Article
Multidisciplinary Sciences
Michael Kalyuzhny, Jeffrey K. Lake, S. Joseph Wright, Annette M. Ostling
Summary: For species to coexist, there must be a decline in performance as conspecific density increases. In this study, it is shown that adults of tropical forest tree species exhibit strong spatial repulsion, indicating substantial niche differences between species. The results demonstrate that conspecific negative density dependence can play a significant role in stabilizing species diversity.
Article
Forestry
Lishunan Yang, Daniel J. Johnson, Zhichun Yang, Xiaochao Yang, Qiulong Yin, Ying Luo, Zhanqing Hao, Shihong Jia
Summary: This study suggests that neglecting habitat heterogeneity and dispersal mode can affect conspecific negative density dependence (CNDD) and community assembly in temperate forests.
Article
Ecology
C. S. Sieger, T. Hovestadt
Summary: The study found an interaction effect between dispersal strategy and spatial variance - lower emigration under habitat-dependent than under random emigration if spatial heterogeneity is low, but eventually a reversal of this ranking if heterogeneity becomes large. Landscapes with sharp transition of habitat attributes result in a high degree of spatial sorting, while fractal landscapes do not. Emigration rates are overall lowest when spatial variation is highest.
ECOLOGICAL PROCESSES
(2021)
Article
Ecology
Mark H. Sorel, Andrew R. Murdoch, Richard W. Zabel, Cory M. Kamphaus, Eric R. Buhle, Mark D. Scheuerell, Sarah J. Converse
Summary: Variation in life-history traits can affect a population's ability to respond to changing environments. In migratory fish, the timing of juvenile emigration can be influenced by population density and environmental conditions, affecting habitat use and population dynamics. We studied Chinook salmon in a river basin in Washington State, finding that the abundance of younger emigrants was influenced by spawner density, while the abundance of older emigrants was influenced by a different set of factors. Higher densities and winter stream discharge were linked to increased early emigration, which may have important implications with climate change. Understanding how environmental conditions affect life-history strategies is crucial for predicting demographic changes in populations.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Yoni Gavish, Eric M. Wood, Sebastian Martinuzzi, Anna M. Pidgeon, Avi Bar-Massada
Summary: This study examines how the Richness-Heterogeneity Relationship (RHR) may vary along different environmental axes and the importance of selecting relevant niche axes in studies of species richness patterns. Findings suggest that predictions of richness patterns improve when more than one heterogeneity axis is included in RHR models.
BASIC AND APPLIED ECOLOGY
(2021)
Article
Ecology
Paul Savary, Jean-Christophe Foltete, Herve Moal, Stephane Garnier
Summary: This article discusses the potential benefits of integrating landscape graphs and genetic graphs in landscape genetics. By comparing different features and partitions of these graphs, the influence of intra-patch features and inter-patch connectivity on genetic structure can be examined, as well as the sensitivity of genetic diversity and differentiation to landscape factors. Additionally, the integration of these graphs through gravity models can enhance their joint use for various theoretical and applied objectives.
Article
Ecology
Johanna Haussler, Remo Ryser, Ulrich Brose
Summary: This study combines trophic network models with spatial network models to investigate the impact of nutrient supply and landscape structure on biological invasions and invasive spread. Results indicate that nutrient supply affects invasion success, with random landscapes facilitating invasive spread.
Review
Biodiversity Conservation
Cendrine Mony, Lea Uroy, Fadwa Khalfallah, Nick Haddad, Philippe Vandenkoornhuyse
Summary: Land use changes have led to a decrease in global biodiversity, and increasing landscape connectivity is proposed as a key strategy to counterbalance the negative effects of habitat fragmentation. However, the existing framework on connectivity has overlooked microorganisms, which represent a significant proportion of Earth's biodiversity. This review explores the influence of connectivity on microorganisms and highlights the need for further research to understand their response to connectivity and its implications for microbial communities and ecosystem services.
