27 results on '"Matthiopoulos, Jason"'
Search Results
2. The role of seabird guano in maintaining North Atlantic summertime productivity
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Browning, Thomas J., Al-Hashem, Ali A., Achterberg, Eric P., Carvalho, Paloma C., Catry, Paulo, Matthiopoulos, Jason, Miller, Julie A.O., and Wakefield, Ewan D.
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- 2023
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3. Strong breeding colony fidelity in northern gannets following high pathogenicity avian influenza virus (HPAIV) outbreak
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Grémillet, David, Ponchon, Aurore, Provost, Pascal, Gamble, Amandine, Abed-Zahar, Mouna, Bernard, Alice, Courbin, Nicolas, Delavaud, Grégoire, Deniau, Armel, Fort, Jérôme, Hamer, Keith C., Jeavons, Ruth, Lane, Jude V., Langley, Liam, Matthiopoulos, Jason, Poupart, Timothée, Prudor, Aurélien, Stephens, Nia, Trevail, Alice, Wanless, Sarah, Votier, Stephen C., and Jeglinski, Jana W.E.
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- 2023
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4. Solving the fourth-corner problem : forecasting ecosystem primary production from spatial multispecies trait-based models
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Sarker, Swapan Kumar, Reeve, Richard, and Matthiopoulos, Jason
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- 2021
5. A statistical calibration tool for methods used to sample outdoor-biting mosquitoes
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Ngowo, Halfan S., Limwagu, Alex J., Ferguson, Heather M., Matthiopoulos, Jason, Okumu, Fredros O., and Nelli, Luca
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- 2022
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6. Using Bayesian state-space models to understand the population dynamics of the dominant malaria vector, Anopheles funestus in rural Tanzania
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Ngowo, Halfan S., Okumu, Fredros O., Hape, Emmanuel E., Mshani, Issa H., Ferguson, Heather M., and Matthiopoulos, Jason
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- 2022
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7. Combining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country
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Chadwick, Fergus J., Clark, Jessica, Chowdhury, Shayan, Chowdhury, Tasnuva, Pascall, David J., Haddou, Yacob, Andrecka, Joanna, Kundegorski, Mikolaj, Wilkie, Craig, Brum, Eric, Shirin, Tahmina, Alamgir, A. S. M., Rahman, Mahbubur, Alam, Ahmed Nawsher, Khan, Farzana, Swallow, Ben, Mair, Frances S., Illian, Janine, Trotter, Caroline L., Hill, Davina L., Husmeier, Dirk, Matthiopoulos, Jason, Hampson, Katie, and Sania, Ayesha
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- 2022
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8. Widespread extinction debts and colonization credits in United States breeding bird communities
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Haddou, Yacob, Mancy, Rebecca, Matthiopoulos, Jason, Spatharis, Sofie, and Dominoni, Davide M.
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- 2022
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9. Landscape drives zoonotic malaria prevalence in non-human primates.
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Johnson, Emilia, Sharma, Reuben Sunil Kumar, Cuenca, Pablo Ruiz, Byrne, Isabel, Salgado-Lynn, Milena, Shahar, Zarith Suraya, Lin, Lee Col, Zulkifli, Norhadila, Mohd Saidi, Nor Dilaila, Drakeley, Chris, Matthiopoulos, Jason, Nelli, Luca, and Fornace, Kimberly
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- 2024
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10. The summer distribution, habitat associations and abundance of seabirds in the sub-polar frontal zone of the Northwest Atlantic
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Wakefield, Ewan D., Miller, David L., Bond, Sarah L., le Bouard, Fabrice, Carvalho, Paloma C., Catry, Paulo, Dilley, Ben J., Fifield, David A., Gjerdrum, Carina, González-Solís, Jacob, Hogan, Holly, Laptikhovsky, Vladimir, Merkel, Benjamin, Miller, Julie A.O., Miller, Peter I., Pinder, Simon J., Pipa, Tânia, Ryan, Peter M., Thompson, Laura A., Thompson, Paul M., and Matthiopoulos, Jason
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- 2021
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11. Author Correction: Widespread extinction debts and colonization credits in United States breeding bird communities
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Haddou, Yacob, Mancy, Rebecca, Matthiopoulos, Jason, Spatharis, Sofie, and Dominoni, Davide M.
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- 2022
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12. HPAIV outbreak triggers short-term colony connectivity in a seabird metapopulation.
