1
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Ruiz-Moreno A, Emslie MJ, Connolly SR. High response diversity and conspecific density-dependence, not species interactions, drive dynamics of coral reef fish communities. Ecol Lett 2024; 27:e14424. [PMID: 38634183 DOI: 10.1111/ele.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Species-to-species and species-to-environment interactions are key drivers of community dynamics. Disentangling these drivers in species-rich assemblages is challenging due to the high number of potentially interacting species (the 'curse of dimensionality'). We develop a process-based model that quantifies how intraspecific and interspecific interactions, and species' covarying responses to environmental fluctuations, jointly drive community dynamics. We fit the model to reef fish abundance time series from 41 reefs of Australia's Great Barrier Reef. We found that fluctuating relative abundances are driven by species' heterogenous responses to environmental fluctuations, whereas interspecific interactions are negligible. Species differences in long-term average abundances are driven by interspecific variation in the magnitudes of both conspecific density-dependence and density-independent growth rates. This study introduces a novel approach to overcoming the curse of dimensionality, which reveals highly individualistic dynamics in coral reef fish communities that imply a high level of niche structure.
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Affiliation(s)
- Alfonso Ruiz-Moreno
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Michael J Emslie
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Sean R Connolly
- Smithsonian Tropical Research Institute, Panama City, Panama
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2
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Fung T, Pande J, Shnerb NM, O'Dwyer JP, Chisholm RA. Processes governing species richness in communities exposed to temporal environmental stochasticity: A review and synthesis of modelling approaches. Math Biosci 2024; 369:109131. [PMID: 38113973 DOI: 10.1016/j.mbs.2023.109131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/10/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Research into the processes governing species richness has often assumed that the environment is fixed, whereas realistic environments are often characterised by random fluctuations over time. This temporal environmental stochasticity (TES) changes the demographic rates of species populations, with cascading effects on community dynamics and species richness. Theoretical and applied studies have used process-based mathematical models to determine how TES affects species richness, but under a variety of frameworks. Here, we critically review such studies to synthesise their findings and draw general conclusions. We first provide a broad mathematical framework encompassing the different ways in which TES has been modelled. We then review studies that have analysed models with TES under the assumption of negligible interspecific interactions, such that a community is conceptualised as the sum of independent species populations. These analyses have highlighted how TES can reduce species richness by increasing the frequency at which a species becomes rare and therefore prone to extinction. Next, we review studies that have relaxed the assumption of negligible interspecific interactions. To simplify the corresponding models and make them analytically tractable, such studies have used mean-field theory to derive fixed parameters representing the typical strength of interspecific interactions under TES. The resulting analyses have highlighted community-level effects that determine how TES affects species richness, for species that compete for a common limiting resource. With short temporal correlations of environmental conditions, a non-linear averaging effect of interspecific competition strength over time gives an increase in species richness. In contrast, with long temporal correlations of environmental conditions, strong selection favouring the fittest species between changes in environmental conditions results in a decrease in species richness. We compare such results with those from invasion analysis, which examines invasion growth rates (IGRs) instead of species richness directly. Qualitative differences sometimes arise because the IGR is the expected growth rate of a species when it is rare, which does not capture the variation around this mean or the probability of the species becoming rare. Our review elucidates key processes that have been found to mediate the negative and positive effects of TES on species richness, and by doing so highlights key areas for future research.
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Affiliation(s)
- Tak Fung
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
| | - Jayant Pande
- Department of Physical and Natural Sciences, FLAME University, Pune, Maharashtra 412115, India
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - James P O'Dwyer
- Department of Plant Biology, School of Integrative Biology, University of Illinois, 505, South Goodwin Avenue, Urbana, IL 61801, United States
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
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3
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George AB, O’Dwyer J. Universal abundance fluctuations across microbial communities, tropical forests, and urban populations. Proc Natl Acad Sci U S A 2023; 120:e2215832120. [PMID: 37874854 PMCID: PMC10622915 DOI: 10.1073/pnas.2215832120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to understand each individual system, a unified analysis of different complex populations is lacking; such an analysis could deepen our understanding of each system and facilitate cross-pollination of tools and insights across fields. Here, we use a shared framework to analyze time-series data of the human gut microbiome, tropical forest, and urban employment. We demonstrate that a single, three-parameter model of stochastic population dynamics can reproduce the empirical distributions of population abundances and fluctuations in all three datasets. The three parameters characterizing a species measure its mean abundance, deterministic stability, and stochasticity. Our analysis reveals that, despite the vast differences in scale, all three systems occupy a similar region of parameter space when time is measured in generations. In other words, although the fluctuations observed in these systems may appear different, this difference is primarily due to the different physical timescales associated with each system. Further, we show that the distribution of temporal abundance fluctuations is described by just two parameters and derive a two-parameter functional form for abundance fluctuations to improve risk estimation and forecasting.
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Affiliation(s)
- Ashish B. George
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - James O’Dwyer
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
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4
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Kessler DA, Shnerb NM. Extinction time distributions of populations and genotypes. Phys Rev E 2023; 108:044406. [PMID: 37978632 DOI: 10.1103/physreve.108.044406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/29/2023] [Indexed: 11/19/2023]
Abstract
Ultimately, the eventual extinction of any biological population is an inevitable outcome. While extensive research has focused on the average time it takes for a population to go extinct under various circumstances, there has been limited exploration of the distributions of extinction times and the likelihood of significant fluctuations. Recently, Hathcock and Strogatz [D. Hathcock and S. H. Strogatz, Phys. Rev. Lett. 128, 218301 (2022)0031-900710.1103/PhysRevLett.128.218301] identified Gumbel statistics as a universal asymptotic distribution for extinction-prone dynamics in a stable environment. In this study we aim to provide a comprehensive survey of this problem by examining a range of plausible scenarios, including extinction-prone, marginal (neutral), and stable dynamics. We consider the influence of demographic stochasticity, which arises from the inherent randomness of the birth-death process, as well as cases where stochasticity originates from the more pronounced effect of random environmental variations. Our work proposes several generic criteria that can be used for the classification of experimental and empirical systems, thereby enhancing our ability to discern the mechanisms governing extinction dynamics. Employing these criteria can help clarify the underlying mechanisms driving extinction processes.
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Affiliation(s)
- David A Kessler
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
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5
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Jops K, O'Dwyer JP. Life history complementarity and the maintenance of biodiversity. Nature 2023:10.1038/s41586-023-06154-w. [PMID: 37286601 DOI: 10.1038/s41586-023-06154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life history, the schedule of when and how fast organisms grow, die and reproduce, is a critical axis along which species differ from each other1-4. In parallel, competition is a fundamental mechanism that determines the potential for species coexistence5-8. Previous models of stochastic competition have demonstrated that large numbers of species can persist over long timescales, even when competing for a single common resource9-12, but how life history differences between species increase or decrease the possibility of coexistence and, conversely, whether competition constrains what combinations of life history strategies complement each other remain open questions. Here we show that specific combinations of life history strategy optimize the persistence times of species competing for a single resource before one species overtakes its competitors. This suggests that co-occurring species would tend to have such complementary life history strategies, which we demonstrate using empirical data for perennial plants.
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Affiliation(s)
- Kenneth Jops
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
| | - James P O'Dwyer
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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6
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Improving the realism of neutral ecological models by incorporating transient dynamics with temporal changes in community size. Theor Popul Biol 2023; 149:12-26. [PMID: 36521555 DOI: 10.1016/j.tpb.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Neutral models in ecology assume that all species are demographically equivalent, such that their abundances differ ultimately because of demographic stochasticity rather than selection. In spite of their simplicity, neutral models have been found to accurately reproduce static patterns of biodiversity for diverse communities. However, the same neutral models have been found to exhibit species abundance dynamics that are far too slow compared to reality, resulting in poor fits to temporally dynamic patterns of biodiversity. Here, we show that one of the root causes of these slow dynamics is the additional assumption that a community has reached an equilibrium with a fixed community size, with species that have a net growth rate close to zero. We removed this additional assumption by constructing and analyzing a neutral model with an expected community size that can change over time and is not necessarily at equilibrium, which thus allows the historical formation of a community to be represented explicitly. Our analysis demonstrated that for the general scenario where a small community rapidly grows in size to a carrying capacity, representing recovery from ecological disturbance or assembly of a new community, the model produced much larger changes in species abundances and much shorter species ages than a neutral model at an equilibrium with fixed community size. In addition, the species abundance distribution was biphasic with a subset of abundant species arising from a founder effect. We confirmed these new results in applications of the new model to the specific scenario of recovery of the Amazon tree community after the end-Cretaceous bolide impact, which involved periods of increasing and decreasing community size. We conclude that incorporating transient dynamics in neutral models improves realism by allowing explicit consideration of how a community is formed over realistic time-scales.
