1
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Luiselli J, Overcast I, Rominger A, Ruffley M, Morlon H, Rosindell J. Detecting the ecological footprint of selection. PLoS One 2024; 19:e0302794. [PMID: 38848435 PMCID: PMC11161045 DOI: 10.1371/journal.pone.0302794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 06/09/2024] Open
Abstract
The structure of communities is influenced by many ecological and evolutionary processes, but the way these manifest in classic biodiversity patterns often remains unclear. Here we aim to distinguish the ecological footprint of selection-through competition or environmental filtering-from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes-species abundances, genetic diversity, and trait variation-to distinguish between mechanistic processes. To correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual's trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly and question the relative roles of neutral and selective processes.
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Affiliation(s)
- Juliette Luiselli
- Département de Biologie, École Normale Supérieure–PSL, Paris, France
- INSA-Lyon, Inria, CNRS, Université Claude Bernard Lyon 1, ECL, Université Lumière Lyon 2, LIRIS UMR5205, Lyon, France
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
| | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- School of Biology and Ecology, University of Maine, Orono, ME, United States of America
| | - Andrew Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, United States of America
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Washington, DC, United States of America
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
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2
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van Nes EH, Pujoni DGF, Shetty SA, Straatsma G, de Vos WM, Scheffer M. A tiny fraction of all species forms most of nature: Rarity as a sticky state. Proc Natl Acad Sci U S A 2024; 121:e2221791120. [PMID: 38165929 PMCID: PMC10786311 DOI: 10.1073/pnas.2221791120] [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: 12/23/2022] [Accepted: 11/11/2023] [Indexed: 01/04/2024] Open
Abstract
Using data from a wide range of natural communities including the human microbiome, plants, fish, mushrooms, rodents, beetles, and trees, we show that universally just a few percent of the species account for most of the biomass. This is in line with the classical observation that the vast bulk of biodiversity is very rare. Attempts to find traits allowing the tiny fraction of abundant species to escape rarity have remained unsuccessful. Here, we argue that this might be explained by the fact that hyper-dominance can emerge through stochastic processes. We demonstrate that in neutrally competing groups of species, rarity tends to become a trap if environmental fluctuations result in gains and losses proportional to abundances. This counter-intuitive phenomenon arises because absolute change tends to zero for very small abundances, causing rarity to become a "sticky state", a pseudoattractor that can be revealed numerically in classical ball-in-cup landscapes. As a result, the vast majority of species spend most of their time in rarity leaving space for just a few others to dominate the neutral community. However, fates remain stochastic. Provided that there is some response diversity, roles occasionally shift as stochastic events or natural enemies bring an abundant species down allowing a rare species to rise to dominance. Microbial time series spanning thousands of generations support this prediction. Our results suggest that near-neutrality within niches may allow numerous rare species to persist in the wings of the dominant ones. Stand-ins may serve as insurance when former key species collapse.
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Affiliation(s)
- Egbert H. van Nes
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
| | - Diego G. F. Pujoni
- Federal University of Minas Gerais, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Laboratório de Limnologia, Ecotoxicologia e Ecologia Aquática, Belo HorizonteMG CEP31270-901, Brazil
| | - Sudarshan A. Shetty
- Laboratory of Microbiology, Wageningen University, WageningenNL-6700 EH, The Netherlands
| | - Gerben Straatsma
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, WageningenNL-6700 EH, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki00014, Finland
| | - Marten Scheffer
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
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3
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Wu L, Yang Y, Ning D, Gao Q, Yin H, Xiao N, Zhou BY, Chen S, He Q, Zhou J. Assessing mechanisms for microbial taxa and community dynamics using process models. MLIFE 2023; 2:239-252. [PMID: 38817815 PMCID: PMC10989933 DOI: 10.1002/mlf2.12076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/27/2023] [Indexed: 06/01/2024]
Abstract
Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.
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Affiliation(s)
- Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental SciencesPeking UniversityBeijingChina
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Daliang Ning
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Huaqun Yin
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Naija Xiao
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Benjamin Y. Zhou
- Department of Mathematics, Lunt HallNorthwestern UniversityEvanstonIllinoisUSA
| | - Si Chen
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Qiang He
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- School of Computer ScienceUniversity of OklahomaNormanOKUSA
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4
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Lin X, Zhang C, Xie W. Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea. Front Microbiol 2023; 14:1185436. [PMID: 37426005 PMCID: PMC10324572 DOI: 10.3389/fmicb.2023.1185436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.
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Affiliation(s)
- Xizheng Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
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5
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Loke LHL, Chisholm RA. Unveiling the transition from niche to dispersal assembly in ecology. Nature 2023:10.1038/s41586-023-06161-x. [PMID: 37286612 DOI: 10.1038/s41586-023-06161-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a 'niche detector' and a tool for assessing when communities are niche versus dispersal assembled.
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Affiliation(s)
- Lynette H L Loke
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, New South Wales, Australia.
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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6
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Lu X, Yu X, Burkovsky I, Esaulov A, Li X, Jiang Y, Mazei Y. Community assembly and co-occurrence network complexity of interstitial microbial communities in the Arctic (investigation of ciliates in the White Sea intertidal zone). MARINE POLLUTION BULLETIN 2023; 188:114656. [PMID: 36731377 DOI: 10.1016/j.marpolbul.2023.114656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Arctic coastal ecosystems play a major role in global environmental system and have been altered significantly by climate changes. To better understanding the response of marine coastal ecosystems towards rapid Arctic climate changes, we examined the variation in diversity and community structure and provided insights into the co-occurrence network and community assembly of interstitial ciliates in the Kandalaksha Gulf of the White Sea from 2009 to 2019. Co-occurrence networks analysis indicated considerably high ration of positive correlations within a community that indicated low competition between interstitial ciliate species. Furthermore, we found that contribution of stochastic processes to the ciliate community assembly was insignificant. Compare with earlier data from the same ecosystem obtained in 1980s-1990s, the role of competitive factors is decreasing, and communities are becoming more spatially and temporally homogeneous. This community simplification is likely due to the response of the entire intertidal ecosystem to global climate change in Arctic.
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Affiliation(s)
- Xiaoteng Lu
- Department of Biology, Shenzhen MSU-BIT University, 1 International University Park Road, Shenzhen 518172, PR China
| | - Xiaowen Yu
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Igor Burkovsky
- Lomonosov Moscow State University, 1 Leninskiye Gory, 119899 Moscow, Russia
| | - Anton Esaulov
- Department of Biology, Shenzhen MSU-BIT University, 1 International University Park Road, Shenzhen 518172, PR China; Penza State University, Krasnaya street 40, 440026 Penza, Russia
| | - Xiaolei Li
- Department of Biology, Shenzhen MSU-BIT University, 1 International University Park Road, Shenzhen 518172, PR China; Lomonosov Moscow State University, 1 Leninskiye Gory, 119899 Moscow, Russia
| | - Yong Jiang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.
| | - Yuri Mazei
- Department of Biology, Shenzhen MSU-BIT University, 1 International University Park Road, Shenzhen 518172, PR China; Lomonosov Moscow State University, 1 Leninskiye Gory, 119899 Moscow, Russia; A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskiy Ave. 33, Moscow 117071, Russia
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7
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Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology. Sci Rep 2023; 13:2859. [PMID: 36801913 PMCID: PMC9938116 DOI: 10.1038/s41598-023-28132-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 01/13/2023] [Indexed: 02/19/2023] Open
Abstract
In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics.
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8
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Princepe D, de Aguiar MAM, Plotkin JB. Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan. Nat Ecol Evol 2022; 6:1992-2002. [PMID: 36216905 DOI: 10.1038/s41559-022-01901-0] [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: 11/08/2021] [Accepted: 09/02/2022] [Indexed: 12/15/2022]
Abstract
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.
