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The concept of potential natural vegetation (PNV) refers to self-sustaining mature vegetation matching the environmental conditions a site offers. Despite its widespread use, the applicability of t...

For community ecologists, “neutral or not?” is a fundamental question, and thus, rejecting neutrality is an important first step before investigating the deterministic processes underlying community dynamics. Hubbell's neutral model is an important contribution to the exploration of community dynamics, both technically and philosophically. However, the neutrality tests for this model are limited by a lack of statistical power, partly because the zero‐sum assumption of the model is unrealistic. In this study, we developed a neutrality test for local communities that implements non‐zero‐sum community dynamics and determines the number of new species (N sp) between observations. For the non‐zero‐sum neutrality test, the model distributed the expected N sp, as calculated by extensive simulations, which allowed us to investigate the neutrality of the observed community by comparing the observed N sp with distributions of the expected N sp derived from the simulations. For this comparison, we developed a new “non‐zero‐sum N sp test,” which we validated by running multiple neutral simulations using different parameter settings. We found that the non‐zero‐sum N sp test rejected neutrality at a near‐significance level, which justified the validity of our approach. For an empirical test, the non‐zero‐sum N sp test was applied to real tropical tree communities in Panama and Malaysia. The non‐zero‐sum N sp test rejected neutrality in both communities when the observation interval was long and N sp was large. Hence, the non‐zero‐sum N sp test is an effective way to examine neutrality and has reasonable statistical power to reject the neutral model, especially when the observed N sp is large. This unique and simple approach is statistically powerful, even though it only employs two temporal sequences of community data. Thus, this test can be easily applied to existing datasets. In addition, application of the test will provide significant benefits for detecting changing biodiversity under climate change and anthropogenic disturbance., In this study, we developed a new neutrality test, so‐called “non‐zero‐sum N sp test,” for local communities that implements non‐zero‐sum community dynamics and examines neutrality based on the number of new species between censuses. For an empirical test, we applied the test to real tropical tree communities in Panama and Malaysia, and it rejected neutrality in both communities.

Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely-related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e. nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the data sets we analyzed showed statistically significant phylogenetic overdispersion.

Biddick & Burns (2021) proposed a null/neutral model that reproduces the island rule as a product of random drift. We agree that it is unnecessary to assume adaptive processes driving island dwarfing or gigantism, but several flaws make their approach unrealistic and thus unsuitable as a stochastic model for evolutionary size changes., This paper is a contribution of the INCT in Ecology, Evolution and Biodiversity Conservation founded by CNPq/FAPEG, in the context of the workshop ‘Fast Evolution on Islands’.

The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.

A cultural practice can spread because it is transmitted with high fidelity, but also because biased transformation leads to its reinvention. The respective effect of these two mechanisms, however, may only be quantified if we can measure and detect high-fidelity transmission. This paper proposes wholesale copying, the reproduction of a set of elements as a set, as an operational definition. Using two corpus of heraldic designs (total n=13,453), we apply information-theoretic tools to detect cases of wholesale copying and gauge their incidence. Heraldic designs are composed according to rigorous combinatorial rules. Wholesale copying causes the frequency of a design to increase out of proportion with the frequency of the motif and tinctures that make it up. Comparing the frequency of designs with that of their component motifs and tinctures, we show that the amount of information carried by a design tracks its inheritance along family lines. A model predicting the frequency of heraldic designs based solely on the frequency of their component parts systematically outperforms one that assumes a mix of wholesale copying and random mutation (with realistic mutation rates). These findings are consistent with low but non-null incidences of wholesale copying in the diffusion of heraldic designs.

In an era of global environmental change, understanding how disturbance affects the dynamics of ecological communities is crucial. However, few studies have theoretically explored the potential influence of disturbance including both intensity and frequency on compositional change over time in communities with stage structure. A spatially explicit, individual‐based model was constructed incorporating the various demographic responses to disturbance of plants at two different growth stages: seedlings and adults. In the model, we assumed that individuals within each stage were demographically equivalent (neutral) but differed between stages. We simulated a common phenomenon that seedlings suffered more from disturbance such as grazing and fire than adults. We showed how stage‐structured communities of seedlings and adults responded to disturbance with various levels of disturbance frequency and intensity. In “undisturbed” simulations, the relationship between average species abundance (defined here as the total number of individuals divided by species richness) and community composition turnover (measured by the Bray–Curtis similarity index) was asymptotic. However, in strongly “disturbed” simulations with the between‐disturbance intervals greater than one, this relationship became unimodal. Stage‐dependent response to disturbance underlay the above discrepancy between undisturbed and disturbed communities.

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions.

