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 research was funded by the project Malaspina (Consolider-Ingenio 2010, CSD2008-00077) and from the European Commission (contract no. 264933, EURO-BASIN: European Union Basin-scale Analysis, Synthesis and Integration).
Abstract: We thank all who contributed to collecting the samples on the different cruises. This study was supported by the UK Natural Environment Research Council through the Atlantic Meridional Transect consortium (this is contribution number 215 of the AMT programme). Special thanks go to D. Harbour, who counted most of the samples to the species level. We acknowledge the contribution of S. Hubbell (Department of Ecology and Evolutionary Biology, University of California) for reviewing carefully this paper and providing useful comments. This research was funded by the project Malaspina (Consolider-Ingenio 2010, CSD2008-00077) and from the European Commission (contract no. 264933, EURO-BASIN: European Union Basin-scale Analysis, Synthesis and Integration). This is contribution 590 from AZTI-Tecnalia Marine Research Division.
100 citations
Cites background or result from "Niches versus neutrality: uncoverin..."
..., 2011) and more specifically to planktonic species assemblages (Alonso et al., 2006; Pueyo, 2006a,b; Dolan et al., 2007; Vergnon et al., 2009; Irigoien et al., 2011)....
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...Global Ecology and Biogeography, ••, ••–••, © 2012 Blackwell Publishing Ltd 9 capturing the largest organisms, which are rare in finite volumes, are always problematic (e.g. Vergnon et al., 2009)....
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...These two findings suggest that phytoplankton communities result from a combination of niche and neutral processes, which is in accordance with the patterns found in an exhaustive phytoplankton time-series dataset (Vergnon et al., 2009)....
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...…2006; Chust et al., 2006a), but since then they have also been applied in marine ecology (e.g. Dornelas et al., 2006; Martiny et al., 2011) and more specifically to planktonic species assemblages (Alonso et al., 2006; Pueyo, 2006a,b; Dolan et al., 2007; Vergnon et al., 2009; Irigoien et al., 2011)....
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TL;DR: The results, taken together with recent studies on tropical forests, suggest that weak interactions among established plants may be a general phenomenon, but that local interactions during colonization are important drivers of community composition.
Abstract: Summary
There is an ongoing debate about whether communities are closely integrated and bound together via interactions such as competition or facilitation, or are disintegrated and dominated by chance. We still lack community-wide data on the intensities of interactions and randomness, and measurements of their impacts on community structure.
Using a long-term data set, we sought to measure the effects of interactions and stochasticity in structuring a highly diverse (>100 species) semi-arid grassland plant community, testing for positive and negative interactions at different stages of population growth of all species.
During the colonization of new patches, most species were facilitated or inhibited by several others. These opposite effects can potentially have a large effect on species abundances, but they were correlated and cancelled out at the community level. Nevertheless, competition during colonization was strong enough to cause poor competitors to have small population sizes.
The subsequent phase of population growth (increase and subsequent change in numbers within occupied patches) was mainly driven by intraspecific density dependence, and we found little evidence for interspecific interactions.
Model results showed that stochasticity and recurrent colonization of transient, favourable patches maintained diversity, keeping poor competitors from becoming extinct.
Synthesis: Our results, taken together with recent studies on tropical forests, suggest that weak interactions among established plants may be a general phenomenon, but that local interactions during colonization are important drivers of community composition. Most of the variance in species abundance in our community was explained by intraspecific competition and stochasticity, with interspecific interactions playing a minor role due to their overall weakness, interaction changes over ontogeny, and the cancellation of opposite-sign interactions when all the species in the community are considered. Despite this, some species were rare seemingly because they cannot withstand interspecific competition. Thus, to untangle the effects of interactions on community structure, future research should focus on interactions occurring at different phases of population growth and on whole communities.
100 citations
TL;DR: The importance of niche-based and neutral processes to species extinction and community assembly across a gradient of habitat loss is unveiled, challenging the predictions of neutral models and underscore the fundamental importance of pro-active measures to prevent human-modified landscapes surpassing critical ecological thresholds.