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Affiliation(s)
- Débora Princepe
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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9
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Chen H(D, Ma Z(S. Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis. Evol Bioinform Online 2022; 18:11769343221128540. [PMID: 36458150 PMCID: PMC9706044 DOI: 10.1177/11769343221128540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/28/2022] [Indexed: 09/10/2024] Open
Abstract
It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats along the DT could be distinguished as 4 types (niches) including (i) stool; (ii) sub-gingival plaques (SubP) and supra-gingival plaques (SupP); (iii) tongue dorsum (TD), throat (TH), palatine tonsils (PT), and saliva (Sal); and (iv) hard palate (HP) and buccal mucosa (BM), and keratinized gingiva (KG). These niches are different not only in composition, but also in metabolic potentials. In a previous study, we applied Harris et al's multi-site neutral and Tang and Zhou's niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan's near-neural model and Ning et al's stochasticity analysis framework to quantify the niche-neutral continuum of the DT microbiome distribution to shed light on the possible ecological/evolutionary mechanism that shapes the continuum. Overall but excluding the stool site, the proportion of neutral OTUs (46%) is slightly higher than that of the positive selection (38%), but significantly higher than negative selection (15%). The gut (stool) exhibited 3 to 12 times lower neutrality than other DT sites. The analysis also cross-verified our previous hypothesis that the KG (keratinized gingiva) is of distinct assembly dynamics in the DT microbiome, should be treated as a fifth niche. Our findings offer new insight on the long-standing debate concerning whether a minimum of 2-mm of KG width is necessary for marginal periodontal health.
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Affiliation(s)
- Hongju (Daisy) Chen
- Department of Mathematics and
Statistics, Honghe University, Yunnan, China
- Computational Biology and Medical
Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of
Zoology, Chinese Academy of Science, Kunming, Yunnan, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical
Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of
Zoology, Chinese Academy of Science, Kunming, Yunnan, China
- Center for Excellence in Animal
Evolution and Genetics, Chinese Academy of Sciences, China
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10
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Chatterjee S, Nag Chowdhury S, Ghosh D, Hens C. Controlling species densities in structurally perturbed intransitive cycles with higher-order interactions. CHAOS (WOODBURY, N.Y.) 2022; 32:103122. [PMID: 36319275 DOI: 10.1063/5.0102599] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel perspective for understanding the influence of higher-order interactions on the evolution of social phenotypes. Our simple model yields a prosperous outlook to demonstrate the impact of perturbations on intransitive competitive higher-order interactions. Using a mathematical technique, we show how alone the perturbed interaction network can quickly determine the coexistence equilibrium of competing species instead of solving a large system of ordinary differential equations. It is possible to split the system into multiple feasible cluster states depending on the number of perturbations. Our analysis also reveals that the ratio between the unperturbed and perturbed species is inversely proportional to the amount of employed perturbation. Our results suggest that nonlinear dynamical systems and interaction topologies can be interplayed to comprehend species' coexistence under adverse conditions. Particularly, our findings signify that less competition between two species increases their abundance and outperforms others.
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Affiliation(s)
- Sourin Chatterjee
- Department of Mathematics and Statistics, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
| | - Sayantan Nag Chowdhury
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | - Dibakar Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | - Chittaranjan Hens
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
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11
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Warren RJ, Costa JT, Bradford MA. Seeing shapes in clouds: the fallacy of deriving ecological hypotheses from statistical distributions. OIKOS 2022. [DOI: 10.1111/oik.09315] [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)
| | - James T. Costa
- Highlands Biological Station&Western Carolina Univ. Highlands NC USA
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12
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Yu X, Li X, Liu Q, Yang M, Wang X, Guan Z, Yang J, Liu M, Yang EJ, Jiang Y. Community assembly and co-occurrence network complexity of pelagic ciliates in response to environmental heterogeneity affected by sea ice melting in the Ross Sea, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155695. [PMID: 35525347 DOI: 10.1016/j.scitotenv.2022.155695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
In the Southern Ocean, the living environment of organisms has changed due to the dramatic increase in melting sea ice and the loss of glaciers, which have consequently caused substantial changes in biodiversity. Samples of pelagic ciliates from 13 sites were collected as bioindicators to demonstrate the relationship between spatial distribution patterns and environmental heterogeneity affected by sea ice melting and to reveal the community assembly mechanisms in the Ross Sea. Univariate analyses and multivariate analyses were effective tools demonstrating clear spatial patterns and providing a sufficient explanation to interpret strong correlations between pelagic ciliate communities and environmental variations, especially the distribution pattern of nutrients and Chl a. Moreover, environmental heterogeneity might affect the co-occurrence network complexity of ciliate communities. Furthermore, our results also indicated that stochastic processes play a significant role in the community assembly of pelagic ciliates. This study examined the controlling mechanisms of environmental heterogeneity affected by sea ice melting on pelagic ciliate communities and provided explanations for the community assembly of pelagic ciliates in polar marine ecosystems.
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Affiliation(s)
- Xiaowen Yu
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xianrong Li
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Mengyao Yang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaoxiao Wang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhenyu Guan
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jinpeng Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Mingjian Liu
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Eun Jin Yang
- Division of Polar Ocean Environment, Korea Polar Research Institute, 213-3 Songdo-dong, Yeonsu-gu, Incheon 406-840, Republic of Korea.
| | - Yong Jiang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
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13
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Chen H(D, Ma Z(S. Niche-Neutral Continuum Seems to Explain the Global Niche Differentiation and Local Drift of the Human Digestive Tract Microbiome. Front Microbiol 2022; 13:912240. [PMID: 36033847 PMCID: PMC9400020 DOI: 10.3389/fmicb.2022.912240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The human digestive tract (DT) is differentiated into diverse niches and harbors the greatest microbiome diversity of our bodies. Segata et al. (2012) found that the microbiome of diverse habitats along the DT may be classified as four categories or niches with different microbial compositions and metabolic potentials. Nonetheless, few studies have offered theoretical interpretations of the observed patterns, not to mention quantitative mechanistic parameters. Such parameters should capture the essence of the fundamental processes that shape the microbiome distribution, beyond simple ecological metrics such as diversity or composition descriptors, which only capture the manifestations of the mechanisms. Here, we aim to get educated guesses for such parameters by adopting an integrated approach with multisite neutral (MSN) and niche-neutral hybrid (NNH) modeling, via reanalyzing Segata’s 16s-rRNA samples covering 10 DT-sites from over 200 healthy individuals. We evaluate the relative importance of the four essential processes (drift, dispersal, speciation, and selection) in shaping the microbiome distribution and dynamics along DT, which are assumed to form a niche-neutral continuum. Furthermore, the continuum seems to be hierarchical: the selection or niche differentiations seem to play a predominant role (> 90% based on NNH) at the global (the DT metacommunity) level, but the neutral drifts seem to be prevalent (> 90% based on MSN/NNH) at the local sites except for the gut site. An additional finding is that the DT appears to have a fifth niche for the DT microbiome, namely, Keratinized gingival (KG), while in Segata’s original study, only four niches were identified. Specifically, in Segata’s study, KG was classified into the same niche type including buccal mucosa (BM), hard palate (HP), and KG. However, it should be emphasized that the proposal of the fifth niche of KG requires additional verification in the future studies.
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Affiliation(s)
- Hongju (Daisy) Chen
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Mathematics, Honghe University, Yunnan, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Zhanshan (Sam) Ma,
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14
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West R, Shnerb NM. Quantitative Characteristics of Stabilizing and Equalizing Mechanisms. Am Nat 2022; 200:E160-E173. [DOI: 10.1086/720665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Zapién-Campos R, Sieber M, Traulsen A. The effect of microbial selection on the occurrence-abundance patterns of microbiomes. J R Soc Interface 2022; 19:20210717. [PMID: 35135298 PMCID: PMC8826141 DOI: 10.1098/rsif.2021.0717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Theoretical models are useful to investigate the drivers of community dynamics. In the simplest case of neutral models, the events of death, birth and immigration of individuals are assumed to only depend on their abundance-thus, all types share the same parameters. The community level expectations arising from these simple models and their agreement to empirical data have been discussed extensively, often suggesting that in nature, rates might indeed be neutral or their differences might not be important. However, how robust are these model predictions to type-specific rates? Also, what are the consequences at the level of types? Here, we address these questions moving from simple neutral communities to heterogeneous communities. For this, we build a model where types are differently adapted to the environment. We compute the equilibrium distribution of the abundances. Then, we look into the occurrence-abundance pattern often reported in microbial communities. We observe that large immigration and biodiversity-common in microbial systems-lead to such patterns, regardless of whether the rates are neutral or non-neutral. We conclude by discussing the implications to interpret and test empirical data.