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Jeglinski, Jana W. E., Lane, Jude V., Votier, Steven C., Furness, Robert W., Hamer, Keith C., McCafferty, Dominic J., Nager, Ruedi G., Sheddan, Maggie, Wanless, Sarah, and Matthiopoulos, Jason
- Abstract
Disease outbreaks can drastically disturb the environment of surviving animals, but the behavioural, ecological, and epidemiological consequences of disease-driven disturbance are poorly understood. Here, we show that an outbreak of High Pathogenicity Avian Influenza Virus (HPAIV) coincided with unprecedented short-term behavioural changes in Northern gannets (Morus bassanus). Breeding gannets show characteristically strong fidelity to their nest sites and foraging areas (2015–2019; n = 120), but during the 2022 HPAIV outbreak, GPS-tagged gannets instigated long-distance movements beyond well-documented previous ranges and the first ever recorded visits of GPS-tagged adults to other gannet breeding colonies. Our findings suggest that the HPAIV outbreak triggered changes in space use patterns of exposed individuals that amplified the epidemiological connectivity among colonies and may generate super-spreader events that accelerate disease transmission across the metapopulation. Such self-propagating transmission from and towards high density animal aggregations may explain the unexpectedly rapid pan-European spread of HPAIV in the gannet. [ABSTRACT FROM AUTHOR]
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- 2024
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13. Fewer pests and more ecosystem service‐providing arthropods in shady African cocoa farms: Insights from a data integration study.
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Jarrett, Crinan, Cyril, Kowo, Haydon, Daniel T., Wandji, Christel Alain, Ferreira, Diogo F., Welch, Andreanna J., Powell, Luke L., and Matthiopoulos, Jason
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MEALYBUGS ,DATA integration ,AGRICULTURE ,ARTHROPODA ,ARTHROPOD pests ,PESTS ,COCOA ,CACAO beans - Abstract
Copyright of Journal of Applied Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
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14. Size‐dependence of food intake and mortality interact with temperature and seasonality to drive diversity in fish life histories.
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Kindsvater, Holly K., Juan‐Jordá, Maria‐José, Dulvy, Nicholas K., Horswill, Cat, Matthiopoulos, Jason, and Mangel, Marc
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PHYSIOLOGICAL effects of climate change ,LIFE history theory ,SIZE of fishes ,SEASONAL temperature variations ,FISH diversity ,REPRODUCTION ,FOOD consumption - Abstract
Understanding how growth and reproduction will adapt to changing environmental conditions is a fundamental question in evolutionary ecology, but predicting the responses of specific taxa is challenging. Analyses of the physiological effects of climate change upon life history evolution rarely consider alternative hypothesized mechanisms, such as size‐dependent foraging and the risk of predation, simultaneously shaping optimal growth patterns. To test for interactions between these mechanisms, we embedded a state‐dependent energetic model in an ecosystem size‐spectrum to ask whether prey availability (foraging) and risk of predation experienced by individual fish can explain observed diversity in life histories of fishes. We found that asymptotic growth emerged from size‐based foraging and reproductive and mortality patterns in the context of ecosystem food web interactions. While more productive ecosystems led to larger body sizes, the effects of temperature on metabolic costs had only small effects on size. To validate our model, we ran it for abiotic scenarios corresponding to the ecological lifestyles of three tuna species, considering environments that included seasonal variation in temperature. We successfully predicted realistic patterns of growth, reproduction, and mortality of all three tuna species. We found that individuals grew larger when environmental conditions varied seasonally, and spawning was restricted to part of the year (corresponding to their migration from temperate to tropical waters). Growing larger was advantageous because foraging and spawning opportunities were seasonally constrained. This mechanism could explain the evolution of gigantism in temperate tunas. Our approach addresses variation in food availability and individual risk as well as metabolic processes and offers a promising approach to understand fish life‐history responses to changing ocean conditions. [ABSTRACT FROM AUTHOR]
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- 2024
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15. Fitness characteristics of the malaria vector Anopheles funestus during an attempted laboratory colonization
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Ngowo, Halfan S., Hape, Emmanuel E., Matthiopoulos, Jason, Ferguson, Heather M., and Okumu, Fredros O.
