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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08 May 2020
TL;DR: In this paper, the authors propose Tiivistelmä (Tiivinen elmä) and Tivinen (Tivinen et al.) this paper ) dictionary.
Abstract: ......................................................................................................4 Tiivistelmä ................................................................................................. 6 Abbreviations .............................................................................................. 7
2 citations
Cites background from "Niches versus neutrality: uncoverin..."
...Exclusion of a species may take a long time in nature, and thus the Theory of Emergent Neutrality takes into account also the neutral coexistence of similar species (Vergnon et al. 2009, Segura et al. 2011)....
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...Classic theories concerning phytoplankton community structure and its drivers include e.g. the Paradox of the Plankton Theory (Hutchinson 1961), the Niche Theory and the Hypothesis of Limiting Similarity (MacArthur & Levins 1967), the C-R-S model (Reynolds 1988), and Theory of Emergent Neutrality (Vergnon et al. 2009, Segura et al. 2011)....
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...…community structure and its drivers include e.g. the Paradox of the Plankton Theory (Hutchinson 1961), the Niche Theory and the Hypothesis of Limiting Similarity (MacArthur & Levins 1967), the C-R-S model (Reynolds 1988), and Theory of Emergent Neutrality (Vergnon et al. 2009, Segura et al. 2011)....
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Dissertation•
01 Jan 2016
TL;DR: It emerges from this exploration that stochastic niche dynamics may result in the spontaneous formation of species clusters, under the qualification that pattern will not form if idiosyncratic regulation mechanisms allow arbitrarily similar species to maintain distinct ecological strategies.
Abstract: From trait patterns to species lifetimes: Effects of niche differentiation on coexistence and community structure by Rafael D’Andrea Rocha Chair: Annette M. Ostling One of the most enduring questions in ecology is what accounts for coexistence among trophically similar organisms. Niche differentiation is one answer, but so is neutrality: species can coexist either because of ecological differences or ecological similarities. Despite being diametrically opposite, these two theories can be difficult to separate in nature. Because neutral theory posits that species traits are irrelevant for ecological performance, trait patterns are commonly used in niche inference, but results are mixed. This dissertation argues that widely accepted ideas about trait pattern driven by niche differentiation must be updated in light of recent findings, and takes the first steps in that direction. We contend that the current theory of trait patterning is incomplete, and progress requires exploring patterns across a variety of niche models. It emerges from this exploration that stochastic niche dynamics may result in the spontaneous formation of species clusters, under the qualification that pattern will not form if idiosyncratic regulation mechanisms allow arbitrarily similar species to maintain distinct ecological strategies. We provide a new metric for identifying and quantifying species clusters, which outperforms existing metrics in rejecting neutrality in our pseudodata. Another major theme is that the null hypothesis is critical in inference tests. Process-based null models are superior to statistical null hypotheses based on randomization of data because the latter destroys pattern caused by forces unrelated to niche differentiation. For example, we show that when species can randomly mutate into similar species, clusters may occur even in the absence of niche differentiation. A final key theme is that the effect of niche differentiation on species xi dynamics and pattern may be more complex than is currently appreciated when stochastic dynamics under immigration is considered. Species richness, lifetimes, and extinction rates in niche-differentiated assemblages may be lower or higher than neutral assemblages, depending on the ratio between regional diversity and the number of niches available. The findings of this dissertation contribute to our theoretical understanding of niche differentiation as an important coexistence mechanism, and to realizing the potential of trait patterns in assessing its prevalence in nature.
2 citations
Cites background from "Niches versus neutrality: uncoverin..."
...(2006) verified this in a Lotka-Volterra model where within-species genotypic diversity promotes coexistence by allowing species to span multiple viable niches and giving them flexibility to respond to selection by converging or diverging from competitors. Yamauchi & Miki (2009) further explored Vellend’s model with the introduction of genetic flow between phenotypes, sexual inheritance of traits, and environmental stochasticity, and reported mixed effects of intraspecific variation on species diversity in simulation outcomes depending on the scenario tested....
