Neutral Theory Of Biodiversity Research Articles

Comment on “Global Correlations in Tropical Tree Species Richness and Abundance Reject Neutrality”

Ricklefs and Renner (Reports, 27 January 2012, p. 464) have argued that the neutral theory of biodiversity and biogeography cannot explain the correlations in family abundances and species richness found between tropical forests from distinct continents. However, we show that such patterns can arise from neutral processes of diversification, migration, and drift over large spatial and temporal scales.

Linking Dispersal and Immigration in Multidimensional Environments

Many problems in ecology require the estimation of rates of dispersal of individuals or propagules across physical boundaries. Such problems arise in invasion ecology, forest dynamics, and the neutral theory of biodiversity. In a forest plot, for example, one might ask what proportion of the seed rain originates from outside the plot. A recent study presented analytical approximations that relate the rate of immigration across a boundary to plot geometry and to the parameters of a dispersal kernel in one- and two-dimensional environments. In this study, we provide a more rigorous derivation of these expressions and we derive a more general expression that applies in environments of arbitrary dimension. We discuss potential applications of the one-, two-, and three-dimensional results to ecological problems.

Positive interactions can produce species-rich communities and increase species turnover through time

Aims The process of facilitation, where a species increases the survival, growth, and fitness of another species, is becoming increasingly recognized as a critical factor in shaping the structure of plant communities. This process is particularly important in stressful environments. Yet few studies have attempted to incorporate positive interactions into community ecological theories such as the neutral theory of biodiversity. Here, we use an equalizing trade-off model as a foundation to study the potential impact of facilitation on species richness and community temporal turnover. Methods Based on a spatially explicit birth–death trade-off model, we assume that the occurrence of facilitation is dependent on the presence of interspecific neighbours. We further propose that the realized birth rate for a given individual subject to facilitation is proportional to the number of interspecific neighbours within its neighbourhood. Thus, in our model, the individuals of rare species will benefit more from the existence of heterospecific individuals than common species. Important Findings As the facilitative coefficient increased, the species richness for simulated communities at the dynamically stochastic equilibrium was also increasing. Simulations also demonstrated that facilitation could increase the replacement of species through time: communities with facilitation become more dissimilar (i.e. have smaller Bray–Curtis similarity values) than communities without or with a lower degree of facilitation after the same time interval. Facilitation from interspecific neighbours on rare species increased their population sizes and consequently made them less prone to extinction, thus enhancing species richness. Meanwhile, in a saturated community, with the increase of species richness, mean population size of entire communities decreased, making species more prone to extinction on average, and thus increased the community temporal turnover. Our results suggest that future experimental work on the effect of facilitation on community-level properties should focus not just on species richness but also on other descriptors of community dynamics such as the temporal species turnover.

The Neutral—Niche Debate: A Philosophical Perspective

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.

Dispersal and recruitment limitation contribute differently to community assembly

The neutral theory of biodiversity has been criticized for being fragile with even slight deviations from its basic assumption of equal fitness among species. In response to this criticism, Hubbell ((2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press) proposed that competitive exclusion can be infinitely delayed by dispersal and recruitment limitation, thus making species effectively neutral. But the theoretical foundation for this claim still remains unclear and controversial, and the effects of dispersal and recruitment limitation are often confounded, especially in field studies. This study aims to provide an affirmative theoretical answer to the question of whether dispersal limitation and recruitment limitation can separately or jointly overwhelm the effects of fitness differences among species and lead to neutral community dynamics. Computer simulations were used to investigate the effects of dispersal and recruitment limitation on delaying competitive exclusion in a homogeneous habitat in a spatially explicit context. We found that even a slight competitive asymmetry would require extremely strong dispersal and recruitment limitation for neutrality to emerge. Most importantly, when the effects of dispersal and recruitment limitation were set apart, it is found that recruitment limitation is more effective in delaying competitive exclusion, whereas dispersal limitation tends to have a stronger impact on the general shape of both species abundance distributions and species-area relationships.

