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Journal ArticleDOI

Niches versus neutrality: uncovering the drivers of diversity in a species-rich community.

01 Oct 2009-Ecology Letters (Blackwell Publishing Ltd)-Vol. 12, Iss: 10, pp 1079-1090
TL;DR: This work provides the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community and suggests this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities.
Abstract: Ecological models suggest that high diversity can be generated by purely niche-based, purely neutral or by a mixture of niche-based and neutral ecological processes. Here, we compare the degree to which four contrasting hypotheses for coexistence, ranging from niche-based to neutral, explain species richness along a body mass niche axis. We derive predictions from these hypotheses and confront them with species body-mass patterns in a highly sampled marine phytoplankton community. We find that these patterns are consistent only with a mechanism that combines niche and neutral processes, such as the emergent neutrality mechanism. In this work, we provide the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community. We suggest this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities.

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Citations
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Journal ArticleDOI
TL;DR: Testing for proportionality infunctionally for functionally defined guilds provides a rapid means for detecting potential mechanisms of co-existence in species-richmeadowcommunities and found evidence that species differing in strategy for spatiallight capture and temporal resource use were more likely to co-exist than expected by chance.
Abstract: Question: Could tests of proportionality for functionally defined guilds providea rapid means of revealing potential mechanisms of co-existence in species-richmeadowcommunities?Studysite:Aspecies-richmeadowinSlovenia.Methods: Species presence/absence was recorded in 830 contiguous0.2 m 9 0.2 m quadrats arranged in a rectangular transect. Evidence for guildproportionality was assessed for guilds defined by (1) taxonomy, (2) growthform and (3) functional group defined by leaf inclination or leaf phenology. Wealso tested whether classifying the graminoid-like forb Scorzenera villosa as agraminoidimprovedevidenceforproportionalityintaxonomicguilds.Results: There was no evidence of guild proportionality for guilds defined byeithertaxonomyorgrowth form.Therewassignificantproportionalityforfunc-tionalgroupsdefinedbyleafphenologyandleafinclination.ClassifyingS. villosaas a graminoid did not improve evidence for proportionality of taxonomicguilds.Conclusions:Testing for proportionality infunctionally defined guilds providesa rapidmeans for detectingpotentialmechanisms ofco-existenceinspecies-richcommunities. We found evidence that species differing in strategy for spatiallight capture (leaf inclination) and temporal resource use (phenology) weremore likely to co-exist than expected by chance. These findings may help toguide future experimental work attempting to confirm co-existence mecha-nismsinmeadowcommunities.Thisapproachmayproveusefulinother poorlystudied,species-richvegetationtypes.IntroductionUnderstanding mechanisms controlling communityassembly is vital for the maintenance of biodiversity, andthusremainsoneofthekeypuzzlesincommunityecology(Grime 2006; Wilson 2007; Mason et al. 2012a). Nichecomplementarity(i.e.complementaritybetweenco-occur-ring species in resource use and acquisition) has long beenidentified as a key mechanism driving the evolution (Dar-win 1859) and maintenance (MacArthur & Levins 1967)of biodiversity. Generally tests for niche complementarityhave combined species niche information, such as func-tional trait measurements or guild classifications, with co-occurrence (Armbruster et al. 1994; Wilson & Roxburgh1994; Stubbs & Wilson 2004; Mason & Wilson 2006) orabundance data (Mason et al. 2008, 2011b; Vergnon et al.2009). These approaches for describing the species nicherepresenttwoextremesinatrade-offbetweenrapidityanddetail. Functional trait measurements yield accurate dataon species resource use and acquisition (Grime 2001;Wrightet al.2004;Masonet al.2012b)andcan beused toobtainaccurateestimatesoffunctionaldiversityusingcon-tinuous indices (Mason et al. 2005, 2011a; Villeger et al.2008; Mouchet et al. 2010; Richardson et al. 2012). How-ever, this requires a large data collection effort, especiallyinspecies-richcommunities. On the other hand, classifica-tion of species into guilds, often based on taxonomy, isvery rapid, but may provide an oversimplified descriptionof the species niche (Wright et al. 2006). One potentialcompromisebetweentheseapproachesistoclassifyspecies