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- 2021
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16. Insecticide resistance and behavioural adaptation as a response to long-lasting insecticidal net deployment in malaria vectors in the Cascades region of Burkina Faso
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Sanou, Antoine, Nelli, Luca, Guelbéogo, W. Moussa, Cissé, Fatoumata, Tapsoba, Madou, Ouédraogo, Pierre, Sagnon, N’falé, Ranson, Hilary, Matthiopoulos, Jason, and Ferguson, Heather M.
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- 2021
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17. Incorporating environmental heterogeneity and observation effort to predict host distribution and viral spillover from a bat reservoir.
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Ribeiro, Rita, Matthiopoulos, Jason, Lindgren, Finn, Tello, Carlos, Zariquiey, Carlos M., Valderrama, William, Rocke, Tonie E., and Streicker, Daniel G.
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BATS , *GAUSSIAN processes , *HETEROGENEITY , *RABIES , *ZOONOSES , *ROOSTING - Abstract
Predicting the spatial occurrence of wildlife is a major challenge for ecology and management. In Latin America, limited knowledge of the number and locations of vampire bat roosts precludes informed allocation of measures intended to prevent rabies spillover to humans and livestock. We inferred the spatial distribution of vampire bat roosts while accounting for observation effort and environmental effects by fitting a log Gaussian Cox process model to the locations of 563 roosts in three regions of Peru. Our model explained 45% of the variance in the observed roost distribution and identified environmental drivers of roost establishment. When correcting for uneven observation effort, our model estimated a total of 2340 roosts, indicating that undetected roosts (76%) exceed known roosts (24%) by threefold. Predicted hotspots of undetected roosts in rabies-free areas revealed high-risk areas for future viral incursions. Using the predicted roost distribution to inform a spatial model of rabies spillover to livestock identified areas with disproportionate underreporting and indicated a higher rabies burden than previously recognized. We provide a transferrable approach to infer the distribution of a mostly unobserved bat reservoir that can inform strategies to prevent the re-emergence of an important zoonosis. [ABSTRACT FROM AUTHOR]
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- 2023
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18. Metapopulation regulation acts at multiple spatial scales: Insights from a century of seabird colony census data.
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Jeglinski, Jana W. E., Wanless, Sarah, Murray, Stuart, Barrett, Robert T., Gardarsson, Arnthor, Harris, Mike P., Dierschke, Jochen, Strøm, Hallvard, Lorentsen, Svein‐Håkon, and Matthiopoulos, Jason
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COLONIAL birds ,COLONIES (Biology) ,POPULATION dynamics ,BIRD populations ,CENSUS ,NATURAL history ,PRECAUTIONARY principle - Abstract
Density‐dependent feedback is recognized as important regulatory mechanisms of population size. Considering the spatial scales over which such feedback operates has advanced our theoretical understanding of metapopulation dynamics. Yet, metapopulation models are rarely fit to time‐series data and tend to omit details of the natural history and behavior of long‐lived, highly mobile species such as colonial mammals and birds. Seabird metapopulations consist of breeding colonies that are connected across large spatial scales, within a heterogeneous marine environment that is increasingly affected by anthropogenic disturbance. Currently, we know little about the strength and spatial scale of density‐dependent regulation and connectivity between colonies. Thus, many important seabird conservation and management decisions rely on outdated assumptions of closed populations that lack density‐dependent regulation. We investigated metapopulation dynamics and connectivity in an exemplar seabird species, the Northern gannet (Morus bassanus), using more than a century of census data of breeding colonies distributed across the Northeast Atlantic. We developed and fitted these data to a novel hierarchical Bayesian state‐space model, to compare increasingly complex scenarios of metapopulation regulation through lagged, local, regional, and global density dependence, as well as different mechanisms for immigration. Models with conspecific attraction fit the data better than the equipartitioning of immigrants. Considering local and regional density dependence jointly improved model fit slightly, but importantly, future colony size projections based on different mechanistic regulatory scenarios varied widely: a model with local and regional dynamics estimated a lower metapopulation capacity (645,655 Apparently Occupied Site [AOS]) and consequently higher present saturation (63%) than a model with local density dependence (1,367,352 AOS, 34%). Our findings suggest that metapopulation regulation in the gannet is more complex than traditionally assumed, and highlight the importance of using models that consider colony connectivity and regional dynamics for conservation management applications guided by precautionary principles. Our study advances our understanding of metapopulation dynamics in long‐lived colonial species and our approach provides a template for the development of metapopulation models for colonially living birds and mammals. [ABSTRACT FROM AUTHOR]
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- 2023
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19. Integrated modelling of seabird-habitat associations from multi-platform data: a review
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Matthiopoulos, Jason, Wakefield, Ewan, Jeglinski, Jana W.E., Furness, Robert W., Trinder, Mark, Tyler, Glen, McCluskie, Aly, Allen, Sophy, Braithwaite, Janelle, and Evans, Tom
