Article
Multidisciplinary Sciences
Justin J. Van Ee, Jacob S. Ivan, Mevin B. Hooten
Summary: Joint species distribution models are commonly used to study species-environment relationships and species dependence. This study introduces a method for measuring community confounding and demonstrates how to orthogonalize the environmental and random species effects in joint species distribution models. The results show that community confounding can lead to computational difficulties, but orthogonalizing the effects can alleviate these difficulties. The implications of community confounding and orthogonalization are discussed through a case study on mammalian responses to a bark beetle epidemic.
SCIENTIFIC REPORTS
(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
Ecology
Daria Bystrova, Giovanni Poggiato, Billur Bektas, Julyan Arbel, James S. Clark, Alessandra Guglielmi, Wilfried Thuiller
Summary: Researchers introduced a Dirichlet process to further reduce model dimension by clustering species in the residual covariance matrix, proposing a framework that includes prior knowledge and demonstrating improved dimension reduction in a case study of plant communities. This approach revealed additional information from the residual covariance matrix and showed how estimated clusters align with plant traits, highlighting their importance in shaping communities.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Joshua S. North, Erin M. Schliep, Gretchen J. A. Hansen, Holly Kundel, Christopher A. Custer, Paul Mclaughlin, Tyler Wagner
Summary: Estimating relative abundance is crucial for conservation and management efforts in freshwater fisheries. This study developed a joint species distribution model (JSDM) that accounts for varying sampling conditions and captures seasonal variation in species life history. The findings show that not accounting for these variations can bias the inference of relative abundance, limiting our ability to detect responses to management interventions and environmental change. The model can be applied to other systems where catchability may vary as a function of space, time, and species.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Ecology
Megan R. Laxton, Oscar Rodriguez de Rivera, Andrea Soriano-Redondo, Janine B. Illian
Summary: The potential for statistical complexity in species distribution models has increased with computational power. Complex models can analyze ecological systems and messy data, but may be difficult to interpret. Founding model complexity in ecological theory can improve insights gained from SDMs. Evaluating a marked point process approach, this study discusses the role of model components and their impacts on predictions. Including complex components can account for spatio-temporal population dynamics not explained by environmental variables. However, the inclusion of certain temporal correlation structures may lead to unrealistic predictions, emphasizing the need for careful consideration of model complexity.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Ramiro Martin-Devasa, Sara Martinez-Santalla, Carola Gomez-Rodriguez, Rosa M. Crujeiras, Andres Baselga
Summary: This study aimed to assess the dependence between the form of the decrease in biological similarity with distance (distance-decay) and species range size, and introduced the use of a sigmoidal model, the Gompertz function, for fitting distance-decay models. The results showed that the functional form of distance-decay patterns depends on species range size, and the Gompertz function accommodates different frequency distributions of species range size.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Ecology
Francis K. C. Hui, David I. Warton, Scott D. Foster, Christopher R. Haak
Summary: We introduce community-level basis function models (CBFMs) as an approach for spatiotemporal joint distribution modelling. CBFMs can be viewed as related to spatiotemporal latent variable models, where the latent variables are replaced by a set of pre-specified spatiotemporal basis functions which are common across species. CBFMs can be used for a variety of reasons, such as inferring patterns of habitat use in space and time, understanding how residual covariation between species varies spatially and/or temporally, and spatiotemporal predictions of species-and community-level quantities.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Jeffrey W. Doser, Andrew O. Finley, Sudipto Banerjee
Summary: Determining the spatial distributions of species and communities is important in ecology and conservation efforts. We developed a spatial factor multi-species occupancy model to explicitly account for species correlations, imperfect detection, and spatial autocorrelation. Ignoring these complexities leads to inferior model predictive performance, and our proposed model had the highest predictive performance among the alternative models.