Evolutionary paleoecologists have proposed many explanations for Phanerozoic trends in ecospace utilization, including escalation, seafood through time, filling of an empty ecospace, and tiering, among others. These hypotheses can be generalized into four models of functional diversification within a life-habit ecospace framework (functional-trait space). The models also incorporate concepts in community assembly, functional diversity, evolutionary diversification, and morphological disparity. The redundancy model produces an ecospace composed of clusters of functionally similar taxa. The partitioning model produces an ecospace that is progressively subdivided by taxa along life-habit gradients. The expansion model produces an ecospace that becomes progressively enlarged by the accumulation of taxa with novel life habits. These models can be caused by a wide range of ecological and evolutionary processes, but they are all caused by particular “driven” mechanisms. A fourth, neutral model also exists, in which ecospace is filled at random by life habits: this model can serve as a passive null model. Each model produces distinct dynamics for functional diversity/disparity statistics when simulated by stochastic simulations of ecospace diversification. In this first of two companion articles, I summarize the theoretical bases of these models, describe their expected statistical dynamics, and discuss their relevance to important paleoecological trends and theories. Although most synoptic interpretations of Phanerozoic ecological history invoke one or more of the driven models, I argue that this conclusion is premature until tests are conducted that provide better statistical support for them over simpler passive models.

Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion. Model simulations incorporating ecological and evolutionary processes uncover five general rules that describe invasions in microbial communities.

AimThe great variation in range sizes among species has fascinated ecologists for decades. In reef-associated fish species, which live in fragmented habitats and adopt a wide range of dispersal strategies, we may expect species with greater dispersal ability to spread over larger ranges. However, empirical evidence for such a positive relationship between dispersal and range size in reef fishes remains scarce. Here, we unveil the more nuanced role of dispersal on the range size distribution of reef associated fishes using empirical data and a novel spatially explicit model.LocationTropical Eastern PacificMajor taxa studiedReef-associated fishesMethodsWe estimated range size distributions for six different guilds of all reef-associated fishes with different dispersal abilities. We used a one-dimensional spatially explicit neutral model, which simulates the distribution of species along a linear coastline to explored the effect of dispersal, speciation and sampling on the distribution of range sizes. Our model adopts a more realistic gradual speciation process (protracted speciation) and incorporates important long distance dispersal events with a fat-tail dispersal kernel. We simulated our model using a highly efficient coalescence approach, which guarantees the metacommunity, is sampled at dynamic equilibrium. We fitted the model to the empirical data using an approximate Bayesian computation approach, with a sequential Monte Carlo algorithm.ResultsStochastic birth, death, speciation and dispersal events alone can accurately explain empirical range size distributions for six different guilds of tropical, reef-associated fishes. Variation in range size distributions among guilds are explained purely by differences in dispersal ability with the best dispersers covering larger ranges.Main conclusionsA simple combination of neutral processes with guild-specific dispersal ability provides a general explanation for both within- and across-guild range size variation. Our results support the theoretically expected, but empirically much debated, hypothesis that dispersal promotes range size.

Despite centuries of interest in species range limits, few studies have taken a whole community into consideration. Actually, multiple species may simultaneously respond to environmental changes, for example, global warming, leading a series of dynamical communities toward the advancing front. We investigated multiple species range expansions through the analysis of a two-species dispersion model and simulations of multiple species assemblages regulated by neutral and fecundity-survival trade-offs (FSTs), respectively, and found that species assemblages regulated by different mechanisms would initiate different expanding patterns in geographic ranges in response to environmental changes. The neutral model generally predicts a higher biodiversity near the core of an expanding range, and a lower community similarity compared with a FST model. Without considering the evolution of life history traits, an assortment of the reproduction ability happens at the advancing front under FSTs at the expense of a higher death rate or lower competitive ability. These results emphasize the importance of community assembly rules to the biodiversity maintenance of range expanding communities.

The neutral model of cultural evolution, which assumes that copying is unbiased, provides precise predictions regarding frequency distributions of traits and the turnover within a popularity-ranked list. Here we study turnover in ranked lists and identify where the turnover departs from neutral model predictions to detect transmission biases in three different domains: color terms usage in English language 20th century books, popularity of early (1880–1930) and recent (1960–2010) USA baby names, and musical preferences of users of the Web site Last.fm. To help characterize the type of transmission bias, we modify the neutral model to include a content-based bias and two context-based biases (conformity and anti-conformity). How these modified models match real data helps us to infer, from population scale observations, when cultural transmission is biased, and, to some extent, what kind of biases are operating at individual level.