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Quantifying current and future overlap between human activities and wildlife is a core and growing aim of ecological study, spurring ever more spatial data collection and diversification of observation techniques (surveys, telemetry, citizen science etc.).\ud To meet this aim, data collected via multiple platforms, across different geographical and temporal regions, may need to be integrated, yet many ecologists remain unclear about the relationships between data types and therefore how they can be combined.\ud In seabird research, these applied questions can be particularly pressing because many human activities (e.g. tidal and wind renewables, fishing, shipping, etc.) are concentrated in coastal waters, where many seabirds also aggregate, especially while breeding. In addition, seabird coloniality and density dependence present unique analytical challenges.\ud We review the relevant literature on data integration and illustrate it with example models and data (in an accompanying R-library and vignette (J Matthiopoulos et al., 2022)), to derive methodological and quantitative guidelines for best practice in conducting joint inference for multi-platform data. We use systematic survey data to motivate the key arguments, but also overview developments in integration with other data (e.g., telemetry tracking, citizen science, mark-recapture).\ud We make recommendations on (1) the use of response and explanatory data, (2) the treatment of survey design and observation errors, (3) exploiting dependencies across space and time, (4) accounting for biological phenomena, such as commuting costs from the colony (i.e., accessibility) and density dependence, and (5) the choice of statistical framework.\ud Synthesis and application: Integrated analysis of multi-platform data turns many of the seabird-specific challenges into opportunities for inferring habitat associations and predicting future distributions. Our review proposes practical recommendations for data collection and analysis that will allow seabird conservation to derive maximal benefits from these opportunities.
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- 2022
20. Generalized functional responses in habitat selection fitted by decision trees and random forests
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Aldossari, Shaykhah, Husmeier, Dirk, Matthiopoulos, Jason, Ladde, Gangaram, and Samia, Noelle
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Species Distribution Models (SDMs) are important regression tools in the ecological sciences that can support distribution predictions using different environmental variables. Most of the research in the area of SDMs has assumed that regression coefficients in these models are fixed. However, species respond differently to different habitats depending on the habitat availability, meaning that regression coefficients change as functions of habitat availability, a phenomenon known as a functional response in habitat selection. The generalized functional response (GFR) is a varying-coefficient extension of the basic SDM framework, designed for more robust forecasts of species distributions in a rapidly changing world. The original GFR model formulated the varying regression coefficients using a polynomial function approach, which led to improvements of forecasting performance in many applications. The purpose of this paper is to improve the out-of-sample performance of the GFR model using a decision tree and Breiman's random forest algorithm. We compare the original GFR model with a decision tree and random forests using the GFR model by applying both models to a real population dataset on house sparrows. The results revealed a noticeable improvement in terms of out-of-sample R² in the decision tree and the random forest approaches over the original GFR model.
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- 2021
21. Integration of mark–recapture and acoustic detections for unbiased population estimation in animal communities.
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Jarrett, Crinan, Haydon, Daniel T., Morales, Juan M., Ferreira, Diogo F., Forzi, Francis Alemanji, Welch, Andreanna J., Powell, Luke L., and Matthiopoulos, Jason
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ANIMAL communities ,ANIMAL populations ,BIRD communities ,COMMUNITIES ,ACOUSTIC devices - Abstract
Abundance estimation methods that combine several types of data are becoming increasingly common because they yield more accurate and precise parameter estimates and predictions than are possible from a single data source. These beneficial effects result from increasing sample size (through data pooling) and complementarity between different data types. Here, we test whether integrating mark–recapture data with passive acoustic detections into a joint likelihood improves estimates of population size in a multi‐guild community. We compared the integrated model to a mark–recapture‐only model using simulated data first and then using a data set of mist‐net captures and acoustic recordings from an Afrotropical agroforest bird community. The integrated model with simulated data improved accuracy and precision of estimated population size and detection parameters. When applied to field data, the integrated model was able to produce, for each bird guild, ecologically plausible estimates of population size and detection parameters, with more precision compared with the mark–recapture model. Overall, our results show that adding acoustic data to mark–recapture analyses improves estimates of population size. With the increasing availability of acoustic recording devices, this data collection technique could readily be added to routine field protocols, leading to a cost‐efficient improvement of traditional mark–recapture population estimation. [ABSTRACT FROM AUTHOR]
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- 2022
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22. Modelling and mapping how common guillemots balance their energy budgets over a full annual cycle.
