Article
Biodiversity Conservation
Roozbeh Valavi, Jane Elith, Jose J. Lahoz-Monfort, Gurutzeta Guillera-Arroita
Summary: This study investigates the poor performance of the random forest algorithm with default parameters in species presence-background modeling, attributing it to class imbalance and class overlap. By proposing solutions and methods to manage imbalance and overlap, the algorithm's performance is improved.
Article
Ecology
Matthew T. Farr, David S. Green, Kay E. Holekamp, Elise F. Zipkin
Summary: Integrated models combining presence-only data and distance sampling data improve accuracy and precision of estimates for species abundance and covariate effects. A case study in the Masai Mara National Reserve in Kenya revealed that human disturbance was a major driver of black-backed jackal abundance patterns. The model showed minimal effects of landscape cover, lion density, and distance to water sources on jackal abundance.
Article
Biodiversity Conservation
Cristina Rueda-Uribe, Leonel Herrera-Alsina, Lesley T. Lancaster, Isabella Capellini, Kara K. S. Layton, Justin M. J. Travis
Summary: This study used citizen science data and boosted regression trees to predict the monthly distributions of 55 hummingbird species in the Andes. The findings reveal complex patterns of altitudinal and ecosystem movements in hummingbirds, with varying magnitude and impact on population trends.
Article
Multidisciplinary Sciences
Juan M. Escamilla Molgora, Luigi Sedda, Peter J. Diggle, Peter M. Atkinson
Summary: Species distribution models are widely used for mapping taxa spatially. However, current models typically rely on presence-absence data, while the available data are mainly presence-only. This study presents a Bayesian-based SDM that operates directly on presence-only data and infers absences, improving the utility of global biodiversity databases.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biodiversity Conservation
Virginia Morera-Pujol, Philip S. Mostert, Kilian J. Murphy, Tim Burkitt, Barry Coad, Barry J. McMahon, Maarten Nieuwenhuis, Kevin Morelle, Alastair I. Ward, Simone Ciuti
Summary: Using geospatial data to predict species distribution is a common tool in management and conservation. However, high-quality data is expensive, so integrated species distribution models (ISDMs) have been developed to combine high-quality presence-absence data with low-quality presence-only data. This study demonstrates the applicability of spatially explicit ISDMs to empirical data in a Bayesian context.
Article
Ecology
Malgorzata Charytanowicz, Kajetan Perzanowski, Maciej Januszczak, Aleksandra Woloszyn-Galeza, Piotr Kulczycki
Summary: This study tested a new method for evaluating the habitat preferences of wisents based on unbiased presence-only data. The results showed that wisents prefer sites with broken canopy closure, especially those on slopes. Regardless of the season, sites with a north aspect and sloping terrain were the most frequent areas of presence for wisents.
ECOLOGICAL INFORMATICS
(2022)
Article
Ecology
Victoria Nolan, Francis Gilbert, Tom Reader
Summary: By converting species presence data into 'pseudo-abundance' and using zero-inflated models to address sampling bias, greater accuracy and reliability can be achieved in species distribution modeling.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biodiversity Conservation
Sara Martino, Daniela Silvia Pace, Stefano Moro, Edoardo Casoli, Daniele Ventura, Alessandro Frachea, Margherita Silvestri, Antonella Arcangeli, Giancarlo Giacomini, Giandomenico Ardizzone, Giovanna Jona Lasinio
Summary: This study proposed a new protocol for presence-only data fusion, incorporating information sources such as social media platforms to reduce uncertainty in species distribution modeling. By analyzing spatial data on two dolphin species with different ecological characteristics and applying different detection functions and thinning methods, the study revealed the impact on ecological findings. The findings provide insights into species distribution in the study area and demonstrate the method's broad applicability.
Article
Ecology
Owain Barton, John R. Healey, Line S. Cordes, Andrew J. Davies, Graeme Shannon
Summary: The study developed a hybrid species distribution model to predict the spread of roe deer in Great Britain and applied the model to the region of Wales. The model utilized commonly available presence-only distribution data and minimal demographic information and simplified population dynamics to a set of generic rules. The study demonstrated the utility of presence-only data for predicting animal species spread and provided a method to reduce model complexity while retaining important environmental details and biological realism.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Vincent A. Landau, Barry R. Noon, David M. Theobald, N. Thompson Hobbs, Clayton K. Nielsen
Summary: Species distribution models are important tools for managing and conserving imperiled species. This study developed an integrated species distribution model to predict habitat suitability for jaguars in the border region between northern Mexico and the southwestern USA. The model results identified rugged terrain and riparian vegetation as the key factors influencing habitat use by jaguars in the study region.
