Article
Engineering, Marine
Mohammed Shahidul Alam, Qun Liu, Petra Schneider, Mohammad Mojibul Hoque Mozumder, Mohammad Zahedur Rahman Chowdhury, Mohammad Muslem Uddin, Md. Mostafa Monwar, Md. Enamul Hoque, Suman Barua
Summary: The Bombay duck fishery in Bangladesh has a significant impact on the local economy, but has never been a priority for regulatory authorities. This study conducted a thorough assessment of the fish stock and recommended measures to ensure sustainability. The fishery is currently overexploited and requires management policies to protect juvenile fishes and reduce fishing pressure.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Environmental Sciences
Beyah Meissa, Mamadou Dia, Braham C. Baye, Moustapha Bouzouma, Ely Beibou, Ruben H. Roa-Ureta
Summary: Several data-poor stock assessment methods were applied to the Mauritanian pink spiny lobster fishery, all indicating the stock being overfished and in need of biomass rebuilding. Despite uncertain estimates, clear management guidance for sustainable exploitation emerged from the study.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Marine & Freshwater Biology
Maria Grazia Pennino, Marta Cousido-Rocha, Catarina Maia, Alberto Rocha, Ivone Figueiredo, Alexandre Alonso-Fernandez, Cristina Silva, Francisco Izquierdo, Jose Castro, Josefina Teruel Gomez, Jose Rodriguez, Santiago Cervino
Summary: This study evaluated the status of the common sole in the Iberian Coast region using three different length-based methods. The results indicate that this stock is being exploited at the maximum sustainable yield level, with good conservation of immature individuals but a relatively low proportion of large mature individuals.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Environmental Sciences
Kui Zhang, Jiajun Li, Gang Hou, Zirong Huang, Dengfu Shi, Zuozhi Chen, Yongsong Qiu
Summary: The Beibu Gulf is one of the most important fishing grounds in the South China Sea, but in recent years signs of overfishing have been observed. This study assessed nine exploited fish species in the area using two length-based methods, revealing that a pressing situation exists with the majority of fish stocks facing growth overfishing and overexploitation. Collaboration between China and Vietnam is recommended to promote the sustainability and recovery of fishery resources in the Beibu Gulf.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Fisheries
Paul Bouch, Coilin Minto, Dave G. Reid
Summary: A study comparing CMSY and SPiCT methods with ICES age-based assessments for 17 data-rich fish stocks found that both methods often differed considerably from the ICES assessment. CMSY tended to overestimate relative fishing mortality and underestimate relative stock biomass, while SPiCT showed the opposite tendency.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Article
Environmental Sciences
Kui Zhang, Jun Zhang, Peng Zhang, Li Su, Xiaofan Hong, Yongsong Qiu, Zuozhi Chen
Summary: This study assessed the status of skipjack tuna stock in the South China Sea using two data-poor methods. The results showed that the stock may be heavily overfished and recommended reducing fishing effort and increasing catchable size.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Multidisciplinary Sciences
Madeline A. E. Peters, Megan A. Greischar, Nicole Mideo
Summary: Inferring biological processes from population dynamics is a challenge in ecology, especially when faced with incomplete data. In this study on rodent malaria infections, researchers found that measurement bias can affect estimates of parasite developmental duration, leading to inferences about extended cycle length. Alternative protocols and statistical methods are discussed to mitigate such misestimation.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)
Article
Fisheries
Arnaud Gruss, Jeremy R. McKenzie, Martin Lindegren, Richard Bian, Simon D. Hoyle, Jennifer A. Devine
Summary: This study utilizes spatio-temporal models to support stock assessments, focusing on the snapper stock in the northeast coast of the North Island in New Zealand. The findings suggest that snapper exhibit seasonal ecological patterns and the current stock structure assumptions are reasonable. The spatio-temporal models provide similar indices of abundance compared to standard models. However, there is a spatial shrinkage issue in estimating age proportions with the spatio-temporal models, which future studies should address through simulation experiments and sensitivity analyses.
FISHERIES RESEARCH
(2023)
Article
Biology
Itamar Sela, Yuri Wolf, Eugene Koonin
Summary: The study shows that different assumptions in modeling gene commonality data distribution can impact the results. When fitting simple models, incorporating a finite gene pool or varying rates of gene loss and gain can reduce overestimation of specific gene numbers.
Article
Fisheries
Giancarlo M. Correa, Carey R. McGilliard, Lorenzo Ciannelli, Claudio Fuentes
Summary: Ignoring variability in fish species somatic growth rates can lead to biased and imprecise estimates in stock assessment models, while incorporating this variability can produce unbiased and precise results. Unequal distribution of fishing mortality across space significantly impacts estimation model performance.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Article
Business, Finance
Albert Bo Zhao, Tingting Cheng
Summary: In this study, we utilize the ensemble learning approach of stacking to refine and combine various linear and nonlinear models for stock return prediction. We find that stacking with a simple structure outperforms traditional benchmarks and other models, both in terms of in- and out-of-sample performance measures, particularly during extreme market downturns.
