Article
Biology
Kawika Pierson
Summary: This paper demonstrates that families of divergence-based evenness measures nest and can be ranked based on uniformity changes. By deriving new distance-based measures, it captures the angular distance between relative abundance vectors, providing a highly reactive approach to changes in uniform assemblages.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Plant Sciences
Maria Papadopoulou, Ioannis Tsiripidis, Sampson Panajiotidis, Georgios Fotiadis, Daniel Veres, Eniko Magyari, Marc Bormann, Sonia Fontana, Lyudmila Shumilovskikh, Konstantinos Panagiotopoulos, Frank Schabitz, Thomas Giesecke
Summary: This study compared pollen assemblages from two different regions in southeastern Europe to the surrounding vegetation and found that pollen assemblages are more effective at reflecting the presence or absence of plants rather than their abundance. Additionally, the bias in pollen assemblages increases with landscape openness and vegetation diversity.
VEGETATION HISTORY AND ARCHAEOBOTANY
(2022)
Article
Ecology
Martin Bitomsky, Hanno Schaefer, Robin J. Pakeman, Jitka Klimesova, Lars Gotzenberger, Martin Duchoslav
Summary: This study investigates the relationship between plant mycorrhizal status diversity and soil nutrient availability, taking into account within-plot mycorrhizal status variability. The results show that within-plot variability is more important than between-plot variability in determining mycorrhizal status. Plant mycorrhizal status diversity is positively related to Ca and Mg, but the relationship with Mg varies depending on phylogeny. There is no clear relationship between mycorrhizal status diversity and P, and the relationship with K is inconsistent.
Article
Forestry
Lin Li, Zhifeng Wen, Shiguang Wei, Juyu Lian, Wanhui Ye
Summary: Functional diversity is crucial for the connection between ecosystem functions and biodiversity, and its understanding is important for community diversity conservation strategies. In this study, a subtropical forest community in China was investigated, and functional diversity indices were calculated based on functional traits of plant species. The results showed significant differences in functional diversity and species diversity indices based on plant habit, as well as correlations among different functional richness and divergence indices. Altitude and other environmental factors also influenced the functional diversity of the community. Soil total phosphorus was identified as the most critical environmental factor. These findings contribute to our understanding of functional diversity in subtropical forests and provide insights for biodiversity conservation in the region.
Article
Environmental Sciences
R. S. K. Barnes
Summary: The study in Knysna estuarine bay revealed complex relationships between species diversity and species-density, with strong correlation with relative evenness and negative correlation with overall assemblage abundance. The presence of specific individual faunal components significantly influenced the results.
MARINE ENVIRONMENTAL RESEARCH
(2021)
Review
Biodiversity Conservation
Andres Felipe Suarez-Castro, Maia Raymundo, Malyon Bimler, Margaret M. Mayfield
Summary: Understanding how ecosystem functioning is influenced by global change requires considering the relationship between species richness and functional diversity at multiple spatial scales. However, most studies focus on single scale analyses and ignore spatial context. This paper emphasizes the need for a spatially explicit, multi-scale framework to better understand this relationship and highlights challenges that could be addressed by integrating approaches from community and landscape ecology.
Article
Agronomy
Fernando H. Oreja, Matthew D. Inman, David L. Jordan, Deepayan Bardhan, Ramon G. Leon
Summary: Herbicide programs can affect weed population density and community composition. Stochastic models can help predict potential community changes resulting from the use of herbicide programs. This study aimed to model the population dynamics of weed species under different herbicide programs and how these dynamics influence weed community diversity over time. The repeated use of glyphosate alone had a minimal effect on richness, but significantly reduced weed diversity and evenness. Programs with more mechanisms of action and the use of both preemergence and postemergence herbicides were more likely to lose weed species, but had a higher probability of maintaining diversity and evenness. Losses in weed community diversity were reversible, but the eradication of species with low reproductive rates decreased diversity and evenness. The effects of herbicide programs on the weed community lasted for several years even after modifications were made.