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Affiliation(s)
| | - Michael Sieber
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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16
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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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17
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Examining the generality of the biphasic transition from niche-structured to immigration-structured communities. THEOR ECOL-NETH 2021. [DOI: 10.1007/s12080-021-00521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Halley JM, Pimm SL. The Dynamic Hypercube as a Niche Community Model. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.686403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Different models of community dynamics, such as the MacArthur–Wilson theory of island biogeography and Hubbell’s neutral theory, have given us useful insights into the workings of ecological communities. Here, we develop the niche-hypervolume concept of the community into a powerful model of community dynamics. We describe the community’s size through the volume of the hypercube and the dynamics of the populations in it through the fluctuations of the axes of the niche hypercube on different timescales. While the community’s size remains constant, the relative volumes of the niches within it change continuously, thus allowing the populations of different species to rise and fall in a zero-sum fashion. This dynamic hypercube model reproduces several key patterns in communities: lognormal species abundance distributions, 1/f-noise population abundance, multiscale patterns of extinction debt and logarithmic species-time curves. It also provides a powerful framework to explore significant ideas in ecology, such as the drift of ecological communities into evolutionary time.
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Roubik DW, Basset Y, Lopez Y, Bobadilla R, Perez F, Ramírez S. JA. Long‐term (1979–2019) dynamics of protected orchid bees in Panama. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- David W. Roubik
- Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Yves Basset
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
- Faculty of Science University of South Bohemia Budejovice Czech Republic
- Institute of Entomology Biology Centre of the Czech Academy of Sciences Budejovice Czech Republic
- Maestría de Entomología Universidad de Panamá Panama City Republic of Panama
| | - Yacksecari Lopez
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Ricardo Bobadilla
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Filonila Perez
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - José Alejandro Ramírez S.
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
- Maestría de Entomología Universidad de Panamá Panama City Republic of Panama
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20
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Ma ZS. Evaluating the Assembly Dynamics in the Human Vaginal Microbiomes With Niche-Neutral Hybrid Modeling. Front Microbiol 2021; 12:699939. [PMID: 34489890 PMCID: PMC8417885 DOI: 10.3389/fmicb.2021.699939] [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: 04/24/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
Using 2,733 longitudinal vaginal microbiome samples (representing local microbial communities) from 79 individuals (representing meta-communities) in the states of healthy, BV (bacterial vaginosis) and pregnancy, we assess and interpret the relative importance of stochastic forces (e.g., stochastic drifts in bacteria demography, and stochastic dispersal) vs. deterministic selection (e.g., host genome, and host physiology) in shaping the dynamics of human vaginal microbiome (HVM) diversity by an integrated analysis with multi-site neutral (MSN) and niche-neutral hybrid (NNH) modeling. It was found that, when the traditional “default” P-value = 0.05 was specified, the neutral drifts were predominant (≥50% metacommunities indistinguishable from the MSN prediction), while the niche differentiations were moderate (<20% from the NNH prediction). The study also analyzed two challenging uncertainties in testing the neutral and/or niche-neutral hybrid models, i.e., lack of full model specificity – non-unique fittings of same datasets to multiple models with potentially different mechanistic assumptions – and lack of definite rules for setting the P-value thresholds (also noted as Pt-value when referring to the threshold of P-value in this article) in testing null hypothesis (model). Indeed, the two uncertainties can be interdependent, which further complicates the statistical inferences. To deal with the uncertainties, the MSN/NNH test results under a series of P-values ranged from 0.05 to 0.95 were presented. Furthermore, the influence of P-value threshold-setting on the model specificity, and the effects of woman’s health status on the neutrality level of HVM were examined. It was found that with the increase of P-value threshold from 0.05 to 0.95, the overlap (non-unique) fitting of MSN and NNH decreased from 29.1 to 1.3%, whereas the specificity (uniquely fitted to data) of MSN model was kept between 55.7 and 82.3%. Also with the rising P-value threshold, the difference between healthy and BV groups become significant. These findings suggested that traditional single P-value threshold (such as the de facto standard P-value = 0.05) might be insufficient for testing the neutral and/or niche neutral hybrid models.
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Affiliation(s)
- Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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21
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Abstract
Animal (human) gut microbiomes have been coevolving with their hosts for many millions of years. Understanding how the coevolution shapes the processes of microbiome assembly and diversity maintenance is important but rather challenging. An effort may start with the understanding of how and why animals and humans may differ in their microbiome neutrality (stochasticity) levels. Here, we attempted to perform layered comparative stochasticity analyses across animal species (including humans), class, and kingdom scales, corresponding to microbial metacommunity, landscape, and global-landscape scales. By analyzing 4,903 microbiome samples from 274 animal species covering 4 major invertebrate classes and all 6 vertebrate classes and including 1,787 human gut microbiome samples, we discovered the following: (i) at the microbial metacommunity (animal species) scale, although the general trend of stochasticity (measured in the relationships between fundamental biodiversity/dispersal numbers of Hubbell’s neutral theory and host species phylogenetic timeline) seems continuous, there seems to be a turning point from animals to humans in the passing rate of neutrality tests (12% to 45% versus 100%). We postulate that it should be the human experiences from agricultural/industrial activities (e.g., diet effects) and frequent social/familial contacts that are responsible for the dramatically rising stochastic neutrality in human gut microbiomes. (ii) At the microbial landscape (animal class) and global landscape (animal kingdom) scales, neutrality is not detectable, suggesting that the landscape is niche differentiated—animal species may possess “home niches” for their coadapted microbiomes. We further analyze the reliabilities of our findings by using variable P value thresholds (type I error) and performing power analysis (type II error) of neutrality tests. IMPORTANCE Understanding how the coevolution (evolutionary time scale) and/or the interactions (ecological time scale) between animal (human) gut microbiomes and their hosts shape the processes of the microbiome assembly and diversity maintenance is important but rather challenging. An effort may start with the understanding of how and why animals and humans may differ in their microbiome neutrality (stochasticity) levels. Here, we attempted to perform layered comparative stochasticity analyses across animal species (including humans), class, and kingdom scales, corresponding to microbial metacommunity, landscape, and global-landscape scales by analyzing 4,903 microbiome samples from 274 animal species covering 4 major invertebrate classes and all 6 vertebrate classes, and including 1,787 human gut microbiome samples. The analyses were implemented by fitting the multisite neutral model and further augmented by checking false-positive and false-negative errors, respectively. It appears that there is a turning (tipping) point in the neutrality level from animal to human microbiomes.
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22
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Nyirabuhoro P, Gao X, Ndayishimiye JC, Xiao P, Mo Y, Ganjidoust H, Yang J. Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir. FEMS Microbiol Ecol 2021; 97:6184044. [PMID: 33755730 DOI: 10.1093/femsec/fiab036] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
Investigation of bacterial community dynamics across different time scales is important for understanding how environmental conditions drive community change over time. Bacterioplankton from the surface waters of a subtropical urban reservoir in southeast China were analyzed through high-frequency sampling over 13 months to compare patterns and ecological processes between short (0‒8 weeks), medium (9‒24 weeks) and long (25‒53 weeks) time intervals. We classified the bacterial community into different subcommunities: abundant taxa (AT); conditionally rare taxa (CRT); rare taxa (RT). CRT contributed > 65% of the alpha-diversity, and temporal change of beta-diversities was more pronounced for AT and CRT than RT. The bacterial community exhibited a directional change in the short- and medium-time intervals and a convergent dynamic during the long-time interval due to a seasonal cycle. Cyanobacteria exhibited a strong succession pattern than other phyla. CRT accounted for > 76% of the network nodes in three stations. The bacteria-environment relationship and deterministic processes were stronger for large sample size at station G (n = 116) than small sample size at stations C (n = 12) and L (n = 22). These findings suggest that a high-frequency sampling approach can provide a better understanding on the time scales at which bacterioplankton can change fast between being abundant or rare, thus providing the facts about environmental factors driving microbial community dynamics. Patterns and processes in alpha- and beta-diversities and community assembly of bacterioplankton differ among different time intervals (short-, medium- and long-time intervals) and different subcommunities (abundant, conditionally rare and rare taxa) in a subtropical urban reservoir, demonstrating the importance of temporal scale and high-frequency sampling in microbial community ecology.
