Article
Ecology
Malcolm O'Toole, Nuno Queiroz, Nicolas E. Humphries, David W. Sims, Ana M. M. Sequeira
Summary: Telemetry datasets are increasingly large and cover a wide range of species, allowing for the understanding of species' spatial use. However, biases in tracking datasets can affect model performance, with tagging location and track length having the greatest impact. Adding less biased tracks can help overcome these biases.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Mathematics, Applied
Alexander Strang, Karen C. Abbott, Peter J. Thomas
Summary: Competitive tournaments are found in various fields and have developed methods for evaluating and ranking competitors. Intransitive tournaments, which contain both cyclic and non-cyclic components, can be accurately described using the discrete Helmholtz-Hodge decomposition (HHD). The HHD naturally emerges from two types of tournaments with simple statistical interpretations, making it a preferred method over others. The traits of competitors play a crucial role in determining their success in competition, and a trait-performance model allows for explicit computation of the degree of intransitivity in the network. Increasing the number of potential competitors promotes cyclic competition, while correlation between performance against different competitors promotes transitive competition.
Article
Mathematics, Interdisciplinary Applications
I. Creus Marti, A. Moya, F. J. Santonja
Summary: This paper presents a Bayesian model for analyzing longitudinal gut microbiome data, taking into account compositional paradigm and principal balances. The proposed model is able to predict future dynamics of microbial community in the short term and analyze microbial interactions using estimated parameters. It is demonstrated to be useful through the analysis of six different datasets and comparison with four alternative models.
Article
Ecology
Jay M. Ver Hoef, Devin Johnson, Robyn Angliss, Matt Higham
Summary: This study analyzed a massive opportunistic dataset of incidental shipboard observations of marine mammals to create species density maps using spatial regression for count data with an effort offset. Two marine mammal species in the Gulf of Alaska and Bering Sea were used as examples. The study employed spatial count regression with random effects and MCMC sampling to estimate abundance and identify hotspots.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Review
Mathematics, Interdisciplinary Applications
Bo-Wen Shen
Summary: This review provides an overview of Lorenz models between 1960 and 2008, classifying them into six categories based on different types of Partial Differential Equations (PDEs). These models have contributed significantly to our understanding of chaos, the butterfly effect, attractor coexistence, and intransitivity (or almost intransitivity) across various scientific fields.
INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS
(2023)
Review
Biodiversity Conservation
Conor Waldock, Rick D. Stuart-Smith, Camille Albouy, William W. L. Cheung, Graham J. Edgar, David Mouillot, Jerry Tjiputra, Loic Pellissier
Summary: The contributions of species to ecosystem functions or services depend on their presence and local abundance, but current predictive spatial models focus more on species occurrence rather than abundance. The study found significant variation in the performance of abundance-based models, with random forests providing the best predictions in certain scenarios.
Article
Ecology
Erik Blystad Solbu, Bert van der Veen, Ivar Herfindal, Knut Anders Hovstad
Summary: This paper demonstrates the use of generalized linear mixed models to study dynamic species abundance distributions, with simulations and case studies on fish and bat communities. The main finding is that species heterogeneity is the main factor influencing community similarity.
Article
Ecology
Xiao Feng, Huijie Qiao
Summary: The study proposed a conceptual framework based on environmental suitability and dispersal to interpret the mixed evidence on species population distribution across space. The results showed that the highest abundance could occur in the geographical centre, niche centre, or somewhere in between, depending on environmental setup and dispersal ability. Geographical and niche centres rarely overlapped, indicating a counteracting effect between the two factors in determining abundance patterns.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Astronomy & Astrophysics
Chengyu Xi, James E. Taylor
Summary: The study presents a new method for quantifying the abundance of satellites around field galaxies and in groups, by identifying galaxies likely to be centrals and using clustering signal to decompose the population. The method assigns probabilities to each galaxy of being a satellite or central, providing a statistical estimate of satellite abundance. Testing the method on data from the COSMOS field, the results are consistent with previous studies and extend over a broader range of central masses.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Plant Sciences
Lian Liu, Junhui Cheng, Yawen Li, Zhichun Lan, Yongfei Bai
Summary: Intransitive competition is an important mechanism promoting species coexistence and biodiversity maintenance, sensitive to nitrogen enrichment and spatial scale. The degree of competitive intransitivity generally decreases with increasing spatial scale, with different effects on common and rare species.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Ecology
Corey T. Callaghan, Diana E. Bowler, Shane A. Blowes, Jonathan M. Chase, Mitchell B. Lyons, Henrique M. Pereira
Summary: Broad-scale biodiversity monitoring relies on citizen scientists. It is important to understand the spatial pattern of citizen scientists' sampling effort and its deviation from an optimal pattern. This study develops a workflow to estimate the optimal distribution of sampling effort for species diversity inference using citizen science data.