JOURNAL OF EMPIRICAL FINANCE
(2022)
Article
Ecology
Richard E. Grewelle, Elizabeth Mansfield, Fiorenza Micheli, Giulio De Leo
Summary: This article discusses the widespread and increasing stressors faced by species and ecosystems, and the lack of data for detailed, quantitative risk assessment. To address this issue, researchers have developed EcoRAMS, a tool that provides statistically robust ecological risk assessments of multiple stressors in data-poor contexts.
ECOLOGICAL INFORMATICS
(2023)
Article
Fisheries
Vanessa Trijoulet, Christoffer Moesgaard Albertsen, Kasper Kristensen, Christopher M. Legault, Timothy J. Miller, Anders Nielsen
Summary: This study shows that using Pearson residuals to analyze goodness of the fit, when data are fitted using a multivariate distribution, is incorrect and one-step-ahead (OSA) or forecast quantile residuals should be used instead. The study describes the calculation of OSA residuals specifically to de-correlate compositional observations for the multivariate distributions most commonly used in assessment models.
FISHERIES RESEARCH
(2023)
Article
Fisheries
Peter-John F. Hulson, Benjamin C. Williams
Summary: This study evaluates the impact of considering ageing error and growth variability on the determination of input sample size (ISS) in statistical catch-at-age assessment models. The results show that including these sources of uncertainty decreases the ISS determined through bootstrap methods. This indicates that there is more variability in age composition and conditional age-at-length data than previously accounted for. Including these sources of uncertainty improves the estimation of ISS and subsequently improves the quality of stock assessment models.
FISHERIES RESEARCH
(2024)
Article
Biochemical Research Methods
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson
Summary: Simulating complex biological and physiological systems and predicting their behaviors remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, aiding in model development and simulation. A general methodology for composing models can improve model composition and ensure physical plausibility, as demonstrated through automated model composition using a human arterial circulation model.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Ecology
James T. Thorson, Mayumi L. Arimitsu, Taal Levi, Gretchen H. Roffler
Summary: This article introduces a new method using a Tweedie generalized linear model (GLM) to analyze compositional data of prey. By statistically deriving the predator foraging process, future theoretical and applied developments can be inspired. The authors provide a new mvtweedie package and use two examples to demonstrate the application of this method and software.
Article
Fisheries
Nicholas D. Ducharme-Barth, Arnaud Gruss, Matthew T. Vincent, Hidetada Kiyofuji, Yoshinori Aoki, Graham Pilling, John Hampton, James T. Thorson
Summary: Abundance indices derived from fisheries-dependent data have the potential for bias, but spatiotemporal delta-GLMMs can better standardize and predict abundance in unfished areas, improving the estimation of fisheries stock assessments. However, further evaluation is needed on the performance of spatiotemporal delta-GLMMs in situations where fisheries spatial sampling patterns change over time.
FISHERIES RESEARCH
(2022)
Article
Fisheries
Kristen L. Omori, James T. Thorson
Summary: This article investigates the management of data-limited species by grouping them into species complexes. By analyzing spatial and temporal similarities among species using cluster analysis and species distribution models, the study finds that some rockfish species can be consistently grouped together, although the arrangement and number of clusters may vary depending on the data used.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Fisheries
Martin Lindegren, Mikael van Deurs, Aurore Maureaud, James T. Thorson, Dorte Bekkevold
Summary: Many marine fish species have wide distribution, but failing to acknowledge distinct populations within these species may lead to overestimation of stock's harvest potential. This study developed a statistical approach to identify population boundaries for European sprat, revealing regional differences in abundance patterns and confirming genetic studies showing reproductive isolation between different regions. The statistical approach can complement genetic methods and guide spatial management efforts for sustainable exploitation under changing climate conditions.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Fisheries
James T. Thorson
Summary: This study demonstrates the importance of density dependence in species distribution models and proposes several new approaches to address density dependence. They find that the impact of species abundance on habitats is spatiotemporally varied, and this relationship can be detected using SDMs.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Fisheries
Matthew R. Siskey, Andre E. Punt, Peter-John F. Hulson, Meaghan D. Bryan, James N. Ianelli, James T. Thorson
Summary: This study developed a framework for evaluating the impact of survey sampling designs on stock assessments and found that decreasing the number of tows sampled led to an increase in the uncertainty of the overfishing limit (OFL). The study also found that reducing the number of otoliths per tow had a smaller impact on OFL uncertainty. Applying this framework to all monitored stocks is important to identify which stocks benefit the most from increased sampling or have the least impact on OFL uncertainty with reduced sampling.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2023)
Article
Fisheries
Julia Indivero, Timothy E. Essington, James N. Ianelli, James T. Thorson
