Neutral Theory of Biodiversity

Le concept de niche imprègne l’écologie. Comme le concept de fitness en biologie évolutive, c’est un concept central, au sens parfois peu explicité, apte à subir des glissements, jusqu’à finalement pouvoir être qualifié de tautologique (Griesemer 1992). Comme définition préliminaire, disons, sans préciser davantage, que la niche est ce qui décrit l’écologie d’une espèce, ce qui peut signifier son rôle dans l’écosystème, son habitat, etc. Le concept, inspiré par la biologie darwinienne, a connu une fortune croissante au cours du XXe siècle, à la croisée des disciplines écologiques en développement, avant de tomber en disgrâce dans les années 1980 (Chase & Leibold 2003). Dans une première partie, nous retraçons l’histoire du concept et de ses sens, de ses diverses fortunes et infortunes. Dans une deuxième partie, nous examinons plus précisément les rapports que le concept entretient avec les explications de la coexistence et de la diversité. Dans une troisième partie, nous exposons la récente controverse entre la théorie basée sur le concept de niche et la théorie neutre, et discutons son bien-fondé. En conclusion, nous revenons sur les vertus et difficultés des différents sens du concept.

In this chapter, we first trace the history of the concept of ecological niche and see how its meanings varied with the search for a theory of ecology. The niche concept has its roots in the Darwinian view of ecosystems that are structured by struggle for survival and, originally, the niche was perceived as an invariant place within the ecosystem, that would preexist the assembly of the ecosystem. The concept then slipped towards a sense in which the niche, no longer a pre-existing ecosystem structure, eventually became a variable that would in turn have to be explained by the competitive exclusion principle and the coevolution of species. The niche concept used at that time, while more operational from an empirical point of view than the previous one, suffered however from an ill-founded definition. A recent refoundation by Chase & Leibold enabled to overcome some of the definitional difficulties.
We then present how, in contemporary ecology, the niche concept is recruited to explain biodiversity and species coexistence patterns. We show how, in parallel, neutralist models, by succeedingly explaining some ecological patterns without resorting to explanations in terms of niche, have questioned the explanatory virtues of the niche concept.
In conclusion, it seems that the forunes and misfortunes of the niche concept can be seen as a reflection of the difficulties of ecology to give birth to a theory that would be both predictive and explanatory.

Using the scriptural based Created Heterozygosity Model and calculating factors regarding physiological, environmental, and rates of geographical expansion. Predictions regarding mutation rates are made on Hominidae (humans and primates), Canid (Wolf, dogs), Vulpes (foxes), Felidae (cats). The implications of rapid mutation changes and increases in diversity has implications in molecular biology, genetics and medicine. Phylogenetic methods are put to the test against pedigree methods for accuracy and determination of when the last bottleneck in animal life is discussed. The worldwide pattern of limited variation among all animal life, tells us that something physically happened in the past that reset all mitochondrial diversity at the same time. What was this? When exactly was this? Is genetic diversity still increasing today? Is a Universal molecular clock explained by neutral theory the best explanation for all the diversity we see in life today and can it explain the patterns observed in nature? Are evolutionary phylogenetic mutation rates more valid than pedigree mutation rates? Can future predictions be made regarding different mutation rate models? These questions demand attention, as many paradoxes exist regarding these controversial topics.

Ant gardens (AGs) are specialized ant-plant associations where arboreal ants build their carton nests in association with epiphytes that use the carton as a substrate. Most of the epiphytes are planted by ants; therefore, seed selection by ants is a key driver of the epiphyte composition of AGs. However, deterministic post-dispersal factors, such as the surrounding environmental conditions and plant succession, may also influence epiphyte composition. Here we ask whether epiphyte composition on a local scale is associated with dispersal constraints, local environmental conditions (light availability, number of branches and nest height) or AG successional stage. We sampled all epiphyte species in 18 AGs formed by Camponotus femoratus and Crematogaster levior in Central Amazon, Brazil. AGs were located within a range of 1 km and at a maximum of 20 m from the edges of a dirt road within a primary forest. Epiphytic composition showed strong spatial structure, decreasing in similarity with increasing distance. Environmental conditions and AG successional stage were not related to AG floristic composition, suggesting a key role of stochastic processes related to seed dispersal. A combination of seed abundance and attractiveness in neighbouring AGs seems to drive the higher similarity in epiphyte composition among closer AGs.