Coexistence of nearly neutral species

Aims The neutral theory of biodiversity provides a powerful framework for modeling macroecological patterns and interpreting species assemblages. However, there remain several unsolved problems, including the effect of relaxing the assumption of strict neutrality to allow for empirically observed variation in vital rates and the ‘problem of time’—empirically measured coexistence times are much shorter than the prediction of the strictly neutral drift model. Here, we develop a nearly neutral model that allows for differential birth and death rates of species. This model provides an approach to study species coexistence away from strict neutrality. Methods Based on Moran’s neutral model, which assumes all species in a community have the same competitive ability and have identical birth and death rates, we developed a model that includes birth–death trade-off but excludes speciation. This model describes a wide range of asymmetry from strictly neutral to nearly neutral to far from neutral and is useful for analyzing the effect of drift on species coexistence. Specifically, we analyzed the effects of the birth–death trade-off on the time and probability of species coexistence and quantified the loss of biodiversity (as measured by Simpson’s diversity) due to drift by varying species birth and death rates. Important Findings We found (i) a birth–death trade-off operating as an equalizing force driven by demographic stochasticity promotes the coexistence of nearly neutral species. Species near demographic trade-offs (i.e. fitness equivalence) can coexist even longer than that predicted by the strictly neutral model; (ii) the effect of birth rates on species coexistence is very similar to that of death rates, but their compensatory effects are not completely symmetric; (iii) ecological drift over time produces a march to fixation. Trade-off-based neutral communities lose diversity more slowly than the strictly neutral community, while non-neutral communities lose diversity much more rapidly; and (iv) nearly neutral systems have substantially shorter time of coexistence than that of neutral systems. This reduced time provides a promising solution to the problem of time.

Review on the Application of Ecosystem Models in Biodiversity Analyses

This paper is an exposition with the sole aim of highlighting the relevance of ecosystem models in the analyses of biodiversity. The structure of ecosystem models enables researchers to design and consequently formulate monitoring programs that will be useful to the conservation of biodiversity. Ecosystem theoretical models discussed in the paper include Lotka and Volterra Predator-Prey Model; Constructal Law; Kleiber’s Law; Metabolic Theory of Ecology; Occupancy-Abundance Relationship; Allometry Scaling; Rapoport’s Rule; Ewin’s Sampling Formula; Thorson’s Rule; Rench’s Rule, Unified Neutral Theory of Biodiversity (UNTB), and Ecosystem Forecasting. Lastly Biodiversity Action Plan as one of the applications of Ecosystem Theoretical models project was explained. Keywords: action plan, biodiversity, ecosystem, models

Time-dependent solutions of the spatially implicit neutral model of biodiversity

Previous research into the neutral theory of biodiversity has focused mainly on equilibrium solutions rather than time-dependent solutions. Understanding the time-dependent solutions is essential for applying neutral theory to ecosystems in which time-dependent processes, such as succession and invasion, are driving the dynamics. Time-dependent solutions also facilitate tests against data that are stronger than those based on static equilibrium patterns. Here I investigate the time-dependent solutions of the classic spatially implicit neutral model, in which a small local community is coupled to a much larger metacommunity through immigration. I present explicit general formulas for the eigenvalues, left eigenvectors and right eigenvectors of the models’s transition matrix. The time-dependent solutions can then be expressed in terms of these eigenvalues and eigenvectors. Some of these results are translated directly from existing results for the classic Moran model of population genetics (the Moran model is equivalent to the spatially implicit neutral model after a reparameterization); others of the results are new. I demonstrate that the asymptotic time-dependent solution corresponding to just these first two eigenvectors can be a good approximation to the full time-dependent solution. I also demonstrate the feasibility of a partial eigendecomposition of the transition matrix, which facilitates direct application of the results to a biologically relevant example in which a newly invading species is initially present in the metacommunity but absent from the local community.