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Affiliation(s)
- Pascaline Nyirabuhoro
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaofei Gao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jean Claude Ndayishimiye
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hossein Ganjidoust
- Faculty of Civil and Environmental Engineering, Environmental Engineering Division, Tarbiat Modares University, P.O. Box 14115-397, Tehran, Iran
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R. China
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23
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Feng G, Huang J, Xu Y, Li J, Zang R. Disentangling Environmental Effects on the Tree Species Abundance Distribution and Richness in a Subtropical Forest. FRONTIERS IN PLANT SCIENCE 2021; 12:622043. [PMID: 33828571 PMCID: PMC8020568 DOI: 10.3389/fpls.2021.622043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
As a transitional vegetation type between evergreen broadleaved forest and deciduous broadleaved forest, evergreen-deciduous broadleaved mixed forest is composed of diverse plant species. This distinctive forest is generally distributed in mountainous areas with complex landforms and heterogeneous microenvironments. However, little is known about the roles of environmental conditions in driving the species diversity patterns of this forest. Here, based on a 15-ha plot in central China, we aimed to understand how and to what extent topographical characteristics and soil nutrients regulate the number and relative abundance of tree species in this forest. We measured environmental factors (terrain convexity, slope, soil total nitrogen, and phosphorus concentrations) and species diversity (species abundance distribution and species richness) in 20 m × 20 m subplots. Species abundance distribution was characterized by skewness, Berger-Parker index, and the proportion of singletons. The generalized additive model was used to examine the variations in diversity patterns caused by environmental factors. The structural equation model was used to assess whether and how topographical characteristics regulate species diversity via soil nutrients. We found that soil nutrients had significant negative effects on species richness and positive effects on all metrics of species abundance distribution. Convexity had significant positive effects on species richness and negative effects on all metrics of species abundance distribution, but these effects were mostly mediated by soil nutrients. Slope had significant negative effects on skewness and the Berger-Parker index, and these effects were almost independent of soil nutrients. Soil nutrients and topographical characteristics together accounted for 9.5-17.1% of variations in diversity patterns and, respectively, accounted for 8.9-13.9% and 3.3-10.7% of the variations. We concluded that soil nutrients were more important than topographical factors in regulating species diversity. Increased soil nutrient concentration led to decreased taxonomic diversity and increased species dominance and rarity. Convexity could be a better proxy for soil nutrients than slope. Moreover, these abiotic factors played limited roles in regulating diversity patterns, and it is possible that the observed patterns are also driven by some biotic and abiotic factors not considered here.
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Affiliation(s)
- Guang Feng
- Key Laboratory of Biodiversity Conservation of the National Forestry and Grassland Administration, Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Jihong Huang
- Key Laboratory of Biodiversity Conservation of the National Forestry and Grassland Administration, Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yue Xu
- Key Laboratory of Biodiversity Conservation of the National Forestry and Grassland Administration, Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Junqing Li
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Runguo Zang
- Key Laboratory of Biodiversity Conservation of the National Forestry and Grassland Administration, Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Ibanez T, Keppel G, Baider C, Birkinshaw C, Florens FBV, Laidlaw M, Menkes C, Parthasarathy N, Rajkumar M, Ratovoson F, Rasingam L, Reza L, Aiba S, Webb EL, Zang R, Birnbaum P. Tropical cyclones and island area shape species abundance distributions of local tree communities. OIKOS 2020. [DOI: 10.1111/oik.07501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Ibanez
- Inst. Agronomique néo‐Calédonien (IAC), Equipe Sol et Végétation (SolVeg) Nouméa New Caledonia
- AMAP, Univ. of Montpellier, and: CIRAD, CNRS, INRAE, IRD Montpellier France
- Dept of Biology, Univ. of Hawai'i at Hilo Hawai'i USA
| | - Gunnar Keppel
- School of Natural and Built Environments and Future Industries Inst., Univ. of South Australia Adelaide SA Australia
- Biodiversity, Macroecology and Biogeography, Univ. of Goettingen Göttingen Germany
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro‐Industry and Food Security Réduit Mauritius
| | - Chris Birkinshaw
- Missouri Botanical Garden – Programme Madagascar Antananarivo Madagascar
| | - F. B. Vincent Florens
- Tropical Island Biodiversity, Ecology and Conservation Pole of Research, Dept of Biosciences and Ocean Studies, Univ. of Mauritius Réduit Mauritius
| | - Melinda Laidlaw
- Queensland Herbarium, Dept of Environment and Science Toowong Australia
| | | | | | - Muthu Rajkumar
- Dept of Ecology and Environmental Sciences, Pondicherry Univ. Puducherry India
- Tropical Forest Research Inst. Madhya Pradesh India
| | - Fidy Ratovoson
- Missouri Botanical Garden, Madagascar Research and Conservation Program Antananarivo Madagascar
| | - Ladan Rasingam
- Botanical Survey of India, Deccan Regional Center Telangana India
| | - Ludovic Reza
- Missouri Botanical Garden, Madagascar Research and Conservation Program Antananarivo Madagascar
| | - Shin‐ichiro Aiba
- Graduate School of Science and Engineering, Kagoshima Univ. Kagoshima Japan
| | - Edward L. Webb
- Dept of Biological Sciences, National Univ. of Singapore Singapore
| | - Runguo Zang
- Key Laboratory of Biodiversity Conservation, The State Forestry and Grassland Administration, Inst. of Forest Ecology, Environment and Protection, Chinese Academy of Forestry Beijing P. R. China
| | - Philippe Birnbaum
- Inst. Agronomique néo‐Calédonien (IAC), Equipe Sol et Végétation (SolVeg) Nouméa New Caledonia
- AMAP, Univ. of Montpellier, and: CIRAD, CNRS, INRAE, IRD Montpellier France
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D’Andrea R, Gibbs T, O’Dwyer JP. Emergent neutrality in consumer-resource dynamics. PLoS Comput Biol 2020; 16:e1008102. [PMID: 32730245 PMCID: PMC7446820 DOI: 10.1371/journal.pcbi.1008102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 08/24/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022] Open
Abstract
Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern. The neutral theory of biodiversity assumes that species are ecologically equivalent. Given the natural history observation of ubiquitous phenotypic differences between species, it is surprising that neutral theory has successfully predicted a broad range of biodiversity patterns, and simultaneously unsurprising that these results have not convinced ecologists that the natural world is neutral. However, we have lacked a description of how neutrality can emerge in a natural way from ecological mechanisms and species differences. Our study sheds light on this question, providing a theoretical backdrop for the success of neutral theory as a description of macroecological pattern. We derive a prediction for the degree to which consumers must differ in preferences for different resources before the resulting biodiversity patterns become distinguishable from neutrality. These predictions, which we confirm using simulations, show that neutral-like outcomes are possible even when resource requirements across consumers are very far from neutral. Our results can be tested in experimental microbial communities, where, equipped with an inferred consumption network, our analysis can yield predictions for biodiversity patterns and community turnover at different taxonomic levels.
