Niches versus neutrality: uncovering the drivers of diversity in a species-rich community.
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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TL;DR: This study shows that changes in community diversity accompany variations in the underlying deterministic-stochastic assembly mechanisms, and is relevant for managing complex microbial systems, which could display similar responses to disturbance, like oceans, soils or the human gut.
Abstract: Disturbance is known to affect ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, diversity, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors were subjected to a range of disturbances in the form of a toxic pollutant, tracking changes in ecosystem function. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, alpha-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in alpha-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Tradeoffs were observed in community function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic-niche assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.
24 citations
Cites result from "Niches versus neutrality: uncoverin..."
...These observed 233 patterns are also in accordance with ecological studies proposing deterministic and stochastic 234 processes balancing each other to allow coexistence (12), with communities exhibiting 235 variations in the strength of stabilization mechanisms and the degree of fitness equivalence 236 among species (11)....
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TL;DR: It is shown that clusters are robust to demographic stochasticity, and can persist under immigration, and introduced and validated metrics which have no free parameters nor require arbitrary trait binning, and weigh species by their abundances rather than relying on a presence-absence count.
Abstract: Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist. It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species, in contrast with the dominant paradigm of greater-than-chance species differences. However, current clustering theory relies largely on heuristic rather than mechanistic models. Furthermore, studies of models incorporating demographic stochasticity and immigration, two key players in community assembly, did not observe clusters. Here we demonstrate clustering under partitioning of resources, partitioning of environmental gradients, and a competition-colonization tradeoff. We show that clusters are robust to demographic stochasticity, and can persist under immigration. While immigration may sustain clusters that are otherwise transient, too much dilutes the pattern. In order to detect and quantify clusters in nature, we introduce and validate metrics which have no free parameters nor require arbitrary trait binning, and weigh species by their abundances rather than relying on a presence-absence count. By generalizing beyond the circumstances where clusters have been observed, our study contributes to establishing them as an update to classical trait patterning theory.
23 citations
TL;DR: The data suggest that the major forces structuring termite communities depend on the presence of this dominant mound-building termite; and that they change to more environmental filtering with disturbance, suggesting Anthropogenic disturbance seems to function as a filter that allows only a specific subset of species to occur.
Abstract: Intensification of land-use threatens biodiversity, especially in tropical ecosystems that harbor the planet's highest species richness. This negative impact of anthropogenic disturbance on species numbers is well established, but the mechanisms underlying the community assembly processes are less well understood. Termites are of fundamental importance in tropical ecosystems where they are critical for nutrient recycling and species diversity. We tested the impact of anthropogenic disturbance on termite species diversity and assembly processes in a West African savanna applying the newest techniques of phylogenetic community analyses. Species richness dropped in areas of intensive land-use and compositional similarity between intensive land-use areas was high. This contrasted with a protected National Park where communities were characterized by high species richness and intermediate species turnover between sites. Slightly disturbed areas in the buffer zone surrounding the park were intermediate, they still had high species richness but similarity between sites increased. Strikingly, the assembly pattern also changed with disturbance from more phylogenetic overdispersion to more clustering (coexisting species became phylogenetically more similar), but only when the fungus-growing termite Macrotermes bellicosus was absent. Our data suggest that the major forces structuring termite communities depend: (1) on the presence of this dominant mound-building termite; and (2) that they change to more environmental filtering with disturbance. Anthropogenic disturbance seems to function as a filter that allows only a specific subset of species to occur. Such an effect might be widespread in ecology but it is difficult to document quantitatively. Phylogenetic community analyses can help to contribute such evidence.