20 citations

Book ChapterDOI
25 Feb 2013
TL;DR: The complexity of species interactions will be illustrated by referring to a number of both direct and indirect interactions in ecosystems that may act together or change in different phases of development.
Abstract: A plant community is composed of individuals of different species that have arrived and established at the site and persist there until they become locally extinct. The presence of species in a plant community depends, apart from the availability of propagules and safe sites, on environmental resources (nutrients, water, light) and conditions (climate, soil pH, human impact) for growth and reproduction, whereas the species ’ abundances in the community can be modifi ed by a variety of interspecifi c interactions structuring the community, both in space and in time. Interactions between species do not only affect community structure, but also provide the community with emergent properties as compared to the sum of the individual plants (cf. Looijen & van Andel 1999 ). The absence of species in a plant community can be due to failure of dispersal or/and lack of appropriate resources and conditions. Ozinga et al . (2009) have shown that losses in plant diversity in north western Europe are at least as much due to a degraded dispersal infrastructure as to effects of, for example, eutrophication. Plants do not only interact with other plants in the community, but also with a large number of fungal and animal species (e.g. van Dam 2009 ). Different types of interaction and their importance in structuring plant communities, in space and time, will be presented and discussed. They will fi rst be defi ned (Section 7.2 ) and then treated one after the other (Sections 7.3 – 7.7 ). Thereafter, the complexity of species interactions will be illustrated by referring to a number of both direct and indirect interactions in ecosystems that may act together or change in different phases of development (Section 7.8 ). Finally, in Section 7.9 , the notion of ‘ assembly rules ’ will be discussed.

20 citations

Journal ArticleDOI
01 Aug 2014-Ecology
TL;DR: A novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism) is proposed.
Abstract: Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I(k) in space and across taxonomic levels to test hypotheses about the ecological and evolutionary drivers of biodiversity patterns.