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7
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Spatial Distribution and Species Association of Dominant Tree Species in Huangguan Plot of Qinling Mountains, China. FORESTS 2022. [DOI: 10.3390/f13060866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The spatial distribution pattern and population structure of trees are shaped by multiple processes, such as species characteristics, environmental factors, and intraspecific and interspecific interactions. Studying the spatial distribution patterns of species, species associations, and their relationships with environmental factors is conducive to uncovering the mechanisms of biodiversity maintenance and exploring the underlying ecological processes of community stability and succession. This study was conducted in a 25-ha Qinling Huangguan forest (warm-temperate, deciduous, broad-leaved) dynamic monitoring plot. We used univariate and bivariate g(r) functions of the point pattern analysis method to evaluate the spatial distribution patterns of dominant tree species within the community, and the intra- and interspecific associations among different life-history stages. Complete spatial randomness and heterogeneous Poisson were used to reveal the potential process of community construction. We also used Berman’s test to determine the effect of three topographic variables on the distribution of dominant species. The results indicated that all dominant species in this community showed small-scale aggregation distribution. When we excluded the influence of environmental heterogeneity, the degree of aggregation distribution of each dominant species tended to decrease, and the trees mainly showed random or uniform distribution. This showed that environmental heterogeneity significantly affects the spatial distribution of tree species. Dominant species mainly showed positive associations with one another among different life-history stages, while negative associations prevailed among different tree species. Furthermore, we found that the associations between species were characterized by interspecific competition. Berman’s test results under the assumption of complete spatial randomness showed that the distribution of each dominant species was mainly affected by slope and convexity.
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8
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Haas H, Reaver NGF, Karki R, Kalin L, Srivastava P, Kaplan DA, Gonzalez-Benecke C. Improving the representation of forests in hydrological models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151425. [PMID: 34748839 DOI: 10.1016/j.scitotenv.2021.151425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Forests play a critical role in the hydrologic cycle, impacting the surface and groundwater dynamics of watersheds through transpiration, interception, shading, and modification of the atmospheric boundary layer. It is therefore critical that forest dynamics are adequately represented in watershed models, such as the widely applied Soil and Water Assessment Tool (SWAT). SWAT's default parameterization generally produces unrealistic forest growth predictions, which we address here through an improved representation of forest dynamics using species-specific re-parameterizations. We applied this methodology to the two dominant pine species in the southeastern U.S., loblolly pine (Pinus taeda L.) and slash pine (Pinus elliotti). Specifically, we replaced unrealistic parameter values related to tree growth with physically meaningful parameters derived from publicly available remote-sensing products, field measurements, published literature, and expert knowledge. Outputs of the default and re-parameterized models were compared at four pine plantation sites across a range of management, soil, and climate conditions. Results were validated against MODIS-derived leaf area index (LAI) and evapotranspiration (ET), as well as field observations of total biomass. The re-parameterized model outperformed the default model in simulating LAI, biomass accumulation, and ET at all sites. The two parametrizations also resulted in substantially different mean annual water budgets for all sites, with reductions in water yield ranging from 13 to 45% under the new parameterization, highlighting the importance of properly parameterizing forest dynamics in watershed models. Importantly, our re-parameterization methodology does not require alteration to the SWAT code, allowing it to be readily adapted and applied in ongoing and future watershed modeling studies.
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Affiliation(s)
- Henrique Haas
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL 36849, USA.
| | | | - Ritesh Karki
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD 20740, USA.
| | - Latif Kalin
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Puneet Srivastava
- College of Agriculture and Natural Resources, University of Maryland, College Park, MD, USA.
| | - David A Kaplan
- Engineering School of Sustainable Infrastructure and Environment, Environmental Engineering Sciences Department, University of Florida, Gainesville, FL 32611, USA.
| | - Carlos Gonzalez-Benecke
- Department of Forest Engineering, Resources and Management, Oregon State University, Corvallis, OR 97331, USA.
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9
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Takeuchi Y, Ohtsuki H, Innan H. Non-zero-sum neutrality test for the tropical rain forest community using long-term between-census data. Ecol Evol 2022; 12:e8462. [PMID: 35136547 PMCID: PMC8809451 DOI: 10.1002/ece3.8462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/01/2021] [Accepted: 11/12/2021] [Indexed: 11/07/2022] Open
Abstract
For community ecologists, "neutral or not?" is a fundamental question, and thus, rejecting neutrality is an important first step before investigating the deterministic processes underlying community dynamics. Hubbell's neutral model is an important contribution to the exploration of community dynamics, both technically and philosophically. However, the neutrality tests for this model are limited by a lack of statistical power, partly because the zero-sum assumption of the model is unrealistic. In this study, we developed a neutrality test for local communities that implements non-zero-sum community dynamics and determines the number of new species (N sp) between observations. For the non-zero-sum neutrality test, the model distributed the expected N sp, as calculated by extensive simulations, which allowed us to investigate the neutrality of the observed community by comparing the observed N sp with distributions of the expected N sp derived from the simulations. For this comparison, we developed a new "non-zero-sum N sp test," which we validated by running multiple neutral simulations using different parameter settings. We found that the non-zero-sum N sp test rejected neutrality at a near-significance level, which justified the validity of our approach. For an empirical test, the non-zero-sum N sp test was applied to real tropical tree communities in Panama and Malaysia. The non-zero-sum N sp test rejected neutrality in both communities when the observation interval was long and N sp was large. Hence, the non-zero-sum N sp test is an effective way to examine neutrality and has reasonable statistical power to reject the neutral model, especially when the observed N sp is large. This unique and simple approach is statistically powerful, even though it only employs two temporal sequences of community data. Thus, this test can be easily applied to existing datasets. In addition, application of the test will provide significant benefits for detecting changing biodiversity under climate change and anthropogenic disturbance.
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Affiliation(s)
- Yayoi Takeuchi
- Biodiversity Division National Institute for Environmental Studies Tsukuba Japan
| | - Hisashi Ohtsuki
- SOKENDAI (The Graduate University for Advanced Studies) Hayama Japan
| | - Hideki Innan
- SOKENDAI (The Graduate University for Advanced Studies) Hayama Japan
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10
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Fung T, O'Dwyer JP, Chisholm RA. Effects of temporal environmental stochasticity on species richness: a mechanistic unification spanning weak to strong temporal correlations. OIKOS 2021. [DOI: 10.1111/oik.08667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tak Fung
- National Univ. of Singapore, Dept of Biological Sciences Singapore Singapore
| | - James P. O'Dwyer
- Dept of Plant Biology, School of Integrative Biology, Univ. of Illinois Urbana IL USA
| | - Ryan A. Chisholm
- National Univ. of Singapore, Dept of Biological Sciences Singapore Singapore
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11
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Murphy SJ, Smith AB. What can community ecologists learn from species distribution models? Ecosphere 2021. [DOI: 10.1002/ecs2.3864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Stephen J. Murphy
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Boulevard Saint Louis Missouri 63110 USA
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University 318 West 12th Avenue Columbus Ohio 43201 USA
| | - Adam B. Smith
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Boulevard Saint Louis Missouri 63110 USA
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12
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Crausbay SD, Sofaer HR, Cravens AE, Chaffin BC, Clifford KR, Gross JE, Knapp CN, Lawrence DJ, Magness DR, Miller-Rushing AJ, Schuurman GW, Stevens-Rumann CS. A Science Agenda to Inform Natural Resource Management Decisions in an Era of Ecological Transformation. Bioscience 2021. [DOI: 10.1093/biosci/biab102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Earth is experiencing widespread ecological transformation in terrestrial, freshwater, and marine ecosystems that is attributable to directional environmental changes, especially intensifying climate change. To better steward ecosystems facing unprecedented and lasting change, a new management paradigm is forming, supported by a decision-oriented framework that presents three distinct management choices: resist, accept, or direct the ecological trajectory. To make these choices strategically, managers seek to understand the nature of the transformation that could occur if change is accepted while identifying opportunities to intervene to resist or direct change. In this article, we seek to inspire a research agenda for transformation science that is focused on ecological and social science and based on five central questions that align with the resist–accept–direct (RAD) framework. Development of transformation science is needed to apply the RAD framework and support natural resource management and conservation on our rapidly changing planet.