The simplest theories often have much merit and many limitations, and in this vein, the value of Neutral Theory (NT) has been the subject of much debate over the past 15 years. NT was proposed at the turn of the century by Stephen Hubbell to explain pervasive patterns observed in the organization of ecosystems. Its originally tepid reception among ecologists contrasted starkly with the excitement it caused among physicists and mathematicians. Indeed, NT spawned several theoretical studies that attempted to explain empirical data and predicted trends of quantities that

Nesse trabalho exploramos os aspectos teóricos da Teoria Neutra da Biodiversidade e Biogeografi a (TNB) proposta por Hubbell , apresentando juntamente um estudo cienciométrico sobre o impacto dessa teoria na comunidade científi ca, seus avanços, principais críticas e algumas perspectivas. A TNB pode facilitar o desenvolvimento de hipóteses nulas testáveis principalmente em comunidades nas quais características espaciais explícitas desempenham um papel marcante, representando uma importante ferramenta conceitual e analítica. A premissa mais provocativa da TNB é que os organismos de todas as espécies têm propriedades ecológicas idênticas. Isso choca com a visão clássica de organização das comunidades por nicho ecológico e até mesmo com a teoria da evolução pela seleção natural. O livro no qual Hubbell apresentou a TNB teve (e ainda tem) grande repercussão na literatura científi ca. Até os dias atuais, essa publicação foi citada por 1.128 artigos, em 239 periódicos científi cos, classifi cados em 21 diferentes categorias de assuntos diferentes. Apesar do impacto em diferentes áreas do conhecimento, Hubbell (2001) foi mais discutido entre ecólogos e biólogos da conservação. As críticas contra a TNB são abundantes, principalmente acerca de seu principal axioma (a equivalência ecológica das espécies). A despeito das críticas, e do fato de que TNB tenha sido refutada em vários estudos, pesquisas recentes corroboram suas predições, apresentando avanços teóricos e novas ferramentas analíticas. Ademais, até mesmo os críticos consideram a TNB uma teoria elegante, facilmente testável e útil para o desenvolvimento teórico na ecologia. Palavras-chave: Modelos Neutros, Metacomunidades, Dispersão, Especiação, Deriva Ecológica.

One of the most popular approaches for investigating the roles of niche and neutral processes driving metacommunity patterns consists of partitioning variation in species data into environmental and spatial components. The logic is that the distance decay of similarity in communities is expected under neutral models. However, because environmental variation is often spatially structured, the decay could also be attributed to environmental factors that are missing from the analysis. Here, we use a spatial autocorrelation analysis protocol, previously developed to detect isolation-by-distance in allele frequencies, to evaluate patterns of species abundances under neutral dynamics. We show that this protocol can be linked with variation partitioning analyses. Moreover, in an attempt to test the neutral model, we derive three predictions to be applied both to original species abundances and to abundances predicted by a pure spatial model species abundances will be uncorrelated; Moran's I correlograms will reveal similar short-distance autocorrelation patterns; an increasing degree of non-neutrality will tend to generate patterns of correlation among abundances within groups of species with similar correlograms (i.e. within species with neutral and non-neutral dynamics). We illustrate our protocol by analyzing spatial patterns in abundance of 28 terrestrially breeding anuran species from Central Amazonia. We recommend that researchers should investigate spatial autocorrelation patterns of abundances predicted by pure spatial models to identify similar patterns of spatial autocorrelation at short distances and lack of correlation between species abundances. Therefore, the hypothesis that spatial patterns in abundances are primarily due to pure neutral dynamics (rather than to missing spatiallystructured environmental factors) can be confirmed after taking environmental variables into account.

Scale is a key to determining which processes drive community structure. We analyse size distributions of phytoplankton to determine time scales at which we can observe either fixed environmental characteristics underlying communities structure or competition-driven size distributions. Using multiple statistical tests, we characterise size distributions of phytoplankton from 20-year time series in two sites of the Baltic Sea. At large temporal scales (5-20 years), size distributions are unimodal, indicating that fundamental barriers to existence are here subtler than in other systems. Frequency distributions of the average size of the species weighted by biovolume are multimodal over large time scales, although this is the product of often unimodal short-term (<1 year) patterns. Our study represents a much-needed structured, high-resolution analysis of phytoplankton size distributions, revealing that short-term analyses are necessary to determine if, and how, competition shapes t...