EUROPEAN JOURNAL OF AGRONOMY
(2022)
Article
Ecology
Oluwafemi D. Olusoji, Gyorgy Barabas, Jurg W. Spaak, Simone Fontana, Thomas Neyens, Frederik De Laender, Marc Aerts
Summary: Individual-level trait diversity is an essential component of trait diversity, but the implications of using species-level trait diversity indices on individual-level traits have not been adequately studied. In this study, we examined various indices to measure individual-level trait diversity and found that only trait divergence indices produced the expected trends. Other indices showed limitations in their applicability and may lead to misinterpretation of trait distribution.
Article
Ecology
Lilia Roa-Fuentes, Lisney A. Villamizar-Pena, Jhon A. Mantilla-Carreno, M. Alejandra Jaramillo
Summary: Functional diversity and species diversity provide information to understand differences between plant communities from a contrasting environment. Research on flooded and unflooded forests in Colombia shows that the plant community in the unflooded forest has higher stem density and lower basal area than flooded forests. Tree communities in the flooded forests had higher specific leaf area, but lower wood density. Species diversity and functional diversity were higher in the plant community from the unflooded forest.
ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Kai Xu, Yeqing Zhou
Summary: The new metric is n-consistent under the conditional mean independence and root-n consistent otherwise. A goodness-of-fit test for single-index models based on this metric is introduced, which is consistent against any global alternatives.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2021)
Article
Statistics & Probability
Anna Klimova, Tamas Rudas
Summary: Relational models generalize log-linear models to arbitrary discrete sample spaces by specifying effects associated with subsets of cells. The properties of maximum likelihood estimates (MLEs) in a relational model with an overall effect resemble those of traditional log-linear models, while without an overall effect, the properties of MLEs are considerably different. The Poisson and multinomial MLEs are not equivalent when an overall effect is absent in the Poisson case.
COMMUNICATIONS IN STATISTICS-THEORY AND METHODS
(2022)
Article
Biochemistry & Molecular Biology
Jamie R. Bucholz, Garrett W. Hopper, Irene Sanchez Gonzalez, Taylor E. Kelley, Colin R. Jackson, Ryan C. Garrick, Carla L. Atkinson, Jeffrey D. Lozier
Summary: Understanding patterns of diversity in freshwater mussels, we found that species density positively influences species richness and intrapopulation genetic diversity, but there is no consistent correlation between genetic diversity and species richness.
Article
Ecology
Kritish De, Amar Paul Singh, Arkojyoti Sarkar, Kritika Singh, Manju Siliwal, Virendra Prasad Uniyal, Syed Ainul Hussain
Summary: This study examined the effects of habitat disturbance on taxonomic distinctness, functional diversity, and local contribution to beta diversity of spider community in the Ganga River. The results showed significant relationships between habitat disturbance and the indices of taxonomic distinctness, functional diversity, and local contribution. Anthropogenic activities such as agriculture, garbage dump, human settlement, and created embankment influenced the spider community's taxonomic distinctness, functional diversity, and local contribution.
ECOLOGICAL PROCESSES
(2023)
Article
Computer Science, Interdisciplinary Applications
Rosa Arboretti, Riccardo Ceccato, Luigi Salmaso
Summary: This paper demonstrates the flexibility and strengths of the Non-Parametric Combination procedure in multivariate contexts, focusing on Goodness-of-Fit and distribution comparison issues. It provides solutions for different scenarios and shows the viability of the procedure in small sample sizes.
JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION
(2021)
Article
Biochemistry & Molecular Biology
Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer
Summary: This study sequenced the polyploid genomes of Brettanomyces bruxellensis yeast strains using long-read sequencing strategy, revealing unique polyploidization history and trajectories in different subpopulations. The genomes contain both genetically close and diverged copies, indicating auto- and allopolyploidization events. Loss of heterozygosity events has influenced the structure of these polyploid genomes.