19 citations

01 Jan 2013
TL;DR: In this paper, the authors tested the influence of different resolution of predictors on the predictive ability of species distribution models and showed that fine resolution predictors could ameliorate the models for some species by giving a better estimation of the micro-topographic condition that species tolerate, but that fine-resolution predictors for climatic factors still need to be amelored.
Abstract: Understanding the distribution and composition of species assemblages and being able to predict them in space and time are highly important tasks io investigate the fate of biodiversity in the current global changes context. Species distribution models are tools that have proven useful to predict the potential distribution of species by relating their occurrences to environmental variables. Species assemblages can then be predicted by combining the prediction of individual species models. In the first part of my thesis, I tested the importance of new environmental predictors to improve species distribution prediction. I showed that edaphic variables, above all soil pH and nitrogen content could be important in species distribution models. In a second chapter, I tested the influence of different resolution of predictors on the predictive ability of species distribution models. I showed that fine resolution predictors could ameliorate the models for some species by giving a better estimation of the micro-topographic condition that species tolerate, but that fine resolution predictors for climatic factors still need to be ameliorated. The second goal of my thesis was to test the ability of empirical models to predict species assemblages' characteristics such as species richness or functional attributes. I showed that species richness could be modelled efficiently and that the resulting prediction gave a more realistic estimate of the number of species than when obtaining it by stacking outputs of single species distribution models. Regarding the prediction of functional characteristics (plant height, leaf surface, seed mass) of plant assemblages, mean and extreme values of functional traits were better predictable than indices reflecting the diversity of traits in the community. This approach proved interesting to understand which environmental conditions influence particular aspects of the vegetation functioning. It could also be useful to predict climate change impacts on the vegetation. In the last part of my thesis, I studied the capacity of stacked species distribution models to predict the plant assemblages. I showed that this method tended to over-predict the number of species and that the composition of the community was not predicted exactly either. Finally, I combined the results of macro- ecological models obtained in the preceding chapters with stacked species distribution models and showed that this approach reduced significantly the number of species predicted and that the prediction of the composition is also ameliorated in some cases. These results showed that this method is promising. It needs now to be tested on further data sets. - Comprendre la maniere dont les plantes se repartissent dans l'environnement et s'organisent en communaute est une question primordiale dans le contexte actuel de changements globaux. Cette connaissance peut nous aider a sauvegarder la diversite des especes et les ecosystemes. Des methodes statistiques nous permettent de predire la distribution des especes de plantes dans l'espace geographique et dans le temps. Ces modeles de distribution d'especes, relient les occurrences d'une espece avec des variables environnementales pour decrire sa distribution potentielle. Cette methode a fait ses preuves pour ce qui est de la prediction d'especes individuelles. Plus recemment plusieurs tentatives de cumul de modeles d'especes individuelles ont ete realisees afin de predire la composition des communautes vegetales. Le premier objectif de mon travail est d'ameliorer les modeles de distribution en testant l'importance de nouvelles variables predictives. Parmi differentes variables edaphiques, le pH et la teneur en azote du sol se sont averes des facteurs non negligeables pour predire la distribution des plantes. Je demontre aussi dans un second chapitre que les predicteurs environnementaux a fine resolution permettent de refleter les conditions micro-topographiques subies par les plantes mais qu'ils doivent encore etre ameliores avant de pouvoir etre employes de maniere efficace dans les modeles. Le deuxieme objectif de ce travail consistait a etudier le developpement de modeles predictifs pour des attributs des communautes vegetales tels que, par exemple, la richesse en especes rencontree a chaque point. Je demontre qu'il est possible de predire par ce biais des valeurs de richesse specifiques plus realistes qu'en sommant les predictions obtenues precedemment pour des especes individuelles. J'ai egalement predit dans l'espace et dans le temps des caracteristiques de la vegetation telles que sa hauteur moyenne, minimale et maximale. Cette approche peut etre utile pour comprendre quels facteurs environnementaux promeuvent differents types de vegetation ainsi que pour evaluer les changements a attendre au niveau de la vegetation dans le futur sous differents regimes de changements climatiques. Dans une troisieme partie de ma these, j'ai explore la possibilite de predire les assemblages de plantes premierement en cumulant les predictions obtenues a partir de modeles individuels pour chaque espece. Cette methode a le defaut de predire trop d'especes par rapport a ce qui est observe en realite. J'ai finalement employe le modele de richesse en espece developpe precedemment pour contraindre les resultats du modele d'assemblage de plantes. Cela a permis l'amelioration des modeles en reduisant la sur-prediction et en ameliorant la prediction de la composition en especes. Cette methode semble prometteuse mais de nouveaux tests sont necessaires pour bien evaluer ses capacites.

19 citations

Journal ArticleDOI
01 Nov 2018-Ecology
TL;DR: The ways in which species' abundance is expected to be relevant to the cross-scale resilience model based on the extensive abundance literature in ecology are detailed and a series of testable hypotheses are put forward to improve the ability to anticipate and quantify how resilience is generated and how ecosystems will buffer recent rapid global changes.
Abstract: The cross-scale resilience model suggests that system-level ecological resilience emerges from the distribution of species' functions within and across the spatial and temporal scales of a system. It has provided a quantitative method for calculating the resilience of a given system and so has been a valuable contribution to a largely qualitative field. As it is currently laid out, the model accounts for the spatial and temporal scales at which environmental resources and species are present and the functional roles species play but does not inform us about how much resource is present or how much function is provided. In short, it does not account for abundance in the distribution of species and their functional roles within and across the scales of a system. We detail the ways in which we would expect species' abundance to be relevant to the cross-scale resilience model based on the extensive abundance literature in ecology. We also put forward a series of testable hypotheses that would improve our ability to anticipate and quantify how resilience is generated, and how ecosystems will (or will not) buffer recent rapid global changes. This stream of research may provide an improved foundation for the quantitative evaluation of ecological resilience.