Differences in the breadth of the pelvis among modern human populations and among extinct hominin species have often been interpreted in the light of thermoregulatory adaptation, whereby a larger pelvic girdle would help preserve body temperature in cold environments while a narrower pelvis would help dissipate heat in tropical climates. There is, however, a theoretical problem in interpreting a pattern of variation as evidence of selection without first accounting for the effects of neutral evolutionary processes (i.e., mutation, genetic drift and migration). Here, we analyse 3D configurations of 27 landmarks on the os coxae of 1494 modern human individuals representing 30 male and 23 female populations from five continents and a range of climatic conditions. We test for the effects of climate on the size and shape of the pelvic bone, while explicitly accounting for population history (i.e., geographically-mediated gene flow and genetic drift). We find that neutral processes account for a substantial proportion of shape variance in the human os coxae in both sexes. Beyond the neutral pattern due to population history, temperature is a significant predictor of shape and size variation in the os coxae, at least in males. The effect of climate on the shape of the pelvic bone, however, is comparatively limited, explaining only a small percentage of shape variation in males and females. In accordance with previous hypotheses, the size of the os coxae tends to increase with decreasing temperature, although the significance of the association is reduced when population history is taken into account. In conclusion, the shape and size of the human os coxae reflect both neutral evolutionary processes and climatically-driven adaptive changes. Neutral processes have a substantial effect on pelvic variation, suggesting such factors will need to be taken into account in future studies of human and fossil hominin coxal variation.

A commonly used null model for species association among forest trees is a well-mixed community (WMC). A WMC represents a non-spatial, or spatially implicit, model, in which species form nearest-neighbor pairs at a rate equal to the product of their community proportions. WMC models assume that the outcome of random dispersal and demographic processes is complete spatial randomness (CSR) in the species’ spatial distributions. Yet, stochastic dispersal processes often lead to spatial autocorrelation (SAC) in tree species densities, giving rise to clustering, segregation, and other nonrandom patterns. Although methods exist to account for SAC in spatially-explicit models, its impact on non-spatial models often remains unaccounted for. To investigate the potential for SAC to bias tests based upon non-spatial models, we developed a spatially-heterogeneous (SH) modelling approach that incorporates measured levels of SAC. Using the mapped locations of individuals in a tropical tree community, we tested the hypothesis that the identity of nearest-neighbors represents a random draw from neighborhood species pools. Correlograms of Moran’s I confirmed that, for 50 of 51 dominant species, stem density was significantly autocorrelated over distances ranging from 50 to 200 m. The observed patterns of SAC were consistent with dispersal limitation, with most species occurring in distinct patches. For nearly all of the 106 species in the community, the frequency of pairwise association was statistically indistinguishable from that projected by the null mod- els. However, model comparisons revealed that non-spatial models more strongly underestimated observed species-pair frequencies, particularly for conspecific pairs. Overall, the CSR models projected more significant facilitative interactions than did SH models, yielding a more liberal test of niche differences. Our results underscore the importance of accounting for stochastic spatial processes in tests of association, regardless of whether spatial or non-spatial models are employed.

Community diversity is expected to reflect variations in local conditions but, recently, ecologists have started to realize that local diversity is also under pressure from global processes. As a result, the traditional view of community structure based on local interspecific interactions was replaced by the idea that community structure is a result of multiple processes acting in different spatial scales. This study is aimed at quantifying the relative importance of spatial, environmental and spatially structured processes on Ephemeroptera community in Cerrado streams in Brazil. Thirty-four rivers and streams in the Brazilian state Mato Grosso were sampled. Ephemeroptera species composition, based on abundance and presence data, was evaluated in relation to niche and neutral predictors by using a partial redundancy analysis (pRDA). Results obtained through the pRDA indicated that both environmental and spatial processes influenced Ephemeroptera abundance. On the other hand, only environmental processes showed effects on community patterns when using species presence data from preserved, altered and large streams and also when looking only at the preserved sites. When streams larger than 20 m were excluded from analysis, both environmental and spatially processes showed influence on Ephemeroptera composition. Adjusted R 2 values were higher for environmental than for spatial processes in all analyses. The relatively high influence of both environmental processes and stream width in the analyses highlights the sensitivity of mayflies assemblies to environmental variation, and emphasizes the importance of local processes, as predicted by niche theory, while neutral processes act to a lesser extent on the structure of the studied communities.