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
Ecology
Alison Johnston, Eleni Matechou, Emily B. Dennis
Summary: The increasing availability and use of citizen science data in biodiversity research and conservation has led to the development of analytical approaches to address the challenges posed by these datasets. This review highlights the outstanding challenges in analyzing citizen science data for biodiversity monitoring and proposes potential solutions, such as collecting additional data or metadata, combining different datasets, and refining statistical models. Further research and development in these areas can significantly enhance biodiversity monitoring and conservation efforts.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Leena Hintsanen, Emma-Liina Marjakangas, Andrea Santangeli, Alison Johnston, Aleksi Lehikoinen
Summary: The role and effectiveness of protected areas in conserving biodiversity under a warming climate are still debated. This study used bird survey data from southern Canada to examine the climate-driven changes in temperature niche compositions of bird communities inside and outside protected areas. Results showed that communities inside protected areas included a higher proportion of cold-dwelling species and exhibited slower shifts towards warm-dwelling species compared to communities outside protected areas. However, as the climate warms, the temperature compositions of bird communities inside protected areas quickly begin to resemble those outside, suggesting that the protection of cold-dwelling species may be compromised.
CONSERVATION BIOLOGY
(2023)
Article
Ecology
Amelia Penny, Maria Dornelas, Anne Magurran
Summary: The composition of ecological assemblages has been rapidly changing in the past century. We developed a quantitative framework to compare the temporal trajectories of this compositional reorganization and applied it to bird and marine fish datasets. The number of changes away from the baseline was found to be a consistent correlate of the overall rate of change, but both fish and birds showed large unreversed changes and time series with accelerating compositional change.
Review
Biology
Maria Dornelas, Jonathan M. Chase, Nicholas J. Gotelli, Anne E. Magurran, Brian J. McGill, Laura H. Antao, Shane A. Blowes, Gergana N. Daskalova, Brian Leung, Ines S. Martins, Faye Moyes, Isla H. Myers-Smith, Chris D. Thomas, Mark Vellend
Summary: Estimating biodiversity change is a critical challenge in the context of human modification. This review examines how biodiversity has changed across scales and taxonomic groups, focusing on species richness, temporal turnover, spatial beta-diversity, and abundance. The findings show mixed patterns of both increases and declines in local scales, with higher prevalence of declining trends in beta-diversity and abundance. At the global scale, extinction rates are likely surpassing speciation rates, although both are elevated. Reducing blind spots in understanding biodiversity change is essential for effective management.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Emma-Liina Marjakangas, Laura Bosco, Martijn Versluijs, Yanjie Xu, Andrea Santangeli, Sari Holopainen, Sanna Makelainen, Sergi Herrando, Verena Keller, Petr Vorisek, Lluis Brotons, Alison Johnston, Karine Prince, Stephen G. Willis, Karen Aghababyan, Vitalie Ajder, Dawn E. Balmer, Taulant Bino, Kerem Ali Boyla, Tomasz Chodkiewicz, Juan Carlos del Moral, Vlatka Dumbovic Mazal, Alessandro Ferrarini, Carlos Godinho, Marco Gustin, Mikhail Kalyakin, Peter Knaus, Tatiana Kuzmenko, Ake Lindstrom, Qenan Maxhuni, Blas Molina, Karoly Nagy, Dimitrije Radisic, Sasa Rajkov, Drazenko Z. Rajkovic, Liutauras Raudoniki, Jovica Sjenicic, Stoycho Stoychev, Tibor Szep, Norbert Teufelbauer, Silvia Ursul, Chris A. M. van Turnhout, Metodija Velevskik, Thomas Vikstrom, Tomasz Wilk, Olga Voltzit, Ingar Jostein Oien, Christoph Sudfeldt, Bettina Gerlach, Aleksi Lehikoinen
Summary: Climate change leads to species' range shifts and local extinctions, causing changes in community composition. Ecological barriers, such as biome boundaries, coastlines, and elevation, can influence the ability of communities to adapt to climate change. However, these barriers are often overlooked in climate change studies, which may hinder accurate predictions of biodiversity shifts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Faye Moyes, Isaac Trindade-Santos, Anne E. E. Magurran