While habitat transformation driven by human activities is the main driver of current biodiversity changes, there is still no framework to explore and forecast the effects of different types of habitat changes on the richness and composition of biological communities. To tackle this issue, we modeled the dynamics of a regional meta-community, composed either of ecologically equivalent species (neutral model) or of generalist and specialist species (specialization model), and explored the impact of the overall reduction, patch conversion or alteration of an original habitat into one or several other habitats of different total carrying capacity on the community metrics at equilibrium. Our simulations reveal strong interactions between the community model considered (neutral or specialization model) and the type of habitat change. Under neutrality, the impact of habitat changes on richness can be approached by a power law species–individual relationship (SIR), which may at constant density be simplified into the widely used power law species–area relationship (SAR), independent of the type of change. However, in the presence of generalist and specialist species, we found that 1) while habitat reduction in area also leads to approximately power law SIRs and SARs, 2) patch conversion and alteration have more complex effects on regional species richness, and 3) habitat alteration elicits the functional homogenization of communities, involving a decrease of their average level of specialization.

A recent model by Currat et al. indicates that when one species colonizes an area already occupied by a closely related species, massive introgression of neutral genes should take place primarily in the direction from the local to the invasive species. Here, I show that this model relies on an assumption that might not capture the true dynamics of how species exchange migrants during admixture. As an alternative, I formulate a new model, based on a different and perhaps more biologically realistic assumption of interbreeding, that demonstrates symmetric introgression as compared to the large and asymmetric introgression predicted by the original model. The new model indicates that asymmetry is not a default property of introgressions, thus necessitating alternative explanations for the common observation of massive asymmetric introgression including sex-biased dispersal.

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species-environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species-environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species-environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species-environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species-environment feedback on community assembly.

Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape ‘terrageny’, which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscapes.

We carried out a simulation study to compare the efficiency of three alternative programs (DFDIST, DETSELD and BAYESCAN) to detect loci under directional selection from genome-wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide range of scenarios, we conclude that BAYESCAN appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.

Heathlands are man-made habitats and their decline during the last century can be contributed to shifts in both agricultural and management practices as well as to hydrological and atmospheric changes. As a result, many heathland sites, including the Kalmthoutse Heide in Belgium, were included in the European Natura 2000 program, a network of protected areas across the European Union. To assure an accurate mapping of the Kalmthoutse Heide and other Natura 2000 sites in Belgium a classification framework for habitat status reporting with remote sensing data and in particular high resolution hyperspectral imagery was started. In this study we propose a simple and fast context based method for mapping heathland heterogeneity using the intermediate, otherwise redundant, classification probabilities as generated by a hard classification algorithm. Our study proved to be successful in using intermediate classification probabilities as a valuable source of ecological information. The delineated areas have been shown to be statistically sound and robust compared to a neutral model. The technique is not limited to a particular hard classification technique and can easily be adopted into current vegetation monitoring efforts. The resulting maps provided accessible maps which can support management of the protected site and enhance the accuracy of EU reportage as required by the habitat directive.

We simulate species-area curves (SACs) using a spatially explicit neutral model. These display three distinct phases with the central phase being well approximated by a "power law" where species richness (S) is related to area (A) by S = cA(z). If seeds are normally distributed in space about their parent, the power law phase of the SAC is unrealistically narrow, and implausibly large speciation rates are required to fit empirical data. However, if dispersal follows a more realistic "fat-tailed" distribution (where long-distance dispersal events are more likely) the SACs fit the empirical data better, have a power law that holds for a much broader range of areas, and require a dramatically smaller speciation rate than when dispersal is normally distributed. Neutral models with biologically plausible dispersal parameters and speciation rates lead to empirically realistic SACs.

Comparative data in invasion ecology show that (i) disturbance enhances community invasibility, (ii) there is a positive relationship between residence time of an invader and its success, (iii) there are broadly constant proportions of newly arrived species to those that become established and dominant (“tens rule”), and (iv) invasive species have higher growth rates in comparison with non-invasive species. I use a simple neutral model to test whether these patterns occur in communities with all species identical and no species-specific interactions. In the model, local communities are grouped into continents with immigration rates smaller between than within the continents. Species coming from the other continent are considered to be alien and their fates are recorded. In the model, disturbance predictably increases species numbers and numbers of individuals of aliens. However, the model makes different predictions on effects of disturbance on three processes involved in alien species spreading: establishment (positive effect of disturbance), naturalization (negative effect) and dominance (positive effect). The predictions do not change if variation of growth rates is incorporated into the model. The model also predicts positive relationship between residence time and abundance. Total community size had little effect on success of alien species. The broad agreement of the predictions of the neutral model with the patterns from the field suggests that some of these general patterns of community invasibility are to some degree fully independent of any specific biological assumptions and by themselves may not provide many insights on underlying biological processes. Aggregate data should therefore be used with great caution and statistical patterns must be removed by means of generating null model predictions.

