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Ecological trade-offs between species are often invoked to explain species coexistence in ecological communities. However, few mathematical models have been proposed for which coexistence conditions can be characterized explicitly in terms of a trade-off. Here we present a model of a plant community which allows such a characterization. In the model plant species compete for sites where each site has a fixed stress condition. Species differ both in stress tolerance and competitive ability. Stress tolerance is quantified as the fraction of sites with stress conditions low enough to allow establishment. Competitive ability is quantified as the propensity to win the competition for empty sites. We derive the deterministic, discrete-time dynamical system for the species abundances. We prove the conditions under which plant species can coexist in a stable equilibrium. We show that the coexistence conditions can be characterized graphically, clearly illustrating the trade-off between stress tolerance and competitive ability. We compare our model with a recently proposed, continuous-time dynamical system for a tolerance-fecundity trade-off in plant communities, and we show that this model is a special case of the continuous-time version of our model., Comment: To be published in Journal of Mathematical Biology. 30 pages, 5 figures, 5 appendices

Gorgona Island, the major insular area in the Colombian Pacific Ocean, is characterized by a remarkably high biological and ecosystem diversity for this area of the world. Coral reefs are well developed and their fish communities have been described using conventional visual surveys. These methods, however, are known to be biased towards detecting larger and more mobile species, tending to ignore small and cryptobenthic species. The two main objectives of this study were to describe the assemblage structure of the cryptobenthic fish fauna and estimate the extent to which this fauna is underestimated by visual surveys.At the beginning and the end of the warm season, we compared the cryptobenthic fish assemblage recorded using visual surveys against the one recorded using “enclosed anesthetic/rotenone samples” on isolated coral colonies (N=54 beginning of warm season; N=17 end of warm season). The crypthobenthic fish fauna associated to coral colonies was characterized by small body sizes and was composed mainly by species of the families Antennaridae, Blennidae, Gobiidae, Labrisomidae, Muraenidae, Serranidae, Scorpaenidae and Syngnathidae. Conventional visual surveys underestimated overall species richness by 28-36% and number of individuals by 16-35%. Noteworthy, four species recorded during this study using “enclosed anesthetic/rotenone samples” were new records for Gorgona Island. Although both sampling methods can detect a largely overlapping group of species, the “enclosed anesthetic/rotenone samples” method was able to detect more individuals and species, including several species that visual surveys fail to detect. Although this study is the first effort to describe the cryptobenthic fish assemblage associated to coral reefs in the Tropical Eastern Pacific, our results suggest that these assemblages are an important component of the reef fish community in the region in terms of biodiversity and functional roles. Rev. Biol. Trop. 62 (Suppl. 1): 359-371. Epub 2014 February 01. Métodos de muestreo convencionales (censos visuales) usados en el estudio de peces arrecifales han llevado a una constante subestimación de la riqueza de especies, ya que estos tienden a ignorar especies pequeñas y crípticas. En este estudio describimos la estructura del ensamblaje de peces criptobentónicos en Isla Gorgona, Colombia y estimamos el grado en que este ensamblaje es subestimado al usar censos visuales. Al comienzo y al final de la estación cálida comparamos la capacidad de detección de censos visuales vs “muestreos cerrados con anestésico/rotenona” (N=54 comienzo; N=17 final). La fauna criptobentónica se caracterizó por mantener individuos de tamaños corporales pequeños, pertenecientes principalmente a las familias Antennaridae, Blennidae, Gobiidae, Labrisomidae, Muraenidae, Serranidae, Scorpaenidae and Syngnathidae. Los censos visuales subestimaron la riqueza de especies en un 28-36% y el número de individuos en un 16-35%. Aunque un gran número de especies son detectadas usando ambos métodos, los “muestreos cerrados con anestésico/rotenona” detectan un mayor rango de especies. Este estudio, el primer esfuerzo para describir el ensamblaje de peces criptobentónicos asociados a arrecifes coralinos en Colombia, sugiere que la fauna criptobentónica puede ser un componente importante de la comunidad arrecifal en términos de biodiversidad y papel funcional.

International audience; Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.