Abstract: Although both niche-based and neutral processes are involved in community assembly, most models on the effects of habitat loss are stochastic, assuming neutral communities mainly affected by ecological drift and random extinction. Given that habitat loss is considered the most important driver of the current biodiversity crisis, unraveling the processes underlying the effects of habitat loss is critical from both a theoretical and an applied perspective. Here we unveil the importance of niche-based and neutral processes to species extinction and community assembly across a gradient of habitat loss, challenging the predictions of neutral models. We draw on a large dataset containing the distribution of 3653 individuals of 42 species, representing 35% of the small mammal species of the Atlantic Forest hotspot, obtained in 68 sites across three continuously-forested landscapes and three adjacent 10 000-ha fragmented landscapes differing in the amount of remaining forest (50%, 30% and 10%). By applying a null-model approach, we investigated β-diversity patterns by detecting deviations of observed community similarity from the similarity between randomly assembled communities. Species extinction following habitat loss was decidedly non-random, in contrast to the notion that fragmented communities are mainly driven by ecological drift. Instead, habitat loss led to a strong biotic homogenization. Moreover, species composition changed abruptly at the same level of landscape-scale habitat loss that has already been associated with a drastic decline in species richness. Habitat loss, as other anthropogenic disturbances, can thus be seen as a strong ecological filter that increases (rather than decreases) the importance of deterministic processes in community assembly. As such, critical advances for the development of conservation science lie on the incorporation of the relevant niche traits associated with extinction proneness into models of habitat loss. The results also underscore the fundamental importance of pro-active measures to prevent human-modified landscapes surpassing critical ecological thresholds.
96 citations
TL;DR: Fractal techniques are used to characterize patterns of cross-scale habitat complexity, and how this relates to body-depth abundance distributions of associated fish assemblages over corresponding spatial scales are examined.
Abstract: Despite a large number of studies focusing on the complexity of coral reef habitats and the characteristics of associated fish assemblages, the relationship between reef structure and fish assemblages remains unclear. The textural discontinuity hypothesis, which proposes that multi-modal body size distributions of organisms are driven by discontinuous habitat structure, provides a theoretical basis that may explain the influence of habitat availability on associated organisms. In this study we use fractal techniques to characterize patterns of cross-scale habitat complexity, and examine how this relates to body-depth abundance distributions of associated fish assemblages over corresponding spatial scales. Our study demonstrates that: (1) Reefs formed from different underlying substrata exhibit distinct patterns of cross-scale habitat complexity; (2) The availability of potential refuges at different scales correlates with patterns in fish body depth distributions, but habitat structure is more strongly related to the relative abundance of fish in the body depth modes, rather than to the number of modes; (3) As reefs change from coral- to algal-dominated states, the complexity of the underlying reef substratum may change, presenting a more homogenous environment to associated assemblages; (4) Individual fish body depth distributions may be multi-modal, however, these distributions are not static characteristics of the fish assemblage and may change to uni-modal forms in response to changing habitat condition. In light of predicted anthropogenic changes, there is a clear need to improve our understanding of the scale of ecological relationships to anticipate future changes and vulnerabilities.
91 citations
TL;DR: It is shown that the multimodal pattern of species abundance distributions is consistent with predictions from the theory of emergent neutrality, suggesting that natural communities may be shaped by the evolutionary emergence of groups of similar species that coexist in niches.
Abstract: Recent analyses of data sampled in communities ranging from corals and fossil brachiopods to birds and phytoplankton suggest that their species abundance distributions have multiple modes, a pattern predicted by none of the existing theories. Here we show that the multimodal pattern is consistent with predictions from the theory of emergent neutrality. This adds to the observations, suggesting that natural communities may be shaped by the evolutionary emergence of groups of similar species that coexist in niches. Such self-organized similarity unifies niche and neutral theories of biodiversity.
79 citations
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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