Evolutionary changes in gene expression account for most phenotypic differences between species. Advances in microarray technology have made the systematic study of gene expression evolution possible. In this study, gene expression patterns were compared between human and mouse genomes using two published methods. Specifically, we studied how gene expression evolution was related to GO terms and tried to decode the relationship between promoter evolution and gene expression evolution. The results showed that (1) the significant enrichment of biological processes in orthologs of expression conservation reveals functional significance of gene expression conservation. The more conserved gene expression in some biological processes than is expected in a purely neutral model reveals negative selection on gene expression. However, fast evolving genes mainly support the neutrality of gene expression evolution, and (2) gene expression conservation is positively but only slightly correlated with promoter conservation based on a motif-count score of the promoter alignment. Our results suggest a neutral model with negative selection for gene expression evolution between humans and mice, and promoter evolution could have some effects on gene expression evolution.

Although only a few studies have explicitly evaluated live-dead agreement of species and community responses to environmental and spatial gradients, paleoecological analyses implicitly assume that death assemblages capture these gradients accurately. We use nine data sets from modern, relatively undisturbed coastal study areas to evaluate how the response of living molluscan assemblages to environmental gradients (water depth and seafloor type; “environmental component” of a gradient) and geographic separation (“spatial component”) is captured by their death assemblages. We find that:1. Living assemblages vary in composition either in response to environmental gradients alone (consistent with a species-sorting model) or in response to a combination of environmental and spatial gradients (mass-effect model). None of the living assemblages support the neutral model (or the patch-dynamic model), in which variation in species abundance is related to the spatial configuration of stations alone. These findings also support assumptions that mollusk species consistently differ in responses to environmental gradients, and suggest that in the absence of postmortem bias, environmental gradients might be accurately captured by variation in species composition among death assemblages. Death assemblages do in fact respond uniquely to environmental gradients, and show a stronger response when abundances are square-root transformed to downplay the impact of numerically abundant species and increase the effect of rare species.2. Species' niche positions (position of maximum abundance) along bathymetric and sedimentary gradients in death assemblages show significantly positive rank correlations to species positions in living assemblages in seven of nine data sets (both square-root-transformed and presence-absence data).3. The proportion of compositional variation explained by environmental gradients in death assemblages is similar to that of counterpart living assemblages. Death assemblages thus show the same ability to capture environmental gradients as do living assemblages. In some instances compositional dissimilarities in death assemblages show higher rank correlation with spatial distances than with environmental gradients, but spatial structure in community composition is mainly driven by spatially structured environmental gradients.4. Death assemblages correctly identify the dominance of niche metacommunity models in mollusk communities, as revealed by counterpart living assemblages. This analysis of the environmental resolution of death assemblages thus supports fine-scale niche and paleoenvironmental analyses using molluscan fossil records. In spite of taphonomic processes and time-averaging effects that modify community composition, death assemblages largely capture the response of living communities to environmental gradients, partly because of redundancy in community structure that is inherently associated with multispecies assemblages. The molluscan data sets show some degree of redundancy as evidenced by the presence of at least two mutually exclusive subsets of species that replicate the community structure, and simple simulations show that between-sample relationships can be preserved and remain significant even when a large proportion of species is randomly removed from data sets.

We use recently developed technical methods to study species-area relationships from a spatially explicit extension of Hubbell's neutral model on an infinite landscape. Our model includes variable dispersal distances and exhibits qualitatively different behaviour from the cases of nearest-neighbour dispersal and finite periodic landscapes that have previously been studied. We show that different dispersal distances and even different dispersal kernels produce identical species-area curves up to rescaling of the two axes. This scaling property provides a straightforward method for fitting the model to empirical data. The species-area curves display all three phases observed empirically and enable the exponent describing the power law relationship for species-area curves to be identified as the gradient at the central phase. This exponent can take all values between 0 and 1 and is given by a simple function of the speciation rate, independent of all other model variables.

As the utility of the neutral theory of biodiversity is increasingly being recognized, there is also an increasing need for proper tools to evaluate the relative importance of neutral processes (dispersal limitation and stochasticity). One of the key features of neutral theory is its close link to data: sampling formulas, giving the probability of a data set conditional on a set of model parameters, have been developed for parameter estimation and model comparison. However, only single local samples can be handled with the currently available sampling formulas, whereas data are often available for many small spatially separated plots. Here, I present a sampling formula for multiple, spatially separated samples from the same metacommunity, which is a generalization of earlier sampling formulas. I also provide an algorithm to generate data sets with the model and I introduce a general test of neutrality that does not require an alternative model; this test compares the probability of the observed data (calculated using the new sampling formula) with the probability of model-generated data sets. I illustrate this with tree abundance data from three large Panamanian neotropical forest plots. When the test is performed with model parameters estimated from the three plots, the model cannot be rejected; however, when parameter estimates previously reported for BCI are used, the model is strongly rejected. This suggests that neutrality cannot explain the structure of the three Panamanian tree communities on the local (BCI) and regional (Panama Canal Zone) scale simultaneously. One should be aware, however, that aspects of the model other than neutrality may be responsible for its failure. I argue that the spatially implicit character of the model is a potential candidate.