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Affiliation(s)
- Rafael D’Andrea
- Department of Plant Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
| | - Theo Gibbs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - James P. O’Dwyer
- Department of Plant Biology, University of Illinois, Urbana, Illinois, United States of America
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Kim D, Ohr S. Coexistence of plant species under harsh environmental conditions: an evaluation of niche differentiation and stochasticity along salt marsh creeks. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s41610-020-00161-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Ecologists have achieved much progress in the study of mechanisms that maintain species coexistence and diversity. In this paper, we reviewed a wide range of past research related to these topics, focusing on five theoretical bodies: (1) coexistence by niche differentiation, (2) coexistence without niche differentiation, (3) coexistence along environmental stress gradients, (4) coexistence under non-equilibrium versus equilibrium conditions, and (5) modern perspectives.
Results
From the review, we identified that there are few models that can be generally and confidently applicable to different ecological systems. This problem arises mainly because most theories have not been substantiated by enough empirical research based on field data to test various coexistence hypotheses at different spatial scales. We also found that little is still known about the mechanisms of species coexistence under harsh environmental conditions. This is because most previous models treat disturbance as a key factor shaping community structure, but they do not explicitly deal with stressful systems with non-lethal conditions. We evaluated the mainstream ideas of niche differentiation and stochasticity for the coexistence of plant species across salt marsh creeks in southwestern Denmark. The results showed that diversity indices, such as Shannon–Wiener diversity, richness, and evenness, decreased with increasing surface elevation and increased with increasing niche overlap and niche breadth. The two niche parameters linearly decreased with increasing elevation. These findings imply a substantial influence of an equalizing mechanism that reduces differences in relative fitness among species in the highly stressful environments of the marsh. We propose that species evenness increases under very harsh conditions if the associated stress is not lethal. Finally, we present a conceptual model of patterns related to the level of environmental stress and niche characteristics along a microhabitat gradient (i.e., surface elevation).
Conclusions
The ecology of stressful systems with non-lethal conditions will be increasingly important as ongoing global-scale climate change extends the period of chronic stresses that are not necessarily fatal to inhabiting plants. We recommend that more ecologists continue this line of research.
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Worden L. Conservation of community functional structure across changes in composition in consumer-resource models. J Theor Biol 2020; 493:110239. [PMID: 32145224 DOI: 10.1016/j.jtbi.2020.110239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 02/04/2023]
Abstract
High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloguing of functional characteristics of microbial community members as well as their phylogenetic identity. Such studies have found that a community's makeup in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than its composition is in terms of taxa. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional structure. This model demonstrates that interaction with essential resources can regulate the community-wide abundances of ecologically relevant traits, keeping them at consistent levels despite large changes in the abundances of the species housing those traits in response to changes in the environment, and across variation between communities in species composition. Functional structure is shown to be able to track differences in environmental conditions faithfully across differences in species composition. Mathematical conditions on consumers' vital rates and functional responses necessary and sufficient to produce conservation of functional community structure across differences in species composition in these models are presented. These conditions imply a nongeneric relation between biochemical rates, and avenues for further research are discussed.
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Affiliation(s)
- Lee Worden
- Francis I. Proctor Foundation for Research in Ophthalmology, Box 0412, University of California, San Francisco, California 94143-0412, United States.
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28
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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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29
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Laroche F, Violle C, Taudière A, Munoz F. Analyzing snapshot diversity patterns with the Neutral Theory can show functional groups' effects on community assembly. Ecology 2020; 101:e02977. [PMID: 31944275 DOI: 10.1002/ecy.2977] [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: 04/24/2018] [Revised: 08/29/2019] [Accepted: 12/04/2019] [Indexed: 11/07/2022]
Abstract
A central question of community ecology is to understand how the interplay between processes of the Neutral Theory (e.g., immigration and ecological drift) and niche-based processes (e.g., environmental filtering, intra- and interspecific density dependence) shape species diversity in competitive communities. The articulation between these two categories of mechanisms can be studied through the lens of the intermediate organizational level of "functional groups" (FGs), defined as clusters of species with similar traits. Indeed, FGs stress ecological differences among species and are thus likely to unravel non-neutral interactions within communities. Here we presented a novel approach to explore how FGs affect species coexistence by comparing species and functional diversity patterns. Our framework considers the Neutral Theory as a mechanistic null hypothesis. It assesses how much the functional diversity deviates from species diversity in communities, and compares this deviation, called the "average functional deviation," to a neutral baseline. We showed that the average functional deviation can indicate reduced negative density dependence or environmental filtering among FGs. We validated our framework using simulations illustrating the two situations. We further analyzed tropical tree communities in Western Ghats, India. Our analysis of the average functional deviation revealed environmental filtering between deciduous and evergreen FGs along a broad rainfall gradient. By contrast, we did not find clear evidence for reduced density dependence among FGs. We predict that applying our approach to new case studies where environmental gradients are milder and FGs are more clearly associated to resource partitioning should reveal the missing pattern of reduced density dependence among FGs.
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Affiliation(s)
| | - Cyrille Violle
- CEFE, Université Paul Valéry Montpellier 3, Université Montpellier, EPHE, CNRS, IRD, Montpellier, France
| | - Adrien Taudière
- CEFE, Université Paul Valéry Montpellier 3, Université Montpellier, EPHE, CNRS, IRD, Montpellier, France
| | - François Munoz
- University Grenoble-Alpes, LECA, 2233 Rue de la Piscine, Grenoble, 38041, France.,Institut Français de Pondichéry, UMIFRE 21 MAEE-CNRS, 11 St. Louis Street, Pondicherry, India
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30
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Neutral and niche forces as drivers of species selection. J Theor Biol 2019; 483:109969. [PMID: 31377398 DOI: 10.1016/j.jtbi.2019.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 11/23/2022]
Abstract
The evolutionary and ecological processes behind the origin of species are among the most fundamental problems in biology. In fact, many theoretical hypothesis on different type of speciation have been proposed. In particular, models of sympatric speciation leading to the formation of new species without geographical isolation, are based on the niche hypothesis: the diversification of the population is induced by the competition for a limited set of available resources. Interestingly, neutral models of evolution have shown that stochastic forces are sufficient to generate coexistence of different species. In this work, we put forward this dichotomy within the context of species formation, studying how neutral and niche forces contribute to sympatric speciation in a model ecosystem. In particular, we study the evolution of a population of individuals with asexual reproduction whose inherited characters or phenotypes are specified by both niche-based and neutral traits. We analyze the stationary state of the dynamics, and study the distribution of individuals in the whole phenotypic space. We show, both numerically and analytically, that there is a non-trivial coupling between neutral and niche forces induced by stochastic effects in the evolution of the population allowing the formation of clusters, that is, species in the phenotypic space. Remarkably, our framework can be generalized also to sexual reproduction or other type of population dynamics.
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31
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Abstract
Background: The abundance of different species in a community often follows the log series distribution. Other ecological patterns also have simple forms. Why does the complexity and variability of ecological systems reduce to such simplicity? Common answers include maximum entropy, neutrality, and convergent outcome from different underlying biological processes. Methods: This article proposes a more general answer based on the concept of invariance, the property by which a pattern remains the same after transformation. Invariance has a long tradition in physics. For example, general relativity emphasizes the need for the equations describing the laws of physics to have the same form in all frames of reference. Results: By bringing this unifying invariance approach into ecology, we show that the log series pattern dominates when the consequences of processes acting on abundance are invariant to the addition or multiplication of abundance by a constant. The lognormal pattern dominates when the processes acting on net species growth rate obey rotational invariance (symmetry) with respect to the summing up of the individual component processes. Conclusions: Recognizing how these invariances connect pattern to process leads to a synthesis of previous approaches. First, invariance provides a simpler and more fundamental maximum entropy derivation of the log series distribution. Second, invariance provides a simple derivation of the key result from neutral theory: the log series at the metacommunity scale and a clearer form of the skewed lognormal at the local community scale. The invariance expressions are easy to understand because they uniquely describe the basic underlying components that shape pattern.
