1
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Ulrich W, Matthews TJ, Biurrun I, Campos JA, Czortek P, Dembicz I, Essl F, Filibeck G, Giusso Del Galdo GP, Güler B, Naqinezhad A, Török P, Dengler J. Environmental drivers and spatial scaling of species abundance distributions in Palaearctic grassland vegetation. Ecology 2022; 103:e3725. [PMID: 35416279 PMCID: PMC9540260 DOI: 10.1002/ecy.3725] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022]
Abstract
Species abundance distributions (SADs) link species richness with species abundances and are an important tool in the quantitative analysis of ecological communities. Niche‐based and sample‐based SAD models predict different spatial scaling properties of SAD parameters. However, empirical research on SAD scaling properties is largely missing. Here we extracted percentage cover values of all occurring vascular plants as proxies of their abundance in 1725 10‐m2 plots from the GrassPlot database, covering 47 regional data sets of 19 different grasslands and other open vegetation types of the Palaearctic biogeographic realm. For each plot, we fitted the Weibull distribution, a model that is able to effectively mimic other distributions like the log‐series and lognormal, to the species–log abundance rank order distribution. We calculated the skewness and kurtosis of the empirical distributions and linked these moments, along with the shape and scale parameters of the Weibull distribution, to plot climatic and soil characteristics. The Weibull distribution provided excellent fits to grassland plant communities and identified four basic types of communities characterized by different degrees of dominance. Shape and scale parameter values of local communities on poorer soils were largely in accordance with log‐series distributions. Proportions of subdominant species tended to be lower than predicted by the standard lognormal SAD. Successive accumulation of plots of the same vegetation type yielded nonlinear spatial scaling of SAD moments and Weibull parameters. This scaling was largely independent of environmental correlates and geographic plot position. Our findings caution against simple generalizations about the mechanisms that generate SADs. We argue that in grasslands, lognormal‐type SADs tend to prevail within a wider range of environmental conditions, including more extreme habitats such as arid environments. In contrast, log‐series distributions are mainly restricted to comparatively species‐rich communities on humid and fertile soils.
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Affiliation(s)
- Werner Ulrich
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Toruń, Poland
| | - Thomas J Matthews
- GEES (School of Geography, Earth and Environmental Sciences) and Birmingham Institute of Forest Research, Birmingham, UK.,CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Depto de Ciências Agráriase Engenharia do Ambiente, PT-9700-042, Angra do Heroísmo, Açores, Portugal
| | - Idoia Biurrun
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Juan Antonio Campos
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Patryk Czortek
- Białowieża Geobotanical Station, Faculty of Biology, University of Warsaw, Sportowa St. 19, 17-230 Białowieża, Poland
| | - Iwona Dembicz
- Department of Ecology and Environmental Conservation, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Żwirki i Wigury St. 101, Warsaw, Poland
| | - Franz Essl
- Bioinvasions, Global Change, Macroecology Group, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Goffredo Filibeck
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | | | - Behlül Güler
- Biology Education, Dokuz Eylul University, Buca, İzmir, Turkey
| | - Alireza Naqinezhad
- Department of Plant Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Péter Török
- MTA-DE Lendület Functional and Restoration Ecology Research Group, University of Debrecen, Egyetem sqr. 1, Debrecen, Hungary.,Polish Academy of Sciences, Botanical Garden - Center for Biological Diversity Conservation in Powsin, Prawdziwka St. 2, 02-973, Warszawa, Poland.,University of Debrecen, Department of Ecology, Egyetem sqr. 1, Debrecen, Hungary
| | - Jürgen Dengler
- Vegetation Ecology, Institute of Natural Resource Management (IUNR) , Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Plant Ecology, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
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2
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How Do Biological and Functional Diversity Change in Invaded Tropical Marine Rocky Reef Communities? DIVERSITY 2021. [DOI: 10.3390/d13080353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evidence so far shows that most alien species (AS) have negative impacts on native biodiversity and are changing biodiversity in almost all environments. Here, we study eight rocky shores at four sites containing reefs with invaded communities and other not-invaded (control) communities, to evaluate the effects of four marine invasive species on biological and functional diversity. We used the adjustment and selection approach of species abundance distribution models (SAD), taxonomic diversity indices and functional diversity indices based on hierarchical grouping matrices (FD—Functional Diversity). In addition to comparing invaded and not-invaded communities, we also performed the same analysis, but removed the invaders (AS removed) from the matrices. The geometric-series model was best adjusted to the majority of communities. The diversity indices suggest that the taxonomic diversity is lower in invaded communities, while the functional diversity indices suggest a change in the functional space of invaded and not-invaded communities, with a greater amount of functional space filled by species in the not-invaded communities. Taxonomic and functional diversity indices were successful in identifying processes that determine the biological diversity of invaded communities, as they seem to obey a pattern that reflects the reduced diversity of invaded communities.