Many statistical tests have been developed for detecting positive selection. Most of these tests draw conclusions based on significant deviations from the patterns of polymorphism predicted by the neutral model. However, many non-equilibrium forces may cause similar deviations, and thus the tests usually have low statistical specificity to positive selection. The main challenge is hence to construct test statistics that are reasonably powerful in detecting positive selection, but are relatively insensitive to other forces. Recently, Zeng et al. (2006) proposed a new test, DH, which is a compound of Tajima's D and Fay and Wu's H, and showed that DH has reasonably high statistical specificity to positive selection. In this report, we expand the idea of a compound test by combining Fay and Wu's H or DH with the Ewens-Watterson (EW) test. We refer to these 2 new tests as HEW and DHEW, respectively. Compared to the DH test, HEW and DHEW are more robust against the presence of recombination, and are also more powerful in detecting positive selection. Furthermore, the DHEW test, similar to DH, is also relatively insensitive to background selection and demography. The HEW test, on the other hand, tends to be somewhat less conservative than DH and DHEW in some cases.

Summary 1 Both spatial and temporal processes are assumed to play an important role in driving seedling dynamics. We assessed the magnitude of these two processes in a neotropical forest in French Guiana. We first quantified temporal changes in seedling community structure, then evaluated the relative importance of environmental heterogeneity and temporal fluctuations in seed arrival in determining seedling dynamics. 2 We monitored the seedling dynamics of 6244 seedlings by censusing 370 1-m 2 seedling plots in 160 stations over 20 months. At each station, we quantified environmental variability (light availability, soil resources, litter depth, topography), and measured temporal fluctuations in seed input by sampling seed arrival into seed traps located in each station. 3 Temporal changes in seedling density and diversity between four consecutive censuses were compared with those predicted by a neutral model assuming random recruitment and mortality. Seedling density fluctuations were considerably more variable over time than expected under the neutral assumption. Diversity changes showed less consistent results. For the two first census intervals, seedling diversity was more constant than under the neutral expectations. For the last census interval, seedling diversity was more variable than expected under neutrality. 4 Seedling recruitment, mortality and diversity of recruits were modelled against environmental variables and seed arrival. Sites with higher light availability and soil fertility had more diverse recruits ( P < 0.01) but lower seedling survival ( P < 0.05). Both density and diversity of local seed arrival had a positive effect, respectively, on density and diversity of recruited seedlings ( P < 0.05). 5 Our results show that temporal pulses in seedling community are mainly driven by large temporal fluctuations in seedling recruitment. Annual variation in seedfall and environmental filtering both contribute to explaining spatio-temporal variation in seedling dynamics to a large degree. Irrespective of species identity, tropical seedling communities are both seed- and establishment-limited. The temporal component of seed-limitation appears to be of critical relevance in the structuring of tropical seedling communities.

Hubbell's (2001) neutral model describes how local communities are structured if population dynamics are statistically identical among species in a constant, possibly patchy, environment with random speciation. Tests of this model have been restricted largely to terrestrial communities. Here we tested the fit of this neutral model to fish, zooplankton and phytoplankton species-abundance distributions from 30 well-studied lake communities varying widely in lake size and productivity. We measured the fit of the communities to the neutral model in three ways. All but two zooplankton (7 of 9) and all but three fish (9 of 12) communities were consistent with all three measures of fit. However, all nine phytoplankton communities did not fit the neutral model by at least one measure. This result for phytoplankton communities represents to date the most consistent failure of the standard neutral model to predict the shape of species-abundance distributions.

A widespread but controversial idea in ecology states that the number of invaders of a species assemblage depends on its species richness. Both negative and positive relationships have been reported. We examined whether a simple neutral model where assemblages are generated by drawing individuals from two pools of identical species (native and alien) can predict this relationship. We performed a meta-analysis of published data on this relationship. The neutral model showed that in communities with low and fixed numbers of indi- viduals, the relationship between the number of aliens and native species is strong and negative. This becomes weaker as the proportion of species from both pools already present in the community increases. The relationship between alien and native species richness becomes positive when the number of individuals is allowed to vary, because the richness depends on number of individuals and/or area sampled. The meta-analysis showed that scale-dependence of the relationship between alien and native species richness is universal and compatible with the neutral model. Unless more evidence is available to refute it, the relationship between native and alien species richness should be considered a result of a neutral processes due to constraints on the number of individuals in the community.