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Affiliation(s)
- Shelley D Crausbay
- Conservation Science Partners, Fort Collins, Colorado, and is a consortium partner for the US Geological Survey's North Central Climate Adaptation Science Center, Boulder, Colorado, United States
| | - Helen R Sofaer
- US Geological Survey Pacific Island Ecosystems Research Center, Hawaii Volcanoes National Park, Hawai'i, United States
| | - Amanda E Cravens
- US Geological Survey's Social and Economic Analysis Branch, Fort Collins, Colorado, United States
| | | | - Katherine R Clifford
- US Geological Survey's Social and Economic Analysis Branch, Fort Collins, Colorado, United States
| | - John E Gross
- US National Park Service Climate Change Response Program, Fort Collins, Colorado, United States
| | | | - David J Lawrence
- US National Park Service Climate Change Response Program, Fort Collins, Colorado, United States
| | - Dawn R Magness
- US Fish and Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States
| | | | - Gregor W Schuurman
- US National Park Service Climate Change Response Program, in Fort Collins, Colorado, United States
| | - Camille S Stevens-Rumann
- Forest and Rangeland Stewardship Department and assistant director of the Colorado Forest Restoration Institute, at Colorado State University, Fort Collins, Colorado, United States
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13
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Chisholm RA, Fung T. Adding stage‐structure to a spatial neutral model: implications for explaining local and regional patterns of biodiversity. OIKOS 2021. [DOI: 10.1111/oik.08489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan A. Chisholm
- Dept of Biological Sciences, National Univ. of Singapore Singapore Singapore
| | - Tak Fung
- Dept of Biological Sciences, National Univ. of Singapore Singapore Singapore
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14
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Pulla S, Suresh H, Dattaraja H, Sukumar R. Plant dynamics in a tropical dry forest are strongly associated with climate and fire and weakly associated with stabilizing neighborhood effects. Oecologia 2021; 197:699-713. [PMID: 34713303 DOI: 10.1007/s00442-021-05066-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
Abstract
Studies comparing the relative strengths of multiple key drivers of forest dynamics are rare, but can inform both our fundamental understanding of plant communities as well as community-ecology theory. We studied the dynamics of a woody plant community in a southern Indian seasonally-dry tropical forest (SDTF) in relation to environmental factors (precipitation, temperature, fire, soil nutrients, and topography) and conspecific and heterospecific plant neighborhoods to identify which of these best predicted recruitment, survival and growth of dominant species over a 24-year study period. We also assessed the relative prevalence of density-independent and density-dependent responses in the community. Climate and fire were more important than plant neighborhoods and topographic and edaphic variables in explaining variation in plant performance. Recruitment, survival and growth were lower during periods of low precipitation and immediately following fires. Recruitment increased, and growth and survival largely decreased, with increasing temperatures. Smaller-sized individuals were disproportionately strongly affected by the vagaries of climate and fire. Conspecific negative density-dependence, a population-fluctuation stabilizing process, was relatively unimportant. Density-dependent effects decayed rapidly with distance from the focal plant (growth, survival) or quadrat (recruitment); positive density-dependence was frequently found in recruitment, possibly resulting from limited dispersal and/or facilitation. Woody plant dynamics in this SDTF appear to be responding largely to fluctuations in environmental conditions, particularly precipitation, temperature, and fire. In contrast to wetter forests, population-fluctuation stabilizing processes in this ecosystem appear to be relatively weak. Changes in climatic or fire regimes are likely to result in large compositional shifts in this SDTF.
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Affiliation(s)
- Sandeep Pulla
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012, India
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, 560012, India
| | - Hebbalalu Suresh
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012, India
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, 560012, India
| | - Handanakere Dattaraja
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012, India
| | - Raman Sukumar
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012, India.
- Divecha Centre for Climate Change, Indian Institute of Science, Bengaluru, 560012, India.
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15
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Shibasaki S, Mobilia M, Mitri S. Exclusion of the fittest predicts microbial community diversity in fluctuating environments. J R Soc Interface 2021; 18:20210613. [PMID: 34610260 PMCID: PMC8492180 DOI: 10.1098/rsif.2021.0613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species' ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Mauro Mobilia
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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16
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Patterns of woody species diversity and structure in Thalewood House permanent preservation plot in Bannerghatta National Park, Bangalore, India. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00169-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Fort H, Grigera TS. A method for predicting species trajectories tested with trees in barro colorado tropical forest. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2021.109504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Sloan WT, Nnaji CF, Lunn M, Curtis TP, Colloms SD, Couto JM, Pinto AJ, Connelly S, Rosser SJ. Drift dynamics in microbial communities and the effective community size. Environ Microbiol 2021; 23:2473-2483. [PMID: 33684262 DOI: 10.1111/1462-2920.15453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/26/2021] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
The structure and diversity of all open microbial communities are shaped by individual births, deaths, speciation and immigration events; the precise timings of these events are unknowable and unpredictable. This randomness is manifest as ecological drift in the population dynamics, the importance of which has been a source of debate for decades. There are theoretical reasons to suppose that drift would be imperceptible in large microbial communities, but this is at odds with circumstantial evidence that effects can be seen even in huge, complex communities. To resolve this dichotomy we need to observe dynamics in simple systems where key parameters, like migration, birth and death rates can be directly measured. We monitored the dynamics in the abundance of two genetically modified strains of Escherichia coli, with tuneable growth characteristics, that were mixed and continually fed into 10 identical chemostats. We demonstrated that the effects of demographic (non-environmental) stochasticity are very apparent in the dynamics. However, they do not conform to the most parsimonious and commonly applied mathematical models, where each stochastic event is independent. For these simple models to reproduce the observed dynamics we need to invoke an 'effective community size', which is smaller than the census community size.
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Affiliation(s)
- William T Sloan
- School of Engineering, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Chioma F Nnaji
- School of Engineering, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Mary Lunn
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Jillian M Couto
- School of Engineering, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Ameet J Pinto
- Department of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Stephanie Connelly
- School of Engineering, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Susan J Rosser
- School of Biological Sciences, Roger Land Building, Alexander Crum Brown Road, The King's Buildings, Edinburgh, EH9 3FF, UK
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19
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Ontiveros VJ, Capitán JA, Casamayor EO, Alonso D. The characteristic time of ecological communities. Ecology 2021; 102:e03247. [PMID: 33217780 PMCID: PMC7900965 DOI: 10.1002/ecy.3247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/09/2020] [Accepted: 09/14/2020] [Indexed: 11/30/2022]
Abstract
A simple description of temporal dynamics of ecological communities may help us understand how community assembly proceeds, predict ecological responses to environmental disturbances, and improve the performance of biological conservation actions. Although community changes take place at multiple temporal scales, the variation of species composition and richness over time across communities and habitats shows general patterns that may potentially reveal the main drivers of community dynamics. We used the simplest stochastic model of island biogeography to propose two quantities to characterize community dynamics: the community characteristic time, as a measure of the typical time scale of species‐richness change, and the characteristic Jaccard index, as a measure of temporal β diversity, that is, the variation of community composition over time. In addition, the community characteristic time, which sets the temporal scale at which null, noninteracting species assemblages operate, allowed us to define a relative sampling frequency (to the characteristic time). Here we estimate these quantities across microbial and macroscopic species assemblages to highlight two related results. First, we illustrated both characteristic time and Jaccard index and their relation with classic time‐series in ecology, and found that the most thoroughly sampled communities, relative to their characteristic time, presented the largest similarity between consecutive samples. Second, our analysis across a variety of habitats and taxa show that communities span a large range of species turnover, from potentially very fast (short characteristic times) to rather slow (long characteristic times) communities. This was in agreement with previous knowledge, but indicated that some habitats may have been sampled less frequently than required. Our work provides new perspectives to explore the temporal component in ecological studies and highlights the usefulness of simple approximations to the complex dynamics of ecological communities.