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Affiliation(s)
- Steven A. Frank
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697-2525, USA
| | - Jordi Bascompte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
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32
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Mitchell EG, Harris S, Kenchington CG, Vixseboxse P, Roberts L, Clark C, Dennis A, Liu AG, Wilby PR. The importance of neutral over niche processes in structuring Ediacaran early animal communities. Ecol Lett 2019; 22:2028-2038. [PMID: 31515929 PMCID: PMC6899650 DOI: 10.1111/ele.13383] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/22/2023]
Abstract
The relative influence of niche vs. neutral processes in ecosystem dynamics is an on-going debate, but the extent to which they structured the earliest animal communities is unknown. Some of the oldest known metazoan-dominated paleocommunities occur in Ediacaran age (~ 565 million years old) strata in Newfoundland, Canada and Charnwood Forest, UK. These comprise large and diverse populations of sessile organisms that are amenable to spatial point process analyses, enabling inference of the most likely underlying niche or neutral processes governing community structure. We mapped seven Ediacaran paleocommunities using LiDAR, photogrammetry and a laser line probe. We found that neutral processes dominate these paleocommunities, with niche processes exerting limited influence, in contrast with the niche-dominated dynamics of modern marine ecosystems. The dominance of neutral processes suggests that early metazoan diversification may not have been driven by systematic adaptations to the local environment, but instead may have resulted from stochastic demographic differences.
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Affiliation(s)
- Emily G. Mitchell
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Simon Harris
- British Geological SurveyNicker HillKeyworth, NottinghamNG12 5GGUK
| | | | - Philip Vixseboxse
- School of Earth SciencesUniversity of BristolWills Memorial Building, Queens RoadBristolBS8 1RJUK
| | - Lucy Roberts
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUK
| | - Catherine Clark
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Alexandra Dennis
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Alexander G. Liu
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Philip R. Wilby
- British Geological SurveyNicker HillKeyworth, NottinghamNG12 5GGUK
- School of Geography, Geology & the EnvironmentUniversity of LeicesterUniversity RoadLeicesterLE1 7RHUK
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33
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Enquist BJ, Feng X, Boyle B, Maitner B, Newman EA, Jørgensen PM, Roehrdanz PR, Thiers BM, Burger JR, Corlett RT, Couvreur TLP, Dauby G, Donoghue JC, Foden W, Lovett JC, Marquet PA, Merow C, Midgley G, Morueta-Holme N, Neves DM, Oliveira-Filho AT, Kraft NJB, Park DS, Peet RK, Pillet M, Serra-Diaz JM, Sandel B, Schildhauer M, Šímová I, Violle C, Wieringa JJ, Wiser SK, Hannah L, Svenning JC, McGill BJ. The commonness of rarity: Global and future distribution of rarity across land plants. SCIENCE ADVANCES 2019; 5:eaaz0414. [PMID: 31807712 PMCID: PMC6881168 DOI: 10.1126/sciadv.aaz0414] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/04/2019] [Indexed: 05/21/2023]
Abstract
A key feature of life's diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth's plant biodiversity that are rare. A large fraction, ~36.5% of Earth's ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth's plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.
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Affiliation(s)
- Brian J. Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Xiao Feng
- Institute of the Environment, University of Arizona, Tucson, AZ 85721, USA
| | - Brad Boyle
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Brian Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Erica A. Newman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Institute of the Environment, University of Arizona, Tucson, AZ 85721, USA
| | | | - Patrick R. Roehrdanz
- Betty and Gordon Moore Center for Science, Conservation International, 2011 Crystal Dr., Arlington, VA 22202, USA
| | - Barbara M. Thiers
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10348, USA
| | - Joseph R. Burger
- Institute of the Environment, University of Arizona, Tucson, AZ 85721, USA
| | - Richard T. Corlett
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden and Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan, China
| | | | - Gilles Dauby
- AMAP, IRD, CIRAD, CNRS, INRA, Université Montpellier, Montpellier, France
| | | | - Wendy Foden
- Cape Research Centre, South African National Parks, Tokai, 7947 Cape Town, South Africa
| | - Jon C. Lovett
- School of Geography, University of Leeds, Leeds, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Pablo A. Marquet
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, CP 8331150 Santiago, Chile
- Instituto de Ecología y Biodiversidad (IEB), Laboratorio Internacional de Cambio Global and Centro de Cambio Global UC, Chile
| | - Cory Merow
- Department of Ecology and Evolutionary Biology, University of Connecticut, CT 06269, USA
| | - Guy Midgley
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Naia Morueta-Holme
- Center for Macroecology, Evolution and University of Copenhagen, Universitetsparken 15, Building 3, DK-2100 Copenhagen Ø, Denmark
| | - Danilo M. Neves
- Department of Botany, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Ary T. Oliveira-Filho
- Department of Botany, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Nathan J. B. Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel S. Park
- Department of Organismic and Evolutionary Biology, Harvard University, MA 02138, USA
| | - Robert K. Peet
- Department of Biology, University of North Carolina, NC 27599, USA
| | - Michiel Pillet
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | - Brody Sandel
- Department of Biology, Santa Clara University, Santa Clara, CA 95053, USA
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, Santa Barbara, CA 93101, USA
| | - Irena Šímová
- Centre for Theoretical Study, Charles University, Prague 1, Czech Republic
- Department of Ecology, Faculty of Sciences, Charles University, Czech Republic
| | - Cyrille Violle
- Université Montpellier, CNRS, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, Leiden, Netherlands
| | | | - Lee Hannah
- Betty and Gordon Moore Center for Science, Conservation International, 2011 Crystal Dr., Arlington, VA 22202, USA
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) and Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| | - Brian J. McGill
- School of Biology and Ecology and Senator George J. Mitchell Center of Sustainability Solutions, University of Maine, Orono, ME 04469, USA
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34
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Chen W, Ren K, Isabwe A, Chen H, Liu M, Yang J. Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons. MICROBIOME 2019; 7:138. [PMID: 31640783 PMCID: PMC6806580 DOI: 10.1186/s40168-019-0749-8] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 09/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons. RESULTS Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes. CONCLUSIONS This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.
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Affiliation(s)
- Weidong Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Alain Isabwe
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Min Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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35
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Viana DS, Chase JM. Spatial scale modulates the inference of metacommunity assembly processes. Ecology 2019; 100:e02576. [PMID: 30516271 DOI: 10.1002/ecy.2576] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/09/2018] [Accepted: 11/06/2018] [Indexed: 11/11/2022]
Abstract
The abundance and distribution of species across the landscape depend on the interaction between local, spatial, and stochastic processes. However, empirical syntheses relating these processes to spatiotemporal patterns of structure in metacommunities remain elusive. One important reason for this lack of synthesis is that the relative importance of the core assembly processes (dispersal, selection, and drift) critically depends on the spatial grain and extent over which communities are studied. To illustrate this, we simulated different aspects of community assembly on heterogeneous landscapes, including the strength of response to environmental heterogeneity (inherent to niche theory) vs. dispersal and stochastic drift (inherent to neutral theory). We show that increasing spatial extent leads to increasing importance of niche selection, whereas increasing spatial grain leads to decreasing importance of niche selection. The strength of these scaling effects depended on environment configuration, dispersal capacity, and niche breadth. By mapping the variation observed from the scaling effects in simulations, we could recreate the entire range of variation observed within and among empirical studies. This means that variation in the relative importance of assembly processes among empirical studies is largely scale dependent and cannot be directly compared. The scaling coefficient of the relative contribution of assembly processes, however, can be interpreted as a scale-integrative estimate to compare assembly processes across different regions and ecosystems. This emphasizes the necessity to consider spatial scaling as an explicit component of studies intended to infer the importance of community assembly processes.