This paper reviews how statistical tests of neutrality have been used to address questions in molecular ecology are reviewed. The work consists of four major parts: a brief review of the current status of the neutral theory; a review of several particularly interesting examples of how statistical tests of neutrality have led to insight into ecological problems; a brief discussion of the pitfalls of assuming a strictly neutral model if it is false; and a discussion of some of the opportunities and problems that molecular ecologists face when using neutrality tests to study natural selection.

We explore how cultural heterogeneity evolves without strong selection pressure or environmental differences between groups. Using a neutral transmission model with an isolation-by-distance spatiality, we test the effect of a simple representation of cultural ‘memory’ on the dynamics of heterogeneity. We find that memory magnifies the effect of affinity while decreasing the effect of individual learning on cultural heterogeneity. This indicates that, while the cost of individual learning governs the frequency of individual learning, memory is important in governing its effect.

Host—parasite interactions often have complex dynamics. At the level of individual allele frequencies, the dynamics are difficult to predict and difficult to measure. However, aggregate properties of polymorphism, such as allelic diversity or the frequency of resistance, may be relatively easy to work with. I study this problem with computer simulations of a host—parasite model. In one example, the simulations show that the allelic diversity at a locus is similar in a host—parasite model and a neutral model in which drift is the only evolutionary process. Allelic diversity is similar in the two models, even though the temporal dynamics of individual allele frequencies are very different. In a second example, the genetic system that would be inferred from analysing samples of hosts and parasites is quite different from the actual specificity that determines the dynamics of the system. Thus, general conclusions about the specificity of host—parasite genetics must be analysed in the context of the expected statistical distributions of polymorphism. The final example shows that the frequency of resistance provides an interesting aggregate measure of host—parasite polymorphism. If the ratio of parasite generation time to the time between the reproductive seasons of the hosts is small, then no regular periodicity in the frequency of resistance occurs. However, if parasites have many generations per reproductive season of the host, then resistance fluctuates with a period equal to the seasonality of the host. The important role of seasonality shown here differs from the emphasis in previous theories on the relative generation times of host and parasite.

Expressions are obtained for the expected levels of linkage disequilibrium under three different equilibrium neutral models that make different assumptions about how recombination takes place. A transformation model is considered in which exchange events involve only one locus at a time. Two conjugation models are considered one with a linear genome and one with a circular genome. In the conjugation models large blocks of genes can be transferred with each conjugation. Consistent with published simulation results, it is found that if the transformation rate per locus is more than twenty times the mutation rate per locus, then the levels of linkage disequilibrium are quite low. If the number of loci being sampled is greater than 10, conjugation with a circular genome can be considerably more effective than transformation in reducing linkage disequilibrium. When recombination rates are high, expected linkage disequilibrium is shown to be proportional to the inverse of the transformation rate (or conjugation rate.)

A higher ratio of substitutional to synonymous changes in between-species than in within-species comparisons has been taken as evidence for positive selection changing amino acids. A model is presented in which a difference of this kind arises as a result of purely neutral mutations, provided that the “species” compared are sufficiently different to approach a steady state between forward and backward mutation. In Neissseria, substitutions are twice as frequent, relative to synonymous changes, in between-species comparisons: it is shown that the data are consistent with the neutral model. The argument does not invalidate evidence for positive selection, for example in Drosophila, when the species compared are fairly similar.

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.

A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale., Author Summary Plant growth is a very complex character impacted by almost any aspect of plant biology and showing continuous variation among natural populations of a single species like Arabidopsis thaliana. Although difficult, it is important to reveal the precise genetic architecture of such a trait's variation to improve our understanding of the mechanisms and evolutionary significance of phenotypic variation. By using recombinant inbred lines derived from a cross between the reference strain ‘Col-0’ and the Irish strain ‘Bur-0’, we have localized several regions of the genome impacting plant growth. When attempting to confirm one of this region's effect, we revealed an even more complex genetic architecture where a first locus (which had remained undetected initially) has a major effect on growth only when a specific genotype was present at a second locus. We have shown here that the reason for this epistatic interaction between the two loci is that the functional allele for a gene important for photosynthesis efficiency and, consequently, growth, had been transposed from one locus to the other in Bur-0 compared to Col-0. This type of structural polymorphism seems to be frequent among strains and, although more difficult to detect, is likely to be of significant evolutionary importance.

Fragmented landscapes alter ecological interactions by modifying the flux of organisms, material, and energy. Fragmented distributions of hypothetical resources and species were represented by several fractal models of landscape patterns at scales ranging from 90 to 2,400 m. Maps of resource aggregations at three scales resulted in multiple-scale notions of "patch," "gap," "edge," "corridor," "source," and "sink." A neutral model of species co-occurrence was developed for analyses conducted at several scales. The neutral model has implications for sampling mutualistic species and for detecting species' responses to changes in environmental conditions. An ecologically meaningful view of landscape pattern depends on the home range size, dispersal ability, or speed with which organisms use resources rather than on the cartographic depiction of the landscape used by humans.