ECOLOGICAL APPLICATIONS
(2022)
Article
Ecology
Florencia Grattarola, Diana E. Bowler, Petr Keil
Summary: Anthropogenic changes affect species' geographic ranges, but data on range dynamics are insufficient and biased. Integrated species distribution models (IDMs) can complement data and account for sampling effort, but are not widely used for temporal change. This study presents a generalizable model and case example to address this issue.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Ecology
Christophe Botella, Alexis Joly, Pierre Bonnet, Francois Munoz, Pascal Monestiez
Summary: This study introduces a method for jointly estimating sampling effort and species densities to avoid biases in species distribution models. The proposed method accurately estimated sampling effort when constant within spatial mesh cells. Inferences were correct and robust to sampling variation within cells, providing reliable SDM for large presence-only datasets.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Ecology
Santeri Karppinen, Tuomas Rajala, Samu Mantyniemi, Ilpo Kojola, Matti Vihola
Summary: This article introduces a statistical modeling framework based on citizen science data for identifying territories and estimating animal populations. The research shows that statistical methods can be used to assess wildlife populations using presence-only data, and provides a practical case study on estimating the number and locations of wolf territories.
ECOLOGICAL MODELLING
(2022)
Article
Statistics & Probability
Guido A. Moreira, Dani Gamerman
Summary: This paper presents an exact modeling approach for the analysis of presence-only ecological data. The proposed method achieves exactness through a data augmentation scheme and shows better performance in predictions and Bayesian inference compared to the standard method.
ANNALS OF APPLIED STATISTICS
(2022)
Article
Statistics & Probability
Ian Laga, Xiaoyue Niu, Le Bao
Summary: The study focused on estimating the size of FSW in Malawi using a Bayesian model for presence-only data from PLACE surveys, which can be utilized to implement targeted HIV prevention and treatment programs and successfully reduce the incidence of HIV and other sexually transmitted infections in FSW communities.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2022)
Article
Biochemistry & Molecular Biology
Florentin Remot, Victor Ronget, Hannah Froy, Benjamin Rey, Jean-Michel Gaillard, Daniel H. Nussey, Jean-Francois Lemaitre
Summary: The study found that telomere length generally decreases with age in adult vertebrates, but this decline is weak and varies among different classes. Detectable telomere length declines with age were only found in studies using TRF with in-gel hybridisation and qFISH methods, while no such trend was observed in studies using other methods.
Article
Ecology
Juliette Seigle-Ferrand, Pascal Marchand, Nicolas Morellet, Jean-Michel Gaillard, A. J. Mark Hewison, Sonia Said, Yannick Chaval, Hugo Santacreu, Anne Loison, Glenn Yannic, Mathieu Garel
Summary: Understanding the impact of linear landscape features on animal movements is crucial, especially in fragmented habitats. Large herbivores primarily use linear features as landmarks to demarcate their home range, with different patterns observed in mountain species. In highly fragmented landscapes, the costs of memorizing key features and the need for sufficient area to meet vital needs constrain large herbivores. Linear features play a significant role in how these animals perceive and utilize the landscape, with consistent patterns observed across sexes and species.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Ecology
Federico Ossi, Stefano Focardi, Bryony A. Tolhurst, Gian Pietro Picco, Amy L. Murphy, Davide Molteni, Noemi Giannini, Jean-Michel Gaillard, Francesca Cagnacci
Summary: Automated contact detection using proximity loggers allows for measuring encounters and time spent near resources. The inference from contact detection is linked to contact distance, which has associated errors. A probabilistic approach was used to model this relationship, showing variations based on distance, radio power, and animal movements.