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Affiliation(s)
- Duarte S Viana
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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36
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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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37
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Pos E, Guevara JE, Molino J, Sabatier D, Bánki OS, Pitman NC, Mogollón HF, García‐Villacorta R, Neill D, Phillips OL, Cerón C, Ríos Paredes M, Núñez Vargas P, Dávila N, Fiore AD, Rivas‐Torres G, Thomas‐Caesar R, Vriesendorp C, Young KR, Tirado M, Wang O, Sierra R, Mesones I, Zagt R, Vasquez R, Ahuite Reategui MA, Palacios Cuenca W, Valderrama Sandoval EH, ter Steege H. Scaling issues of neutral theory reveal violations of ecological equivalence for dominant Amazonian tree species. Ecol Lett 2019; 22:1072-1082. [PMID: 30938488 PMCID: PMC6849817 DOI: 10.1111/ele.13264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/17/2019] [Accepted: 03/07/2019] [Indexed: 11/26/2022]
Abstract
Neutral models are often used as null models, testing the relative importance of niche versus neutral processes in shaping diversity. Most versions, however, focus only on regional scale predictions and neglect local level contributions. Recently, a new formulation of spatial neutral theory was published showing an incompatibility between regional and local scale fits where especially the number of rare species was dramatically under-predicted. Using a forward in time semi-spatially explicit neutral model and a unique large-scale Amazonian tree inventory data set, we show that neutral theory not only underestimates the number of rare species but also fails in predicting the excessive dominance of species on both regional and local levels. We show that although there are clear relationships between species composition, spatial and environmental distances, there is also a clear differentiation between species able to attain dominance with and without restriction to specific habitats. We conclude therefore that the apparent dominance of these species is real, and that their excessive abundance can be attributed to fitness differences in different ways, a clear violation of the ecological equivalence assumption of neutral theory.
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Affiliation(s)
- Edwin Pos
- Ecology & Biodiversity GroupUtrecht UniversityPadualaan 8Utrecht3584 CHThe Netherlands
| | - Juan Ernesto Guevara
- Grupo de Investigación en BiodiversidadMedio Ambiente y Salud‐BIOMAS‐ Universidad de las AméricasCampus QueriQuito Ecuador
| | - Jean‐François Molino
- AMAPIRDCiradCNRSINRAUniversité de MontpellierTA A‐51/PS2, Bd. de la LirondeMontpellier34398France
| | - Daniel Sabatier
- AMAPIRDCiradCNRSINRAUniversité de MontpellierTA A‐51/PS2, Bd. de la LirondeMontpellier34398France
| | - Olaf S. Bánki
- Naturalis Biodiversity CenterPO Box 9517Leiden2300 RAThe Netherlands
| | - Nigel C.A. Pitman
- Science and EducationThe Field Museum1400 S. Lake Shore DriveChicagoIL60605‐2496USA
| | - Hugo F. Mogollón
- Endangered Species Coalition8530 Geren Rd.Silver SpringMD20901USA
| | - Roosevelt García‐Villacorta
- Institute of Molecular Plant SciencesUniversity of EdinburghMayfield RdEdinburghEH3 5LRUK
- Royal Botanic Garden Edinburgh20a Inverleith Row, EdinburghScotlandEH3 5LRUK
| | - David Neill
- Ecosistemas, Biodiversidad yConservación de EspeciesUniversidad Estatal AmazónicaKm. 2 1/2 vía a Tena (Paso Lateral)Puyo, PastazaEcuador
| | | | - Carlos Cerón
- Escuela de Biología Herbario Alfredo ParedesUniversidad CentralAp. Postal 17.01.2177QuitoPichinchaEcuador
| | | | - Percy Núñez Vargas
- Herbario VargasUniversidad Nacional de San Antonio Abad del CuscoAvenida de la CulturaNro 733Cusco, CuzcoPeru
| | - Nállarett Dávila
- Biologia VegetalUniversidade Estadual de CampinasCaixa Postal6109CampinasSP13.083‐970Brazil
| | - Anthony Di Fiore
- Department of AnthropologyUniversity of Texas at AustinSAC 5.150, 2201, Speedway Stop C3200AustinTX78712USA
| | - Gonzalo Rivas‐Torres
- Colegio de Ciencias Biológicas y Ambientales‐COCIBA & Galapagos Institute for the Arts and Sciences‐GAIASUniversidad San Francisco de Quito‐USFQQuitoPichinchaEcuador
- Department of Wildlife Ecology and ConservationUniversity of Florida110 Newins‐Ziegler HallGainesvilleFL32611USA
| | | | - Corine Vriesendorp
- Science and EducationThe Field Museum1400 S. Lake Shore DriveChicagoIL60605‐2496USA
| | - Kenneth R. Young
- Geography and the EnvironmentUniversity of Texas at Austin305 E. 23rd Street, CLA buildingAustinTX78712USA
| | - Milton Tirado
- GeoISEl Día 369 y El Telégrafo, 3° PisoQuitoPichinchaEcuador
| | - Ophelia Wang
- Environmental Science and PolicyNorthern Arizona UniversityFlagstaffAZ86011USA
| | - Rodrigo Sierra
- GeoISEl Día 369 y El Telégrafo, 3° PisoQuitoPichinchaEcuador
| | - Italo Mesones
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCA94720–3140USA
| | - Roderick Zagt
- Tropenbos InternationalLawickse Allee 11PO Box 232Wageningen6700 AEThe Netherlands
| | | | | | | | - Elvis H. Valderrama Sandoval
- Department of BiologyUniversity of MissouriSt. LouisMO63121USA
- Facultad de BiologiaUniversidad Nacional de la Amazonia PeruanaPevas 5ta cdraIquitos, LoretoPeru
| | - Hans ter Steege
- Systems EcologyFree UniversityDe Boelelaan 1087Amsterdam1081 HVNetherlands
- Biodiversity DynamicsNaturalis Biodiversity CenterPO Box 9517Leiden2300 RAThe Netherlands
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Wu Y, Chen Y, Shen TJ. Comparing Allee effect-based and dispersal-based neutral models for species abundance distribution patterns. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Burgess MG, Fredston-Hermann A, Tilman D, Loreau M, Gaines SD. Broadly inflicted stressors can cause ecosystem thinning. THEOR ECOL-NETH 2019; 12:207-223. [PMID: 31723368 PMCID: PMC6853792 DOI: 10.1007/s12080-019-0417-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/12/2019] [Indexed: 11/26/2022]
Abstract
Many anthropogenic stressors broadly inflict mortality or reduce fecundity, including habitat destruction, pollution, climate change, invasive species, and multispecies harvesting. Here, we show-in four analytical models of interspecies competition-that broadly inflicted stressors disproportionately cause competitive exclusions within groups of ecologically similar species. As a result, we predict that ecosystems become progressively thinner-that is, they have progressively less functional redundancy-as broadly inflicted stressors become progressively more intense. This may negatively affect the temporal stability of ecosystem functions, but it also buffers ecosystem productivity against stress by favoring species less sensitive to the stressors. Our main result follows from the weak limiting similarity principle: species with more similar ecological niches compete more strongly, and their coexistence can be upset by smaller perturbations. We show that stressors can cause indirect competitive exclusions at much lower stressor intensity than needed to directly cause species extinction, consistent with the finding of empirical studies that species interactions are often the proximal drivers of local extinctions. The excluded species are more sensitive to the stressor relative to their ecologically similar competitors. Moreover, broadly inflicted stressors may cause hydra effects-where higher stressor intensity results in higher abundance for a species with lower sensitivity to the stressor than its competitors. Correlations between stressor impacts and ecological niches reduce the potential for indirect competitive exclusions, but they consequently also reduce the buffering effect of ecosystem thinning on ecosystem productivity. Our findings suggest that ecosystems experiencing stress may continue to provision ecosystem services but lose functional redundancy and stability.
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Affiliation(s)
- Matthew G. Burgess
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, 216 UCB, Boulder, CO 80309, USA
- Environmental Studies Program, University of Colorado, Boulder, CO 80303, USA
| | - Alexa Fredston-Hermann
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA
| | - David Tilman
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Michel Loreau
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS, 09200 Moulis, France
| | - Steven D. Gaines
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
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Optimal Microbiome Networks: Macroecology and Criticality. ENTROPY 2019; 21:e21050506. [PMID: 33267220 PMCID: PMC7514995 DOI: 10.3390/e21050506] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
The human microbiome is an extremely complex ecosystem considering the number of bacterial species, their interactions, and its variability over space and time. Here, we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model, we detected potential species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detected an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and how these should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest Pareto total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not necessarily at the phase transition between healthy and unhealthy states. We stress the importance of considering portfolios of interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their interactions (i.e., species collective behavior) that shape transition from healthy to unhealthy states. The macroecological characterization of the microbiome is useful for public health and disease diagnosis and etiognosis, while species-specific analyses can detect beneficial species leading to personalized design of pre- and probiotic treatments and microbiome engineering.