Article
Environmental Sciences
Yin-Zheng Lai, Chih-Wei Tu, Chih-hao Hsieh, Chia-Ying Ko
Summary: Environmental and climatic changes are expected to redistribute species, altering the strengths of species interaction networks. One way to infer species interaction networks is by analyzing their geographical overlaps, which provides indices of species interdependence. Integrating MSR and MSS further allows us to assess community coexistence stability and structure, with a stronger negative relationship between MSR and MSS within a community suggesting a more stable community.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Stephanie Elizabeth Hogg, Yan Wang, Lewi Stone
Summary: Joint species distribution models (JSDMs) that explicitly account for imperfect detection can accurately estimate intrinsic correlation between species with sufficient survey sites and replications. However, reducing the number of survey sites decreases precision of estimates, while reducing the number of survey replications can lead to biased estimates. For low detection probabilities, a large number of survey replications may be required to remove bias from estimates. JSDMs not explicitly accounting for detection have limited ability to disentangle detection from occupancy, reducing their ability to accurately infer species distribution spatially.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Ecology
Stephen J. Murphy, Adam B. Smith
Summary: Species distribution and ecological niche models are widely used tools in research and conservation, but their potential in understanding community-level patterns is an emerging field. This review discusses important topics such as predicting community attributes and rare species detection, highlighting the role these models can play in advancing community ecology.
Article
Ecology
Maximilian Pichler, Florian Hartig
Summary: The newly developed sjSDM model can rapidly and accurately analyze large-scale community data, avoiding the use of latent variables, thus providing important applications for JSDMs in ecology.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Environmental Sciences
Alan E. Gelfand, Shinichiro Shirota
Summary: Joint species distribution modeling is gaining attention due to the limitations of individual level modeling in capturing species interactions. These joint models capture species dependence through correlation matrices and spatial dependence. Odds ratios and spatial odds ratios are used to better understand the practical dependence between species. The study uses data from South Africa to illustrate the spatial distribution of odds ratios for positively and negatively correlated species pairs under the joint species distribution model.
ENVIRONMENTAL AND ECOLOGICAL STATISTICS
(2021)
Article
Biodiversity Conservation
Alice Monnier-Corbel, Alexandre Robert, Yves Hingrat, Blas M. Benito, Anne-Christine Monnet
Summary: Habitat Suitability Index (HSI) derived from Species Distribution Model (SDM) has been used to infer or predict local demographic properties such as abundance for many species. However, the relationship between HSI and abundance has been a topic of debate, with some studies showing a lack of correlation. To better understand this relationship, we studied the temporal variation of HSI and abundance using data from a 10-year monitoring of a Houbara bustard population in Morocco. Our results showed a triangular relationship between local abundance and HSI, with the upper limit of abundance increasing with HSI. Additionally, sites with the highest HSI had the least variation in abundance. These findings provide empirical evidence supporting the importance of investigating the relationship between HSI and abundance using temporal variation.
GLOBAL ECOLOGY AND CONSERVATION
(2023)
Article
Ecology
Alba Cervantes-Loreto, Carolyn A. Ayers, Emily K. Dobbs, Berry J. Brosi, Daniel B. Stouffer
Summary: Animals change their behavior in the presence of other species and the environment, impacting population dynamics. A framework using pollinator functional responses was proposed to examine how behavioral changes influence the interactions between pollinators and the environment. The study found that co-foragers interfere with the focal pollinator, with interference being strongest at higher resource levels and pesticide exposure.
Article
Ecology
Stefan J. G. Vriend, Vidar Grotan, Marlene Gamelon, Frank Adriaensen, Markus P. Ahola, Elena Alvarez, Liam D. Bailey, Emilio Barba, Jean-Charles Bouvier, Malcolm D. Burgess, Andrey Bushuev, Carlos Camacho, David Canal, Anne Charmantier, Ella F. Cole, Camillo Cusimano, Blandine F. Doligez, Szymon M. Drobniak, Anna Dubiec, Marcel Eens, Tapio Eeva, Kjell Einar Erikstad, Peter N. Ferns, Anne E. Goodenough, Ian R. Hartley, Shelley A. Hinsley, Elena Ivankina, Rimvydas Juskaitis, Bart Kempenaers, Anvar B. Kerimov, John Atle Kalas, Claire Lavigne, Agu Leivits, Mark C. Mainwaring, Jesus Martinez-Padilla, Erik Matthysen, Kees van Oers, Markku Orell, Rianne Pinxten, Tone Kristin Reiertsen, Seppo Rytkonen, Juan Carlos Senar, Ben C. Sheldon, Alberto Sorace, Janos Torok, Emma Vatka, Marcel E. Visser, Bernt-Erik Saether
Summary: Identifying the environmental drivers of variation in fitness-related traits is important in ecology and evolution. This study examined the influence of local climatic variables on spatial synchrony in fitness-related traits among bird populations in Europe. The researchers found that temperature strongly affected spatial synchrony in laying date for blue tits and great tits but not for pied flycatchers. Understanding how environmental conditions influence trait values improves our understanding of environmental impacts on populations.