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3
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Antão LH, Magurran AE, Dornelas M. The Shape of Species Abundance Distributions Across Spatial Scales. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Species abundance distributions (SADs) describe community structure and are a key component of biodiversity theory and research. Although different distributions have been proposed to represent SADs at different scales, a systematic empirical assessment of how SAD shape varies across wide scale gradients is lacking. Here, we examined 11 empirical large-scale datasets for a wide range of taxa and used maximum likelihood methods to compare the fit of the logseries, lognormal, and multimodal (i.e., with multiple modes of abundance) models to SADs across a scale gradient spanning several orders of magnitude. Overall, there was a higher prevalence of multimodality for larger spatial extents, whereas the logseries was exclusively selected as best fit for smaller areas. For many communities the shape of the SAD at the largest spatial extent (either lognormal or multimodal) was conserved across the scale gradient, despite steep declines in area and taxonomic diversity sampled. Additionally, SAD shape was affected by species richness, but we did not detect a systematic effect of the total number of individuals. Our results reveal clear departures from the predictions of two major macroecological theories of biodiversity for SAD shape. Specifically, neither the Neutral Theory of Biodiversity (NTB) nor the Maximum Entropy Theory of Ecology (METE) are able to accommodate the variability in SAD shape we encountered. This is highlighted by the inadequacy of the logseries distribution at larger scales, contrary to predictions of the NTB, and by departures from METE expectation across scales. Importantly, neither theory accounts for multiple modes in SADs. We suggest our results are underpinned by both inter- and intraspecific spatial aggregation patterns, highlighting the importance of spatial distributions as determinants of biodiversity patterns. Critical developments for macroecological biodiversity theories remain in incorporating the effect of spatial scale, ecological heterogeneity and spatial aggregation patterns in determining SAD shape.
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4
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de Lima RAF, Condé PA, Banks-Leite C, Campos RC, Hernández MIM, Rodrigues RR, Prado PI. Disentangling the effects of sampling scale and size on the shape of species abundance distributions. PLoS One 2020; 15:e0238854. [PMID: 32915868 PMCID: PMC7485778 DOI: 10.1371/journal.pone.0238854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/25/2020] [Indexed: 11/19/2022] Open
Abstract
Many authors have tried to explain the shape of the species abundance distribution (SAD). Some of them have suggested that sampling spatial scale is an important factor shaping SADs. These suggestions, however, did not consider the indirect and well-known effect of sample size, which increases as samples are combined to generate SADs at larger spatial scales. Here, we separate the effects of sample size and sampling scale on the shape of the SAD for three groups of organisms (trees, beetles and birds) sampled in the Brazilian Atlantic Forest. We compared the observed SADs at different sampling scales with simulated SADs having the same richness, relative abundances but comparable sample sizes, to show that the main effect shaping SADs is sample size and not sampling spatial scale. The effect of scale was minor and deviations between observed and simulated SADs were present only for beetles. For trees, the match between observed and simulated SADs was improved at all spatial scales when we accounted for conspecific aggregation, which was even more important than the sampling scale effect. We build on these results to propose a conceptual framework where observed SADs are shaped by three main factors, in decreasing order of importance: sample size, conspecific aggregation and beta diversity. Therefore, studies comparing SADs across sites or scales should use sampling and/or statistical approaches capable of disentangling these three effects on the shape of SADs.