Functional trade-offs have long been recognised as important mechanisms of species coexistence, but direct experimental evidence for such mechanisms is extremely rare. Here, we test the effect of one classical trade-offa negative correlation between seed size and seed numberby establishing microcosm plant communities with positive, negative and no correlation between seed size and seed number and analysing the effect of the seed size/number correlation on species richness. Consistent with theory, a negative correlation between seed size and seed number led to a higher number of species in the communities and a corresponding wider range of seed size (a measure of functional richness) by promoting coexistence of large-and small-seeded species. Our study provides the first direct evidence that a seed size/number trade-off may contribute to species coexistence, and at a wider context, demonstrates the potential role of functional trade-offs in maintaining species diversity.

Los inventarios de biodiversidad en sitios contrastantes obtienen datos con distribuciones normales y lognormales, utiles para cuantificar como el cambio climatico afecta a los bosques del mundo. Sin embargo, casi todos los biologos estan familiarizados con la normal, pero menos discuten el por que la distribucion lognormal de frecuencias relativas de especies ocurre en tantas comunidades bioticas. Pretendemos incorporar a mas estudiosos a dicha discusion. Tanto la normal como la lognormal tienen medias y valores extremos. Ello es consistente con el teorema del limite central; valido cuando los datos de un muestreo provienen de procesos aleatorios y el muestreo ha sido estocastico y representativo. Segun la Teoria Neutral Unificada de la Biodiversidad y la Biogeografia de Steve Hubbell, basta considerar que la natalidad, mortalidad, migraciones y especiacion en una comunidad, y desde la metacomunidad circundante, ocurren al azar y simetricamente entre especies, para explicar que las...

Functional trade-offs have long been recognised as important mechanisms of species coexistence, but direct experimental evidence for such mechanisms is extremely rare. Here, we test the effect of one classical trade-offa negative correlation between seed size and seed numberby establishing microcosm plant communities with positive, negative and no correlation between seed size and seed number and analysing the effect of the seed size/number correlation on species richness. Consistent with theory, a negative correlation between seed size and seed number led to a higher number of species in the communities and a corresponding wider range of seed size (a measure of functional richness) by promoting coexistence of large-and small-seeded species. Our study provides the first direct evidence that a seed size/number trade-off may contribute to species coexistence, and at a wider context, demonstrates the potential role of functional trade-offs in maintaining species diversity.

Neutral community models have shown that limited migration can have a pervasive influence on the taxonomic composition of local communities even when all individuals are assumed of equivalent ecological fitness. Notably, the spatially implicit neutral theory yields a single parameter I for the immigration-drift equilibrium in a local community. In the case of plants, seed dispersal is considered as a defining moment of the immigration process and has attracted empirical and theoretical work. In this paper, we consider a version of the immigration parameter I depending on dispersal limitation from the neighbourhood of a community. Seed dispersal distance is alternatively modelled using a distribution that decreases quickly in the tails (thin-tailed Gaussian kernel) and another that enhances the chance of dispersal events over very long distances (heavily fat-tailed Cauchy kernel). Our analysis highlights two contrasting situations, where I is either mainly sensitive to community size (related to ecological drift) under the heavily fat-tailed kernel or mainly sensitive to dispersal distance under the thin-tailed kernel. We review dispersal distances of rainforest trees from field studies and assess the consistency between published estimates of I based on spatially-implicit models and the predictions of the kernel-based model in tropical forest plots. Most estimates of I were derived from large plots (10-50 ha) and were too large to be accounted for by a Cauchy kernel. Conversely, a fraction of the estimates based on multiple smaller plots (1 ha) appeared too small to be consistent with reported ranges of dispersal distances in tropical forests. Very large estimates may reflect within-plot habitat heterogeneity or estimation problems, while the smallest estimates likely imply other factors inhibiting migration beyond dispersal limitation. Our study underscores the need for interpreting I as an integrative index of migration limitation which, besides the limited seed dispersal, possibly includes habitat filtering or fragmentation.