19 citations


Cites background from "Niches versus neutrality: uncoverin..."

  • ...2; Hypothesis 1) (Walker et al. 1999, Sugihara and Bersier 2003, Vergnon et al. 2009, 2012, Magurran and Henderson 2012)....

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  • ...Vergnon et al. (2009) found that the most abundant phytoplankton species were far apart in terms of body size (the scale domain at which they operated), suggesting that strong interspecific competition prevents similarly sized species from attaining high abundances....

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  • ...2; Damuth 1981, Petchey and Gaston 2006, Vergnon et al. 2009, Magurran and Henderson 2012)....

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References
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Book
30 May 2017
TL;DR: In this article, a simple linear model is proposed to describe the geometry of linear models, and a general linear model specification in R is presented. But the theory of linear model theory is not discussed.
Abstract: LINEAR MODELS A simple linear model Linear models in general The theory of linear models The geometry of linear modelling Practical linear models Practical modelling with factors General linear model specification in R Further linear modelling theory Exercises GENERALIZED LINEAR MODELS The theory of GLMs Geometry of GLMs GLMs with R Likelihood Exercises INTRODUCING GAMS Introduction Univariate smooth functions Additive models Generalized additive models Summary Exercises SOME GAM THEORY Smoothing bases Setting up GAMs as penalized GLMs Justifying P-IRLS Degrees of freedom and residual variance estimation Smoothing Parameter Estimation Criteria Numerical GCV/UBRE: performance iteration Numerical GCV/UBRE optimization by outer iteration Distributional results Confidence interval performance Further GAM theory Other approaches to GAMs Exercises GAMs IN PRACTICE: mgcv Cherry trees again Brain imaging example Air pollution in Chicago example Mackerel egg survey example Portuguese larks example Other packages Exercises MIXED MODELS and GAMMs Mixed models for balanced data Linear mixed models in general Linear mixed models in R Generalized linear mixed models GLMMs with R Generalized additive mixed models GAMMs with R Exercises APPENDICES A Some matrix algebra B Solutions to exercises Bibliography Index

8,393 citations


"Niches versus neutrality: uncoverin..." refers methods in this paper

  • ...All GAM fitting was performed using the R mgcv package (Wood 2006)....

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Book
01 Jan 2001
TL;DR: A study of the issue indicates that it is not a serious problem for neutral theory, and there is sometimes a difference between some of the simulation-based results of Hubbell and the analytical results of Volkov et al. (2003).
Abstract: study of the issue indicates that it is not a serious problem for neutral theory, for reasons we discuss below. First, a bit of background. Hubbell (2001) derived the analytical expression for the stochastic mean and variance of the abundance of a single arbitrary species in a neutral community undergoing immigration from a metacommunity source area. However, his approach did not lend itself to an analytical solution for the distribution of relative species abundance (RSA) in a multispecies community for community sizes larger than a handful of individuals. As a result, all of Hubbell's RSA distributions for local communities were based on simulations. This problem was solved by Volkov et al. (2003), who derived an analytical expression for the RSA distribution in local communities of arbitrary size. However, as Chisholm and Burgman noted, there is sometimes a difference between some of the simulation-based results of Hubbell and the analytical results of Volkov et al. (2003). Chisholm and Burgman computed Volkov's equation and resimulated Hubbell's results for the four cases

5,317 citations

Journal ArticleDOI
TL;DR: Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time.
Abstract: ▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...

5,240 citations


"Niches versus neutrality: uncoverin..." refers background in this paper

  • ...Niche-based models assume differences in resource use between species; species thereby avoid competition and are able to coexist (Gause 1934; Hardin 1960; Chesson 2000)....