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Dunn, Ruth E., Green, Jonathan A., Wanless, Sarah, Harris, Mike P., Newell, Mark A., Bogdanova, Maria I., Horswill, Catharine, Daunt, Francis, and Matthiopoulos, Jason
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OCEAN temperature ,CALORIC expenditure ,ANIMAL populations ,SEVERE storms ,ENERGY budget (Geophysics) ,REPRODUCTION ,POPULATION dynamics ,BAYESIAN analysis - Abstract
The ability of individual animals to balance their energy budgets throughout the annual cycle is important for their survival, reproduction and population dynamics. However, the annual cycles of many wild, mobile animals are difficult to observe and our understanding of how individuals balance their energy budgets throughout the year therefore remains poor.We developed a hierarchical Bayesian state‐space model to investigate how key components of animal energy budgets (namely individual energy gain and storage) varied in space and time. Our model used biologger‐derived estimates of time‐activity budgets, locations and energy expenditure to infer year‐round time series of energy income and reserves. The model accounted for seasonality in environmental drivers such as sea surface temperature and daylength, allowing us to identify times and locations of high energy gain.Our study system was a population of common guillemots Uria aalge breeding at a western North Sea colony. These seabirds manage their energy budgets by adjusting their behaviour and accumulating fat reserves. However, typically during severe weather conditions, birds can experience an energy deficit over a sustained period, leading to starvation and large‐scale mortality events.We show that guillemot energy gain varied in both time and space. Estimates of guillemot body mass varied throughout the annual cycle and birds periodically experienced losses in mass. Mass losses were likely to have either been adaptive, or due to energetic bottlenecks, the latter leading to increased susceptibility to mortality. Guillemots tended to be lighter towards the edge of their spatial distribution.We describe a framework that combines biologging data, time‐activity budget analysis and Bayesian state‐space modelling to identify times and locations of high energetic reward or potential energetic bottlenecks in a wild animal population. Our approach can be extended to address ecological and conservation‐driven questions that were previously unanswerable due to logistical complexities in collecting data on wild, mobile animals across full annual cycles. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]
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- 2022
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23. Individual-Level Memory Is Sufficient to Create Spatial Segregation among Neighboring Colonies of Central Place Foragers.
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Aarts, Geert, Mul, Evert, Fieberg, John, Brasseur, Sophie, van Gils, Jan A., Matthiopoulos, Jason, and Riotte-Lambert, Louise
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ENVIRONMENTAL degradation ,COLONIES ,COLONIES (Biology) ,SPATIAL memory ,BEE colonies ,SPATIAL ability ,HABITAT partitioning (Ecology) - Abstract
Central place foragers often segregate in space, even without signs of direct agonistic interactions. Using parsimonious individual-based simulations, we show that for species with spatial cognitive abilities, individual-level memory of resource availability can be sufficient to cause spatial segregation in the foraging ranges of colonial animals. The shapes of the foraging distributions are governed by commuting costs, the emerging distribution of depleted resources, and the fidelity of foragers to their colonies. When colony fidelity is weak and foragers can easily switch to colonies located closer to favorable foraging grounds, this leads to space partitioning with equidistant borders between neighboring colonies. In contrast, when colony fidelity is strong—for example, because larger colonies provide safety in numbers or individuals are unable to leave—it can create a regional imbalance between resource requirements and resource availability. This leads to nontrivial space-use patterns that propagate through the landscape. Interestingly, while better spatial memory creates more defined boundaries between neighboring colonies, it can lower the average intake rate of the population, suggesting a potential trade-off between an individual's attempt for increased intake and population growth rates. [ABSTRACT FROM AUTHOR]
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- 2021
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24. Transferable species distribution modelling: Comparative performance of Generalised Functional Response models.
