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: It is suggested that the net effect of disturbance on the relative importance of niche and neutral processes in community assembly varies non-monotonically with the severity of disturbance, in contrast to the prevailing view that disturbance promotes niche processes.
Abstract: Many ecosystems experience strong temporal variability in environmental conditions; yet, a clear picture of how niche and neutral processes operate to determine community assembly in temporally variable systems remains elusive. In this study, we constructed neutral metacommunity models to assess the relative importance of neutral processes in a spatially and temporally variable ecosystem. We analyzed macroinvertebrate community data spanning multiple seasons and years from 20 sites in a Sonoran Desert river network in Arizona. The model goodness-of-fit was used to infer the importance of neutral processes. Averaging over eight stream flow conditions across three years, we found that neutral processes were more important in perennial streams than in non-perennial streams (intermittent and ephemeral streams). Averaging across perennial and non-perennial streams, we found that neutral processes were more important during very high flow and in low flow periods; whereas, at very low flows, the relative importance of neutral processes varied greatly. These findings were robust to the choice of model parameter values. Our study suggested that the net effect of disturbance on the relative importance of niche and neutral processes in community assembly varies non-monotonically with the severity of disturbance. In contrast to the prevailing view that disturbance promotes niche processes, we found that neutral processes could become more important when the severity of disturbance is beyond a certain threshold such that all organisms are adversely affected regardless of their biological traits and strategies.
5 citations
TL;DR: This paper analyzed tree species diversity and composition of urban green space (UGS) types and urban zones and examined the links between species and life history trait diversity and species productivity (carbon storage) in Kumasi, Ghana.
Abstract: Urban biodiversity is essential to creating resilient and sustainable cities. Nevertheless, there is paucity of data on the characterization of microhabitat effects on species/trait diversity and diversity-functional relationships in urban landscapes especially in developing countries. The objectives of this study were to; 1) analyze tree species diversity and composition of urban green space (UGS) types and urban zones, (2) describe the life history diversity of UGS types and urban zones and 3) examine the links between species and life history trait diversity and species productivity (carbon storage) in Kumasi, Ghana. Stratified random sampling was adopted in surveying 470 sampling plots and six streets of lengths ranging from 50 m to 1 km. About 176 tree species in 46 families were recorded within Kumasi. About 96 species were in an adjacent natural forest located at the outskirts of the city. Home gardens, institutional compounds, and public parks had the highest species richness of 76, 75 and 71, respectively while urban rangelands and farmlands were the least species rich with 6 and 23, respectively. Species richness (S) in the peri-urban (LDUZ, S = 142) and core urban (HDUZ, S = 108) were significantly different (Χ2 = 15.7, p < 0.0001, n = 1). Native species richness was lowest in the core urban area and highest in the natural forest. Pioneers and anthropochory dispersed species were the most abundant, suggesting that this urban landscape is shaped by both environment and social filters. Tree species diversity and distribution depend on the type of UGS and portrays a perturbed landscape in the early seres of succession with the overall ecosystem function sustained by both species and life history trait diversities. The implications of these findings for improving urban biodiversity conservation and overall urban sustainability are discussed.
4 citations
Dissertation•
07 Jul 2010
4 citations
Cites background from "Niches versus neutrality: uncoverin..."
...…of niche-based and neutral perspectives (Chase 2003, Chave 2004, Tilman 2004, Chase 2005, Orrock and Fletcher 2005, Gravel et al. 2006, Holyoak and Loreau 2006, Leibold and McPeek 2006, Adler et al. 2007, Cadotte 2007, Chase 2007, Jabot et al. 2008, Vergnon et al. 2009, Orrock and Watling 2010)....
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01 Jan 2012
TL;DR: In this article, the authors investigated the role of competition for resources in phytoplankton communities in the North Sea and found that both changes in N:P ratios and changes in absolute nutrient loads affected the PHYTOPLankton species composition.
Abstract: The aim of this thesis was to better understand the ways in which changes in nutrient loads impact phytoplankton communities. As nutrients entering coastal systems become more and more influenced by anthropogenic activities, so too comes the responsibility to understand what potential consequences may result. The North Sea is a key example of a coastal system experiencing large shifts in nutrient loading, with a particularly strong reduction in phosphorus (P) loads in recent decades. Bioassay experiments conducted during research cruises revealed that this has resulted in a spatial gradient from P limitation of phytoplankton growth in nearshore waters to nitrogen (N) limitation in the central North Sea. Effects of reduced P loads varied among phytoplankton groups, which may lead to shifts in community composition and a potential rise of harmful dino- and nanoflagellates. Field samples and controlled chemostat experiments showed that P limitation reduced the nutritional quality of phytoplankton, which may have negative impacts on the productivity of higher trophic levels in the food web. Chemostat experiments using North Sea phytoplankton were conducted to investigate the role of competition for resources. The results showed that both changes in N:P ratios and changes in absolute nutrient loads affected the phytoplankton species composition, in agreement with theoretical predictions of the nutrient-load hypothesis. This work supports calls for continued and improved monitoring of the North Sea. Furthermore, this research demonstrates that future de-eutrophication efforts in any aquatic system should be done with more balanced reductions of N and P as a core tenet.
4 citations
Cites background from "Niches versus neutrality: uncoverin..."
...Some studies have applied the neutral theory to phytoplankton community data and from this developed a “clumpy distribution” concept where species abundances seem to aggregate along trait lines such as cell size (Vergnon et al., 2009; Segura et al., 2013)....
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TL;DR: It is shown that when competition acts in concert with stochasticity and dispersal, communities spontaneously organize into clusters of similar species, and clusters feature generally across different niche mechanisms, and even under the confounding influence of environmental filters.
Abstract: Patterns of trait distribution among coexisting species can potentially reveal the processes by which species assemble into communities. The dominant paradigm, that competition causes species to differ more than expected by chance, has limited empirical support. Here we show that when competition acts in concert with stochasticity and dispersal, communities spontaneously organize into clusters of similar species. Further, we show clusters feature generally across different niche mechanisms, and even under the confounding influence of environmental filters. While clusters have been previously reported as transient or else persisting under restricted circumstances, our results show they persist broadly under immigration. Previous stochastic niche studies missed this effect because they only explored extremely low immigration. We provide parameter-free metrics for detecting clusters in field data, which we validate using simulations. We conclude that clusters are a more general pattern than overdispersion, and trait-based searches for niche differentiation may be more successful once they account for this fact.
4 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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