Summary: Recent research has shown rapid reorganization in ecological assemblages, especially in marine ecosystems. However, it is not well understood how changes in taxonomic diversity correspond to changes in functional diversity. This study analyzed 30 years of trawl data and found that taxonomic rarity aligns with changes in assemblage size, while functional rarity actually increases with larger assemblages. These findings highlight the significance of assessing both taxonomic and functional dimensions when studying biodiversity change.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Alessandra R. R. Kortz, Faye Moyes, Vania R. Pivello, Petr Pysek, Maria Dornelas, Piero Visconti, Anne E. E. Magurran
Summary: Alien species are often associated with changes in biodiversity, but their impact on the reshaping of ecological communities is not well understood. In this study, we used the BioTIME database to examine the relationship between alien species and compositional change in vascular plant assemblages. We found that, although rare, the presence of alien species was linked to increased rates of compositional turnover. This suggests that alien species play a role in driving rapid changes in ecological communities.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Ornithology
Wesley M. Hochachka, Viviana Ruiz-Gutierrez, Alison Johnston
Summary: This study explores the use of eBird data for estimating occupancy rates and finds that combining data from repeated visits and single visits improves the accuracy of estimates. The conclusion is that eBird data can be used to estimate occupancy rates in many cases.
Article
Ecology
Anne Chao, Simon Thorn, Chun-Huo Chiu, Faye Moyes, Kai-Hsiang Hu, Robin L. Chazdon, Jessie Wu, Luiz Fernando S. Magnago, Maria Dornelas, David Zeleny, Robert K. Colwell, Anne E. Magurran
Summary: In this study, we propose a rigorous standardization method to measure and compare beta diversity across datasets based on sampling data. Our approach is built upon the assumption of a statistical sampling model, treating the sampling data as a representative sample from an assemblage. We introduce the concept of standardized, coverage-based beta diversity by standardizing alpha and gamma diversity at the same level of sample coverage. Our extension of the iNEXT method to beta diversity ensures the removal of the dependence on gamma and alpha values, allowing us to quantify the pure among-assemblage differentiation. The proposed standardization is demonstrated with various spatial, temporal, and spatiotemporal datasets.
ECOLOGICAL MONOGRAPHS
(2023)
Article
Limnology
Angel Galvez, Andreu Castillo-Escriva, Anne Magurran, Ivan Alambiaga, Fabian Bonilla, Antonio Camacho, Eduardo M. Garcia-Roger, Sanda Iepure, Javier Miralles-Lorenzo, Juan S. Monros, Carla Olmo, Antonio Picazo, Carmen Rojo, Juan Rueda, Mahmood Sasa, Mati Segura, Xavier Armengol, Francesc Mesquita-Joanes
Summary: This study compares the diversity of multiple taxa inhabiting tropical and Mediterranean temporary ponds using a spatial and temporal approach. The results show higher gamma and alpha diversity in tropical ponds, but phytoplankton and microinvertebrates from the Mediterranean region matched or exceeded tropical alpha diversity on some occasions. Spatial beta diversity did not differ between regions, and temporal beta diversity showed similar patterns. However, macroinvertebrates and amphibians exhibited differential effects on community variation observable only in animals with longer life-spans.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Ecology
Juan D. D. Bogota-Gregory, David G. G. Jenkins, Flavio C. T. Lima, Anne E. E. Magurran, William G. R. Crampton
Summary: Explaining the mechanisms of spatial and temporal variation in community composition is challenging. This study focuses on the temporal variation in community composition at different habitat types in the Amazon, and investigates the influence of seasonality and landscape connectivity. The results show that river-floodplain systems have higher temporal turnover compared to stream systems, indicating the importance of considering temporal dynamics and hydrological seasonality in the conservation of aquatic biodiversity in the Amazon.