Article
Ecology
Veera Norros, Panu Halme, Anna Norberg, Otso Ovaskainen
Summary: The study found that spore production in fungi is influenced by environmental conditions and species traits. The timing and patterns of spore release are important for dispersal. There is a trade-off between spore size and number, and different species have different strategies in spore release timing.
FUNCTIONAL ECOLOGY
(2023)
Article
Ecology
Benjamin Weigel, Niina Kotamaki, Olli Malve, Kristiina Vuorio, Otso Ovaskainen
Summary: Lake phytoplankton communities have undergone significant changes due to eutrophication, land-use, and climate change, resulting in the emergence of novel community types and functional differences. The spatio-temporal dynamics have strongly influenced the assembly mechanisms of phytoplankton communities.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Biology
Sara Hamis, Panu Somervuo, J. Arvid Agren, Dagim Shiferaw Tadele, Juha Kesseli, Jacob G. G. Scott, Matti Nykter, Philip Gerlee, Dmitri Finkelshtein, Otso Ovaskainen
Summary: Spatial cumulant models (SCMs) provide a mathematical framework to accurately describe the dynamics of theoretical cancer cell populations generated by spatio-temporal point processes (STPPs). By using SCMs, we can study cell-cell interactions and design more effective treatment strategies to inhibit population growths.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Statistics & Probability
Georgia Papadogeorgou, Carolina Bello, Otso Ovaskainen, David B. Dunson
Summary: Reductions in natural habitats require a better understanding of species' interconnection and how ecosystems respond to environmental changes. This study focuses on bird-plant interactions, specifically on potential fruit consumption and seed dispersal. The researchers develop a method for predicting species' interactions that addresses biases in existing studies and incorporates covariates to inform the latent factors.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Article
Ecology
Joao Carlos Pena, Otso Ovaskainen, Ian MacGregor-Fors, Camila Palhares Teixeira, Milton Cezar Ribeiro
Summary: The urbanization process leads to changes in bird communities, with highly urbanized areas exhibiting a reduced number of bird species sharing few functional traits. However, most urban bird studies have focused on temperate cities and vegetation patches. This study investigates how urban environmental attributes modulate species occurrences and the distribution of functional traits across the streetscape of a tropical metropolis, predicting diverse trait-environment relationships but fewer species with generalist traits in highly urbanized contexts.
LANDSCAPE AND URBAN PLANNING
(2023)
Article
Ecology
Adrian Barrero, Otso Ovaskainen, Juan Traba, Julia Gomez-Catasus
Summary: The study investigates the co-occurrence patterns of steppe passerines in a natural habitat and suggests that competition and dominance processes play a significant role in shaping bird assemblages. The Eurasian skylark appears to be the dominant species in the community, negatively associating with many coexistent species.
Article
Ecology
Koen de Koning, Jeroen Broekhuijsen, Ingolf Kuehn, Otso Ovaskainen, Franziska Taubert, Dag Endresen, Dmitry Schigel, Volker Grimm
Summary: Digital twins are emerging as a new tool in monitoring and understanding systems and processes, with the potential to transform ecology digitally. However, it is crucial to avoid misguided developments and instead combine data, models, and domain knowledge and align them with the real world.
TRENDS IN ECOLOGY & EVOLUTION
(2023)
Article
Ecology
Camila Leandro, Mirkka Jones, William Perrin, Pierre Jay-Robert, Otso Ovaskainen
Summary: Mediterranean landscapes in Europe have recently experienced changes in biodiversity, with human activities and habitat fragmentation affecting dung beetles and their responses to landscape composition being rarely investigated.