JOURNAL OF WILDLIFE MANAGEMENT
(2022)
Article
Biochemistry & Molecular Biology
Jean-Francois Lemaitre, Benjamin Rey, Jean-Michel Gaillard, Corinne Regis, Emmanuelle Gilot-Fromont, Francois Debias, Jeanne Duhayer, Sylvia Pardonnet, Maryline Pellerin, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Steve Horvath
Summary: This study explores the relationship between DNA methylation and chronological age in wild roe deer populations living in different ecological contexts. Three DNA methylation-based age estimators were developed, showing that older females may exhibit a lower degree of biological aging compared to males. The research also identifies specific epigenetic alterations with distinct aging patterns between the two sexes.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Remi Fay, Sandra Hamel, Martijn van de Pol, Jean-Michel Gaillard, Nigel G. Yoccoz, Paul Acker, Matthieu Authier, Benjamin Larue, Christie Le Coeur, Kaitlin R. Macdonald, Alex Nicol-Harper, Christophe Barbraud, Christophe Bonenfant, Dirk H. Van Vuren, Emmanuelle Cam, Karine Delord, Marlene Gamelon, Maria Moiron, Fanie Pelletier, Jay Rotella, Celine Teplitsky, Marcel E. Visser, Caitlin P. Wells, Nathaniel T. Wheelwright, Stephanie Jenouvrier, Bernt-Erik Saether
Summary: Temporal correlations among demographic parameters are common, with positive correlations more frequent than negative correlations. These correlations vary significantly among species and are not strongly associated with life history pace. Ignoring temporal correlations may lead to underestimation of extinction risks in most species.
Review
Ecology
Rocio Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero, Mathieu Basille
Summary: This article provides a quantitative assessment of the research within the movement ecology framework (MEF), with a focus on animal movement. Using a text mining approach, the contents of over 8000 papers from 2009 to 2018 were analyzed, and the linkages between the components of MEF were assessed. The study reveals that while the publication rate has increased and there have been major technological changes in the field, animal movement research still primarily focuses on the effect of environmental factors, with little attention given to motion and navigation.
Article
Ecology
Sha Jiang, Harman Jaggi, Wenyun Zuo, Madan K. Oli, Tim Coulson, Jean-Michel Gaillard, Shripad Tuljapurkar
Summary: In this study, the relationship between reproductive dispersion and generation time in 633 species of animals and plants was analyzed. It was found that reproductive dispersion scales isometrically with generation time, while damping time does not. The findings suggest that damping time is influenced by factors other than allometric constraints.
Article
Forestry
William Gaudry, Jean-Michel Gaillard, Sonia Said, Anders Marell, Christophe Baltzinger, Agnes Rocquencourt, Christophe Bonenfant
Summary: The study suggests that browsing damage in forests is influenced by a complex interaction between herbivore density, forest understory composition, and relative availability. Browsing intensity increases with both plant availability and roe deer density, especially when plant availability is low.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Editorial Material
Multidisciplinary Sciences
Jean-Francois Lemaitre, Jean-Michel Gaillard, Eric Gilson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Clement Calenge, Emmanuel Menoni, Blandine Milhau, Kevin Foulche, Jules Chiffard, Stephane Marchandeau
Summary: We implemented a participatory monitoring program for the capercaillie population in the French Pyrenees based on lek censuses. By sampling known leks and searching for unknown leks, we estimated the total numbers of cocks on all leks at different spatial scales. Our findings showed that the capercaillie cock population remained stable from 2010 to 2017, but experienced a slight decrease in the foothill area and western part.