Article
Multidisciplinary Sciences
Tyler Wagner, Erin M. Schliep, Joshua S. North, Holly Kundel, Christopher A. Custer, Jenna K. Ruzich, Gretchen J. A. Hansen
Summary: By combining observations of species abundance and environmental conditions with laboratory-derived data on the physiological response of poikilotherms to temperature, a physiologically guided abundance (PGA) model was developed to predict species geographical distributions and abundance in response to climate change. The model incorporates uncertainty in laboratory-derived thermal response curves and provides estimates of thermal habitat suitability and extinction probability based on site-specific conditions. The results show that considering physiological information greatly affects temperature-driven changes in distributions, local extinction, and abundance of cold, cool, and warm-adapted species. Failure to account for species-specific physiological constraints could lead to unrealistic predictions under a warming climate.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biodiversity Conservation
Alexander Zizka, Alexandre Antonelli, Daniele Silvestro
Summary: Geo-referenced species occurrences from public databases are essential for biodiversity research and conservation, but are often limited by geographical biases. The sampbias algorithm and software can quantify accessibility biases in species occurrence data, and has been successfully used on a dataset of mammal occurrences from the island of Borneo.
Article
Computer Science, Artificial Intelligence
Rami Al-Hmouz, Witold Pedrycz, Ahmed Chiheb Ammari, Ahmed Al-Hmouz
Summary: In this study, the level of difficulty in designing a model based on training data is discussed, and a variability index is proposed to quantify the nature of data. The index is model-neutral and can describe and quantify the modeling challenge irrespective of the specific model. Additionally, a method of reducing the variability index through nonlinear transformation and fuzzy rule-based model is introduced, and the concept of adversarial data is quantified using granular features.
INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS
(2022)
Article
Biochemical Research Methods
Fan Xu, Shike Wang, Xinnan Dai, Piyushkumar A. Mundra, Jie Zheng
Summary: In this study, different machine learning methods were compared and ensemble learning was found to outperform neural network models, with Random Forest performing the best overall. The feature importance scores from Random Forest were used to interpret biological mechanisms underlying the prediction, aiding in improving prediction performance. This research demonstrates the effectiveness of ensemble learning for reliable protein abundance prediction using single-cell multimodal omics data, and opens up avenues for knowledge discovery through mining large-scale single-cell multi-omics data.
Article
Ecology
Nicholas J. Gotelli, Douglas B. Booher, Mark C. Urban, Werner Ulrich, Andrew Suarez, David K. Skelly, David J. Russell, Rebecca J. Rowe, Matthew Rothendler, Nelson Rios, Sandra M. Rehan, George Ni, Corrie S. Moreau, Anne E. Magurran, Faith A. M. Jones, Gary R. Graves, Cristina Fiera, Ulrich Burkhardt, Richard B. Primack
Summary: Using museum specimens can be a valuable method to estimate species' relative abundance, although the estimates for rare species tend to be overestimated. However, the relative abundance estimated from museum records has a strong correlation with the estimates from standardized field surveys.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Jan Christian Habel, Werner Ulrich, Jonas Eberle, Thomas Schmitt
Summary: Standardised biodiversity assessment is crucial for understanding community structures and population dynamics of animals. Different methods exist for monitoring biodiversity, with advantages and disadvantages. The choice of method depends on the target species group, research aim, habitat conditions, and season. In this study, transect counts and bait trapping were used to assess butterfly diversity in the dryland savannah biome of south-eastern Kenya. Transect counts recorded significantly more species and individuals than bait trapping, but bait trapping was better at capturing larger and more mobile species. Seasonality and land-use had a more pronounced effect on transect data than trap data.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Geochemistry & Geophysics
Yanchuang Zhao, Emilio Guirado, Juan J. Gaitan, Fernando T. Maestre
Summary: Emerging evidence suggests that increasing atmospheric aridity, a key aspect of climate change, leads to multiple thresholds in ecosystem responses across global drylands. In Patagonia, Argentina, the relationship between nutrient cycling index (a proxy for ecosystem functioning) and remote sensing indicators varies significantly along different aridity gradients, with distinct thresholds identified. The study indicates that empirical models relying solely on reflectance inputs are unreliable under the most arid conditions, emphasizing the importance of considering aridity thresholds when using remote sensing to monitor changes in ecosystem functioning.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Plant Sciences
Concha Cano-Diaz, Fernando T. Maestre, Juntao Wang, Jing Li, Brajesh K. Singh, Victoria Ochoa, Beatriz Gozalo, Manuel Delgado-Baquerizo
Summary: Photoautotrophic soil cyanobacteria play essential ecological roles and their diversity and abundance remain relatively stable during soil development, while vegetation change has a significant impact on the composition of soil cyanobacterial communities.