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Aldossari, Shaykhah, Husmeier, Dirk, and Matthiopoulos, Jason
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SPECIES distribution ,RADIAL basis functions ,HABITAT selection ,HABITATS ,RANDOM forest algorithms ,REGULARIZATION parameter ,REGRESSION trees - Abstract
Predictive species distribution models (SDMs) are becoming increasingly important in ecology, in the light of rapid environmental change. However, the predictions of most current SDMs are specific to the habitat composition of the environments in which they were fitted. This may limit SDM predictive power because species may respond differently to a given habitat depending on the availability of all habitats in their environment, a phenomenon known as a functional response in resource selection. The Generalised Functional Response (GFR) framework captures this dependence by formulating the SDM coefficients as functions of habitat availability. The original GFR implementation used global polynomial functions of habitat availability to describe the functional responses. In this study, we develop several refinements of this approach and compare their predictive performance using two simulated and two real datasets. We first use local radial basis functions (RBF), a more flexible approach than global polynomials, to represent the habitat selection coefficients, and balance bias with precision via regularization to prevent overfitting. Second, we use the RBF-GFR and GFR models in combination with the classification and regression tree CART, which has more flexibility and better predictive powers for non-linear modelling. As further extensions, we use random forests (RFs) and extreme gradient boosting (XGBoost), ensemble approaches that consistently lead to variance reduction in generalization error. We find that the different methods are ranked consistently across the datasets for out-of-data prediction. The traditional stationary approach to SDMs and the GFR model consistently perform at the bottom of the ranking (simple SDMs underfit, and polynomial GFRs overfit the data). The best methods in our list provide non-negligible improvements in predictive performance, in some cases taking the out-of-sample R2 from 0.3 up to 0.7 across datasets. At times of rapid environmental change and spatial non-stationarity ignoring the effects of functional responses on SDMs, results in two different types of prediction bias (under-prediction or mis-positioning of distribution hotspots). However, not all functional response models perform equally well. The more volatile polynomial GFR models can generate biases through over-prediction. Our results indicate that there are consistently robust GFR approaches that achieve impressive gains in transferability across very different datasets. [ABSTRACT FROM AUTHOR]
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- 2022
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25. Combining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country
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Fergus J. Chadwick, Jessica Clark, Shayan Chowdhury, Tasnuva Chowdhury, David J. Pascall, Yacob Haddou, Joanna Andrecka, Mikolaj Kundegorski, Craig Wilkie, Eric Brum, Tahmina Shirin, A. S. M. Alamgir, Mahbubur Rahman, Ahmed Nawsher Alam, Farzana Khan, Ben Swallow, Frances S. Mair, Janine Illian, Caroline L. Trotter, Davina L. Hill, Dirk Husmeier, Jason Matthiopoulos, Katie Hampson, Ayesha Sania, Chadwick, Fergus J [0000-0001-8650-1938], Clark, Jessica [0000-0003-1692-899X], Chowdhury, Shayan [0000-0001-5153-9055], Chowdhury, Tasnuva [0000-0003-0660-9784], Pascall, David J [0000-0002-7543-0860], Kundegorski, Mikolaj [0000-0002-0982-9371], Wilkie, Craig [0000-0003-0805-0195], Brum, Eric [0000-0002-0244-7178], Rahman, Mahbubur [0000-0001-8577-8281], Alam, Ahmed Nawsher [0000-0002-7962-0725], Swallow, Ben [0000-0002-0227-2160], Illian, Janine [0000-0002-6130-2796], Trotter, Caroline L [0000-0003-4000-2708], Hill, Davina L [0000-0001-9085-6192], Husmeier, Dirk [0000-0003-1673-7413], Matthiopoulos, Jason [0000-0003-3639-8172], Hampson, Katie [0000-0001-5392-6884], Apollo - University of Cambridge Repository, Pascall, David [0000-0002-7543-0860], Trotter, Caroline [0000-0003-4000-2708], and University of St Andrews. School of Mathematics and Statistics
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Bangladesh ,Multidisciplinary ,Models, Statistical ,article ,General Physics and Astronomy ,COVID-19 ,DAS ,General Chemistry ,692/700/478/174 ,General Biochemistry, Genetics and Molecular Biology ,692/700/139 ,692/1807 ,SDG 3 - Good Health and Well-being ,692/699/255/2514 ,RA0421 ,RA0421 Public health. Hygiene. Preventive Medicine ,Humans ,Epidemics ,Sentinel Surveillance ,631/326/596/4130 ,Z721 - Abstract
Funder: Juniper Consortium MR/V038613/1, Funder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation), Diagnostics for COVID-19 detection are limited in many settings. Syndromic surveillance is often the only means to identify cases but lacks specificity. Rapid antigen testing is inexpensive and easy-to-deploy but can lack sensitivity. We examine how combining these approaches can improve surveillance for guiding interventions in low-income communities in Dhaka, Bangladesh. Rapid-antigen-testing with PCR validation was performed on 1172 symptomatically-identified individuals in their homes. Statistical models were fitted to predict PCR-status using rapid-antigen-test results, syndromic data, and their combination. Under contrasting epidemiological scenarios, the models' predictive and classification performance was evaluated. Models combining rapid-antigen-testing and syndromic data yielded equal-to-better performance to rapid-antigen-test-only models across all scenarios with their best performance in the epidemic growth scenario. These results show that drawing on complementary strengths across rapid diagnostics, improves COVID-19 detection, and reduces false-positive and -negative diagnoses to match local requirements; improvements achievable without additional expense, or changes for patients or practitioners.