In six different environments of the Towada-Hachimantai National Park, the forest floor coleopterons were sampled by means of pitfall traps with five different baits. Their niche breadths and niche overlaps were assessed for the electivity of habitat, bait, and habitat × bait, and compared with those expected from neutral models constructed randomly. The niche breadths in the observed assemblages were smaller than those expected from the neutral model, while the niche overlaps were more widely distributed than those expected from the neutral model. Mean overlaps between species neighbors in niche space, cluster analyses, and ordinations of species revealed a guild for habitat, bait and habitat × bait. Lawlor’s (1979) gamma matrices concerning the habitat electivity show that the rates of mutualism resulted from indirect interspecific competitions are significantly smaller in the guild than in the whole assemblage. This suggests that the interspecific competition among the guild members is mitigated or even converted into mutualism by joining of the species which do not belong to the guild. The rates of mutualism were also significantly larger in the resource state of two dimensions (habitat × bait) than in that of either one. Therefore, if niche overlaps are measured on the basis of resource state of multi-dimensions, the rates of mutualism may increase further.

Diversity (or biodiversity) is typically measured by a species count (richness) and sometimes with an evenness index; it may also be measured by a proportional statistic that combines both measures (e.g., Shannon-Weiner index or H'). These diversity measures are hypothesized to be positively and strongly correlated, but this null hypothesis has not been tested empirically. We used the results of Caswell's neutral model to generate null relationships between richness (S), evenness (J'), and proportional diversity (H'). We tested predictions of the null model against empirical relationships describing data in a literature survey and in four individual studies conducted across various scales. Empirical relationships between log S or J' and H' differed from the null model when10 species were tested and in plants, vertebrates, and fungi. The empirical relationships were similar to the null model when10 and100 species were tested and in invertebrates. If100 species were used to estimate diversity, the relation between log S and H' was negative. The strongest predictive models included log S and J'. A path analysis indicated that log S and J' were always negatively related, that empirical observations could not be explained without including indirect effects, and that differences between the partials may indicate ecological effects, which suggests that S and J' act like diversity components or that diversity should be measured using a compound statistic.

International audience; Despite hundreds of reports involving both plants and animals, the mechanisms underlying introgression remain obscure, even if some form of selection is frequently invoked. Introgression has repeatedly been reported in species that have recently colonized a new habitat, suggesting that demographic processes should be given more attention for understanding the mechanisms of introgression. Here we show by spatially explicit simulations that massive introgression of neutral genes takes place during the invasion of an occupied territory if interbreeding is not severely prevented between the invading and the local species. We also demonstrate that introgression occurs almost exclusively from the local to the invading species, especially for populations located far away from the source of the invasion, and this irrespective of the relative densities of the two species. This pattern is strongest at markers experiencing reduced gene flow, in keeping with the observation that organelle genes are often preferentially introgressed across species boundaries. A survey of the literature shows that a majority of published empirical studies of introgression during range expansions, in animals and in plants, follow the predictions of our model. Our results imply that speciation genes can be identified by comparing genomes of interfertile native and invading species pairs.

Neutral community models embody the idea that individuals are ecologically equivalent, having equal fitness over all environmental conditions, and describe how the spatial dynamics and speciation of such individuals can produce a wide range of patterns of distribution, diversity, and abundance. Neutral models have been controversial, provoking a rush of tests and comments. The debate has been spurred by the suggestion that we should test mechanisms. However, the mechanisms and the spatial scales of interest have never clearly been described, and consequently, the tests have often been only peripherally relevant. At least two mechanisms are present in spatially structured neutral models. Dispersal limitation causes clumping of a species, which increases the strength of intraspecific competition and reduces the strength of interspecific competition. This may prolong coexistence and enhance local and regional diversity. Speciation is present in some neutral models and gives a donor-controlled input of new species, many of which remain rare or are short lived, but which directly add to species diversity. Spatial scale is an important consideration in neutral models. Ecological equivalence and equal fitness have implicit spatial scales because dispersal limitation and its emergent effects operate at population levels, and populations and communities are defined at a chosen spatial scale in recent neutral models; equality is measured relative to a metacommunity, and this necessitates defining the spatial scale of that metacommunity. Furthermore, dispersal has its own scales. Thorough empirical tests of neutral models will require both tests of mechanisms and pattern-producing ability, and will involve coupling theoretical models and experiments.

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists–how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, as suming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j–th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant- rate speciation model, or the coalescent model.