Zusammenfassung
Die Intensivierung der Landnutzung bedroht die Artenvielfalt besonders in tropischen Okosystemen, die den weltweit grosten Artenreichtum beherbergen. Dieser negative Einfluss anthropogener Storung auf Artenzahlen ist gut bekannt, weniger wissen wir jedoch uber seine Wirkung auf die Mechanismen, die die Artenzusammensetzung steuern. Termiten sind von fundamentaler Bedeutung in tropischen Okosystemen, wo sie eine masgebliche Rolle im Nahrstoffkreislauf, fur die Bodenfruchtbarkeit und fur die generelle Artenvielfalt spielen. Wir haben die Wirkung von anthropogener Storung auf die Artenvielfalt von Termiten und die Regulationsprozesse der Zusammensetzung von Termitengemeinschaften unter Anwendung neuester Methoden phylogenetischer Gemeinschaftsanalysen untersucht. Die Artenvielfalt sank in Gegenden intensiver Landnutzung stark und die Ahnlichkeit der Zusammensetzung zwischen den untersuchten Flachen war hoch. Dies stand in deutlichem Gegensatz zu einem geschutzten Nationalpark, in dem die Termitengemeinschaften durch eine hohe Artenvielfalt und mittlere ‚turnover’-Raten zwischen den Flachen charakterisiert waren. Leicht gestorte Areale in der Pufferzone des Nationalparks lagen dazwischen. Sie wiesen noch eine hohe Artenvielfalt auf, wobei die Ahnlichkeit zwischen den Flachen aber erhoht war. Auffallig ist, dass sich das Muster der Artenzusammensetzung mit steigender Storung von einer eher phylogenetischen Uberverteilung zu einer starkeren phylogenetischen Klumpung anderte (d.h. koexistierende Arten waren bei Storung phylogenetisch naher verwandt als ohne Storung), aber nur wenn die pilzzuchtende Termitenart Macrotermes bellicosus fehlte. Dies deutet daraufhin, dass die Mechanismen, die die Artengemeinschaften strukturieren, abhangen von (1) der Anwesenheit dieser dominanten Hugel-bauenden Termite und (2) dass Storung zu einem starkeren Einfluss von ‚ Umweltfilterung’ fuhrt. Anthropogene Storung scheint als Filter zu wirken, der es nur bestimmten Arten erlaubt vorzukommen. Solch ein Effekt konnte in der Okologie weit verbreitet sein, er ist jedoch quantitativ schwer nachzuweisen. Phylogenetische Analysen von Artengemeinschaften konnen erheblich dazu beitragen, Hinweise zu liefern.
22 citations
TL;DR: In this paper, the authors compile tree species diversity of different green space (GS) types and examine the links between species and life history trait diversity to GS and species productivity (carbon storage).
21 citations
TL;DR: It is concluded that large-scale processes such as passive dispersal and recurrent habitat recolonization dominate the distribution of species, and sampling protocols and data analyses must be improved in order to obtain estimates of diversity that are comparable across ecosystems.
Abstract: Aim We analysed marine phytoplankton diversity data as a function of latitude, temperature, primary production and several environmental and biological variables to ascertain whether large-scale variability in the diversity of marine nano- and microphytoplankton (including diatoms, dinoflagellates and coccolithophores) follows similar patterns to those observed for macroorganisms. For the first time we explored these relationships after correcting the observed patterns of species richness by sampling effort. Location The global ocean. Methods To standardize the estimates of species richness by sampling effort we used interpolation and extrapolation based on Hill numbers and shareholder quorum subsampling (SQS) methods. Then, we fitted linear and quadratic models to species richness data to explore their variability with latitude, inverse temperature and biomass. These relationships were compared with the patterns obtained from non-standardized data. In addition, we used a stepwise multiple linear regression model to explain the variability of species richness as the combined effect of multiple drivers acting together. Results Marine phytoplankton diversity was weakly correlated with latitude, temperature or biomass. The hotspots of species richness at intermediate latitudes largely vanished after standardization for sampling effort. Neither latitude, temperature, primary production (as diagnostics of energy supply) nor any other variable or combination of variables, explained the patterns of phytoplankton species richness. Main conclusions None of the hypotheses tested explained a significant amount of the variability in species richness. The patterns observed for microorganisms in previous studies may have resulted at least partially from differences in sampling effort along productivity gradients and systematic undersampling of species. We conclude that large-scale processes such as passive dispersal and recurrent habitat recolonization dominate the distribution of species. Sampling protocols and data analyses must be improved in order to obtain estimates of diversity that are comparable across ecosystems.
21 citations
Cites background from "Niches versus neutrality: uncoverin..."
...Emergent hypotheses (Holt, 2006; Vergnon et al., 2009; Segura et al., 2011) suggest that neutrality can arise from ecological and evolutionary interactions among species, giving rise to groups of ecologically similar coexisting...
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...Emergent hypotheses (Holt, 2006; Vergnon et al., 2009; Segura et al., 2011) suggest that neutrality can arise from ecological and evolutionary interactions among species, giving rise to groups of ecologically similar coexisting species....
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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 2001TL;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
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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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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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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