International audience; The roles of species richness, resource use, and resource availability are central to many hypotheses explaining the diversityinvasion phenomenon but are generally not investigated together. Here, we created a large diversity gradient of soil microbial communities by either assembling communities of pure bacterial strains or removing the diversity of a natural soil. Using data on the resource-use capacities of the soil communities and an invader that were gathered from 71 carbon sources, we quantified the niches available to both constituents by using the metrics community niche and remaining niche available to the invader. A strong positive relationship between species richness and community niche across both experiments indicated the presence of resource complementarity. Moreover, community niche and the remaining niche available to the invader predicted invader abundance well. This suggested that increased competition in communities of higher diversity limits community invasibility and underscored the importance of resource availability as a key mechanism through which diversity hinders invasions. As a proof of principle, we subjected selected invaded communities to a resource pulse, which progressively uncoupled the link between soil microbial diversity and invasion and allowed the invader to rebound after nearly being eliminated in some communities. Our results thus show that (1) resource competition suppresses invasion, (2) biodiversity increases resource competition and decreases invasion through niche preemption, and (3) resource pulses that cannot be fully used, even by diverse communities, are favorable to invasion.

Plant-pollinator interactions are among the best known and ubiquitous plant-animal mutualisms and are crucial for ecosystem functioning and the maintenance of biodiversity. Most pollinators are insects with several life-stages (e.g. egg, larva, pupa, adult) and the mutualistic interaction depends on the pollinator surviving these different life-stages. However, to our knowledge, pollinator population structure has been ignored in most theoretical models of plant-pollinator dynamics, and we lack understanding of the role of different life-stages in determining the stability of the mutualism. Here we therefore develop a simple plant-pollinator model with a facultative plant and an obligate pollinator with stage-structure. Our model predicts a globally stable equilibrium when pollinator demography is dominated by adults and a locally stable equilibrium when the plants are strongly dependent on pollination and pollinator demography is dominated by the larval stage. In the latter case, the mutualism is vulnerable to fluctuations in the pollinator population size or structure caused by external factors (e.g. pesticides) reducing larval development and increasing adult mortality. This may cause a sudden collapse rather than gradual decrease of the mutualism, after which the pollination service cannot be recovered by reducing these detrimental external factors, but must be accompanied by large increases in pollinator populations. This highlights the importance of considering population structure in plant-pollinator interactions. (C) 2014 Elsevier Ltd. All rights reserved.

International audience; Animal seed dispersal provides an important ecosystem service by strongly benefiting plant communities. There are several theoretical studies on the ecology of plant-animal seed-disperser interactions, but few studies have explored the evolution of this mutualism. Moreover, these studies ignore plant life history and frugivore foraging behaviour. Thus, it remains an open question what the conditions for the diversification of fruit traits are, in spite of the multitude of empirical studies on fruit trait diversity. Here, we study the evolution of fruit traits using a spatially explicit individual-based model, which considers the costs associated with adaptations inducing dispersal by frugivory, as well as frugivore foraging behaviour and abundance. Our model predicts that these costs are the main determinants of the evolution of fruit traits and that when the costs are not very high, the evolution of larger fruit traits (e.g. fleshy/colourful fruits) is controlled by the choosiness and response thresholds of the frugivores as well as their numerical abundance.Keywords: endozoochory; frugivory; fruit evolution; fruit traits; mutualism; seed dispersal.

Recently, Warren [1] argued that correlative modelling of species distribution and environmental data should be described as Ecological Niche Modelling (ENM) rather than Species Distribution Modelling (SDM). Although discussions of terminology could be posed as semantics and nit-picking, they are symptomatic of deeper challenges to robustly define the philosophy, methodology, and theory of this science. Terminology should standardise definitions and facilitate understanding and communication, while enabling synthesis and innovation.

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne & Rosindell (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed in Lambert (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable., 27 pages, 5 figures

