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: The results suggest that increases in species richness occurring as energy availability increases may be isolated to specific niches, e.g., the body size classes, especially in communities developing on discrete and energetically isolated resources such as deep sea wood falls.
Abstract: Theoretical and empirical studies suggest that the total energy available in natural communities influences body size as well as patterns of abundance and diversity. But the precise mechanisms underlying relationships or how these three ecological properties relate remain elusive. We identify five hypotheses relating energy availability, body size distributions, abundance, and species richness within communities, and we use experimental deep sea wood fall communities to test their predicted effects both on descriptors describing the species richness-body size distribution, and on trends in species richness within size classes over an energy gradient (size class-richness relationships). Invertebrate communities were taxonomically identified, weighed, and counted from 32 Acacia sp. logs ranging in size from 0.6 to 20.6 kg (corresponding to different levels of energy available) which were deployed at 3203 m in the Northeast Pacific Ocean for between 5 and 7 years. Trends in both the species richness-body size distribution and the size class-richness distribution with increasing wood fall size provide support for the Increased Packing hypothesis: species richness increases with increasing wood fall size but only in the modal size class. Furthermore, species richness of body size classes reflected the abundance of individuals in that size class. Thus, increases in richness in the modal size class with increasing energy were concordant with increases in abundance within that size class. The results suggest that increases in species richness occurring as energy availability increases may be isolated to specific niches, e.g. the body size classes, especially in communities developing on discrete and energetically isolated resources such as deep sea wood falls.
10 citations
Cites background from "Niches versus neutrality: uncoverin..."
...However non-competitive neutral mechanisms (Etienne and Olff 2004, Vergnon et al. 2009) have also been proposed to explain community body size distributions....
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TL;DR: Substantial reduction in the isotopic niche of P. bifascistus and a shift toward aquatic invertebrates can facilitate coexistence during this season of resource shortage, which could be an important mechanism that contributes to the resource partitioning and coexistence of dominant omnivores in Neotropical streams.
Abstract: Coexistence of ecomorphologically similar species in diverse Neotropical ecosystems has been a focus of long-term debate among ecologists and evolutionary biologists. Such coexistence can be promoted by trophic plasticity and seasonal changes in omnivorous feeding. We combined stomach content and stable isotope analyses to determine how seasonal variation in resource availability influences the consumption and assimilation of resources by two syntopic fish species, Psalidodon aff. gymnodontus and P. bifasciatus, in the Lower Iguacu basin. We also tested the impact of seasonality on trophic niche breadth and diet overlap of these two dominant omnivores. Seasonal changes in resource availability strongly influenced the consumption and assimilation of resources by the two fish species. Both species exhibited high levels of omnivory, characterized by high diversity of allochthonous resources in the wet season. Terrestrial invertebrates were the main component of diet during this season. However, in the dry season, both species reduced their isotopic niches, indicating diet specialization. High diet overlap was observed in both seasons, but the isotopic niche overlap was smaller in the dry season. Substantial reduction in the isotopic niche of P. bifascistus and a shift toward aquatic invertebrates can facilitate coexistence during this season of resource shortage. Feeding plasticity allows omnivorous fish to adjust their trophic niches according to seasonality, promoting the exploitation of different resources during periods of greater resource diversity. This seasonal variation could be an important mechanism that contributes to the resource partitioning and coexistence of dominant omnivores in Neotropical streams.
10 citations
TL;DR: The authors revisited this relation and associated relations between richness and abundance (as "effective number of species" and coral cover, used as a proxy for disturbance and competition) and found consistent evidence of regional enrichment, a finding subsequently questioned on methodological grounds.
Abstract: The degree to which biotic communities are regionally enriched or locally saturated, and roles of key structuring processes, remain enduring ecological questions. Prior studies of reef-building corals of the Indo-west Pacific (IWP) found consistent evidence of regional enrichment, a finding subsequently questioned on methodological grounds. Here we revisit this relation, and associated relations between richness and abundance (as ‘Effective Number of Species’), and coral cover, used as a proxy for disturbance and competition. From 1994 to 2017, we sampled > 2,900 sites on shallow (typically 200 species, > 40 percent of regional pools and > 25 percent of the IWP total. For deep and shallow sites combined, the highest local tally reached 280 species ha-1. These places may represent the asymptote of local richness in reef-building corals, rare examples of the ecological complexity for which these increasingly endangered communities are justly renowned.
9 citations
TL;DR: A stochastic, spatially explicit model is used that spans a continuum from neutral to niche communities, and is driven by the intensity of hierarchical competition, to study the spatial aspect of a critical transition and propose early warning signals to detect it.
Abstract: The dynamics of ecological communities have been described by neutral and niche theories that are now increasingly integrated into unified models. It is known that a critical transition exists between these two states, but the spatial aspect of this transition has not been studied. Our aim is to study the spatial aspect of the transition and propose early warning signals to detect it. We used a stochastic, spatially explicit model that spans a continuum from neutral to niche communities, and is driven by the intensity of hierarchical competition. The transition is indicated by the emergence of a large patch formed by one species that connects the whole area. The properties of this patch can be used as early warning indicators of a critical transition. If competition intensity increases beyond the critical point, our model shows a sudden decrease of the Shannon diversity index and a gentle decline in species richness. The critical point occurs at a very low value of competitive intensity, with the rate of migration from the metacommunity greatly influencing the position of this critical point. As an example, we apply our new method of early warning indicators to the Barro Colorado Tropical forest, which, as expected, appears to be far from a critical transition. Low values of competitive intensity were also reported by previous studies for different high-diversity real communities, suggesting that these communities are located before the critical point. A small increase of competitive interactions could push them across the transition, however, to a state in which diversity is much lower. Thus this new early warnings indicator could be used to monitor high diversity ecosystems that are still undisturbed.
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9 citations
16 May 2021
TL;DR: In this article, the importance of deterministic or stochastic processes in the succession dynamic is defined, and new successional studies provide answers to different mechanisms of community assemblage.
Abstract: The study of ecological succession to determine how plant communities re-assemble after a natural or anthropogenic disturbance has always been an important topic in ecology. The understanding of these processes forms part of the new theories of community assembly and species coexistence, and is attracting attention in a context of expanding human impacts. Specifically, new successional studies provide answers to different mechanisms of community assemblage, and aim to define the importance of deterministic or stochastic processes in the succession dynamic. Biotic limits, which depend directly on biodiversity (i.e., species competition), and abiotic filtering, which depends on the environment, become particularly important when they are exceeded, making the succession process more complicated to reach the previous disturbance stage. Plant functional traits (PFTs) are used in secondary succession studies to establish differences between abandonment stages or to compare types of vegetation or flora, and are more closely related to the functioning of plant communities. Dispersal limitation is a PFT considered an important process from a stochastic point of view because it is related to the establishing of plants. Related to it the soil seed bank plays an important role in secondary succession because it is essential for ecosystem functioning. Soil compounds and microbial community are important variables to take into account when studying any succession stage. Chronosequence is the best way to study the whole process at different time scales. Finally, our objective in this review is to show how past studies and new insights are being incorporated into the basis of classic succession. To further explore this subject we have chosen old-field recovery as an example of how a number of different plant communities, including annual and perennial grasslands and shrublands, play an important role in secondary succession.
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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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