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Journal ArticleDOI
29 Apr 1960-Science
TL;DR: By emphasizing the very aspects that might result in their denial of them were they less plain the authors can keep the principle explicitly present in their minds untit they see if its implications are, or are noty as unpleasant as their subconscious might suppose.
Abstract: because of a belief that it is best to use that wording which is least likely to hide the fact that we still do not comprehend the exact limits of the principle. For the present, I think the 6'threat of clarity\" (3) is a serious one that is best miniInized by using a formulation that is admittedly unclear; thus can we keep in the forefront of our minds the unfinished work before us. The wording given has, I think, another point of superiority in that it seems brutal and dogmatic. By emphasizing the very aspects that might result in our denial of them were they less plain we can keep the principle explicitly present in our minds untit we see if its implications are, or are noty as unpleasant as our subconscious might suppose. The meaning of these somewhat cryptic remarks should be come clear further on iIl the discussion. What does the exclusion principle mean? Itoughly this: that (i) if two noninterbreeding populations \"do the same thing\"-that is, occupy precisely the same ecological niche in Elton's sense (4)-and (ii) if they are \"sympatric\"that is, if they occupy the same geographic territory-and (iii) if population A multiplies even the least bit faster than population B, then ultimately A will completely displace B, which will become extinct. This is the 44weak form' of the principle. A1ways in practice a stronger form is used, based on the removal of the hypothetical character of condition (iii). We do this because we adhere to what may be caIled the axiom of inequality, which states that no two things or processes

3,062 citations


"Niches versus neutrality: uncoverin..." refers background in this paper

  • ...Niche-based models assume differences in resource use between species; species thereby avoid competition and are able to coexist (Gause 1934; Hardin 1960; Chesson 2000)....

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Journal ArticleDOI
TL;DR: The problem that is presented by the phytoplankton is essentially how it is possible for a number of species to coexist in a relatively isotropic or unstructured environment all competing for the same sorts of materials.
Abstract: The problem that I wish to discuss in the present contribution is raised by the very paradoxical situation of the plankton, particularly the phytoplankton, of relatively large bodies of water. We know from laboratory experiments conducted by many workers over a long period of time (summary in Provasoli and Pintner, 1960) that most members of the phytoplankton are phototrophs, able to reproduce and build up populations in inorganic media containing a source of CO2, inorganic nitrogen, sulphur, and phosphorus compounds and a considerable number of other elements (Na, K, Mg, Ca, Si, Fe, Mn, B, C1, Cu, Zn, Mo, Co and V) most of which are required in small concentrations and not all of which are known to be required by all groups. In addition, a number of species are known which require one or more vitamins, namely thiamin, the cobalamines (B or related compounds), or biotin. The problem that is presented by the phytoplankton is essentially how it is possible for a number of species to coexist in a relatively isotropic or unstructured environment all competing for the same sorts of materials. The problem is particularly acute because there is adequate evidence from enrichment experiments that natural waters, at least in the summer, present an environment of striking nutrient deficiency, so that competition is likely to be extremely severe. According to the principle of competitive exclusion (Hardin, 1960) known by many names and developed over a long period of time by many investigators (see Rand, 1952; Udvardy, 1959; and Hardin, 1960, for historic reviews), we should expect that one species alone would outcompete all the others so that in a final equilibrium situation the assemblage would reduce to a population of a single species. The principle of competitive exclusion has recently been under attack from a number of quarters. Since the principle can be deduced mathematically from a relatively simple series of postulates, which with the ordinary postulates of mathematics can be regarded as forming an axiom system, it follows that if the objections to the principle in any cases are valid, some or all the biological axioms introduced are in these cases incorrect. Most objections to the principle appear to imply the belief that equilibrium under a given set of environmental conditions is never in practice obtained. Since the deduction of the principle implies an equilibrium system, if such sys-

2,898 citations


"Niches versus neutrality: uncoverin..." refers background in this paper

  • ...…a century of research, it is still not understood how species-rich communities are maintained in the face of the theoretical prediction that single-species dominance is more likely than the stable coexistence of numerous species competing for small numbers of common resources (Hutchinson 1961)....

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