Neutral models provide an alternative to niche-based assembly rules of ecological communities by assuming that communities' properties are shaped by the stochastic interplay between ecological drift, migration and speciation. The recent and ongoing interest about neutral assumptions has produced many developments on the theoretical side, with nevertheless limited echoes in terms of analyses of real-world data. The present review paper aims to help bridge the widening gap between modellers and field ecologists through two objectives. First, to provide a multi-criteria typology of the main neutral models, including those from population genetics that have not yet been transposed to ecology, by considering how the fundamental processes of ecological drift, speciation and migration are modelled and, specifically, how space is taken into account. Second, to review methods recently proposed to estimate models parameters from field data, a point that should be mastered to allow for broader applications.

Neutral community models have shown that limited migration can have a pervasive influence on the taxonomic composition of local communities even when all individuals are assumed of equivalent ecological fitness. Notably, the spatially implicit neutral theory yields a single parameter I for the immigration-drift equilibrium in a local community. In the case of plants, seed dispersal is considered as a defining moment of the immigration process and has attracted empirical and theoretical work. In this paper, we consider a version of the immigration parameter I depending on dispersal limitation from the neighbourhood of a community. Seed dispersal distance is alternatively modelled using a distribution that decreases quickly in the tails (thin-tailed Gaussian kernel) and another that enhances the chance of dispersal events over very long distances (heavily fat-tailed Cauchy kernel). Our analysis highlights two contrasting situations, where I is either mainly sensitive to community size (related to ecological drift) under the heavily fat-tailed kernel or mainly sensitive to dispersal distance under the thin-tailed kernel. We review dispersal distances of rainforest trees from field studies and assess the consistency between published estimates of I based on spatially-implicit models and the predictions of the kernel-based model in tropical forest plots. Most estimates of I were derived from large plots (10-50 ha) and were too large to be accounted for by a Cauchy kernel. Conversely, a fraction of the estimates based on multiple smaller plots (1 ha) appeared too small to be consistent with reported ranges of dispersal distances in tropical forests. Very large estimates may reflect within-plot habitat heterogeneity or estimation problems, while the smallest estimates likely imply other factors inhibiting migration beyond dispersal limitation. Our study underscores the need for interpreting I as an integrative index of migration limitation which, besides the limited seed dispersal, possibly includes habitat filtering or fragmentation.

This letter discusses the difference between neutral theory as an observation of present evolutionary dynamics compared to neutral theory as a more-or-less comprehensive theory of evolution.  The letter suggests that prior information, not neutral evolution itself, creates the patterns in the genome in ways that make the dynamics described by neutral theory possible in modern organisms.

Periphyton is an aquatic community composed by algae, bacteria, fungi, and other microorganisms that can develop a complex architecture comparable to tropical forests. We analyzed the spatial pattern of a periphyton community along a succession developed in experimental tanks. Our aim was to identify regularities that may help us to explain the patchiness of this community. Therefore, we estimated the spatial pattern of periphyton biomass using a non-destructive image analysis technique to obtain a temporal series of the spatial distribution. These were analyzed using multifractal techniques. Multifractals are analogous to fractals but they look at the geometry of quantities instead of the geometry of pattern. To use these techniques the object of study must show scale invariance and then can be characterized by a spectra of fractal dimensions. Self-organization describes the evolution of complex structures that emerge spontaneously driven internally by variations of the system itself. The spatial distribution of biomass showed scale invariance at all stages of succession and as the periphyton developed in a homogeneous landscape, in a demonstration of self-organized behavior. Self-organization to a critical state (SOC) is presented in the complex systems literature as a general explanation for scale invariance in nature. SOC requires a mechanism where the history of past events in a place influence the actual dynamics, this was termed ecological memory. The scale invariance was found from the very beginning of the succession thus selforganized criticality is a very improbable explanation for the pattern because there would be not enough time for the build-up of ecological memory. Positive interactions between algae and bacteria, and the existence of different spatial scales of colonization and growth are the likely causes of this pattern. Our work is a demonstration of how large scale patterns emerge from local biotic interactions.