Coexistence of Insect Species Competing for a Pulsed Resource: Toward a Unified Theory of Biodiversity in Fluctuating Environments

BackgroundOne major challenge in understanding how biodiversity is organized is finding out whether communities of competing species are shaped exclusively by species-level differences in ecological traits (niche theory), exclusively by random processes (neutral theory of biodiversity), or by both processes simultaneously. Communities of species competing for a pulsed resource are a suitable system for testing these theories: due to marked fluctuations in resource availability, the theories yield very different predictions about the timing of resource use and the synchronization of the population dynamics between the competing species. Accordingly, we explored mechanisms that might promote the local coexistence of phytophagous insects (four sister species of the genus Curculio) competing for oak acorns, a pulsed resource.Methodology/Principal FindingsWe analyzed the time partitioning of the exploitation of oak acorns by the four weevil species in two independent communities, and we assessed the level of synchronization in their population dynamics. In accordance with the niche theory, overall these species exhibited marked time partitioning of resource use, both within a given year and between different years owing to different dormancy strategies between species, as well as distinct demographic patterns. Two of the four weevil species, however, consistently exploited the resource during the same period of the year, exhibited a similar dormancy pattern, and did not show any significant difference in their population dynamics.Conclusions/SignificanceThe marked time partitioning of the resource use appears as a keystone of the coexistence of these competing insect species, except for two of them which are demographically nearly equivalent. Communities of consumers of pulsed resources thus seem to offer a promising avenue for developing a unifying theory of biodiversity in fluctuating environments which might predict the co-occurrence, within the same community, of species that are ecologically either very similar, or very different.

NEUTRAL BIODIVERSITY THEORY CAN EXPLAIN THE IMBALANCE OF PHYLOGENETIC TREES BUT NOT THE TEMPO OF THEIR DIVERSIFICATION

Numerous evolutionary studies have sought to explain the distribution of diversity across the limbs of the tree of life. At the same time, ecological studies have sought to explain differences in diversity and relative abundance within and among ecological communities. Traditionally, these patterns have been considered separately, but models that consider processes operating at the level of individuals, such as neutral biodiversity theory (NBT), can provide a link between them. Here, we compare evolutionary dynamics across a suite of NBT models. We show that NBT can yield phylogenetic tree topologies with imbalance closely resembling empirical observations. In general, metacommunities that exhibit greater disparity in abundance are characterized by more imbalanced phylogenetic trees. However, NBT fails to capture the tempo of diversification as represented by the distribution of branching events through time. We suggest that population-level processes might therefore help explain the asymmetry of phylogenetic trees, but that tree shape might mislead estimates of evolutionary rates unless the diversification process is modeled explicitly.

The spatial limitations of current neutral models of biodiversity.

The unified neutral theory of biodiversity and biogeography is increasingly accepted as an informative null model of community composition and dynamics. It has successfully produced macro-ecological patterns such as species-area relationships and species abundance distributions. However, the models employed make many unrealistic auxiliary assumptions. For example, the popular spatially implicit version assumes a local plot exchanging migrants with a large panmictic regional source pool. This simple structure allows rigorous testing of its fit to data. In contrast, spatially explicit models assume that offspring disperse only limited distances from their parents, but one cannot as yet test the significance of their fit to data. Here we compare the spatially explicit and the spatially implicit model, fitting the most-used implicit model (with two levels, local and regional) to data simulated by the most-used spatially explicit model (where offspring are distributed about their parent on a grid according to either a radially symmetric Gaussian or a ‘fat-tailed’ distribution). Based on these fits, we express spatially implicit parameters in terms of spatially explicit parameters. This suggests how we may obtain estimates of spatially explicit parameters from spatially implicit ones. The relationship between these parameters, however, makes no intuitive sense. Furthermore, the spatially implicit model usually fits observed species-abundance distributions better than those calculated from the spatially explicit model's simulated data. Current spatially explicit neutral models therefore have limited descriptive power. However, our results suggest that a fatter tail of the dispersal kernel seems to improve the fit, suggesting that dispersal kernels with even fatter tails should be studied in future. We conclude that more advanced spatially explicit models and tools to analyze them need to be developed.