Article
Multidisciplinary Sciences
Andrea Santangeli, Benjamin Weigel, Laura H. Anto, Elina Kaarlejaervi, Maria Haellfors, Aleksi Lehikoinen, Andreas Linden, Maija Salemaa, Tiina Tonteri, Paeivi Merilae, Kristiina Vuorio, Otso Ovaskainen, Jarno Vanhatalo, Tomas Roslin, Marjo Saastamoinen
Summary: Protected areas have mixed impacts on reducing local extinctions, with only a small proportion of species benefiting explicitly. The benefits of protection are related to the size and establishment time of the protected areas, but unrelated to the conservation status or traits of species. Improving coverage, connectivity, and management will be crucial to enhance the effectiveness of protected areas in slowing down biodiversity loss.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Ryan C. Burner, Joerg G. Stephan, Lukas Drag, Maria Potterf, Tone Birkemoe, Juha Siitonen, Jorg Mueller, Otso Ovaskainen, Anne Sverdrup-Thygeson, Tord Snaell
Summary: Functional trait approaches in ecology often face challenges due to the lack of clear hypotheses about trait-niche relationships. This study investigated how different metrics affect inferences about trait-niche relationships using saproxylic beetles in fragmented Finnish forests. The results showed that community-weighted mean trait values (CWMs) were more likely than hierarchical joint species distribution models (JSDMs) to support trait-niche relationships.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Helena Wirta, Mirkka Jones, Pablo Pena-Aguilera, Camilo Chacon-Duque, Eero Vesterinen, Otso Ovaskainen, Nerea Abrego, Tomas Roslin
Summary: This study investigated the impact of seasonality and management on honeybee interactions by analyzing DNA content in beehive samples collected during the honey-storing period in Finland. The results showed that honeybee interactions with other taxa varied among different taxonomic and functional groups, with relatively minor effects of seasonality.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Benjamin Weigel, Caio Graco-Roza, Jenni Hultman, Virpi Pajunen, Anette Teittinen, Maria Kuzmina, Evgeny V. V. Zakharov, Janne Soininen, Otso Ovaskainen
Summary: Understanding how species respond to land-use change is crucial for the expansion of agricultural areas and increasing pressures from land-use. Microbial communities display the fastest responses to environmental change and provide key ecosystem functions. However, regional land-use effects on local environmental conditions are often underestimated, highlighting the importance of considering these effects when studying community responses.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Laura Bosco, Valentin Moser, Mirkka M. M. Jones, Oystein Opedal, Otso Ovaskainen, Gerber Sonja, Roel Van Klink, Samuel A. A. Cushman, Raphael Arlettaz, Alain Jacot
Summary: Fragmentation of habitat caused by intensive agriculture can harm local biodiversity, but it is unclear whether this is due to loss of habitat area or increased fragmentation, as well as how habitat quality factors in. We found that increased ground vegetation density and larger habitat areas favor more diverse and abundant insect communities, while fragmentation effects vary and depend on the species. Therefore, implementing nature-friendly farming practices and maintaining high ground vegetation density in vineyards can promote diverse insect communities.
ECOLOGICAL SOLUTIONS AND EVIDENCE
(2023)
Article
Ecology
Sonja Saine, Reijo Penttila, Brendan Furneaux, Norman Monkhouse, Evgeny V. Zakharov, Otso Ovaskainen, Nerea Abrego
Summary: This study compares wood-inhabiting fungal communities between naturally fallen spruce logs and logs felled for restoration using DNA metabarcoding. The results show that felled logs still hold a relatively high fungal diversity, although there are differences in the composition of pioneering fungal communities between natural and felled logs. Orders Polyporales and Hymenochaetales, including species of conservation concern, are more likely to occur in natural logs. Rare species are more specialized in their habitat requirements than common ones. The study highlights the importance of retaining existing natural deadwood for restoration.
RESTORATION ECOLOGY
(2023)