Mutualistische interacties komen overal voor in de natuur en zijn cruciaal voor de overleving en reproductie van veel soorten. Sinds kort wordt pas erkend dat mutualistische interaties belangrijk zijn voor de verbindingen tussen soorten, voor de modulatie van ecosysteemfunctionering en voor het behoud van biodiversiteit. Mutualistische gemeenschappen, zoals plant-bestuiver gemeenschappen, kunnen worden beschreven als netwerken van interacties tussen mutualistiche partners (bijv. planten en dieren). Met behulp van deze aanpak hebben vele studies hun licht kunnen schijnen op de structuur van mutualistische gemeenschappen en hun eco-evolutionaire patronen. De vraag is: welke ecologische en evolutionaire processen liggen ten grondslag aan de opbouw van mutualistische gemeenschappen? We hebben wiskundige modellen en simulaties ontwikkeld en deze gecombineerd met data analyse om deze vragen te kunnen beantwoorden voor een scala aan mutualistische systemen, waarbij we vooral gefocust hebben op mutualistische plant-dier interacties. We hebben gevonden dat spatio-temporele variabiliteit de belangrijkste factor is van de mutualistische netwerk structuur. De combinatie van ruimtelijke structuur en de variabiliteit in de timing van interacties tussen soorten (fenologie) is wat het meest de mutualistische netwerkstructuur bepaald. De stabiliteit en diversiteit van deze gemeenschappen hangt echter af van de balans van deze processen met andere typen ecologische interacties en de life-history van de soort. Bovendien blijkt het dat veel voorkomende evolutionaire patronen in mutualistiche netwerken, zoals evolutionaire convergentie en complementariteit, lijken te ontstaan uit simpele ecologische (bijv. dispersielimitatie en ecologische drift) en evolutionaire (bijv. mutatie, recombinatie en genetische drift) processen. We concluderen dat: 1) neutrale eco-evolutionare processen niet moeten worden genegeerd bij het bestuderen van de evolutie van ecologische netwerken en 2) ruimtelijke processen (dispersielimitatie, immigratie) en fenologie van essentieel belang zijn voor de samenstelling van mutualistische netwerken, en waarschijnlijk voor ecologische netwerken in het algemeen.

Janzen-Connell effect draagt bij aan genetische en fylogenetische diversiteit Het proefschrift van Xubing Liu geeft een beter begrip van de Janzen-Connellhypothese. Hij beargumenteert dat het Janzen-Connelleffect niet alleen bijdraagt aan het behoud van soortendiversiteit, maar ook van genetische en fylogenetische diversiteit.Honderden studies hebben aangetoond dat veel boomsoorten patronen vertonen die consistent zijn met het Janzen-Connell effect, maar er is nauwelijks studie verricht naar variatie binnen en tussen de soorten. De Janzen-Connell hypothese beschrijft een dichtheids- en/of afstandsafhankelijk effect, veroorzaakt door natuurlijke vijanden (pathogenen en herbivoren), dat een hoge diversiteit in tropische en subtropische bossen in stand kan houden.Het belangrijkste doel van het onderzoek van Xubing Liu is het onderzoeken van het belang van interspecifieke en intraspecifieke variatie voor de Janzen-Connell hypothese door middel van fylogenetische en moleculair-evolutionaire benaderingen. Hij heeft hiertoe grote veldstudies opgezet van 2008 tot 2012 om de sterkte te meten van dichtheids- en/of afstandsafhankelijke effecten in natuurlijke levensgemeenschappen van planten en bodemmicro-organismen.Xubing Liu heeft duidelijk aangetoond met observationele en experimentele data dat door pathogenen veroorzaakte zaailingsterfte afneemt met toenemende fylogenetische afstand tot naburige bomen. Hij toonde ook aan dat het Janzen-Connell effect dat ervaren wordt door de zaailingen van een populatie omringd door pathogenen van een andere populatie afneemt met afnemende similariteit in functionele kenmerken tussen de twee populaties. Vervolgens heeft hij de pathogene schimmels geïdentificeerd die geassocieerd worden met zieke bladeren, rottende zaden en geïnfecteerde zaailingen en gevonden dat fylogenetisch verwante gastheren aan de ene kant en fylogenetisch gerelateerde pathogenen aan de andere kant co-evolueren. Hoewel bodempathogenen een significante reductie van zaailingoverleving tot gevolg hebben, vergroten AMF-schimmels (Arbuscular mycorrhizal fungi) de groei van zaailingen. De antagonistische interactie tussen AMF en pathogenen bepaalt de prestaties van zaailingen en daarmee co-existentie van soorten.