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Wu A, Deng X, He H, Ren X, Jing Y, Xiang W, Ouyang S, Yan W, Fang X. Responses of species abundance distribution patterns to spatial scaling in subtropical secondary forests. Ecol Evol 2019; 9:5338-5347. [PMID: 31110683 PMCID: PMC6509376 DOI: 10.1002/ece3.5122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 11/08/2022] Open
Abstract
To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state-owned forest farm, two 1-ha permanent study plots (100-m × 100-m) were established. We selected four diversity indices including species richness, Shannon-Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken-stick, niche preemption, and Zipf-Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov-Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad-leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump-shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad-leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes.
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Affiliation(s)
- Anchi Wu
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
| | - Xiangwen Deng
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
| | - Honglin He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institution of Geographic Sciences and Natural Resources ResearchChinese Academy of ScienceBeijingChina
- Graduate University of Chinese Academy of SciencesBeijingChina
| | - Xiaoli Ren
- Graduate University of Chinese Academy of SciencesBeijingChina
| | - Yiran Jing
- Chinese Research Academy of Environmental SciencesBeijingChina
| | - Wenhua Xiang
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
| | - Shuai Ouyang
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
| | - Wende Yan
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
| | - Xi Fang
- Faculty of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
- National Engineering Laboratory for Applied Technology of Forestry&Ecology in South ChinaChangshaChina
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan ProvinceHuitongChina
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Chaves DA, Ribeiro-Silva S, Proença CEB, Oliveira WL, Bringel JBA, Medeiros MB. Geographic space, relief, and soils predict plant community patterns of Asteraceae in rupestrian grasslands, Brazil. Biotropica 2019. [DOI: 10.1111/btp.12636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel A. Chaves
- Departamento de Botânica; Instituto de Ciências Biológicas - Universidade de Brasília; Brasília Distrito Federal Brazil
| | - Suelma Ribeiro-Silva
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado - CBC; Brasília Distrito Federal Brazil
| | - Carolyn E. B. Proença
- Departamento de Botânica; Instituto de Ciências Biológicas - Universidade de Brasília; Brasília Distrito Federal Brazil
| | - Washington L. Oliveira
- Programa de Pós-Graduação em Botânica; Instituto de Ciências Biológicas - Universidade de Brasília; Brasília Distrito Federal Brasil
| | - João Bernardo A. Bringel
- Embrapa Recursos Genéticos e Biotecnologia - Embrapa; Parque Estação Biológica, PqEB; Brasília Distrito Federal Brazil
| | - Marcelo B. Medeiros
- Embrapa Recursos Genéticos e Biotecnologia - Embrapa; Parque Estação Biológica, PqEB; Brasília Distrito Federal Brazil
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Species coexistence through competition and rapid evolution. Proc Natl Acad Sci U S A 2019; 116:2407-2409. [PMID: 30692267 DOI: 10.1073/pnas.1822091116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Laan A, de Polavieja GG. Species diversity rises exponentially with the number of available resources in a multi-trait competition model. Proc Biol Sci 2018; 285:20181273. [PMID: 30158308 PMCID: PMC6125918 DOI: 10.1098/rspb.2018.1273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/06/2018] [Indexed: 11/12/2022] Open
Abstract
Theoretical studies of ecosystem models have generally concluded that large numbers of species will not stably coexist if the species are all competing for the same limited set of resources. Here, we describe a simple multi-trait model of competition where the presence of N resources will lead to the stable coexistence of up to 2 N species. Our model also predicts that the long-term dynamics of the population will lie on a neutral attractor hyperplane. When the population shifts within the hyperplane, its dynamics will behave neutrally, while shifts which occur perpendicular to the hyperplane will be subject to restoring forces. This provides a potential explanation of why complex ecosystems might exhibit both niche-like and neutral responses to perturbations. Like the neutral theory of biodiversity, our model generates good fits to species abundance distributions in several datasets but does so without needing to evoke inter-generational stochastic effects, continuous species creation or immigration dynamics. Additionally, our model is able to explain species abundance correlations between independent but similar ecosystems separated by more than 1400 km inside the Amazonian forests.
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Affiliation(s)
- Andres Laan
- Champalimaud Research, Champalimaud Center for the Unknown, Lisbon, Portugal
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46
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Rael RC, D'Andrea R, Barabás G, Ostling A. Emergent niche structuring leads to increased differences from neutrality in species abundance distributions. Ecology 2018; 99:1633-1643. [PMID: 29655259 DOI: 10.1002/ecy.2238] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/27/2018] [Accepted: 03/21/2018] [Indexed: 11/09/2022]
Abstract
Species abundance distributions must reflect the dynamic processes involved in community assembly, but whether and when specific processes lead to distinguishable signals is not well understood. Biodiversity and species abundances may be shaped by a variety of influences, but particular attention has been paid to competition, which can involve neutral dynamics, where competitor abundances are governed only by demographic stochasticity and immigration, and dynamics driven by trait differences that enable stable coexistence through the formation of niches. Key recent studies of the species abundance patterns of communities with niches employ simple models with pre-imposed niche structure. These studies suggest that species abundance distributions are insensitive to the relative contributions of niche and neutral processes, especially when diversity is much higher than the number of niches. Here we analyze results from a stochastic population model with competition driven by trait differences. With this model, niche structure emerges as clumps of species that persist along the trait axis, and leads to more substantial differences from neutral species abundance distributions than have been previously shown. We show that heterogeneity in "between-niche" interaction strength (i.e., in the strength of competition between species in different niches) plays the dominant role in shaping the species abundances along the trait axis, acting as a biotic filter favoring species at the centers of niches. Furthermore, we show that heterogeneity in "within-niche" interactions (i.e., in the competition between species in the same niche) counteracts the influence of heterogeneity in "between-niche" interactions on the SAD to some degree. Our results suggest that competitive interactions that produce niches can also influence the shapes of SADs.
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Affiliation(s)
- Rosalyn C Rael
- Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109-1048, USA
| | - Rafael D'Andrea
- Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109-1048, USA
| | - György Barabás
- Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109-1048, USA
| | - Annette Ostling
- Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109-1048, USA
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47
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Saravia LA, Momo FR. Biodiversity collapse and early warning indicators in a spatial phase transition between neutral and niche communities. OIKOS 2018. [DOI: 10.1111/oik.04256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leonardo A. Saravia
- Inst. de Ciencias, Univ. Nacional de General Sarmiento, J. M. Gutierrez 1159 (1613), Los Polvorines Buenos Aires Argentina
| | - Fernando R. Momo
- Inst. de Ciencias, Univ. Nacional de General Sarmiento, J. M. Gutierrez 1159 (1613), Los Polvorines Buenos Aires Argentina
- INEDES, Univ. Nacional de Luj n Luj n Argentina
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49
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Affiliation(s)
- Bart Haegeman
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station CNRS and Paul Sabatier University 2 route du CNRS 09200 Moulis France
| | - Rampal S. Etienne
- Groningen Institute for Evolutionary Life Sciences University of Groningen Box 11103 9700 CC Groningen The Netherlands
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50
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Carmel Y, Suprunenko YF, Kunin WE, Kent R, Belmaker J, Bar-Massada A, Cornell SJ. Using exclusion rate to unify niche and neutral perspectives on coexistence. OIKOS 2017. [DOI: 10.1111/oik.04380] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yohay Carmel
- Faculty of Civil and Environmental Engineering, The Technion; Haifa Israel
| | | | | | - Rafi Kent
- Dept of Geography and Environment, Bar-Ilan Univ.; Ramat-Gan Israel
| | - Jonathan Belmaker
- Dept of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv Univ; Tel Aviv Israel
| | - Avi Bar-Massada
- Dept of Biology and Environment, Univ. of Haifa at Oranim; Kiryat Tivon Israel
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