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- 2022
26. Effects of culling vampire bats on the spatial spread and spillover of rabies virus.
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Viana M, Benavides JA, Broos A, Ibañez Loayza D, Niño R, Bone J, da Silva Filipe A, Orton R, Valderrama Bazan W, Matthiopoulos J, and Streicker DG
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- Animals, Humans, Bayes Theorem, Peru epidemiology, Livestock, Animals, Wild, Rabies virus genetics, Chiroptera, Rabies epidemiology, Rabies prevention & control
- Abstract
Controlling pathogen circulation in wildlife reservoirs is notoriously challenging. In Latin America, vampire bats have been culled for decades in hopes of mitigating lethal rabies infections in humans and livestock. Whether culls reduce or exacerbate rabies transmission remains controversial. Using Bayesian state-space models, we show that a 2-year, spatially extensive bat cull in an area of exceptional rabies incidence in Peru failed to reduce spillover to livestock, despite reducing bat population density. Viral whole genome sequencing and phylogeographic analyses further demonstrated that culling before virus arrival slowed viral spatial spread, but reactive culling accelerated spread, suggesting that culling-induced changes in bat dispersal promoted viral invasions. Our findings question the core assumptions of density-dependent transmission and localized viral maintenance that underlie culling bats as a rabies prevention strategy and provide an epidemiological and evolutionary framework to understand the outcomes of interventions in complex wildlife disease systems.
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- 2023
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27. A protocol for a longitudinal, observational cohort study of infection and exposure to zoonotic and vector-borne diseases across a land-use gradient in Sabah, Malaysian Borneo: a socio-ecological systems approach.
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Fornace K, Manin BO, Matthiopoulos J, Ferguson HM, Drakeley C, Ahmed K, Khoon KT, Ewers RM, Daim S, and Chua TH
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Introduction. Landscape changes disrupt environmental, social and biological systems, altering pathogen spillover and transmission risks. This study aims to quantify the impact of specific land management practices on spillover and transmission rates of zoonotic and vector-borne diseases within Malaysian Borneo. This protocol describes a cohort study with integrated ecological sampling to assess how deforestation and agricultural practices impact pathogen flow from wildlife and vector populations to human infection and detection by health facilities. This will focus on malaria, dengue and emerging arboviruses (Chikungunya and Zika), vector-borne diseases with varying contributions of simian reservoirs within this setting. Methods. A prospective longitudinal observational cohort study will be established in communities residing or working within the vicinity of the Stability of Altered Forest Ecosystems (SAFE) Project, a landscape gradient within Malaysian Borneo encompassing different plantation and forest types. The primary outcome of this study will be transmission intensity of selected zoonotic and vector-borne diseases, as quantified by changes in pathogen-specific antibody levels. Exposure will be measured using paired population-based serological surveys conducted at the beginning and end of the two-year cohort study. Secondary outcomes will include the distribution and infection rates of Aedes and Anopheles mosquito vectors, human risk behaviours and clinical cases reported to health facilities. Longitudinal data on human behaviour, contact with wildlife and GPS tracking of mobility patterns will be collected throughout the study period. This will be integrated with entomological surveillance to monitor densities and pathogen infection rates of Aedes and Anopheles mosquitoes relative to land cover. Within surrounding health clinics, continuous health facility surveillance will be used to monitor reported infections and febrile illnesses. Models will be developed to assess spillover and transmission rates relative to specific land management practices and evaluate abilities of surveillance systems to capture these risks., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Fornace K et al.)
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- 2022
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