Article
Ecology
Werner Ulrich, Buntarou Kusumoto, Takayuki Shiono, Akinori Fuji, Yasuhiro Kubota
Summary: This study examines the expression and variability of major reproductive traits in Japanese angiosperm woody plants at different latitudes. The results show strong latitudinal gradients in different traits, which may be attributed to ecological filtering and increased numbers of generalist pollinators at higher latitudes.
ECOLOGICAL RESEARCH
(2023)
Article
Mathematics, Applied
Piotr Juszczyk, Wojciech Kryszewski
Summary: The Darboux theorem states the intermediate value property of the derivative of a real function, with numerous counterparts in multivariate calculus and infinite-dimensional settings. This paper discusses some infinite-dimensional variants of the Darboux theorem and explores different notions of nonsmooth differentiability and compactness conditions.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Review
Agriculture, Multidisciplinary
Enrique G. de la Riva, Werner Ulrich, Peter Batary, Julia Baudry, Lea Beaumelle, Roman Bucher, Andrea Cerevkova, Maria R. Felipe-Lucia, Robert Galle, Emmanuelle Kesse-Guyot, Ewa Rembialkowska, Adrien Rusch, Verena Seufert, Dara Stanley, Klaus Birkhofer
Summary: Agricultural intensification has contributed to global food security and well-being, but it has also led to negative impacts on species diversity and ecosystem functioning. This review proposes a conceptual framework to understand the relationship between functional diversity and human well-being, highlighting the need for further research on this topic.
AGRICULTURAL SYSTEMS
(2023)
Article
Ecology
Pierrick Bourrat, William Godsoe, Pradeep Pillai, Tarik C. Gouhier, Werner Ulrich, Nicholas J. Gotelli, Matthijs van Veelen
Summary: The Dialogue series aims to foster critical thinking and encourage the expression of opposing viewpoints on important ecological topics. In this instance, seven researchers engage in a debate over the use of the Price equation, a long-standing framework in evolutionary analysis. The Dialogue provides insight into diverse philosophical and mathematical perspectives on applying the Price equation to ecological questions, such as the relationship between biodiversity and ecosystem functioning. The goal is for the broader scientific community to benefit from these contrasting viewpoints.
Article
Ecology
Francesco Vitali, Jan Christian Habel, Werner Ulrich, Thomas Schmitt
Summary: Temperature increases and land-use changes are affecting the annual activity periods and species composition of longhorn beetles in Luxembourg. Through the analysis of long-term data sets from 1864 to 2014, it was found that higher annual temperatures are associated with earlier annual appearances of the beetles. Additionally, the study revealed changes in beetle communities and an increase in species richness over the past 40 years.
Article
Plant Sciences
Werner Ulrich, Markus Klemens Zaplata
Summary: Habitat filtering, species interactions, neutral colonization and extinction dynamics are important factors determining the sequence of community assembly and functional diversity during primary plant succession. Through analyzing data on plant seed traits from 107 study plots over 7 years, we found that temporal changes in functional diversity were influenced by trait expression, species richness and plant cover. Species richness and community composition played a dominant role in shaping functional diversity.