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Affiliation(s)
- Vicente J Ontiveros
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Acces Cala St. Francesc 14, Blanes, E-17300, Spain
| | - José A Capitán
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Acces Cala St. Francesc 14, Blanes, E-17300, Spain.,Complex Systems Group, Department of Applied Mathematics, Universidad Politécnica de Madrid, Avenida Juan de Herrera, 6, Madrid, E-28040, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, Blanes, E-17300, Spain
| | - David Alonso
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Acces Cala St. Francesc 14, Blanes, E-17300, Spain
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20
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Pande J, Shnerb NM. Taming the diffusion approximation through a controlling-factor WKB method. Phys Rev E 2020; 102:062410. [PMID: 33466058 DOI: 10.1103/physreve.102.062410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/17/2020] [Indexed: 11/07/2022]
Abstract
The diffusion approximation (DA) is widely used in the analysis of stochastic population dynamics, from population genetics to ecology and evolution. The DA is an uncontrolled approximation that assumes the smoothness of the calculated quantity over the relevant state space and fails when this property is not satisfied. This failure becomes severe in situations where the direction of selection switches sign. Here we employ the WKB (Wentzel-Kramers-Brillouin) large-deviations method, which requires only the logarithm of a given quantity to be smooth over its state space. Combining the WKB scheme with asymptotic matching techniques, we show how to derive the diffusion approximation in a controlled manner and how to produce better approximations, applicable for much wider regimes of parameters. We also introduce a scalable (independent of population size) WKB-based numerical technique. The method is applied to a central problem in population genetics and evolution, finding the chance of ultimate fixation in a zero-sum, two-types competition.
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Affiliation(s)
- Jayant Pande
- Department of Physics, Bar-Ilan University, Ramat-Gan IL52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan IL52900, Israel
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21
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Steinmetz B, Kalyuzhny M, Shnerb NM. Intraspecific variability in fluctuating environments: mechanisms of impact on species diversity. Ecology 2020; 101:e03174. [PMID: 32860217 DOI: 10.1002/ecy.3174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/19/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
Recent studies have found considerable trait variations within species. The effect of such intraspecific trait variability (ITV) on the stability, coexistence, and diversity of ecological communities received considerable attention and in many models it was shown to impede coexistence and decrease species diversity. Here we present a numerical study of the effect of genetically inherited ITV on species persistence and diversity in a temporally fluctuating environment. Two mechanisms are identified. First, ITV buffers populations against varying environmental conditions (portfolio effect) and reduces variation in abundances. Second, the interplay between ITV and environmental variations tends to increase the mean fitness of diverse populations. The first mechanism promotes persistence and tends to increase species richness, while the second reduces the chance of a rare species population (which is usually homogeneous) to invade, thus decreasing species richness. We show that for large communities the portfolio effect is dominant, leading to ITV promoting species persistence and richness.
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Affiliation(s)
- Bnaya Steinmetz
- Department of Physics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Michael Kalyuzhny
- Department of Ecology, Evolution, and Behavior, Institute of Life Sciences, Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat Gan, 52900, Israel
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22
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Grilli J. Macroecological laws describe variation and diversity in microbial communities. Nat Commun 2020; 11:4743. [PMID: 32958773 PMCID: PMC7506021 DOI: 10.1038/s41467-020-18529-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/27/2020] [Indexed: 11/15/2022] Open
Abstract
How the coexistence of many species is maintained is a fundamental and unresolved question in ecology. Coexistence is a puzzle because we lack a mechanistic understanding of the variation in species presence and abundance. Whether variation in ecological communities is driven by deterministic or random processes is one of the most controversial issues in ecology. Here, I study the variation of species presence and abundance in microbial communities from a macroecological standpoint. I identify three macroecological laws that quantitatively characterize the fluctuation of species abundance across communities and over time. Using these three laws, one can predict species' presence and absence, diversity, and commonly studied macroecological patterns. I show that a mathematical model based on environmental stochasticity, the stochastic logistic model, quantitatively predicts the three macroecological laws, as well as non-stationary properties of community dynamics.
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Affiliation(s)
- Jacopo Grilli
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, 34151, Italy.
- Santa Fe Institute, Santa Fe, NM, 87501, USA.
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23
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Abstract
AbstractA goal of ecology is to identify the stabilizing mechanisms that maintain species diversity in the face of competitive exclusion and drift. For tropical forest tree communities, it has been hypothesized that high diversity is maintained via Janzen-Connell effects, whereby host-specific natural enemies prevent any one species from becoming too abundant. Here we explore the plausibility of this hypothesis with theoretical models. We confirm a previous result that when added to a model with drift but no competitive exclusion-that is, a neutral model where intrinsic fitnesses are perfectly equalized across species-Janzen-Connell effects maintain very high species richness that scales strongly with community size. However, when competitive exclusion is introduced-that is, when intrinsic fitnesses vary across species-the number of species maintained by Janzen-Connell effects is substantially reduced and scales much less strongly with community size. Because fitness variation is pervasive in nature, we conclude that the potential of Janzen-Connell effects to maintain diversity is probably weak and that the mechanism does not yet provide a sufficient explanation for the observed high diversity of tropical forest tree communities. We also show that, surprisingly, dispersal limitation can further reduce the ability of Janzen-Connell effects to maintain diversity.
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24
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Taitelbaum A, West R, Assaf M, Mobilia M. Population Dynamics in a Changing Environment: Random versus Periodic Switching. PHYSICAL REVIEW LETTERS 2020; 125:048105. [PMID: 32794803 DOI: 10.1103/physrevlett.125.048105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/13/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment modeled by a carrying capacity switching either randomly or periodically between states of abundance and scarcity. The population dynamics is characterized by demographic noise (birth and death events) coupled to a varying environment. We elucidate the similarities and differences of the evolution subject to a stochastically and periodically varying environment. Importantly, the population size distribution is generally found to be broader under intermediate and fast random switching than under periodic variations, which results in markedly different asymptotic behaviors between the fixation probability of random and periodic switching. We also determine the detailed conditions under which the fixation probability of the slow strain is maximal.
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Affiliation(s)
- Ami Taitelbaum
- Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Robert West
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michael Assaf
- Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Mauro Mobilia
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
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25
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Guillin A, Jabot F, Personne A. On the Simpson index for the Wright–Fisher process with random selection and immigration. INT J BIOMATH 2020. [DOI: 10.1142/s1793524520500461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Moran or Wright–Fisher processes are probably the most well known models to study the evolution of a population under environmental various effects. Our object of study will be the Simpson index which measures the level of diversity of the population, one of the key parameters for ecologists who study for example, forest dynamics. Following ecological motivations, we will consider, here, the case, where there are various species with fitness and immigration parameters being random processes (and thus time evolving). The Simpson index is difficult to evaluate when the population is large, except in the neutral (no selection) case, because it has no closed formula. Our approach relies on the large population limit in the “weak” selection case, and thus to give a procedure which enables us to approximate, with controlled rate, the expectation of the Simpson index at fixed time. We will also study the long time behavior (invariant measure and convergence speed towards equilibrium) of the Wright–Fisher process in a simplified setting, allowing us to get a full picture for the approximation of the expectation of the Simpson index.
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Affiliation(s)
- Arnaud Guillin
- Laboratoire de Mathématiques Blaise Pascal, CNRS UMR 6620, Université Clermont-Auvergne, avenue des Landais, F-63177 Aubière, France
| | - Franck Jabot
- Laboratoire d’Ingéniérie pour les Systèmes Complexes, IRSTEA, Campus des Cézeaux 9, avenue Blaise Pascal - CS 20085 63178 Aubière, France
| | - Arnaud Personne
- Laboratoire de Mathématiques Blaise Pascal, CNRS UMR 6620, Université Clermont-Auvergne, avenue des Landais, F-63177 Aubière, France
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26
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Dean AM, Shnerb NM. Stochasticity‐induced stabilization in ecology and evolution: a new synthesis. Ecology 2020; 101:e03098. [DOI: 10.1002/ecy.3098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/16/2020] [Accepted: 02/24/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Antony M. Dean
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul Minnesota55108USA
- BioTechnology Institute University of Minnesota St. Paul Minnesota55108USA
| | - Nadav M. Shnerb
- Department of Physics Bar‐Ilan University Ramat Gan52900Israel
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27
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Abstract
Neutral models of evolution assume the absence of natural selection. Formerly confined to ecology and evolutionary biology, neutral models are spreading. In recent years they've been applied to explaining the diversity of baby names, scientific citations, cryptocurrencies, pot decorations, literary lexica, tumour variants and much more besides. Here, we survey important neutral models and highlight their similarities. We investigate the most widely used tests of neutrality, show that they are weak and suggest more powerful methods. We conclude by discussing the role of neutral models in the explanation of diversity. We suggest that the ability of neutral models to fit low-information distributions should not be taken as evidence for the absence of selection. Nevertheless, many studies, in increasingly diverse fields, make just such claims. We call this tendency 'neutral syndrome'.