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...In addition to local peaks in richness on the trait axis, ? and ? also found evidence of local peaks in abundance, like those predicted in Lotka-Volterra models, using an abundance-weighted trait distance metric and a test looking for peaks in Shannon-Weaver diversity respectively....
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...In sum, clusters appear in nature and feature in Lotka-Volterra competition models, as well as evolutionary models....
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...In the case of no fitness differences, the niche-axis Lotka-Volterra model proposed by ? does not allow for stable coexistence between three or more arbitrarily similar species....
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...Using a simple Lotka-Volterra competition model with species arranged along an axis of resource preference, and assuming that the strength of competition between species is proportional to the overlap in resource preference (“niche overlap”), they obtained a quantitative limit to species similarity consistent with coexistence....
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TL;DR: In this article , the authors used population growth models that consider interspecific interactions parameterized for 35 species using field data and simulated the expected community dynamics under different species-interaction scenarios, suggesting that differences in unmeasured niche axes stabilise coexistence within clusters.
Abstract: Clustering of species with similar niches or traits occurs in communities, but the mechanisms behind this pattern are still unclear. In the emergent neutrality model, species with similar niches and competitive ability self-organise into clusters. In the hidden-niche model, unaccounted-for niche differences stabilise coexistence within clusters. Finally, clustering may occur through alliances of species that facilitate each other. We tested these hypotheses using population-growth models that consider interspecific interactions parameterised for 35 species using field data. We simulated the expected community dynamics under different species-interaction scenarios. Interspecific competition was weaker within rather than between clusters, suggesting that differences in unmeasured niche axes stabilise coexistence within clusters. Direct facilitation did not drive clustering. In contrast, indirect facilitation seemingly promoted species alliances in clusters whose members suppressed common competitors in other clusters. Such alliances have been overlooked in the literature on clustering, but may arise easily when within cluster competition is weak.
2 citations
TL;DR: In this article, the authors explored the response of plant assemblages to environmental drivers among four riparian zones (Amobia, Ninian, Pame and Owname), in Ashanti Region, Ghana, West Africa.
Abstract: The aim of the study was to explore the response of plant assemblages to environmental drivers among four riparian zones (Amobia, Ninian, Pame and Owname), in Ashanti Region, Ghana, West Africa. A 120 sample plots of 10 × 10 m2 for trees and shrubs and 0.5 × 2 m2 for grasses and herbs, were randomly laid perpendicular to the environmental gradients, and from both sides of the four classified riparian zones. Number of individuals were counted per plot and percentage cover estimated per species. MacArthur broken stick model (BS), Chao-1 estimates and Hill numbers were calculated to quantify community assemblages, while constrained ordination (CCA) was applied to examine the relationship between species assemblages and the distribution of associated environmental factors. A total of 1589 individuals belonging to 48 families and 141 species were registered. Species from the Fabaceae, were the highest (14.2%). Overall, species abundance, richness and diversity, differed significantly across the four zones. Aspilia africana and Panicum maximum were the single most abundant tree and grass species, respectively. Infrequent species including Bussea occidentalis, Celtis zenkarii constituted 0.4% of the total species sampled. Although Pame was found to be species poor, it tended to be the most diverse, while Ninian was the least diverse. CCA analysis showed that farming, bushfire, erosion and logging, accounted for 43.13% (axis I = 23.24% and axis II = 19.89%) patterns of species variability across sites. Though disturbances tend to promote diversity through the creation of evenness in species distribution and richness, but in severe scenarios, sensitive indigenous species may go extinct, leaving only stress-tolerant alien invasive like Arthraxon hispidus and Chromolaena odorota.
1 citations
TL;DR: It is found that no one sample in the lung microbial communities of the sputum samples of Exacerbation group, nor those of End-of-treatment group satisfied the predictions of neutral model, suggesting that the neutral-process does not dominate in CF patients before and after antibiotic treatments.
1 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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