Climatic niche models based on native-range climatic data accurately predict invasive-range distributions in the majority of species. However, these models often do not account for ecological and evolutionary processes, which limit the ability to predict future range expansion. This might be particularly problematic in the case of invaders that occupy environments that would be considered marginal relative to the climatic niche in the native range of the species. Here, we assess the potential for future range expansion in the shrub Chromolaena odorata that is currently invading mesic savannas (>650 mm MAP) in South Africa that are colder and drier than most habitats in its native range. In a greenhouse experiment we tested whether its current distribution in South Africa can be explained by increased competitive ability and/or differentiation in drought tolerance relative to the native population. We compared aboveground biomass, biomass allocation, water use efficiency and relative yields of native and invasive C. odorata and the resident grass Panicum maximum in wet and dry conditions. Surprisingly, we found little differentiation between ranges. Invasive C. odorata showed no increased competitive ability or superior drought tolerance compared to native C. odorata. Moreover we found that P. maximum was a better competitor than either native or invasive C. odorata. These results imply that C. odorata is unlikely to expand its future range towards more extreme, drier, habitats beyond the limits of its current climatic niche and that the species' invasiveness most likely depends on superior light interception when temporarily released from competition by disturbance. Our study highlights the fact that species can successfully invade habitats that are at the extreme end of their ranges and thereby contributes towards a better understanding of range expansion during species invasions.

Variation in species richness across environmental gradients may be associated with an expanded volume or increased packing of ecological niche space. However, the relative importance of these alternative scenarios remains unknown, largely because standardized information on functional traits and their ecological relevance is lacking for major diversity gradients. Here, we combine data on morphological and ecological traits for 523 species of passerine birds distributed across an Andes-to-Amazon elevation gradient. We show that morphological traits capture substantial variation in species dietary (75%) and foraging niches (60%) when multiple independent trait dimensions are considered. Having established these relationships, we show that the 14-fold increase in species richness towards the lowlands is associated with both an increased volume and density of functional trait space. However, we find that increases in volume contribute little to changes in richness, with most (78%) lowland species occurring within the range of trait space occupied at high elevations. Taken together, our results suggest that high species richness is mainly associated with a denser occupation of functional trait space, implying an increased specialization or overlap of ecological niches, and supporting the view that niche packing is the dominant trend underlying gradients of increasing biodiversity towards the lowland tropics.

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an ultimate goal of the niche by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word niche. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling.

Ricklefs and Renner (Reports, 27 January 2012, p. 464) showed correlations of species richness and individual abundance within families across continents and claimed that neutral theory predicts no such correlation. However, they did not substantiate this claim quantitatively with a neutral model. Here, we show that neutral theory can be consistent with these correlations and, consequently, that the correlations alone cannot reject neutrality.

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity., Author Summary The role of sex in driving genetic variation and the speed at which new species emerge has been debated for over a century. There is experimental and theoretical evidence that sex increases genetic variation and the speed at which new species emerge, although evidence that sex reduces variation and slows the formation of new species also exists. Surprisingly, given the link between sex and genetic variation, little work has been done on the impact of sex on biodiversity. In the present theoretical study we show that a faster evolutionary rate can decrease the abundance of newly formed species and thus decrease long-term biodiversity. This leads to the paradoxical result that sexual reproduction can increase genetic variation but reduce species diversity. These results suggest that reducing the rate of appearance of genetic variation and the speed at which new species emerge may increase biodiversity in the long-term. This unexpected link between reproductive mode, the speed of evolution and biodiversity suggests that a high evolutionary rate may not be required to yield a large number of species in natural ecosystems.

Several network properties have been identified as determinants of the stability and complexity of mutualistic networks. However, it is unclear which mechanisms give rise to these network properties. Phenology seems important, because it shapes the topology of mutualistic networks, but its effects on the dynamics of mutualistic networks have scarcely been studied. Here, we study these effects with a general dynamical model of mutualistic and competitive interactions where the interaction strength depends on the temporal overlap between species resulting from their phenologies. We find a negative complexitystability relationship, where phenologies maximising mutualistic interactions and minimising intraguild competitive interactions generate speciose, nested and poorly connected networks with moderate asymmetry and low resilience. Moreover, lengthening the season increases diversity and resilience. This highlights the fragility of real mutualistic communities with short seasons (e.g. Arctic environments) to drastic environmental changes.

