Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

Species-specific traits plus stabilizing processes best explain coexistence in biodiverse fire-prone plant communities

Coexistence in fire-prone Mediterranean-type shrublands has been explored in the past using both neutral and niche-based models. However, distinct differences between plant functional types (PFTs), such as fire-killed vs resprouting responses to fire, and the relative similarity of species within a PFT, suggest that coexistence models might benefit from combining both neutral and niche-based (stabilizing) approaches. We developed a multispecies metacommunity model where species are grouped into two PFTs (fire-killed vs resprouting) to investigate the roles of neutral and stabilizing processes on species richness and rank-abundance distributions. Our results show that species richness can be maintained in two ways: i) strictly neutral species within each PFT, or ii) species within PFTs differing in key demographic properties, provided that additional stabilizing processes, such as negative density regulation, also operate. However, only simulations including stabilizing processes resulted in structurally realistic rank-abundance distributions over plausible time scales. This result underscores the importance of including both key species traits and stabilizing (niche) processes in explaining species coexistence and community structure.

Thirty years of forest census at Barro Colorado and the importance of immigration in maintaining diversity

The neutral theory of community ecology can predict diversity and abundances of tropical trees, but only under the assumption of steady input of new species into the community. Without input, diversity of a neutral community collapses, so the theory's predictions are not relevant unless novel species evolve or immigrate. We derive analytically the species input needed to maintain a target tree diversity, and find that a rate close to per recruit would maintain the observed diversity of 291 species in the Barro Colorado 50-ha tree plot in Panama. We then measured the rate empirically by comparing species present in one complete enumeration of the plot to those present five years later. Over six census intervals, the observed rate of input was to species per recruit, suggesting that there is adequate immigration of novel species to maintain diversity. Species interactions, niche partitioning, or density-dependence, while they may be present, do not appear to enhance tree species richness at Barro Colorado.

Hybrid niche-neutral models outperform an otherwise equivalent neutral model for fitting coral reef data

Niche theory and neutral theory are two major developments aiming at explaining patterns of biodiversity observed in nature. Both theories have been found relevant either separately or simultaneously in some real communities, and it has been theoretically demonstrated that they can produce similar species abundance distributions. However, it remains controversial whether the two theories can produce similar patterns via different mechanisms, or can interact to jointly produce the observed diversity patterns, or whether the patterns generated by the neutral model are robust to niche structure. Here we show that, although the neutral model proposed for spatially discrete communities remains robust to strong niche structure for high-diversity communities, the inclusion of more realistic niche differentiation modes greatly improves the goodness of fit to Indo-Pacific coral reefs. Actually, the multiple discrete communities' neutral model, due to its underestimation of the number or abundance of common species, fails to capture the combination of many rare species and a few highly abundant species that characterize the Indo-Pacific coral reef communities. By incorporating niche structure into the multiple discrete communities' model, the hybrid niche-neutral models can successfully reproduce both the species-based and individual-based abundance distribution patterns observed in the coral reefs. We proposed that both niche theory and neutral theory may be involved in explaining the structure of such communities. Our results also suggest a negative relationship between per capita birth to death ratio and immigration among different guilds of coral species, which clearly deserves further investigation.

Species differences drive nonneutral structure in pleistocene coral communities

Although ecological assemblages frequently depart from neutral model predictions, these discrepancies have not been unambiguously attributed to neutral theory's core assumption: that community structure is primarily the result of chance variation in birth, death, speciation, and dispersal, rather than the manifestation of demographic differences among species. Using coral communities in Barbados from four time periods during the Pleistocene, we demonstrate that the neutral theory cannot explain coral community similarity distributions, species' regional abundance distributions, or their local occupancy. Furthermore, discrepancies between the neutral theory and the observed communities can be attributed to violation of the core assumption of species equivalence. In particular, species' variable growth rates are driving departures from neutral predictions. Our results reinforce an understanding of reef coral community assembly that invokes trade-offs in species' demographic strategies. The results further suggest that conservation management actions will fail if they are based on the neutral assumption that different coral species are equally able to create live coral cover in the shallow-water reef environment. These findings highlight the importance of developing biodiversity theory that can parsimoniously incorporate species differences in coral reef communities, rather than further elaborating neutral theory.