ECOLOGICAL APPLICATIONS
(2022)
Editorial Material
Ecology
Roberto Salguero-Gomez, Darren M. Evans, Jean-Michel Gaillard, Lesley Lancaster, Nathan J. Sanders, Kirsty Scandrett, Jennifer Meyer
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Evolutionary Biology
Andres Valenzuela-Sanchez, Benedikt R. Schmidt, Claudio Azat, Soledad Delgado, Andrew A. Cunningham, Jean-Francois Lemaitre, Jean-Michel Gaillard, Hugo Cayuela
Summary: Actuarial senescence, the increase in adult mortality risk with increasing age, is a widespread phenomenon. While between-species variation in ageing rate is well documented, there is debate about variation within a species. This study found significant within-species variation in the ageing rates of southern Darwin's frogs, with faster-paced populations exhibiting higher ageing rates. Amphibians, including the southern Darwin's frog, are emerging models for studying intraspecific variation in ageing rate.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Ecology
Natasha Gillies, Henri Weimerskirch, Jack Thorley, Thomas A. Clay, Lucia Martina Martin Lopez, Rocio Joo, Mathieu Basille, Samantha C. Patrick
Summary: Behavioural plasticity allows populations to adjust to environmental change, especially when genetic evolution is too slow. This study examined the relationship between boldness and behavioural plasticity in wandering albatrosses in response to wind conditions. The findings showed that movement decisions varied with boldness, with bolder birds preferring travel and shyer birds preferring search. The study also highlighted the importance of behavioural plasticity in population responses to climate change, as individual variation may limit adaptive capabilities.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Multidisciplinary Sciences
Natasha Gillies, Lucia Martina Martin Lopez, Olivier F. C. den Ouden, Jelle D. Assink, Mathieu Basille, Thomas A. Clay, Susana Clusella-Trullas, Rocio Joo, Henri Weimerskirchi, Mario Zampolli, Jeffrey N. Zeyl, Samantha C. Patrick
Summary: This study investigated whether wandering albatrosses respond to microbarom infrasound at sea. The results showed that albatrosses not only respond to winds encountered in situ but also move toward source regions associated with higher sound pressure levels. This suggests that albatrosses may be responding to long-range infrasonic cues, which are important for optimizing their flight over long distances.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Jeffrey N. Zeyl, Edward P. Snelling, Maelle Connan, Mathieu Basille, Thomas A. Clay, Rocio Joo, Samantha C. Patrick, Richard A. Phillips, Pierre A. Pistorius, Peter G. Ryan, Albert Snyman, Susana Clusella-Trullas
Summary: Birds exhibit wide variation in their use of aquatic environments, and some diving birds have the ability to detect and respond to sound underwater, possibly due to modifications in their ear structure. This study measured a suite of morphological traits related to aerial and aquatic hearing in bird ears and found significant differences in ear structure between diving birds and terrestrial species. These results confirm adaptations of the middle ear to aquatic lifestyles in birds.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Florian Lecorvaisier, Dominique Pontier, Benoit Soubeyrand, David Fouchet
Summary: Research has found that the use of vaccines that do not entirely block pathogen transmission may lead to the evolution of more virulent strains. High vaccine coverage favors the emergence and prevalence of avirulent strains, and competition between strains is crucial for the eradication of toxigenic strains when these vaccines are used.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Monica E. Barros, Ana Arriagada, Hugo Arancibia, Sergio Neira
Summary: The stock biomass of carrot prawn in the south-central area of Chile has decreased in the past 12 years, mainly due to fishing mortality. Predation mortality has been less studied and quantified, so it is important to estimate and compare predation and fishing mortality to understand their effects on fishing stocks. A food web model was built to analyze the biomass changes and evaluate the relative contribution of different mortality factors. The results showed that predation mortality was the main component of total mortality for carrot prawns and yellow prawns.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Shubham Krishna, Victoria Peterson, Luisa Listmann, Jana Hinners
Summary: This study incorporated viral dynamics into an ecosystem model to investigate the effects of viruses on ecosystem dynamics under current and future climatic conditions. The results showed that the presence of viruses increased nutrient retention in the upper water column, leading to a reduction in phytoplankton biomass and transfer of biomass to higher trophic levels.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Zahra Dehghan Manshadi, Parastoo Parivar, Ahad Sotoudeh, Ali Morovati Sharifabadi
Summary: This study demonstrates the importance of strategies such as limiting built-up areas, preserving green spaces, and protecting water resources on the urban carrying capacity in arid and semi-arid regions. Implementing a combination of policies aimed at enhancing urban green spaces and regulating water demand is found to be the most effective in terms of health and urban carrying capacity.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Shay S. Keretz, Daelyn A. Woolnough, Todd J. Morris, Edward F. Roseman, David T. Zanatta
Summary: This study surveyed native freshwater mussels in the St. Clair-Detroit River system and found 14 live unionids representing 9 species. However, the model used to predict their presence in the main channels was not successful. The study also revealed characteristic differences between the St. Clair and Detroit Rivers.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Zhengrong Zhang, Xuemei Li, Xinyu Liu, Kaixin Zhao