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity–function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of ( i ) differentially constructed culturable bacterial communities, and ( ii ) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

1. Theory predicts that small grazers are regulated by the digestive quality of grass, while large grazers extract sufficient nutrients from low-quality forage and are regulated by its abundance instead. In addition, predation potentially affects populations of small grazers more than large grazers, because predators have difficulty capturing and handling large prey. 2. We analyse the spatial distribution of five grazer species of different body size in relation to gradients of food availability and predation risk. Specifically, we investigate how the quality of grass, the abundance of grass biomass and the associated risks of predation affect the habitat use of small, intermediate and large savanna grazers at a landscape level. 3. Resource selection functions of five mammalian grazer species surveyed over a 21-year period in Serengeti are calculated using logistic regressions. Variables included in the analyses are grass nitrogen, rainfall, topographic wetness index, woody cover, drainage lines, landscape curvature, water and human habitation. Structural equation modelling (SEM) is used to aggregate predictor variables into 'composites' representing food quality, food abundance and predation risk. Subsequently, SEM is used to investigate species' habitat use, defined as their recurrence in 5 x 5 km cells across repeated censuses. 4. The distribution of small grazers is constrained by predation and food quality, whereas the distribution of large grazers is relatively unconstrained. The distribution of the largest grazer (African buffalo) is primarily associated with forage abundance but not predation risk, while the distributions of the smallest grazers (Thomson's gazelle and Grant's gazelle) are associated with high grass quality and negatively with the risk of predation. The distributions of intermediate sized grazers (Coke's hartebeest and topi) suggest they optimize access to grass biomass of sufficient quality in relatively predator-safe areas. 5. The results illustrate how top-down (vegetation-mediated predation risk) and bottom-up factors (biomass and nutrient content of vegetation) predictably contribute to the division of niche space for herbivores that vary in body size. Furthermore, diverse grazing assemblages are composed of herbivores of many body sizes (rather than similar body sizes), because these herbivores best exploit the resources of different habitat types.

The ability of species to modulate environmental conditions and resources has long been of interest. In the past three decades the impacts of these biotic modifiers have been investigated as ecosystem engineers, niche constructors, facilitators and keystone species. This environmental modulation can vary spatially from extremely local to global, temporally from days to geological time, and taxonomically from a few to a very large number of species. Modulation impacts are pervasive and affect, inter alia, the climate, structural environments, disturbance rates, soils and the atmospheric chemical composition. Biotic modifiers may profoundly transform the projected environmental conditions, and consequently have a significant impact on the predicted occurrence of the focal species in species distribution models (SDMs). This applies especially when these models are projected into different geographical regions or into the future or the past, where these biotic modifiers may be absent, or other biotic modifiers may be present. We show that environmental modulation can be represented in SDMs as additional variables. In some instances it is possible to use the species (e.g. biotic modifiers) in order to reflect the modulation. This would apply particularly to cases where the effect is the result of a single or a small number of species (e.g. elephants transforming woodland to grassland). Where numerous species generate an effect (such as tree species making a forest, or grasses facilitating fire) that modulates the abiotic environment, the effect itself might be a better descriptor for the aggregated action of the numerous species. We refer to this effect as the modulator. Much of the information required to incorporate environmental modulation effects in SDMs is already available from remote-sensing data and vegetation models.

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.

Ecological neutral theory has elicited strong opinions in recent years. Here, we review these opinions and strip away some unfortunate problems with semantics to reveal three major underlying questions. Only one of these relates to neutral theory and the importance of ecological drift, whereas the others involve the link between pattern and process, the tradeoff between simplicity and complexity in modeling, and the role of stochasticity and drift in ecology. We explain how neutral theory cannot be simultaneously used both as a null hypothesis and as an,approximation. However, we also show how neutral theory always has a valuable use in one of these two roles even though the real world is not neutral.