Productivity and disturbance are major determinants of species diversity, and results from theoretical models predict that species richness should peak at intermediate levels of both factors. Such “unimodal” responses have been documented in many field and laboratory studies and have usually been attributed to differences among species in competitive ability and/or trade‐offs between competitive ability and tolerance to disturbance. Here we show that most documented patterns of disturbance‐richness and productivity‐richness relationships, as well as the observed interactions between the two factors, can be explained by a simple neutral model where all species are ecologically identical and lack trade‐offs in species characteristics. This finding suggests that current neutral theories can be extended to explain patterns of species responses to productivity and disturbance.

A critical but poorly understood pattern in macroecology is the often unimodal species - body size distribution ( also known as body size - diversity relationship) in a local community ( embedded in a much larger regional species pool). Purely neutral community models that assume functional equivalence among species are incapable of explaining this pattern because body size is the key determinant of functional differences between species. Several niche-based explanations have been offered, but none of them is completely satisfactory. Here we develop a simple model that unites a neutral community model with niche-based theory to explain the relationship. In the model, species of similar size are assumed to belong to the same size guild. Within a size guild, all individuals are equivalent in their competition for resources, sensu Hubbell's neutral community model; they have the same speciation rate and dispersal capacities. Between size guilds, however, the total number of individuals, the speciation rate, and the dispersal capacities differ, but using known allometric scaling laws for these properties, we can describe the differences between size guilds. Our model predicts that species richness reaches an optimum at an intermediate body size, in agreement with observations. The optimum at intermediate body size is basically the result of a trade-off between, on the one hand, allometric scaling laws for the number of individuals and the speciation rate that decrease with body size and, on the other hand, the scaling law for active dispersal that increases with body size.

The most simple neutral model of molecular evolution predicts that the number of substitutions within a lineage in T generations ought to be Poisson distributed. Therefore, the variance in the number of substitutions ought to equal the mean number. The ratio of the variance to the mean number of substitutions is called the index of dispersion, R(T). Assuming infinite sites, no recombination model of the gene, and a haploid, Moran population structure, R(T) is derived for a general stationary model of molecular evolution. R(T) is shown to be affected by fluctuations in parameters only when they occur on a very slow time scale. In order for parameter fluctuations to cause R(T) to deviate significantly from one, the time between parameter changes must be roughly as large, or larger, than the time between substitutions.

The patterns of abundance generated by a simple stochastic birth-death-immigration model are described in order to characterize the diversity of neutral communities of ecologically equivalent species. Diversity is described by species number S and the variance of frequency or log abundance q∼. The frequency distribution of abundance is very generally lognormal, skewed to the left by immigration and resembling descriptions of natural communities. Increased immigration and community size always cause S to increase. Their effect on q∼ is more complicated, but given biologically reasonable assumptions, S and q∼ will be positively correlated in most circumstances. Larger samples contain more species; the graph of log S on log individuals, equivalent to a species-area curve, is generally convex upward but becomes linear with a slope of about +0.25 when immigration is low and births exceed deaths. When individuals invade a new, vacant environment, both S and q∼ increase through time. Thus, a positive correlation between S and q∼ will usually be generated when sites of differing size or age are surveyed. At equilibrium, communities maintain roughly constant levels of S and q∼ but change in composition through time; composition may remain similar, however, for many generations. Many prominent patterns observed in natural communities can therefore be generated by a strictly neutral model. This does not show that community structure is determined exclusively by demographic stochasticity, but rather demonstrates the necessity for an appropriate null model when functional hypotheses are being tested.

Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, however, to distinguish selection that acted in the distant past from ongoing selection. However, under a neutral model, polymorphisms usually reflect more recent mutations than fixed differences between species and may, therefore, be useful for inferring recent selection. If the ancestral state is preferred, selection should shift the frequency distribution of derived states/site toward lower values; if the ancestral is unpreferred, selection should increase the number of derived states/site. Polymorphisms were classified as ancestrally preferred or unpreferred for several genes of D. simulans and D. melanogaster. A computer simulation of coalescence was employed to derive the expected frequency distributions of derived states/site under various modifications of the Wright–Fisher neutral model, and distributions of test statistics (t and Mann–Whitney U) were derived by appropriate sampling. One-tailed tests were applied to transformed frequency data to assess whether the two frequency distributions deviated from neutral expectations in the direction predicted by selection on codon usage. Several genes from D. simulans appear to be subject to recent selection on synonymous codons, including one gene with low codon bias, esterase-6. Selection may also be acting in D. melanogaster.

The 2002 Annual Symposium of the British Ecological Society on Macroecology: reconciling divergent perspectives on large-scale ecological patterns was held at the University of Birmingham, UK from 17 to 19 April 2002.