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28
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Swenson NG, Hulshof CM, Katabuchi M, Enquist BJ. Long‐term shifts in the functional composition and diversity of a tropical dry forest: a 30‐yr study. ECOL MONOGR 2020. [DOI: 10.1002/ecm.1408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nathan G. Swenson
- Department of Biology University of Maryland College Park Maryland 20742 USA
| | - Catherine M. Hulshof
- Department of Biology Virginia Commonwealth University Richmond Virginia 23284 USA
| | - Masatoshi Katabuchi
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Yunnan 666303 China
- W.K. Kellogg Biology Station Michigan State University Hickory Corners Michigan 49060 USA
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA
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29
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Landscape Representation by a Permanent Forest Plot and Alternative Plot Designs in a Typhoon Hotspot, Fushan, Taiwan. REMOTE SENSING 2020. [DOI: 10.3390/rs12040660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Permanent forest dynamics plots have provided valuable insights into many aspects of forest ecology. The evaluation of their representativeness within the landscape is necessary to understanding the limitations of findings from permanent plots at larger spatial scales. Studies on the representativeness of forest plots with respect to landscape heterogeneity and disturbance effect have already been carried out, but knowledge of how multiple disturbances affect plot representativeness is lacking—particularly in sites where several disturbances can occur between forest plot censuses. This study explores the effects of five typhoon disturbances on the Fushan Forest Dynamics Plot (FFDP) and its surrounding landscape, the Fushan Experimental Forest (FEF), in Taiwan where typhoons occur annually. The representativeness of the FFDP for the FEF was studied using four topographical variables derived from a digital elevation model and two vegetation indices (VIs), Normalized Difference Vegetation Index (NDVI) and Normalized Difference Infrared Index (NDII), calculated from Landsat-5 TM, Landsat-7 ETM+, and Landsat-8 OLI data. Representativeness of four alternative plot designs were tested by dividing the FFDP into subplots over wider elevational ranges. Results showed that the FFDP neither represents landscape elevational range (<10%) nor vegetation cover (<7% of the interquartile range, IQR). Although disturbance effects (i.e., ΔVIs) were also different between the FFDP and the FEF, comparisons showed no under- or over-exposure to typhoon damage frequency or intensity within the FFDP. In addition, the ΔVIs were of the same magnitudes in the plots and the reserve, and the plot covered 30% to 75.9% of IQRs of the reserve ΔVIs. Unexpectedly, the alternative plot designs did not lead to increased representation of damage for 3 out of the 4 tested typhoons and they did not suggest higher representativeness of rectangular vs. square plots. Based on the comparison of mean Euclidian distances, two rectangular plots had smaller distances than four square or four rectangular plots of the same area. Therefore, this study suggests that the current FFDP provides a better representation of its landscape disturbances than alternatives, which contained wider topographical variation and would be more difficult to conduct ground surveys. However, upscaling needs to be done with caution as, in the case of the FEF, plot representativeness varied among typhoons.
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30
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Pande J, Fung T, Chisholm R, Shnerb NM. Mean growth rate when rare is not a reliable metric for persistence of species. Ecol Lett 2019; 23:274-282. [DOI: 10.1111/ele.13430] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/03/2019] [Accepted: 10/28/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Jayant Pande
- Department of Physics Bar‐Ilan University Ramat Gan 52900 Israel
| | - Tak Fung
- Department of Biological Sciences National University of Singapore Singapore 117543 Republic of Singapore
| | - Ryan Chisholm
- Department of Biological Sciences National University of Singapore Singapore 117543 Republic of Singapore
| | - Nadav M. Shnerb
- Department of Physics Bar‐Ilan University Ramat Gan 52900 Israel
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31
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Fung T, Chisholm RA, Anderson-Teixeira K, Bourg N, Brockelman WY, Bunyavejchewin S, Chang-Yang CH, Chitra-Tarak R, Chuyong G, Condit R, Dattaraja HS, Davies SJ, Ewango CEN, Fewless G, Fletcher C, Gunatilleke CVS, Gunatilleke IAUN, Hao Z, Hogan JA, Howe R, Hsieh CF, Kenfack D, Lin Y, Ma K, Makana JR, McMahon S, McShea WJ, Mi X, Nathalang A, Ong PS, Parker G, Rau EP, Shue J, Su SH, Sukumar R, Sun IF, Suresh HS, Tan S, Thomas D, Thompson J, Valencia R, Vallejo MI, Wang X, Wang Y, Wijekoon P, Wolf A, Yap S, Zimmerman J. Temporal population variability in local forest communities has mixed effects on tree species richness across a latitudinal gradient. Ecol Lett 2019; 23:160-171. [PMID: 31698546 DOI: 10.1111/ele.13412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/04/2019] [Accepted: 09/29/2019] [Indexed: 11/28/2022]
Abstract
Among the local processes that determine species diversity in ecological communities, fluctuation-dependent mechanisms that are mediated by temporal variability in the abundances of species populations have received significant attention. Higher temporal variability in the abundances of species populations can increase the strength of temporal niche partitioning but can also increase the risk of species extinctions, such that the net effect on species coexistence is not clear. We quantified this temporal population variability for tree species in 21 large forest plots and found much greater variability for higher latitude plots with fewer tree species. A fitted mechanistic model showed that among the forest plots, the net effect of temporal population variability on tree species coexistence was usually negative, but sometimes positive or negligible. Therefore, our results suggest that temporal variability in the abundances of species populations has no clear negative or positive contribution to the latitudinal gradient in tree species richness.