Article
Ecology
Xiaozhou Ye, Shaopeng Wang
Summary: The effects of dispersal and habitat heterogeneity on biodiversity depend on the fitness-dependent dispersal mode. Random dispersal increases local food web diversity but decreases across-community dissimilarity and regional food web diversity. However, fitness-dependency can alter the effects of dispersal on biodiversity, with higher fitness-dependency resulting in increased diversity. Both biodiversity-habitat heterogeneity and connectivity relationships also depend on the dispersal mode.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Ecology
Laurane Winandy, Felix Pellerin, Lucie Di Gesu, Delphine Legrand, Julien Cote
Summary: Using a semi-natural experiment, this study investigated the potential synergetic effects of climate warming and habitat connectivity on a single amphibian species. The results showed that warmer climates decreased the abundance of adult newts and altered the phenotypic composition of populations, but connectivity between climates cancelled out these effects. Additionally, the study found that population isolation disrupted the relationship between emigration propensity and certain morphological traits. These findings highlight the importance of microclimatic refuges and their accessibility in buffering the impacts of climate change on amphibian populations.
Article
Biodiversity Conservation
Jingjing Zhang, Jennifer L. Pannell, Bradley S. Case, Graham Hinchliffe, Margaret C. Stanley, Hannah L. Buckley
Summary: Enhancing functional connectivity in an agricultural landscape is crucial for sustainable agroecosystems. Our study compared the landscape connectivity between two native bird species with different dispersal abilities, highlighting the importance of ecological traits and habitat patches in shaping connectivity networks. Through network analysis, we found that conservation strategies should consider species' life-histories and movement traits for creating connected ecological networks in a functional agricultural landscape.
ECOLOGICAL INDICATORS
(2021)
Article
Biodiversity Conservation
Pascaline Le Gouar, Dominique Vallet, Aude Ernoult, Eric J. Petit, Yann Rantier, Stephane Dreano, Mohamed Qarro, Nelly Menard
Summary: The study revealed that even in geographic proximity, remote areas beyond 1 km from the forest edge as well as human-dominated areas act as barriers to Barbary macaque movement, disrupting gene flow and indicating an ongoing process of isolation through the detection of private alleles in each population.
BIOLOGICAL CONSERVATION
(2021)
Article
Ecology
Hakan Sand, Mark Jamieson, Henrik Andren, Camilla Wikenros, Joris Cromsigt, Johan Mansson
Summary: The study explored the impact of wolf recolonization on moose habitat selection using long-term data. Results showed that moose reduced their use of one type of open habitat after wolf establishment, but there was no change in the use of other habitat types. The study also found that the effect of wolves varied among different habitat types, and there was no consistent support for a behavioral effect of wolves' establishment on moose habitat use.
Article
Ecology
Karold Viviana Coronado-Franco, Pablo A. Tedesco, Matthew A. Kolmann, Samuel R. Borstein, Kristine O. Evans, Sandra Bibiana Correa
Summary: This study examines how differences in dietary preferences influence the spatial distribution and habitat associations of fish species. The results show that different feeding guilds lead to divergent habitat association patterns among species. The findings highlight the importance of understanding species habitat associations in relation to food resource dynamics and floodplain dependence.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Ecology
Calum Anderson, Justin M. J. Travis, Stephen C. F. Palmer, Humphrey Q. P. Crick, Lesley T. Lancaster
Summary: The width and spatial orientations of linear landscape elements play a crucial role in determining connectivity across landscapes. Increasing connecting-edges improves connectivity whereas increasing transecting-edges reduces it, potentially limiting animals' movement and navigation abilities.