Animal behavior is unique in influencing both components of the process of transmission of disease: exposure to infectious agents, and susceptibility to infection once exposed. To date, the influence of behavior on exposure versus susceptibility has largely been considered separately. Here, we ask whether these two key mechanisms act in concert in natural populations, whereby individuals who are most exposed to infectious agents or have the most contact with conspecifics are also the most susceptible or infectious. We propose three mechanisms that can generate covariation between these two key elements of the transmission of disease within and among hosts, and we provide empirical examples of each. We then use a mathematical model to examine the effect of this covariation on the dynamics of disease at the population level. First, we show that the empirical mechanisms generating covariation between behavioral and physiological components of disease transmission are widespread and include endocrine mediators of behavior, mate choice, group size, sickness behaviors, and behavioral avoidance of infectious conspecifics. The diversity of these empirical mechanisms underscores the potential importance and breadth of covariation in the disease process. Second, we show mathematically that the variability in hosts' exposure to infectious agents and susceptibility or infectiousness, and how tightly they are coupled, strongly influences the ability of a disease to invade a host population. Overall, we propose that covariation between behavioral and physiological components of transmission is likely widespread in natural populations, and can have important consequences for the dynamics of disease at the population level as well as for our understanding of sexual selection, social behavior, and animal communication.

The mathematical structure of the two models is summarized in Table 1. The metacommunity composition inside a niche is given by Hubbell’s metacommunity distribution. The model of CP10 imposes the zero-sum constraint, whereas our model does not. Hence, the two models differ only in the sizes of the metacommunity niches. The absolute niche sizes (i.e. the number of individuals in a niche) are infinite in both models; the relative niche sizes (i.e. the fraction of individuals in a niche) are fixed in the model of CP10, and are randomly distributed in our model. This distribution tends to the fixed niche sizes of CP10’s model for high diversity, so that the two models coincide for highly diverse metacommunities. The local community is a sample from the metacommunity, that can be taken with or without dispersal limitation. For both models, the local community SAD inside a niche is given by the Ewens (without dispersal limitation; Ewens 1972) or the Etienne (with dispersal limitation; Etienne 2005) distribution. The models only differ in the niche sizes: fixed in the model of CP10, and randomly distributed in our model. Again, the latter distribution tends to the fixed niche sizes of CP10’s model when the diversity in the local community is high, so that the two models coincide for highly diverse communities.

Most hosts are infected with multiple parasites, and responses of the immune system to co occurring parasites may influence disease spread. Helminth infection can bias the host immune response toward a T-helper type 2 Th2) over a type 1 Th1) response, impairing the host's ability to control concurrent intracellular microparasite infections and potentially modifying disease dynamics. In humans, immune-mediated interactions between helminths and microparasites can alter host susceptibility to diseases such as HIV, tuberculosis TB), and malaria. However, the extent to which similar processes operate in natural animal populations and influence disease spread remains unknown. We used cross-sectional, experimental, and genetic studies to show that gastrointestinal nematode infection alters immunity to intracellular microparasites in free-ranging African buffalo Syncerus caffer). Buffalo that were more resistant to nematode infection had weaker Th1 responses, there was significant genotypic variation in nematode resistance, and anthelminthic treatment enhanced Th1 immunity. Using a disease dynamic model parameterized with empirical data, we found that nematode-induced immune suppression can facilitate the invasion of bovine TB in buffalo. In the absence of nematodes, TB failed to invade the system, illustrating the critical role nematodes may play in disease establishment. Our results suggest that helminths, by influencing the likelihood of microparasite invasion, may influence patterns of disease emergence in the wild.

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

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

Over evolutionary time, the number of species in a community reflects the balance between the rate of speciation and the rate of extinction. Over shorter time-scales local species richness is also affected by how often species move into and out of the local community. These processes are at the heart of Hubbell's 'unified neutral theory of biodiversity' (Hubbell 2001). Hubbell's spatially implicit, dispersal-limited neutral model is the most widely used of the many implementations of neutral theory and it provides an estimate of the rate of speciation in a metacommunity (if metacommunity size is known) and the rate at which species migrate into the local community from the wider metacommunity. Recently, this neutral model has been used to compare rates of speciation and migration in the species-rich fynbos of South Africa and in neotropical forests. Here we use new analytical methods for estimating the neutral model's parameters to infer speciation and dispersal rates for three sites in species-rich sclerophyll shrublands (equivalent to fynbos) in Western Australia (WA). Our estimates suggest that WA shrublands are intermediate between fynbos and tropical rainforest in terms of speciation and dispersal. Although a weak test, the model predicts species abundance distributions and species accumulation curves similar to those observed at the three sites. The neutral model's predictions also remain plausible when confronted with independent data describing: (1) known edaphic relationships between sites, (2) estimates of metacommunity species richness and (3) rates of speciation among resprouters and nonsprouters. Two of the site pairs, however, show species turnovers significantly different from those predicted by the spatially implicit form of the neutral model that we use. This suggests that non-neutral processes, in this case probably edaphic specialisation, are important in the WA shrubland metacommunity. The neutral model predicts similar rates of speciation in resprouter and sprouter taxa, a finding supported by recent molecular phylogenies. Finally, when converted into temporally scaled speciation rates and species longevities, the estimates produced by the neutral model seem implausible. The apparent departure from neutrality in the turnover of species between some sites and the implausible temporal dynamics may be due to the particular model chosen and does not reduce the significance of our other results, which confirm that local dispersal limitation, coupled with broader scale edaphic fidelity, combine to structure this biodiverse metacommunity.