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Affiliation(s)
- Tak Fung
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Kristina Anderson-Teixeira
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panamá.,Smithsonian Conservation Biology Institute, 1500 Remount Road, Front Royal, Virginia, 22630, USA
| | - Norm Bourg
- Smithsonian Conservation Biology Institute, 1500 Remount Road, Front Royal, Virginia, 22630, USA
| | - Warren Y Brockelman
- National Biobank of Thailand, BIOTEC, National Science and Technology Development Agency, Science Park, Klong Luang, Pathum Thani, Thailand.,Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Sarayudh Bunyavejchewin
- Research Office, Department of National Parks, Wildlife and Plant Conservation, Bangkok, 10900, Thailand
| | - Chia-Hao Chang-Yang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung
| | - Rutuja Chitra-Tarak
- Los Alamos National Laboratory, Los Alamos, P.O. Box 1663, New Mexico, 87545, USA
| | - George Chuyong
- Department of Botany and Plant Physiology, University of Buea, PO Box 63, Buea, SWP, Cameroon
| | - Richard Condit
- Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL, 60605, USA
| | | | - Stuart J Davies
- Smithsonian Institution Global Earth Observatory, Center for Tropical Forest Science, Smithsonian Institution, P.O. Box 37012, Washington, 20013, USA
| | | | - Gary Fewless
- Department of Natural and Applied Sciences, Lab Sciences 413, University of Wisconsin-Green Bay, 2420 Nicolet Drive, Green Bay, Wisconsin, 54311, USA
| | - Christine Fletcher
- Forest Research Institute Malaysia, 52109, Kepong, Selangor Darul Ehsan, Malaysia
| | - C V Savitri Gunatilleke
- Faculty of Science, Department of Botany, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - I A U Nimal Gunatilleke
- Faculty of Science, Department of Botany, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Zhanqing Hao
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning
| | - J Aaron Hogan
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, Florida, 33199, USA
| | - Robert Howe
- Department of Natural and Applied Sciences, Lab Sciences 413, University of Wisconsin-Green Bay, 2420 Nicolet Drive, Green Bay, Wisconsin, 54311, USA
| | - Chang-Fu Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei
| | - David Kenfack
- Smithsonian Institution Global Earth Observatory, Center for Tropical Forest Science, Smithsonian Institution, P.O. Box 37012, Washington, 20013, USA
| | - YiChing Lin
- Department of Life Science, Tunghai University, Taichung
| | - Keping Ma
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing
| | | | - Sean McMahon
- Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, Maryland, 21037, USA
| | - William J McShea
- Smithsonian Conservation Biology Institute, 1500 Remount Road, Front Royal, Virginia, 22630, USA
| | - Xiangcheng Mi
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing
| | - Anuttara Nathalang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Klong Luang, Pathum Thani, 12120, Thailand
| | - Perry S Ong
- Institute of Biology, University of the Philippines, Diliman, Quezon City, Philippines
| | - Geoffrey Parker
- Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, Maryland, 21037, USA
| | - E-Ping Rau
- Master 1 Mention Écologie, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Jessica Shue
- Smithsonian Environmental Research Center, P.O. Box 28, Edgewater, Maryland, 21037, USA
| | - Sheng-Hsin Su
- Forest Management Division, Taiwan Forestry Research Institute, Taipei
| | - Raman Sukumar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.,Divecha Centre for Climate Change, Indian Institute of Science, Bangalore, 560012, India
| | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien
| | - Hebbalalu S Suresh
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.,Divecha Centre for Climate Change, Indian Institute of Science, Bangalore, 560012, India
| | - Sylvester Tan
- Smithsonian Institution Global Earth Observatory, Center for Tropical Forest Science, Smithsonian Institution, P.O. Box 37012, Washington, 20013, USA
| | - Duncan Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill Thompson
- Department of Environmental Science, University of Puerto Rico, P.O. Box 70377, San Juan, PR, 00936-8377, USA.,Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK
| | - Renato Valencia
- Departamento de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Apartado 17-01-2184, Quito, Ecuador
| | - Martha I Vallejo
- Calle 37, Instituto Alexander von Humboldt, Number 8-40 Mezzanine, Bogotá, Colombia
| | - Xugao Wang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning
| | - Yunquan Wang
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing
| | - Pushpa Wijekoon
- Faculty of Science, Department of Statistics & Computer Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Amy Wolf
- Department of Natural and Applied Sciences, Lab Sciences 413, University of Wisconsin-Green Bay, 2420 Nicolet Drive, Green Bay, Wisconsin, 54311, USA
| | - Sandra Yap
- Institute of Arts and Sciences, Far Eastern University Manila, Manila, Philippines
| | - Jess Zimmerman
- Department of Environmental Science, University of Puerto Rico, P.O. Box 70377, San Juan, PR, 00936-8377, USA
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Bongalov B, Burslem DFRP, Jucker T, Thompson SED, Rosindell J, Swinfield T, Nilus R, Clewley D, Phillips OL, Coomes DA. Reconciling the contribution of environmental and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy. Ecol Lett 2019; 22:1608-1619. [PMID: 31347263 PMCID: PMC6852337 DOI: 10.1111/ele.13357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/08/2019] [Accepted: 07/01/2019] [Indexed: 11/29/2022]
Abstract
Both niche and stochastic dispersal processes structure the extraordinary diversity of tropical plants, but determining their relative contributions has proven challenging. We address this question using airborne imaging spectroscopy to estimate canopy β-diversity for an extensive region of a Bornean rainforest and challenge these data with models incorporating niches and dispersal. We show that remotely sensed and field-derived estimates of pairwise dissimilarity in community composition are closely matched, proving the applicability of imaging spectroscopy to provide β-diversity data for entire landscapes of over 1000 ha containing contrasting forest types. Our model reproduces the empirical data well and shows that the ecological processes maintaining tropical forest diversity are scale dependent. Patterns of β-diversity are shaped by stochastic dispersal processes acting locally whilst environmental processes act over a wider range of scales.
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Affiliation(s)
- Boris Bongalov
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - David F R P Burslem
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, UK
| | - Tommaso Jucker
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Samuel E D Thompson
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.,National University of Singapore, 21 Lower Kent Ridge Road, 119077, Singapore
| | - James Rosindell
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Tom Swinfield
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Centre for Conservation Science, Royal Society for Protection of Birds, David Attenborough Building, Cambridge, CB2 3QZ, UK
| | - Reuben Nilus
- Forest Research Centre, Sabah Forestry Department, Sandakan, Malaysia
| | | | | | - David A Coomes
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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33
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Yahalom Y, Steinmetz B, Shnerb NM. Comprehensive phase diagram for logistic populations in fluctuating environment. Phys Rev E 2019; 99:062417. [PMID: 31330701 DOI: 10.1103/physreve.99.062417] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Indexed: 06/10/2023]
Abstract
Population dynamics reflects an underlying birth-death process, where the rates associated with different events may depend on external environmental conditions and on the population density. A whole family of simple and popular deterministic models (such as logistic growth) supports a transcritical bifurcation point between an extinction phase and an active phase. Here we provide a comprehensive analysis of the phases of that system, taking into account both the endogenous demographic noise (random birth and death events) and the effect of environmental stochasticity that causes variations in birth and death rates. Three phases are identified: in the inactive phase the mean time to extinction T is independent of the carrying capacity N and scales logarithmically with the initial population size. In the power-law phase T∼N^{q}, and in the exponential phase T∼exp(αN). All three phases and the transitions between them are studied in detail. The breakdown of the continuum approximation is identified inside the power-law phase, and the accompanying changes in decline modes are analyzed. The applicability of the emerging picture to the analysis of ecological time series and to the management of conservation efforts is briefly discussed.
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Affiliation(s)
- Yitzhak Yahalom
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Bnaya Steinmetz
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
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34
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Natural disturbance and soils drive diversity and dynamics of seasonal dipterocarp forest in Southern Thailand. JOURNAL OF TROPICAL ECOLOGY 2019. [DOI: 10.1017/s0266467419000075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractIn 2000, we established a 24-ha plot in Peninsular Thailand to investigate how forest composition, structure and dynamics vary with spatial heterogeneity in resource availability. Detailed soil and topographic surveys were used to describe four edaphic habitats in the plot. Disturbance history was inferred from historical records and floristic analysis. The plot included >119 000 trees ≥1 cm dbh in 578 species, and was recensused in 2010. Species distributions, floristic turnover, stand structure, demographic rates and biomass dynamics were strongly influenced by heterogeneity in soils, topography and disturbance history. Over 75% of species were aggregated on specific edaphic habitats leading to strong compositional turnover across the plot. Soil chemistry more strongly affected species turnover than topography. Forest with high biomass and slow dynamics occurred on well-drained, low fertility ridges. The distribution and size structure of pioneer species reflected habitat-specific differences in disturbance history. Overall, above-ground biomass (AGB) increased by 0.64 Mg ha−1 y−1, from 385 to 392 Mg ha−1, an increase that was entirely attributable to recovery after natural disturbance. Forest composition and stand structure, by reflecting local disturbance history, provide insights into the likely drivers of AGB change in forests. Predicting future changes in tropical forests requires improved understanding of how soils and disturbance regulate forest dynamics.
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35
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Fung T, O'Dwyer JP, Chisholm RA. Partitioning the effects of deterministic and stochastic processes on species extinction risk. ECOLOGICAL COMPLEXITY 2019. [DOI: 10.1016/j.ecocom.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Yahalom Y, Shnerb NM. Phase Diagram for Logistic Systems under Bounded Stochasticity. PHYSICAL REVIEW LETTERS 2019; 122:108102. [PMID: 30932639 DOI: 10.1103/physrevlett.122.108102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 06/09/2023]
Abstract
Extinction is the ultimate absorbing state of any stochastic birth-death process; hence, the time to extinction is an important characteristic of any natural population. Here we consider logistic and logisticlike systems under the combined effect of demographic and bounded environmental stochasticity. Three phases are identified: an inactive phase where the mean time to extinction T increases logarithmically with the initial population size, an active phase where T grows exponentially with the carrying capacity N, and a temporal Griffiths phase, with a power-law relationship between T and N. The system supports an exponential phase only when the noise is bounded, in which case the continuum (diffusion) approximation breaks down within the Griffiths phase. This breakdown is associated with a crossover between qualitatively different survival statistics and decline modes. To study the power-law phase we present a new WKB scheme, which is applicable both in the diffusive and in the nondiffusive regime.