Summary: Environmental conditions can lead to variability in growth and distribution processes, but current stock assessment methods often neglect these patterns. This study used data on walleye pollock in the Bering Sea to demonstrate a feasible approach for incorporating spatially unbalanced size-at-age samples into stock assessments. The analysis revealed extensive variation in size-at-age at fine spatial scales, with year-to-year differences in spatial patterning. Integrating spatiotemporally explicit size-at-age processes improved stock assessment consistency and provided insights into demographic processes. This approach could enhance stock-assessment forecasts under climate change.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Ecology
Merja Elo, Mira H. Kajanus, Jere Tolvanen, Vincent Devictor, Jukka T. Forsman, Aleksi Lehikoinen, Mikko Monkkonen, James T. Thorson, Maximilian G. R. Vollstadt, Sami M. Kivela
Summary: This study investigates the impacts of environmental filtering and biotic interactions on spatial and temporal associations among bird species using a novel hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity. The findings suggest that the aggregation of species is mainly driven by environmental filtering and heterospecific attraction, with no evidence of competition.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Fisheries
Arnaud Gruss, James T. Thorson, Owen F. Anderson, Richard L. O'Driscoll, Madison Heller-Shipley, Scott Goodman
Summary: This study developed a spatio-temporal modelling framework that integrates research survey data and other data sources. It demonstrated the effectiveness of this framework through two case studies.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2023)
Article
Biodiversity Conservation
James T. Thorson, Cheryl L. Barnes, Sarah T. Friedman, Janelle L. Morano, Margaret C. Siple
Summary: Species distribution models (SDMs) are commonly used to analyze the relationship between species occurrence/density and environmental conditions, often including a spatially correlated variable. Spatially varying coefficients (SVCs) in SDMs have received less attention but have the potential to improve interpretability and descriptive power. This article reviews the benefits of using SVCs in ecological contexts such as ecological teleconnections, density-dependent habitat selection, spatially varying detectability, and interactions with unmeasured covariates. Detailed examples using the vector autoregressive spatio-temporal (VAST) model illustrate the advantages of SVCs in analyzing decadal trends, community assembly, and population dynamics. SVCs extend the capabilities of SDMs and enhance our understanding of ecological processes.
Article
Ecology
James T. T. Thorson, Aurore A. A. Maureaud, Romain Frelat, Bastien Merigot, Jennifer S. S. Bigman, Sarah T. T. Friedman, Maria Lourdes D. Palomares, Malin L. L. Pinsky, Samantha A. A. Price, Peter Wainwright
Summary: This study extends previous methods by using structural equation models and associations among categorical traits to achieve mixed-trait imputation. Results show that a one-degree increase in habitat temperature is associated with an average 3.5% increase in natural mortality and a 3.0% decrease in fecundity.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Fisheries
A. Gruess, A. R. Charsley, J. T. Thorson, O. F. Anderson, R. L. O'Driscoll, B. Wood, O. N. Breivik, C. A. O'Leary
Summary: Species distribution models often require multiple data sources to achieve their objectives. In this study, we developed a spatio-temporal modelling framework that integrated research survey data and observer data from fishing vessels, while accounting for physical barriers. Applying this framework to deepwater fisheries in New Zealand, we found that using both observer-only data and integrated data is essential for mapping fish biomass at a large scale and interpolating local biomass indices in years without survey data. We also demonstrated the importance of considering the reliability of interannual variability when choosing between models relying on integrated data or survey-only data for a given geographic area. Moreover, our simulation experiment revealed that the predictions of our spatio-temporal models were not significantly affected by the presence of physical barriers.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Fisheries
J. J. Badger, S. Large, J. T. Thorson
Summary: Many economic sectors rely on marine ecosystem services, and integrated ecosystem assessments (IEAs) are necessary for holistic management and sustainable use. This study demonstrates the utility of spatially and temporally explicit ecological indicators in assessing ecosystem performance and identifying localized processes. The examples highlight the benefits of spatio-temporal methods for integrated ecosystem analysis in the northeast US Shelf Ecosystem.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Fisheries
Daniel Ovando, Darcy Bradley, Echelle Burns, Lennon Thomas, James Thorson
Summary: Designing effective spatial management strategies for marine ecosystems is challenging due to their complexity and uncertainties. This paper presents a modelling framework called marlin, which can simulate the bio-economic dynamics of marine systems efficiently. The framework can be used for both management and research purposes. The study demonstrates the capabilities of marlin through two case studies on marine protected areas (MPAs) and their impacts on conservation and food production. It shows how the framework can assess the distributional outcomes and climate resilience of different MPA design strategies and fishing fleets. The paper highlights the importance of intermediate complexity simulation in predicting and managing trade-offs among conservation, fisheries yields, and distributional outcomes of management policies affected by spatial bio-economic dynamics.
FISH AND FISHERIES
(2023)
Article
Fisheries
James T. Thorson
Summary: Phylogenetic comparative methods (PCM) and phylogenetic structural equation models (PSEM) can replace linear models and improve performance in fisheries meta-analyses, but they are rarely applied in fisheries science.
FISH AND FISHERIES
(2023)