COMPUTER SIMULATIONS OF PLANT BIODIVERSITY IN STABLE AND UNSTABLE ENVIRONMENTS: A TEST OF THE NEUTRAL BIODIVERSITY THEORY

The Neutral Biodiversity Theory (NBT) argues that community-level patterns are not determined by trait differences among species, but rather by demographic stochasticity. If true, deterministic patterns of species co-existence, transient or otherwise, should not occur. We tested this critical prediction using a spatially explicit, reiterative algorithm (SERA) that incorporates demographic stochasticity to examine how artificial plant species compete for light and space. An additional level of ecological realism was added by simulating species competition in heterogeneous and disturbed environments. Across 108 simulations, small niche differences influenced interspecific competition and persistence, particularly in spatiotemporally heterogeneous environments. One species re-emerged as the dominant, and the identities of subdominant and rare species remained constant. Although stochastic processes played an important role, the results of these simulations are inconsistent with NBT, i.e., very small niche differences dictated patterns even when all species obey the same simple physical rules.

Neutral theory as a predictor of avifaunal extinctions after habitat loss

The worldwide loss of natural habitats leads not only to the loss of habitat-endemic species but also to further and protracted extinctions in the reduced areas that remain. How rapid is this process? We use the neutral theory of biodiversity to answer this question, and we compare the results taken with observed rates of avifaunal extinctions. In the neutral model, we derive an exact solution for the rate of species loss in a closed community. The simple, closed-form solution exhibits hyperbolic decay of species richness with time, which implies a potentially rapid initial decline followed by much slower rates long term. Our empirical estimates of extinction times are based on published studies for avifaunal extinctions either on oceanic islands or in forest fragments, which span a total of six orders of magnitude in area. These estimates show that the time to extinction strongly depends on the area. The neutral-theory predictions agree well with observed rates over three orders of magnitude of area (between 100 and 100,000 ha) both for islands and forest fragments. Regarding the species abundance distribution, extinction times based on a broken-stick model led to better agreement with observation than if a log-series model was used. The predictions break down for very small or very large areas. Thus, neutrality may be an affordable assumption for some applications in ecology and conservation, particularly for areas of intermediate size.

Ecological incumbency impedes stochastic community assembly in Holocene foraminifera from the Huon Peninsula, Papua New Guinea

Persistence in the structure of ecological communities can be predicted both by deterministic and by stochastic theory. Evaluating ecological patterns against the neutral theory of biodiversity provides an appropriate methodology for differentiating between these alternatives. We traced the history of benthic foraminiferal communities from the Huon Peninsula, Papua New Guinea. From the well-preserved uplifted reef terrace at Bonah River we reconstructed the benthic foraminiferal communities during a 2200-year period (9000–6800 yr B.P.) of reef building during the Holocene transgressive sea-level rise. We found that the similarity of foraminiferal communities was consistently above 60%, even when comparing communities on either side of a massive volcanic eruption that smothered the existing reef system with ash. Similarly, species diversity and rank dominance were unchanged through time. However, similarity dropped dramatically in the final stages of reef growth, when accommodation space was reduced as sea-level rise slowed. We compared the community inertia index (CII) computed from the observed species abundances with that predicted from neutral theory. Despite the differences in foraminiferal community composition in the younger part of the reef sequence, we found an overall greater degree of community inertia with less variance in observed communities than was predicted from neutral theory, regardless of foraminiferal community size or species migration rate. Thus, persistent species assemblages could not be ascribed to neutral predictions. Ecological incumbency of established foraminiferal species likely prevented stochastic increases in both migrant and rare taxa at the Bonah River site. Regardless of the structuring mechanisms, our reconstruction of Holocene foraminiferal assemblages provides historical context for the management and potential restoration of degraded species assemblages.