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.

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily divergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically divergent hosts. Here we use a sampling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.

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.

On the statistical mechanics of species abundance distributions

A central issue in ecology is that of the factors determining the relative abundance of species within a natural community. The proper application of the principles of statistical physics to species abundance distributions (SADs) shows that simple ecological properties could account for the near universal features observed. These properties are (i) a limit on the number of individuals in an ecological guild and (ii) per capita birth and death rates. They underpin the neutral theory of Hubbell (2001), the master equation approach of Volkov et al. (2003, 2005) and the idiosyncratic (extreme niche) theory of Pueyo et al. (2007); they result in an underlying log series SAD, regardless of neutral or niche dynamics. The success of statistical mechanics in this application implies that communities are in dynamic equilibrium and hence that niches must be flexible and that temporal fluctuations on all sorts of scales are likely to be important in community structure.

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

The theoretical description of the forces that shape ecological communities focuses around two classes of models. In niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. Species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to deduce ecological dynamics from typical measures of diversity and community structure. Here, we show that the fusion of species abundance data with genome-derived measures of evolutionary distance can provide a clear indication of ecological dynamics, capable of quantifying the relative roles played by niche and neutral forces. We apply this technique to six gastrointestinal microbiomes drawn from three different domesticated vertebrates, using high-resolution surveys of microbial species abundance obtained from carefully curated deep 16S rRNA hypervariable tag sequencing data. Although the species abundance patterns are seemingly well fit by the neutral theory of metacommunity assembly, we show that this theory cannot account for the evolutionary patterns in the genomic data; moreover, our analyses strongly suggest that these microbiomes have, in fact, been assembled through processes that involve a significant nonneutral (niche) contribution. Our results demonstrate that high-resolution genomics can remove the ambiguities of process inference inherent in classic ecological measures and permits quantification of the forces shaping complex microbial communities.

The coherence problem with the Unified Neutral Theory of Biodiversity

The Unified Neutral Theory of Biodiversity (UNTB), proposed as an alternative to niche theory, has been viewed as a theory that species coexist without niche differences, without fitness differences, or with equal probability of success. Support is claimed when models lacking species differences predict highly aggregated metrics, such as species abundance distributions (SADs) or species area distributions (SARs). Here, I summarize why UNTB generates confusion, and is not actually relevant to niche theory (i.e. an explanation for why and how many species coexist). Equal probability is not a theory, but lack of one; it does not include or exclude any process relevant to coexistence of competitors. Models lacking explicit species can make useful predictions, but this does not support neutral theory. I provide s suggestions that could help reduce confusion generated by the debate.

Biological diversity of fish communities: pattern and process

For over 150 years, ecologists have been striving to explain fundamental patterns of biological diversity, such as the observation that communities invariably consist of common and rare species, and to unravel the processes that underpin these patterns. This task is increasingly urgent given the accelerating loss of biological diversity. Although fishes are the most diverse vertebrate taxon and fish communities occur in a wide range of habitats, they have been relatively little studied in the quest to elucidate the processes that shape patterns of biological diversity. Here, some of the topics that investigations of fish assemblages can illuminate are highlighted. These include the characteristics of ecological communities and the role that dispersal limitation plays in structuring them, the distinction between core and occasional species, the insights that evaluating abundance in different currencies can bring and the assessment of community capacity. Questions are identified that future investigations of fish communities might tackle and a case study of a biodiverse ecoregion (Thailand and Peninsula Malaysia) is used to illustrate the need for better links between these ecological questions and effective conservation practice.

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.