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Affiliation(s)
- Yitzhak Yahalom
- Department of Physics, Bar-Ilan University, Ramat-Gan IL52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan IL52900, Israel
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37
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Rajala T, Olhede SC, Murrell DJ. When do we have the power to detect biological interactions in spatial point patterns? THE JOURNAL OF ECOLOGY 2019; 107:711-721. [PMID: 31007275 PMCID: PMC6472561 DOI: 10.1111/1365-2745.13080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/07/2018] [Accepted: 09/12/2018] [Indexed: 05/27/2023]
Abstract
Uncovering the roles of biotic interactions in assembling and maintaining species-rich communities remains a major challenge in ecology. In plant communities, interactions between individuals of different species are expected to generate positive or negative spatial interspecific associations over short distances. Recent studies using individual-based point pattern datasets have concluded that (a) detectable interspecific interactions are generally rare, but (b) are most common in communities with fewer species; and (c) the most abundant species tend to have the highest frequency of interactions. However, it is unclear how the detection of spatial interactions may change with the abundances of each species, or the scale and intensity of interactions. We ask if statistical power is sufficient to explain all three key results.We use a simple two-species model, assuming no habitat associations, and where the abundances, scale and intensity of interactions are controlled to simulate point pattern data. In combination with an approximation to the variance of the spatial summary statistics that we sample, we investigate the power of current spatial point pattern methods to correctly reject the null model of pairwise species independence.We show the power to detect interactions is positively related to both the abundances of the species tested, and the intensity and scale of interactions, but negatively related to imbalance in abundances. Differences in detection power in combination with the abundance distributions found in natural communities are sufficient to explain all the three key empirical results, even if all pairwise interactions are identical. Critically, many hundreds of individuals of both species may be required to detect even intense interactions, implying current abundance thresholds for including species in the analyses are too low. Sy n thesis. The widespread failure to reject the null model of spatial interspecific independence could be due to low power of the tests rather than any key biological process. Since we do not model habitat associations, our results represent a first step in quantifying sample sizes required to make strong statements about the role of biotic interactions in diverse plant communities. However, power should be factored into analyses and considered when designing empirical studies.
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Affiliation(s)
- Tuomas Rajala
- Department of Statistical ScienceUniversity College LondonLondonUK
| | | | - David John Murrell
- Centre for Biodiversity and Environment ResearchUniversity College LondonLondonUK
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38
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Feng G, Li J, Zang R, Ding Y, Ai X, Yao L. Variation in three community features across habitat types and scales within a 15-ha subtropical evergreen-deciduous broadleaved mixed forest dynamics plot in China. Ecol Evol 2018; 8:11987-11998. [PMID: 30598793 PMCID: PMC6303768 DOI: 10.1002/ece3.4655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 08/15/2018] [Accepted: 09/21/2018] [Indexed: 11/20/2022] Open
Abstract
The evergreen and deciduous broadleaved mixed forests (EDBMFs) belong to one of the ecosystems most sensitive to environmental change, however, little is known about the environmental determinants for their plant diversity and forest structure at different habitat types and spatial scales. Here, we used data from a 15-ha (300 × 500 m) forest dynamic plot (FDP) of an old-growth EDBMF to examine the patterns and determinants of the three community features (stem abundance, rarefied species richness and basal area [BA]) in three habitat types (ridge, hillside and foothill) and at three spatial scales (20 × 20 m, 50 × 50 m, and 100 × 100 m). We found that the three community features significantly changed with habitat type, but only one of them (rarefied richness) changed with scale. Among spatial scales, the principle environmental factors that widely affected community features were pH, soil organic matter, and total phosphorus, while these effects only taken place at certain habitat. Variations in the three community features explained by soil conditions were generally greater than those explained by topographical conditions. With changes in habitat type, the proportion of variations explained by environmental conditions was 31%-53%, 8%-25%, and 18%-26% for abundance, rarefied richness, and BA, respectively. With increasing spatial scale, the variations explained by environmental conditions were 44%-75% for abundance, 28%-95% for rarefied richness, and 18%-86% for BA. Our study demonstrated that environmental factors had great impacts on the plant diversity and forest structure in the EDBMFs, especially the soil factors such as pH. In addition, the importance of the environmental determinants on these community features was highly related to the spatial scale.
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Affiliation(s)
- Guang Feng
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Key Laboratory of Forest Ecology and Environment, State Forestry Administration, Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Jun‐Qing Li
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
| | - Run‐Guo Zang
- Key Laboratory of Forest Ecology and Environment, State Forestry Administration, Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
| | - Yi Ding
- Key Laboratory of Forest Ecology and Environment, State Forestry Administration, Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
| | - Xun‐Ru Ai
- School of Forestry and HorticultureHubei University for NationalitiesEnshiHubeiChina
| | - Lan Yao
- School of Forestry and HorticultureHubei University for NationalitiesEnshiHubeiChina
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39
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Katabuchi M, Wright SJ, Swenson NG, Feeley KJ, Condit R, Hubbell SP, Davies SJ. Contrasting outcomes of species- and community-level analyses of the temporal consistency of functional composition. Ecology 2018; 98:2273-2280. [PMID: 28722127 DOI: 10.1002/ecy.1952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/14/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022]
Abstract
Multiple anthropogenic drivers affect every natural community, and there is broad interest in using functional traits to understand and predict the consequences for future biodiversity. There is, however, no consensus regarding the choice of analytical methods. We contrast species- and community-level analyses of change in the functional composition for four traits related to drought tolerance using three decades of repeat censuses of trees in the 50-ha Forest Dynamics Plot on Barro Colorado Island, Panama. Community trait distributions shifted significantly through time, which may indicate a shift toward more drought tolerant species. However, at the species level, changes in abundance were unrelated to trait values. To reconcile these seemingly contrasting results, we evaluated species-specific contributions to the directional shifts observed at the community level. Abundance changes of just one to six of 312 species were responsible for the community-level shifts observed for each trait. Our results demonstrate that directional changes in community-level functional composition can result from idiosyncratic change in a few species rather than widespread community-wide changes associated with functional traits. Future analyses of directional change in natural communities should combine community-, species-, and possibly individual-level analyses to uncover relationships with function that can improve understanding and enable prediction.
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Affiliation(s)
- Masatoshi Katabuchi
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, 32611, USA
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Panama
| | - Nathan G Swenson
- Department of Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Kenneth J Feeley
- Department of Biology, University of Miami, Coral Gables, Florida, 33146, USA
| | - Richard Condit
- Field Museum, Chicago, Illinois, 60605, USA.,Morton Arboretum, Lisle, Illinois, 60532, USA
| | - Stephen P Hubbell
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Panama.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
| | - Stuart J Davies
- Center for Tropical Forest Science, Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, D.C., 20013, USA
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40
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The Frequency of Cyclonic Wind Storms Shapes Tropical Forest Dynamism and Functional Trait Dispersion. FORESTS 2018. [DOI: 10.3390/f9070404] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Cross-scale neutral ecology and the maintenance of biodiversity. Sci Rep 2018; 8:10200. [PMID: 29976959 PMCID: PMC6033888 DOI: 10.1038/s41598-018-27712-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/31/2018] [Indexed: 11/08/2022] Open
Abstract
One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.
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42
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Meyer I, Shnerb NM. Noise-induced stabilization and fixation in fluctuating environment. Sci Rep 2018; 8:9726. [PMID: 29950588 PMCID: PMC6021438 DOI: 10.1038/s41598-018-27982-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/05/2018] [Indexed: 01/07/2023] Open
Abstract
The dynamics of a two-species community of N competing individuals are considered, with an emphasis on the role of environmental variations that affect coherently the fitness of entire populations. The chance of fixation of a mutant (or invading) population is calculated as a function of its mean relative fitness, the amplitude of fitness variations and their typical duration. We emphasize the distinction between the case of pairwise competition and the case of global competition; in the latter a noise-induced stabilization mechanism yields a higher chance of fixation for a single mutant. This distinction becomes dramatic in the weak selection regime, where the chance of fixation for a single deleterious mutant is an N-independent constant for global competition and decays like (ln N)−1 in the pairwise competition case. A Wentzel-Kramers-Brillouin (WKB) technique yields a general formula for the chance of fixation of a deleterious mutant in the strong selection regime. The possibility of long-term persistence of large [\documentclass[12pt]{minimal}
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\begin{document}$${\mathscr{O}}$$\end{document}O(N)] suboptimal (and extinction-prone) populations is discussed, as well as its relevance to stochastic tunneling between fitness peaks.