Article
Multidisciplinary Sciences
Christine Howard, Emma-Liina Marjakangas, Alejandra Moran-Ordonez, Pietro Milanesi, Aleksandre Abuladze, Karen Aghababyan, Vitalie Ajder, Volen Arkumarev, Dawn E. Balmer, Hans-Guenther Bauer, Colin M. Beale, Taulant Bino, Kerem Ali Boyla, Ian J. Burfield, Brian Burke, Brian Caffrey, Tomasz Chodkiewicz, Juan Carlos Del Moral, Vlatka Dumbovic Mazal, Nestor Fernandez, Lorenzo Fornasari, Bettina Gerlach, Carlos Godinho, Sergi Herrando, Christina Ieronymidou, Alison Johnston, Mihailo Jovicevic, Mikhail Kalyakin, Verena Keller, Peter Knaus, Drazen Kotrosan, Tatiana Kuzmenko, Domingos Leito, Ake Lindstroem, Qenan Maxhuni, Tomaz Mihelic, Tibor Mikuska, Blas Molina, Karoly Nagy, David Noble, Ingar Jostein Olen, Jean-Yves Paquet, Clara Pladevall, Danae Portolou, Dimitrije Radisic, Sasa Rajkov, Drazenko Z. Rajkovic, Liutauras Raudonikis, Thomas Sattler, Darko Saveljic, Paul Shimmings, Jovica Sjenicic, Karel Stastny, Stoycho Stoychev, Iurii Strus, Christoph Sudfeldt, Elchin Sultanov, Tibor Szep, Norbert Teufelbauer, Danka Uzunova, Chris A. M. van Turnhout, Metodija Velevski, Thomas Vikstrom, Alexandre Vintchevski, Olga Voltzit, Petr Vorisek, Tomasz Wilk, Damaris Zurell, Lluis Brotons, Aleksi Lehikoinen, Stephen G. Willis
Summary: Climate change has an uncertain role in driving recent range shifts in species' distributions, while the effects of other factors are also important. This study uses long-term data on European breeding bird species to investigate the drivers of range dynamics, finding that climate and land cover alone cannot accurately predict observed range shifts. Initial climate conditions and species' traits have a greater influence on local colonization and extinction events, highlighting the need for more comprehensive approaches in forecasting future changes in species' ranges.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Daniel Fink, Alison Johnston, Matt Strimas-Mackey, Tom Auer, Wesley M. Hochachka, Shawn Ligocki, Lauren Oldham Jaromczyk, Orin Robinson, Chris Wood, Steve Kelling, Amanda D. Rodewald
Summary: Citizen and community science datasets are collected using flexible protocols, but the lack of structure in these protocols can complicate the estimation of population trends. To address this issue, a novel modelling approach based on Double machine learning is proposed, which uses machine learning methods to estimate population change and adjust for confounding in the data. The approach has the ability to control for confounding and model spatial heterogeneity in trends, and it was demonstrated to accurately estimate spatially varying trends in a simulation study using eBird data.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Tom Bradfer-Lawrence, Camille Desjonqueres, Alice Eldridge, Alison Johnston, Oliver Metcalf
Summary: The rise of passive acoustic monitoring and the growth in large audio datasets have driven the development of analysis methods for ecological inferences from acoustic data. Acoustic indices are widely used in ecoacoustics but can be challenging to interpret, leading to conflicting results and questioning their value. To improve the use of acoustic indices, this article provides nine points of guidance for study design, analysis, and interpretation, emphasizing the importance of understanding the links between soundscape patterns and acoustic indices. Overall, acoustic indices can offer valuable insights for biodiversity monitoring, conservation, and future research in ecoacoustics.
METHODS IN ECOLOGY AND EVOLUTION
(2023)