature size-rule as they had less statistical support than models that allowed spatial effects to vary by age. Overall, our work highlights that relationships among size, growth, temperature, and oxygen may not be as straightforward as theory suggests and illustrates that modeling decisions can have a large effect on tests of ecological theory, and more broadly, our ability to understand biological responses to climate change.

ecology↗

'surveyjoin': A Standardized Database of Fisheries Bottom Trawl Surveys in the Northeast Pacific Ocean

Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected by NOAA Fisheries and Fisheries and Oceans Canada in the Northeast Pacific Ocean. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This effort standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines changes in the spatial distribution of groundfish species across marine heatwave and non-heatwave years, highlighting species-specific and community-level responses to warming events. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision-making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.

ecology↗

Confronting preferential sampling in wildlife surveys: diagnosis and model-based triage

SummaryO_LIWildlife surveys are often used to estimate the density, abundance, or distribution of animal populations. Recently, model-based approaches to analyzing survey data have become popular because one can more readily accommodate departures from pre-planned survey routes and construct more detailed maps than one can with design-based procedures.\nC_LIO_LISpecies distribution models fitted to wildlife survey data often make the implicit assumption that locations chosen for sampling and animal abundance at those locations are conditionally independent given modeled covariates. However, this assumption is likely violated in many cases when survey effort is non-randomized, leading to preferential sampling.\nC_LIO_LIWe develop a hierarchical statistical modeling framework for detecting and alleviating the biasing effects of preferential sampling in species distribution models fitted to count data. The approach works by jointly modeling wildlife state variables and the locations selected for sampling, and specifying a dependent correlation structure between the two models.\nC_LIO_LIUsing simulation, we show that moderate levels of preferential sampling can lead to large (e.g. 40%) bias in estimates of animal density, and that our modeling approach can considerably reduce this bias.\nC_LIO_LIWe apply our approach to aerial survey counts of bearded seals (Erignathus barbatus) in the eastern Bering Sea. Models that included a preferential sampling effect led to lower estimates of abundance than models without, but the effect size of the preferential sampling parameter decreased in models that included explanatory environmental covariates.\nC_LIO_LIWhen wildlife surveys are conducted without a well-defined sampling frame, ecologists should recognize the potentially biasing effects of preferential sampling. Joint models, such as those described in this paper, can be used to test and correct for such biases. Predictive covariates are also useful for bias reduction, but ultimately the best way to avoid preferential sampling bias is to incorporate design-based principles such as randomization and/or systematic sampling into survey design.\nC_LI

ecology↗