Review
Biodiversity Conservation
Jacques Roy, Francois Rineau, Hans J. De Boeck, Ivan Nijs, Thomas Putz, Samuel Abiven, John A. Arnone, Craig V. M. Barton, Natalie Beenaerts, Nicolas Bruggemann, Matteo Dainese, Timo Domisch, Nico Eisenhauer, Sarah Garre, Alban Gebler, Andrea Ghirardo, Richard L. Jasoni, George Kowalchuk, Damien Landais, Stuart H. Larsen, Vincent Leemans, Jean-Francois Le Galliard, Bernard Longdoz, Florent Massol, Teis N. Mikkelsen, Georg Niedrist, Clement Piel, Olivier Ravel, Joana Sauze, Anja Schmidt, Jorg-Peter Schnitzler, Leonardo H. Teixeira, Mark G. Tjoelker, Wolfgang W. Weisser, Barbro Winkler, Alexandru Milcu
Summary: Ecotrons are advanced controlled environmental facilities that allow for simulation of a wide range of natural environmental conditions, enabling researchers to study ecosystem processes under controlled conditions. These facilities play a crucial role in enhancing mechanistic understanding and predictive capacity of ecosystem research in the face of environmental changes.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Biology
Sachi Yamaguchi, Yoh Iwasa
Summary: Androdioecy, the coexistence of hermaphrodites and males, is rare in vertebrates, but occurs in mangrove killifish. The advantages of outcrossing-oriented hermaphrodites and the production of males strongly affect each other. Different models are studied to explain the discrepancy between the predicted high male fraction and the observed low male fraction.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Biology
Yoh Iwasa, Sachi Yamaguchi
Summary: In species with separate sexes, males provide nuptial gifts containing nutrition to their mates, which can affect the male's reproductive success and bring direct and indirect benefits to the female. By formalizing and analyzing a quantitative genetics model describing the coevolution of nuptial gift size and female's propensity to remate, it was found that various evolutionary equilibriums exist, including scenarios with no nuptial gifts or remating, as well as scenarios where males produce nuptial gifts and females engage in multiple matings.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Behavioral Sciences
Yoh Iwasa, Sachi Yamaguchi
Summary: This study investigated the reasons why subordinate individuals in most sex-changing fishes choose to be female or are forced to give up their male function, finding that subordinates are only evicted by dominant males when there is a significant difference in reproductive resources.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2022)
Article
Biology
Yuka Uchiyama, Yoh Iwasa, Sachi Yamaguchi
Summary: This study developed a dynamic optimization model to investigate the chloride cell composition of individuals living in an environment with fluctuating salinity. The research found that the optimal fraction of generalist chloride cells is influenced by the frequency of salinity changes, the time needed for new cell functionality, and the maintenance cost.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Rena Hayashi, Shingo Iwami, Yoh Iwasa
Summary: After infecting a host, a viral strain may rapidly increase and produce mutants with a faster proliferation rate than the original virus. However, most mutants become extinct due to the stochasticity caused by a small number of infected cells. The study calculated the fraction of mutants that could escape stochastic extinction based on a continuous-time branching process with a time-dependent growth rate.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Yoh Iwasa, Yoichi Yusa, Sachi Yamaguchi
Summary: This paper develops an evolutionary game to examine the conditions for different life-cycle types to succeed in a seasonal environment. The study finds that planktotrophy is favored when the planktonic stages are more efficient in terms of biomass gain, while lecithotrophy or direct development is more advantageous under specific conditions.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Yoh Iwasa, Rena Hayashi
Summary: This study presents a simple model that couples social and epidemiological dynamics, revealing the relationship between people's activities and waves of infection. The model shows different oscillation patterns and variations, as well as the control conditions of infection.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Review
Biology
Yoh Iwasa, Sachi Yamaguchi
Summary: Marine animals exhibit diverse and flexible sexual systems. This review focuses on theoretical studies in the last decade, highlighting advancements in understanding sex change in coral fishes, diverse sexual patterns in barnacles, larval production strategies, and temperature-based sex determination in fish and reptiles. The game model provides a valuable framework to comprehend the diversity of sexual patterns, considering various constraints and incorporating physiological and molecular mechanisms.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Cell Biology
Yoh Iwasa
Summary: We reviewed mathematical models and concepts in developmental biology, including the feedback vertex set in ascidian embryos, tissue deformation in chick limb bud formation, mechanobiology and its impact on cell shape and gene expression, and the adaptive design of development in response to fluctuating environments.