In a recent paper, I presented a sampling formula for species abundances from multiple samples according to the prevailing neutral model of biodiversity, but practical implementation for parameter estimation was only possible when these samples were from local communities that were assumed to be equally dispersal limited. Here I show how the same sampling formula can also be used to estimate model parameters using maximum likelihood when the samples have different degrees of dispersal limitation. Moreover, it performs better than other, approximate, parameter estimation approaches. I also show how to calculate errors in the parameter estimates, which has so far been largely ignored in the development of and debate on neutral theory. (C) 2008 Elsevier Ltd. All rights reserved.

aeres : ACL; International audience; Hubbell's neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et al. have argued that other assumptions on the speciation process could be more realistic, for example, that every species has the same probability to speciate (Etienne, et al. in Oikos 116:241-258, 2007). They introduced a number of neutral community models with a different speciation process, and conjectured formulas for their stationary species abundance distribution. Here we study a generalised neutral community model, encompassing these modified models, and derive its stationary distribution, thus proving the conjectured formulas.

Monitoring of large herbivores is central to research and management activities in many protected areas. Monitoring programs were originally developed to estimate (trends in) population sizes of individual species. However, emphasis is shifting increasingly towards conservation of diversity and communities instead of individual species, as a growing literature shows the importance of herbivore diversity for ecosystem functioning. We argue that the design of monitoring programs has not yet been adapted well to this new conservation paradigm. Using large herbivore census data from Hluhluwe-iMfolozi Park, South Africa, we studied how monitoring methodology (observational counts vs. dung counts) and spatial scale interact in influencing estimates of large herbivore species richness and diversity. Dung counts resulted in higher herbivore species richness and diversity estimates than direct observational counts, especially at finer monitoring resolutions (grid cells smaller than 25 km(2)). At monitoring resolutions coarser than 25 km(2) both methods gave comparable diversity estimates. The methods also yielded different spatial diversity estimates, especially at finer resolutions. Grid cells with high diversity according to the dung count data did not necessarily have high diversity according to the observational counts, as shown by low correlation of grid cell values of both methods. We discuss these results in the light of estimates of the sampling effort of each method and, hence, suggest new monitoring designs that are more suitable for tracking temporal and spatial trends in large herbivore diversity and community composition.

Epidemiological studies typically focus on single-parasite systems, although most hosts harbor multiple parasite species; thus, the potential impacts of co-infection on disease dynamics are only beginning to be recognized. Interactions between macroparasites, such as gastrointestinal nematodes, and microparasites causing diseases like TB, AIDS, and malaria are particularly interesting because co-infection may favor transmission and progression of these important diseases. Here we present evidence for strong interactions between gastrointestinal worms and bovine tuberculosis (TB) in free-ranging African buffalo (Syncerus caffer). TB and worms are negatively associated at the population, among-herd, and within-herd scales, and this association is not solely the result of demographic heterogeneities in infection. Combining data from 1362 buffalo with simple mechanistic models, we find that both accelerated mortality of co-infected individuals and TB transmission heterogeneity caused by trade-offs in immunity to the two types of parasites likely contribute to observed infection patterns. This study is one of the first to examine the relevance of within-host immunological trade-offs for understanding parasite distribution patterns in natural populations.