Development, Application and Place of Neutral Theory in Ecology and Biogeography

AbstractClassical ecological theory predicts that ecological communities should only contain as many species as there are resources. Many ecosystems, however, seem to contain many more species than classical theory allows. Understanding this paradox is central to community ecology and biogeography. Niche‐based models consider that differences and trade‐offs between species’ life history traits stabilise species interactions and so allow coexistence. In stark contrast, neutral models assume that individuals at the same trophic level interact identically with conspecifics and heterospecifics (i.e. all species are equivalent), and this equivalence allows coexistence. Despite it seeming unlikely that species are equivalent, neutral models do predict some of the macroscopic properties of ecological communities surprisingly well. Although there are many neutral models, the best‐known neutral model in the context of community ecology is that described by Hubbell (2001) in the Unified Neutral Theory of Biodiversity. We review the development of neutral theory in ecology and biogeography, consider its predictions and how they can be evaluated, and look at how neutral theory may develop in the future. This article focuses on species‐rich plant communities, as they are, for the most part, the test‐bed for the recent development and application of neutral models, but we also consider the application of neutral approaches to other taxonomic groups and ecosystem types.

Synthesizing traditional biogeography with microbial ecology: the importance of dormancy

AbstractThe discovery of biogeographical patterns among microbial communities has led to a focus on the empirical evaluation of the importance of dispersal limitation in microbial biota. As a result, the spatial distribution of microbial diversity has been increasingly studied while the synthesis of biogeographical theory with microbial ecology remains undeveloped. To make biogeographical theory relevant to microbial ecology, microbial traits that potentially affect the distribution of microbial diversity need to be considered. Given that many microorganisms in natural environments are in a state of dormancy and that dormancy is an important microbial fitness trait, I provide a first attempt to account for the effects of dormancy on microbial biogeography by treating dormancy as a fundamental biogeographical response. I discuss the effects of dormancy on the equilibrium theory of island biogeography and on the unified neutral theory of biodiversity and biogeography, and suggest how the equilibrium theory of island biogeography can produce predictions approaching those of the Baas‐Becking hypothesis (i.e. everything is everywhere, but the environment selects). In addition, I present a conceptual model of the unified neutral theory of biodiversity and biogeography, generalized to account for dormancy, from which a full model can be constructed for species with or without dormant life history stages.

Speciation and the neutral theory of biodiversity

The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size ("ecological drift"), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non-neutral modes of speciation, such as adaptive radiations.

Protracted speciation revitalizes the neutral theory of biodiversity

Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies - without compromising any of the original model's existing achievements and retaining computational and analytical tractability - by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of 'incipient' species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non-neutral models should also model speciation as a gradual process rather than an instantaneous one.

The neutral theory of biodiversity with random fission speciation

The neutral theory of biodiversity and biogeography emphasizes the importance of dispersal and speciation to macro-ecological diversity patterns. While the influence of dispersal has been studied quite extensively, the effect of speciation has not received much attention, even though it was already claimed at an early stage of neutral theory development that the mode of speciation would leave a signature on metacommunity structure. Here, we derive analytical expressions for the distribution of abundances according to the neutral model with recruitment (i.e., dispersal and establishment) limitation and random fission speciation which seems to be a more realistic description of (allopatric) speciation than the point mutation mode of speciation mostly used in neutral models. We find that the two modes of speciation behave qualitatively differently except when recruitment is strongly limited. Fitting the model to six large tropical tree data sets, we show that it performs worse than the original neutral model with point mutation speciation but yields more realistic predictions for speciation rates, species longevities, and rare species. Interestingly, we find that the metacommunity abundance distribution under random fission is identical to the broken-stick abundance distribution and thus provides a dynamical explanation for this grand old lady of abundance distributions.

Unified neutral theory of biodiversity and biogeography

Unified neutral theory of biodiversity and biogeography