Summary: This study examines land use change in the Chinese Tianshan mountainous region using system dynamics and patch-generating land use simulation models. The results show an expansion in forest and construction land, a decline in grassland area, and an increase in cultivated land area from 2005 to 2020. By 2040, unused land, grassland, and water are expected to decrease while other land types increase, with construction land showing the most significant increase. The study provides insights for future ecological and environmental management in the region.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Amira Khelifa, Nadjia El Saadi
Summary: This paper develops an agent-based model to study malaria disease transmission, taking into account the interactions between hosts, vectors, and aquatic habitats, as well as their geographical locations. The simulation results highlight the significant role of aquatic habitats in infection transmission and disease persistence, and demonstrate the effectiveness of eliminating these habitats in limiting disease transmission.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Guillaume Peron
Summary: The theory for movement-based coexistence between species often overlooks small-scale, station-keeping movements. However, at this scale, there are many instances where positive correlations exist between species traits that are expected to be negatively correlated based on current theory. Through simulations, the researcher presents a counter-example to demonstrate that functional tradeoffs are not a necessary condition for movement-based coexistence. This study highlights the significance of species-specific space use patterns under the time allocation tradeoff hypothesis.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Sandra Y. Mendiola, Nicole M. Gerardo, David J. Civitello
Summary: Research on the use of insect microbial symbionts as a means of controlling the spread of insect vectors and the pathogens they carry has made significant progress in the last decade. This study focused on the relative importance of simultaneous effects caused by a symbiont called Caballeronia spp. on the ability of squash bugs to transmit phytopathogenic Serratia marcescens. The researchers found that infection with Caballeronia significantly reduced pathogen titers and cleared S. marcescens in bugs, thus reducing the vectoring potential of these pests. The study also showed that maximizing symbiont prevalence in the vector population is crucial for effectively mitigating plant infections.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Shirui Hao, Dongryeol Ryu, Andrew W. Western, Eileen Perry, Heye Bogena, Harrie Jan Hendricks Franssen
Summary: This study investigates the sensitivity of model yield prediction to uncertainties in model parameters and inputs using the Sobol' method. The results show that yield is more sensitive to changes in water availability and nitrogen availability, depending on soil, management, and weather conditions.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Nitika Mundetia, Devesh Sharma, Aditya Sharma
Summary: This study focused on assessing groundwater sustainability using different modeling approaches in a river basin in Rajasthan, India. The results showed a decrease in future groundwater recharge and emphasized the need for better management and conservation practices to achieve sustainable development goals.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Sukdev Biswas, Sk Golam Mortoja, Ritesh Kumar Bera, Sabyasachi Bhattacharya
Summary: Bacteria play a crucial role in regulating the nutrient cycle of ecosystems, and maintaining a thriving bacterial population is essential for the sustainability of these environments. This study introduces the concept of cooperation as a group defense mechanism employed by bacteria and incorporates it into the functional response, offering a more comprehensive understanding of the complex tritrophic food chain dynamics. The results highlight the importance of a balance between strong group defense and moderate cooperation for bacteria sustainability and overall system stability.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
D. Z. M. Le Gouvello, S. Heye, L. R. Harris, J. Temple-Boyer, P. Gaspar, M. G. Hart-Davis, C. Louro, R. Nel
Summary: This study modeled the dispersal pathways and compared potential dispersal corridors of different sea turtle species in the Western Indian Ocean. The results showed that ocean currents play a major role in driving dispersal, with species and years exhibiting differences in dispersal patterns. Active swimming had little influence on dispersal during the first year.
ECOLOGICAL MODELLING
(2024)
Review
Ecology
Yingying Duan, Haina Rong, Gexiang Zhang, Sergey Gorbachev, Dunwu Qi, Luis Valencia-Cabrera, Mario J. Perez-Jimenez
Summary: Computing models are an effective way to study population dynamics of endangered species like giant pandas. This paper proposes a unified framework and conducts a comprehensive survey of computing models for giant panda ecosystems. Multi-factor computing models are more suitable for studying giant panda ecosystems.
ECOLOGICAL MODELLING
(2024)
Article
Ecology
Samantha Lai, Theophilus Zhi En Teo, Arief Rullyanto, Jeffery Low, Karenne Tun, Peter A. Todd, Siti Maryam Yaakub
Summary: Understanding the exchange of genetic material among populations in the marine environment is crucial for conservation efforts. Agent-based models are increasingly used to predict dispersal pathways, including for seagrasses. This study highlights the importance of considering both sexual propagules and asexual vegetative fragments when evaluating seagrass connectivity.
ECOLOGICAL MODELLING
(2024)