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Affiliation(s)
- Renato A. Ferreira de Lima
- Laboratório de Ecologia Teórica (LET), Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
| | - Paula Alves Condé
- Laboratório de Ecologia Teórica (LET), Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Renata C. Campos
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Malva I. Medina Hernández
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Ricardo R. Rodrigues
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, Brazil
| | - Paulo I. Prado
- Laboratório de Ecologia Teórica (LET), Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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5
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Thompson SED, Chisholm RA, Rosindell J. Characterising extinction debt following habitat fragmentation using neutral theory. Ecol Lett 2019; 22:2087-2096. [PMID: 31612627 DOI: 10.1111/ele.13398] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 09/09/2019] [Indexed: 01/13/2023]
Abstract
Habitat loss leads to species extinctions, both immediately and over the long term as 'extinction debt' is repaid. The same quantity of habitat can be lost in different spatial patterns with varying habitat fragmentation. How this translates to species loss remains an open problem requiring an understanding of the interplay between community dynamics and habitat structure across temporal and spatial scales. Here we develop formulas that characterise extinction debt in a spatial neutral model after habitat loss and fragmentation. Central to our formulas are two new metrics, which depend on properties of the taxa and landscape: 'effective area', measuring the remaining number of individuals and 'effective connectivity', measuring individuals' ability to disperse through fragmented habitat. This formalises the conventional wisdom that habitat area and habitat connectivity are the two critical requirements for long-term preservation of biodiversity. Our approach suggests that mechanistic fragmentation metrics help resolve debates about fragmentation and species loss.
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Affiliation(s)
- Samuel E D Thompson
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.,Department of Life Sciences, Imperial College London, Silwood Park campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Ryan A Chisholm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
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6
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Fung T, Xiao S, Chisholm RA. Spatial scaling of species richness–productivity relationships for local communities: analytical results from a neutral model. THEOR ECOL-NETH 2019. [DOI: 10.1007/s12080-019-0431-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Yakimov BN, Gelashvili DB, Zhang Y, Markelov IN, Zhang S, Ma K. Quantification of non-power-law diversity scaling with local multifractal analysis. ECOL INFORM 2018. [DOI: 10.1016/j.ecoinf.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Chen Y, Shen TJ, Condit R, Hubbell SP. Community-level species' correlated distribution can be scale-independent and related to the evenness of abundance. Ecology 2018; 99:2787-2800. [PMID: 30347110 DOI: 10.1002/ecy.2544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 08/29/2018] [Accepted: 10/02/2018] [Indexed: 11/10/2022]
Abstract
The spatial distribution of species is not random; instead, individuals tend to gather, resulting in a non-random pattern. Previous studies used the independent negative binomial distribution (NBD) to model the distributional aggregation of a single species, in which the independence of the distribution of individuals of a species in different quadrats had been assumed. This way of analyzing aggregation will result in the scale-dependent estimation of the aggregation or shape parameter. However, because non-random (and therefore non-independent) distribution of individuals of a species in a finite area can be caused by either correlated or clumped distribution of individuals of a species between neighboring sites, an alternative model would assume that the distribution of individuals of a species over different sampling areas is multinomial. Here, we showed that, by assuming that regional species abundance followed a NBD while using a multinomial distribution to assign individuals of species in different non-overlapped sampling quadrats that are from a partition of the entire region (quantifying positive correlation or synchrony), the estimation of the shape parameter in this probabilistic model, which is the negative multinomial distribution (NMD), was scale-invariant (i.e., the estimated shape parameter is identical across different partitions of the study region). Accordingly, the estimation of the shape parameter was related to regional species distribution alone. This implied that, the shape parameter at the community level, using the NMD model, reflected the evenness of interspecific abundance. As a comparison, if the distribution of individuals of a single species followed independent NBDs as studied previously, the shape parameter would measure the evenness of intraspecific abundance (quantifying single-species' distributional aggregation). Moreover, our study highlighted the necessity for adjusting the model for the effects of unsampled species when studying community-level distributional patterns. Collectively, as long as a target area is partitioned into non-overlapping quadrats (no matter how their sizes vary), the proposed NMD model in this study, along with the independent NBDs model, can be jointly formulated as a framework to reconcile the scale-dependent debate on the shape parameter, unifying the relationship between inter- or intraspecific abundance and distributional patterns.
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Affiliation(s)
- Youhua Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Tsung-Jen Shen
- Institute of Statistics & Department of Applied Mathematics, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan
| | - Richard Condit
- Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, Illinois, 60605, USA.,Morton Arboretum, 4100 Illinois Rte. 53, Lisle, Illinois, 60532, USA
| | - Stephen P Hubbell
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Panama.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
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9
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Cross-scale neutral ecology and the maintenance of biodiversity. Sci Rep 2018; 8:10200. [PMID: 29976959 PMCID: PMC6033888 DOI: 10.1038/s41598-018-27712-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/31/2018] [Indexed: 11/08/2022] Open
Abstract
One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.
