Review
Oceanography
Arnaud Gruss, James T. Thorson, Christine C. Stawitz, Jonathan C. P. Reum, Sean K. Rohan, Cheryl L. Barnes
Summary: By applying EOF analysis to examine fish demographic processes in the eastern Bering Sea, the study found a strong correlation between prey-biomass-per-predator-mass and the spatial extent of bottom temperatures (CPE), indicating a bottom-up environmental influence on demographic processes. Anomalous years, such as 1999 and 2010 with a large CPE and high indices for demographic variables, as well as 2016-2019 with a small CPE and low indices, were identified. These findings suggest the potential for using CPE projections to forecast changes in demographic process variables in the future.
PROGRESS IN OCEANOGRAPHY
(2021)
Article
Fisheries
Cecilia A. O'Leary, Lukas B. DeFilippo, James T. Thorson, Stan Kotwicki, Gerald R. Hoff, Vladimir V. Kulik, James N. Ianelli, Andre E. Punt
Summary: As oceans warm, the distribution of groundfish species shifts, which can complicate management efforts. This study developed model-based biomass estimates for three Bering Sea groundfish species by combining data from the US and Russia. The results show that groundfish densities have shifted northward and high-density areas now span across the international border.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Jaclyn Clement Kinney, Wieslaw Maslowski, Robert Osinski, Younjoo J. Lee, Christina Goethel, Karen Frey, Anthony Craig
Summary: The seasonal sea ice cover in the Bering Sea plays a crucial role in the formation of a cold bottom water pool (<2 degrees C) and affects the distribution of arctic and subarctic demersal fish species. Recent declines in sea ice cover have led to a smaller Cold Pool area, impacting food security. The retreat of the Cold Pool may result in the migration of subarctic species towards the Chukchi Sea.
Article
Physics, Applied
Thomas W. Pfeifer, John A. Tomko, Eric Hoglund, Ethan A. Scott, Khalid Hattar, Kenny Huynh, Michael Liao, Mark Goorsky, Patrick E. Hopkins
Summary: In this study, a new method for analyzing the thermal conductivity variations in a material with spatial distribution of defects is developed using time-domain thermoreflectance. The near-surface thermal conductivity of silicon wafers irradiated with Kr+ ions is measured using this method. The results are validated using transmission electron microscopy, which confirms the spatial variation of the sub-surface silicon structure. The drastic reduction in silicon thermal conductivity is primarily attributed to structural defects and boundary scattering between amorphous and crystalline regions.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Acoustics
Jennifer J. Johnson, Jennifer L. Miksis-Olds, Thomas C. Lippmann, J. Michael Jech, Kerri D. Seger, James M. Pringle, Ernst Linder
Summary: A characteristic feature of the eastern Bering Sea is the presence of a subsurface layer called the cold pool, which is linked to seasonal sea ice and plays a role in zooplankton and fish dynamics. This study used acoustic backscatter data collected from 2008 to 2018 to investigate the relationship between biological scattering communities and cold pool variation. The results showed that during the cold regime, acoustic backscatter was significantly higher than during the warm regime, and there was a shift in the frequency-dependent scattering communities. The study also found that the cold pool proxy of sea ice concentration was a stronger predictor for biological scattering than bottom temperature in the cold regime. These findings suggest that the cold pool and frequency-dependent scattering dynamics could serve as indicators of regime shifts and have implications for ecosystem management in the Arctic.
JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Luke Thomas, Jim N. Underwood, Noah H. Rose, Zachary L. Fuller, Zoe T. Richards, Laurence Dugal, Camille M. Grimaldi, Ira R. Cooke, Stephen R. Palumbi, James P. Gilmour
Summary: This study investigates the mechanisms of coral resilience to climate change in the Rowley Shoals of Western Australia. By studying coral samples from different habitats and using various molecular techniques, the researchers found that there were genetic differences between corals living in lagoon and reef slope habitats. Corals from the lagoon were found to be more resistant to bleaching and showed distinct differences in gene expression compared to corals from the reef slope.
Article
Computer Science, Information Systems
Zhensheng Wang, Feidong Lu, Zhaohui Liu, Wei Tu, Ke Nie, Qingyun Du, Qingquan Li, Zhiqiang Wu
Summary: Understanding the relationship between mixed land use and urban vibrancy is crucial for advanced urban planning. This study presents a Bayesian spatially varying coefficient (SVC) model to explore this relationship while considering other factors. The results show that including spatially structured and unstructured components can improve the model's accuracy, and considering spatial heterogeneity further enhances its performance.
INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE
(2023)
Article
Fisheries
Kevin D. Friedland, Travis Miles, Andrew G. Goode, Eric N. Powell, Damian C. Brady
Summary: The study describes changes in the extent and thermal properties of the Cold Pool in the Middle Atlantic Bight (MAB). Observations and models indicate a significant warming trend and reduced spatial extent of the Cold Pool during the study period. These changes are likely to have implications for the distribution of boreal species and overall ecosystem productivity.
FISHERIES OCEANOGRAPHY
(2022)
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
Ecology
Mira H. Kajanus, Jukka T. Forsman, Maximilian G. R. Vollstadt, Vincent Devictor, Merja Elo, Aleksi Lehikoinen, Mikko Monkkonen, James T. Thorson, Sami M. Kivela
Summary: Titmice can serve as indicators of bird density in Northern European forest bird communities, encouraging the use of titmice observations by even less-experienced observers in citizen science monitoring.
ECOLOGY AND EVOLUTION
(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)