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Affiliation(s)
- Immanuel Meyer
- Department of Physics, Bar-Ilan University, Ramat-Gan, IL52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan, IL52900, Israel.
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43
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Olivares I, Karger DN, Kessler M. Assessing species saturation: conceptual and methodological challenges. Biol Rev Camb Philos Soc 2018; 93:1874-1890. [PMID: 29733121 DOI: 10.1111/brv.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Is there a maximum number of species that can coexist? Intuitively, we assume an upper limit to the number of species in a given assemblage, or that a lineage can produce, but defining and testing this limit has proven problematic. Herein, we first outline seven general challenges of studies on species saturation, most of which are independent of the actual method used to assess saturation. Among these are the challenge of defining saturation conceptually and operationally, the importance of setting an appropriate referential system, and the need to discriminate among patterns, processes and mechanisms. Second, we list and discuss the methodological approaches that have been used to study species saturation. These approaches vary in time and spatial scales, and in the variables and assumptions needed to assess saturation. We argue that assessing species saturation is possible, but that many studies conducted to date have conceptual and methodological flaws that prevent us from currently attaining a good idea of the occurrence of species saturation.
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Affiliation(s)
- Ingrid Olivares
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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44
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Fung T, O’Dwyer JP, Chisholm RA. Quantifying species extinction risk under temporal environmental variance. ECOLOGICAL COMPLEXITY 2018. [DOI: 10.1016/j.ecocom.2017.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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45
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Tropical forest dynamics in unstable terrain: a case study from New Guinea. JOURNAL OF TROPICAL ECOLOGY 2018. [DOI: 10.1017/s0266467418000123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract:Long-term forest dynamics plots in the tropics tend to be situated on stable terrain. This study investigated forest dynamics on the north coast of New Guinea where active subduction zones are uplifting lowland basins and exposing relatively young sediments to rapid weathering. We examined forest dynamics in relation to disturbance history, topography and soil nutrients based on partial re-census of the 50-ha Wanang Forest Dynamics Plot in Papua New Guinea. The plot is relatively high in cations and phosphorus but low in nitrogen. Soil nutrients and topography accounted for 29% of variation in species composition but only 4% of variation in basal area. There were few areas of high biomass and most of the forest was comprised of small-diameter stems. Approximately 18% of the forest was less than 30 y old and the annual tree mortality rate of nearly 4% was higher than in other tropical forests in South-East Asia and the neotropics. These results support the reputation of New Guinea's forests as highly dynamic, with frequent natural disturbance. Empirical documentation of this hypothesis expands our understanding of tropical forest dynamics and suggests that geomorphology might be incorporated in models of global carbon storage especially in regions of unstable terrain.
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46
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Danino M, Shnerb NM. Theory of time-averaged neutral dynamics with environmental stochasticity. Phys Rev E 2018; 97:042406. [PMID: 29758719 DOI: 10.1103/physreve.97.042406] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 06/08/2023]
Abstract
Competition is the main driver of population dynamics, which shapes the genetic composition of populations and the assembly of ecological communities. Neutral models assume that all the individuals are equivalent and that the dynamics is governed by demographic (shot) noise, with a steady state species abundance distribution (SAD) that reflects a mutation-extinction equilibrium. Recently, many empirical and theoretical studies emphasized the importance of environmental variations that affect coherently the relative fitness of entire populations. Here we consider two generic time-averaged neutral models; in both the relative fitness of each species fluctuates independently in time but its mean is zero. The first (model A) describes a system with local competition and linear fitness dependence of the birth-death rates, while in the second (model B) the competition is global and the fitness dependence is nonlinear. Due to this nonlinearity, model B admits a noise-induced stabilization mechanism that facilitates the invasion of new mutants. A self-consistent mean-field approach is used to reduce the multispecies problem to two-species dynamics, and the large-N asymptotics of the emerging set of Fokker-Planck equations is presented and solved. Our analytic expressions are shown to fit the SADs obtained from extensive Monte Carlo simulations and from numerical solutions of the corresponding master equations.
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Affiliation(s)
- Matan Danino
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
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47
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Danino M, Shnerb NM. Fixation and absorption in a fluctuating environment. J Theor Biol 2018; 441:84-92. [DOI: 10.1016/j.jtbi.2018.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
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48
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Wiegand T, May F, Kazmierczak M, Huth A. What drives the spatial distribution and dynamics of local species richness in tropical forest? Proc Biol Sci 2018; 284:rspb.2017.1503. [PMID: 28931739 DOI: 10.1098/rspb.2017.1503] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/22/2017] [Indexed: 11/12/2022] Open
Abstract
Understanding the structure and dynamics of highly diverse tropical forests is challenging. Here we investigate the factors that drive the spatio-temporal variation of local tree numbers and species richness in a tropical forest (including 1250 plots of 20 × 20 m2). To this end, we use a series of dynamic models that are built around the local spatial variation of mortality and recruitment rates, and ask which combination of processes can explain the observed spatial and temporal variation in tree and species numbers. We find that processes not included in classical neutral theory are needed to explain these fundamental patterns of the observed local forest dynamics. We identified a large spatio-temporal variability in the local number of recruits as the main missing mechanism, whereas variability of mortality rates contributed to a lesser extent. We also found that local tree numbers stabilize at typical values which can be explained by a simple analytical model. Our study emphasized the importance of spatio-temporal variability in recruitment beyond demographic stochasticity for explaining the local heterogeneity of tropical forests.
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Affiliation(s)
- Thorsten Wiegand
- Department of Ecological Modelling, Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Biodiversity Synthesis, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Felix May
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Biodiversity Synthesis, Deutscher Platz 5e, 04103 Leipzig, Germany .,Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Martin Kazmierczak
- Department of Ecological Modelling, Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Andreas Huth
- Department of Ecological Modelling, Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Biodiversity Synthesis, Deutscher Platz 5e, 04103 Leipzig, Germany.,Institute of Environmental Systems Research, University of Osnabrück, 49069 Osnabrück, Germany
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49
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Danino M, Kessler DA, Shnerb NM. Stability of two-species communities: Drift, environmental stochasticity, storage effect and selection. Theor Popul Biol 2018; 119:57-71. [DOI: 10.1016/j.tpb.2017.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 10/03/2017] [Accepted: 11/15/2017] [Indexed: 11/16/2022]
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50
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D'Andrea R, Ostling A. Biodiversity maintenance may be lower under partial niche differentiation than under neutrality. Ecology 2017; 98:3211-3218. [PMID: 28898396 DOI: 10.1002/ecy.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 08/22/2017] [Accepted: 08/29/2017] [Indexed: 11/08/2022]
Abstract
Niche differentiation is normally regarded as a key promoter of species coexistence in competitive systems. One might therefore expect that relative to neutral assemblages, niche-differentiated communities should support more species with longer persistence and lower probability of extinction. Here we compare stochastic niche and neutral dynamics in simulated assemblages, and find that when local dynamics combine with immigration from a regional pool, the effect of niches can be more complex. Trait variation that lessens competition between species will not necessarily give all immigrating species their own niche to occupy. Such partial niche differentiation protects certain species from local extinction, but precipitates exclusion of others. Differences in regional abundances and intrinsic growth rates have similar impacts on persistence times as niche differentiation, and therefore blur the distinction between niche and neutral dynamical patterns-although niche dynamics will influence which species persist longer. Ultimately, unless the number of niches available to species is sufficiently high, niches may actually heighten extinction rates and lower species richness and local persistence times. Our results help make sense of recent observations of community dynamics, and point to the dynamical observations needed to discern the influence of niche differentiation.
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Affiliation(s)
- Rafael D'Andrea
- Department of Ecology and Evolutionary Biology, University of Michigan, 2004 Kraus Natural Sciences, 830 North University Avenue, Ann Arbor, Michigan, 48109, USA
| | - Annette Ostling
- Department of Ecology and Evolutionary Biology, University of Michigan, 2004 Kraus Natural Sciences, 830 North University Avenue, Ann Arbor, Michigan, 48109, USA.,Centre for Macroecology, Evolution and Climate, Building 3, 2nd floor, Universitetsparken 15, 2100, København Ø, Denmark
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