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10
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McLeish MJ, Fraile A, García-Arenal F. Ecological Complexity in Plant Virus Host Range Evolution. Adv Virus Res 2018; 101:293-339. [PMID: 29908592 DOI: 10.1016/bs.aivir.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.
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11
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Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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12
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Zhou J, Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol Mol Biol Rev 2017. [PMID: 29021219 DOI: 10.1128/mmbr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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13
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Jordan SMR, Barraclough TG, Rosindell J. Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150221. [PMID: 26977062 PMCID: PMC4810815 DOI: 10.1098/rstb.2015.0221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.
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Affiliation(s)
- Sean M R Jordan
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
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14
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Saravia LA. A new method to analyse species abundances in space using generalized dimensions. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Leonardo A. Saravia
- Instituto de Ciencias Básicas Universidad Nacional de General Sarmiento J.M. Gutierrez 1159 (1613) Los Polvorines Buenos Aires Argentina
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15
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Blonder B, Sloat L, Enquist BJ, McGill B. Separating macroecological pattern and process: comparing ecological, economic, and geological systems. PLoS One 2014; 9:e112850. [PMID: 25383874 PMCID: PMC4226609 DOI: 10.1371/journal.pone.0112850] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/16/2014] [Indexed: 11/18/2022] Open
Abstract
Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form ('first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns ('second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.
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Affiliation(s)
- Benjamin Blonder
- Sky School, University of Arizona, Tucson, Arizona, United States of America
| | - Lindsey Sloat
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Brian McGill
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America
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16
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Connolly SR, MacNeil MA, Caley MJ, Knowlton N, Cripps E, Hisano M, Thibaut LM, Bhattacharya BD, Benedetti-Cecchi L, Brainard RE, Brandt A, Bulleri F, Ellingsen KE, Kaiser S, Kröncke I, Linse K, Maggi E, O'Hara TD, Plaisance L, Poore GCB, Sarkar SK, Satpathy KK, Schückel U, Williams A, Wilson RS. Commonness and rarity in the marine biosphere. Proc Natl Acad Sci U S A 2014; 111:8524-9. [PMID: 24912168 PMCID: PMC4060690 DOI: 10.1073/pnas.1406664111] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Explaining patterns of commonness and rarity is fundamental for understanding and managing biodiversity. Consequently, a key test of biodiversity theory has been how well ecological models reproduce empirical distributions of species abundances. However, ecological models with very different assumptions can predict similar species abundance distributions, whereas models with similar assumptions may generate very different predictions. This complicates inferring processes driving community structure from model fits to data. Here, we use an approximation that captures common features of "neutral" biodiversity models--which assume ecological equivalence of species--to test whether neutrality is consistent with patterns of commonness and rarity in the marine biosphere. We do this by analyzing 1,185 species abundance distributions from 14 marine ecosystems ranging from intertidal habitats to abyssal depths, and from the tropics to polar regions. Neutrality performs substantially worse than a classical nonneutral alternative: empirical data consistently show greater heterogeneity of species abundances than expected under neutrality. Poor performance of neutral theory is driven by its consistent inability to capture the dominance of the communities' most-abundant species. Previous tests showing poor performance of a neutral model for a particular system often have been followed by controversy about whether an alternative formulation of neutral theory could explain the data after all. However, our approach focuses on common features of neutral models, revealing discrepancies with a broad range of empirical abundance distributions. These findings highlight the need for biodiversity theory in which ecological differences among species, such as niche differences and demographic trade-offs, play a central role.