Article
Environmental Sciences
Jan Christian Habel, Werner Ulrich, Patrick Gros, Mike Teucher, Thomas Schmitt
Summary: Climate change has a significant impact on biodiversity and ecosystem functions, causing species to shift their distributions and communities to change. In a study of lowland butterflies and burnet moths in Salzburg, Austria, it was found that these species have shifted their occurrence uphill by more than 300 meters in the past 70 years. Habitat generalists and mobile species showed the strongest shifts, while specialists and sedentary species showed the weakest shifts. These findings highlight the increasing impact of climate change on species distribution patterns and local community composition.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Amy K. Hahs, Bertrand Fournier, Myla F. J. Aronson, Charles H. Nilon, Adriana Herrera-Montes, Allyson B. Salisbury, Caragh G. Threlfall, Christine C. Rega-Brodsky, Christopher A. Lepczyk, Frank A. La Sorte, Ian MacGregor-Fors, J. Scott MacIvor, Kirsten Jung, Max R. Piana, Nicholas S. G. Williams, Sonja Knapp, Alan Vergnes, Aldemar A. Acevedo, Alison M. Gainsbury, Ana Rainho, Andrew J. Hamer, Assaf Shwartz, Christian C. Voigt, Daniel Lewanzik, David M. Lowenstein, David O'Brien, Desiree Tommasi, Eduardo Pineda, Ela Sita Carpenter, Elena Belskaya, Gabor L. Loevei, James C. Makinson, Joanna L. Coleman, Jon P. Sadler, Jordan Shroyer, Julie Teresa Shapiro, Katherine C. R. Baldock, Kelly Ksiazek-Mikenas, Kevin C. Matteson, Kyle Barrett, Lizette Siles, Luis F. Aguirre, Luis Orlando Armesto, Marcin Zalewski, Maria Isabel Herrera-Montes, Martin K. Obrist, Rebecca K. Tonietto, Sara A. Gagne, Sarah J. Hinners, Tanya Latty, Thilina D. Surasinghe, Thomas Sattler, Tibor Magura, Werner Ulrich, Zoltan Elek, Jennifer Castaneda-Oviedo, Ricardo Torrado, D. Johan Kotze, Marco Moretti
Summary: Cities can support diverse and distinct biological communities, but urbanization also leads to the loss of habitats and species. This global analysis on vertebrate and invertebrate species shows that urbanization causes taxon-specific changes in trait composition, with reproductive strategy traits showing the strongest response. Maximizing opportunities to support different urban trait syndromes is crucial for conservation and management programs in cities.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Werner Ulrich, Thomas Schmitt, Patrick Gros, Robert Trusch, Jan Christian Habel
Summary: The study analyzes museum data of butterflies and burnet moths from Germany and Austria to understand the spatiotemporal variability in insect abundances. The results show that population fluctuations and long-term trends in community composition are positively correlated across larger spatial distances and are influenced by global factors such as land use and urbanization. The study also highlights the importance of natural landscapes for conservation strategies due to their association with higher faunal compositional variability.
Article
Statistics & Probability
Akinori Fuji, Buntarou Kusumoto, Takayuki Shiono, Yasuhiro Kubota, Werner Ulrich, John B. Dickie, Si-Chong Chen
Summary: Seed dormancy is associated with seed mass and dispersal mode, and these associations can help us understand trait-based community assembly and plant biogeography. The geographic patterns of dormancy/non-dormancy strategies are shaped by climate factors and indicate the filtering/sorting processes related to seed traits.
JAPANESE JOURNAL OF STATISTICS AND DATA SCIENCE
(2023)
Review
Biodiversity Conservation
Werner Ulrich, Peter Batary, Julia Baudry, Lea Beaumelle, Roman Bucher, Andrea Cerevkova, Enrique G. de la Riva, Maria R. Felipe-Lucia, Robert Galle, Emmanuelle Kesse-Guyot, Ewa Rembialkowska, Adrien Rusch, Dara Stanley, Klaus Birkhofer
Summary: There is ample evidence suggesting that species diversity has positive effects on ecosystem functioning and services in both natural and agricultural landscapes. However, the effects of such diversity on human well-being are less clear and have been subject to debate. This is partly due to methodological difficulties in evaluating and quantifying these effects and the lack of precise conceptual frameworks. In this article, a conceptual framework is proposed that links different aspects of diversity to ecosystem functioning, ecosystem services and disservices, and different aspects of well-being. Despite the progress, there are still shortcomings and obstacles in the current approaches and it is important to establish stricter terminology and evaluate each step in the pathways from diversity to well-being. Long-term socio-ecological research platforms are also needed to gather relevant data on ecosystem functioning and well-being.