DEVELOPMENT GROWTH & DIFFERENTIATION
(2023)
Article
Biodiversity Conservation
Stef Haesen, Jonas J. Lembrechts, Pieter De Frenne, Jonathan Lenoir, Juha Aalto, Michael B. Ashcroft, Martin Kopecky, Miska Luoto, Ilya Maclean, Ivan Nijs, Pekka Niittynen, Johan van den Hoogen, Nicola Arriga, Josef Bruna, Nina Buchmann, Marek Ciliak, Alessio Collalti, Emiel De Lombaerde, Patrice Descombes, Mana Gharun, Ignacio Goded, Sanne Govaert, Caroline Greiser, Achim Grelle, Carsten Gruening, Lucia Hederova, Kristoffer Hylander, Juergen Kreyling, Bart Kruijt, Martin Macek, Frantisek Malis, Matej Man, Giovanni Manca, Radim Matula, Camille Meeussen, Sonia Merinero, Stefano Minerbi, Leonardo Montagnani, Lena Muffler, Roma Ogaya, Josep Penuelas, Roman Plichta, Miguel Portillo-Estrada, Jonas Schmeddes, Ankit Shekhar, Fabien Spicher, Mariana Ujhazyova, Pieter Vangansbeke, Robert Weigel, Jan Wild, Florian Zellweger, Koenraad Van Meerbeek
Summary: Microclimate research has gained renewed interest in the past decade, and its importance for ecological processes is increasingly recognized. To improve ecological models, there is a growing need for high-resolution microclimatic temperature grids across broad spatial extents. In this study, we present a new set of open-access bioclimatic variables for microclimate temperatures of European forests at a resolution of 25 x 25 m(2).
GLOBAL CHANGE BIOLOGY
(2023)
Article
Soil Science
Lingjuan Li, Ivan Nijs, Hans De Boeck, Olga Vinduskova, Simon Reynaert, Chase Donnelly, Lin Zi, Erik Verbruggen
Summary: Climate change is causing longer alternating wet and dry spells, which affect soil water availability and soil microbial communities. Intermediate regimes of wet and dry spells increase stochasticity of microbial community assembly, while longer wet or dry periods reduce fungal diversity and network connectivity.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Genetics & Heredity
Yoh Iwasa, Sou Tomimoto, Akiko Satake
Summary: Genomic sequencing reveals that somatic mutations cause genetic differentiation of cells within a single tree. A mathematical model for stem cell proliferation in the shoot apical meristem (SAM) was studied. Phylogenetic distance between cells sampled from different parts of a shoot was evaluated, indicating genetic differences due to mutations accumulated during shoot elongation. The tissue's cell walls suppress cell location exchange, resulting in genetic differentiation according to shoot angle and increased genetic variance among cells.
Article
Agronomy
Simon Reynaert, Arthur Vienne, Hans J. De Boeck, Tommy D'Hose, Ivan Janssens, Ivan Nijs, Miguel Portillo-Estrada, Erik Verbruggen, Sara Vicca
Summary: Global warming is changing the variability of precipitation patterns in the mid-latitudes, leading to longer dry and wet spells. This fluctuation can negatively affect the soil water and nutrient dynamics of managed ecosystems, impacting their functioning. This study found that the addition of basalt can mitigate the effects of persistent precipitation regimes on agricultural grassland, improving productivity and soil nutrient availability without compromising fodder quality.
AGRICULTURAL AND FOREST METEOROLOGY
(2023)
Article
Biology
Rena Hayashi, Yoh Iwasa
Summary: A high mutation rate of the RNA virus can result in the emergence of novel mutants that may evade the immunity of the original strain. However, many of these mutants go extinct due to the stochasticity of initial infected cell numbers. This study examines the impact of escaping host immune reactions and concludes that the chance of a mutant strain being established decreases with time since the wild-type infection.
BULLETIN OF MATHEMATICAL BIOLOGY
(2023)
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)