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Affiliation(s)
- Sean R Connolly
- School of Marine and Tropical Biology, and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia;
| | - M Aaron MacNeil
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - M Julian Caley
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013;
| | - Ed Cripps
- School of Mathematics and Statistics, University of Western Australia, Perth, WA 6009, Australia
| | - Mizue Hisano
- School of Marine and Tropical Biology, and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Loïc M Thibaut
- School of Marine and Tropical Biology, and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | | | | | - Russell E Brainard
- Coral Reef Ecosystem Division, Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI 96818
| | - Angelika Brandt
- Biocenter Grindel and Zoological Museum, University of Hamburg, 20146 Hamburg, Germany
| | - Fabio Bulleri
- Dipartimento di Biologia, University of Pisa, I-56126 Pisa, Italy
| | - Kari E Ellingsen
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, 9296 Tromsø, Norway
| | - Stefanie Kaiser
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, 26382 Wilhelmshaven, Germany
| | - Ingrid Kröncke
- Marine Research Department, Senckenberg am Meer, 26382 Wilhelmshaven, Germany
| | - Katrin Linse
- British Antarctic Survey, Cambridge CB3 0ET, United Kingdom
| | - Elena Maggi
- Dipartimento di Biologia, University of Pisa, I-56126 Pisa, Italy
| | | | - Laetitia Plaisance
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013
| | | | - Santosh K Sarkar
- Department of Marine Science, University of Calcutta, Calcutta 700 019, India
| | - Kamala K Satpathy
- Environment and Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India; and
| | - Ulrike Schückel
- Marine Research Department, Senckenberg am Meer, 26382 Wilhelmshaven, Germany
| | - Alan Williams
- Commonwealth Scientific and Industrial Research Organization, Marine and Atmospheric Research, Marine Laboratories, Hobart, TAS 7001, Australia
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Matthews TJ, Whittaker RJ. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives. Ecol Evol 2014; 4:2263-77. [PMID: 25360266 PMCID: PMC4201439 DOI: 10.1002/ece3.1092] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 11/14/2022] Open
Abstract
Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.
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Affiliation(s)
- Thomas J Matthews
- Conservation Biogeography and Macroecology Programme, School of Geography and the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, UK ; Azorean Biodiversity Group (ABG CITA-A) and Portuguese Platform for Enhancing Ecological Research and Sustainability (PEERS), Departamento de Ciências Agrárias, University of the Azores Rua Capitão João d'Ávila, Pico da Urze, 9700-042, Angra do Heroísmo, Portugal
| | - Robert J Whittaker
- Conservation Biogeography and Macroecology Programme, School of Geography and the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, UK ; Center for Macroecology, Evolution and Climate, Department of Biology, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
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Yakimov BN, Iudin DI, Solntsev LA, Gelashvili DB. Multifractal analysis of neutral community spatial structure. J Theor Biol 2014; 343:44-53. [DOI: 10.1016/j.jtbi.2013.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 09/16/2013] [Accepted: 10/19/2013] [Indexed: 10/26/2022]
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Do spatially-implicit estimates of neutral migration comply with seed dispersal data in tropical forests? PLoS One 2013; 8:e72497. [PMID: 23977307 PMCID: PMC3747097 DOI: 10.1371/journal.pone.0072497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 07/16/2013] [Indexed: 11/19/2022] Open
Abstract
Neutral community models have shown that limited migration can have a pervasive influence on the taxonomic composition of local communities even when all individuals are assumed of equivalent ecological fitness. Notably, the spatially implicit neutral theory yields a single parameter I for the immigration-drift equilibrium in a local community. In the case of plants, seed dispersal is considered as a defining moment of the immigration process and has attracted empirical and theoretical work. In this paper, we consider a version of the immigration parameter I depending on dispersal limitation from the neighbourhood of a community. Seed dispersal distance is alternatively modelled using a distribution that decreases quickly in the tails (thin-tailed Gaussian kernel) and another that enhances the chance of dispersal events over very long distances (heavily fat-tailed Cauchy kernel). Our analysis highlights two contrasting situations, where I is either mainly sensitive to community size (related to ecological drift) under the heavily fat-tailed kernel or mainly sensitive to dispersal distance under the thin-tailed kernel. We review dispersal distances of rainforest trees from field studies and assess the consistency between published estimates of I based on spatially-implicit models and the predictions of the kernel-based model in tropical forest plots. Most estimates of I were derived from large plots (10–50 ha) and were too large to be accounted for by a Cauchy kernel. Conversely, a fraction of the estimates based on multiple smaller plots (1 ha) appeared too small to be consistent with reported ranges of dispersal distances in tropical forests. Very large estimates may reflect within-plot habitat heterogeneity or estimation problems, while the smallest estimates likely imply other factors inhibiting migration beyond dispersal limitation. Our study underscores the need for interpreting I as an integrative index of migration limitation which, besides the limited seed dispersal, possibly includes habitat filtering or fragmentation.
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