The zero-sum assumption is one of the ingredients of the standard neutral model of biodiversity by Hubbell. It states that the community is saturated all the time, which in this model means that the total number of individuals in the community is constant over time, and therefore introduces a coupling between species abundances. It was shown recently that a neutral model with independent species, and thus without any coupling between species abundances, has the same sampling formula (given a fixed number of individuals in the sample) as the standard model [Etienne, R.S., Alonso, D., McKane, A.J., 2007. The zero-sum assumption in neutral biodiversity theory. J. Theor. Biol. 248, 522-536]. The equilibria of both models are therefore equivalent from a practical point of view. Here we show that this equivalence can be extended to a class of neutral models with density-dependence on the community-level. This result can be interpreted as robustness of the model, i.e. insensitivity of the model to the precise interaction of the species in a neutral community. It can also be interpreted as a lack of resolution, as different mechanisms of interactions between neutral species cannot be distinguished using only a single snapshot of species abundance data. (C) 2008 Elsevier Ltd. All rights reserved.

Este artículo contiene 13 páginas, Species abundance distributions (SADs) have played a historical role in the development ofcommunity ecology. They summarize information about the number and the relativeabundance of the species encountered in a sample from a given community. For yearsecologists have developed theory to characterize species abundance patterns, and the studyof these patterns has received special attention in recent years. In particular, ecologists havedeveloped statistical sampling theories to predict the SAD expected in a sample taken froma region. Here, we emphasize an important limitation of all current sampling theories: theyignore species identity. We present an alternative formulation of statistical sampling theorythat incorporates species asymmetries in sampling and dynamics, and relate, in a generalway, the community-level SAD to the distribution of population abundances of the speciesintegrating the community. We illustrate the theory on a stochastic community model thatcan accommodate species asymmetry. Finally, we discuss the potentially important role ofspecies asymmetries in shaping recently observed multi-humped SADs and in comparisonsof the relative success of niche and neutral theories at predicting SADs

Hubbell's neutral theory of biodiversity has generated much debate over the need for niches to explain biodiversity patterns. Discussion of the theory has focused on its neutrality assumption, i.e. the functional equivalence of species in competition and dispersal. Almost no attention has been paid to another critical aspect of the theory, the assumptions on the nature of the speciation process. In the standard version of the neutral theory each individual has a fixed probability to speciate. Hence, the speciation rate of a species is directly proportional to its abundance in the metacommunity. We argue that this assumption is not realistic for most speciation modes because speciation is an emergent property of complex processes at larger spatial and temporal scales and, consequently, speciation rate can either increase or decrease with abundance. Accordingly, the assumption that speciation rate is independent of abundance (each species has a fixed probability to speciate) is a more natural starting point in a neutral theory of biodiversity. Here we present a neutral model based on this assumption and we confront this new model to 20 large data sets of tree communities, expecting the new model to fit the data better than Hubbell's original model. We find, however, that the data sets are much better fitted by Hubbell's original model. This implies that species abundance data can discriminate between different modes of speciation, or, stated otherwise, that the mode of speciation has a large impact on the species abundance distribution. Our model analysis points out new ways to study how biodiversity patterns are shaped by the interplay between evolutionary processes (speciation, extinction) and ecological processes (competition, dispersal).

The neutral theory of S. P. Hubbell postulates a two-scale hierarchical framework consisting of a metacommunity following the speciation - drift equilibrium characterized by the "biodiversity number'' theta, and local communities following the migration - drift equilibrium characterized by the "migration rate'' m ( or the "fundamental dispersal number'' I). While Etienne's sampling formula allows simultaneous estimation of h and m from a single sample of a local community, its applicability to a network of ( rather small) samples is questionable. We de. ne here an alternative two-stage approach estimating h from an adequate subset of the individuals sampled in the field ( using Ewens' sampling formula) and m from community samples ( using Etienne's sampling formula). We compare its results with the simultaneous estimation of theta and m ( one-stage estimation), for simulated neutral samples and for 50 1-ha plots of evergreen forest in South India. The one-stage approach exhibits problems of bias and of poor differentiability between high-theta, low-m and low-theta, high-m solution domains. Conversely, the two-stage approach yielded reasonable estimates and is to be preferred when several small, scattered plots are available instead of a single large one.

The neutral theory of biodiversity as put forward by Hubbell in his 2001 monograph has received much criticism for its unrealistic simplifying assumptions. These are the assumptions of functional equivalence among different species (neutrality), the assumption of point mutation speciation, and the assumption that resources are continuously saturated, such that constant resource availability implies constant community size (zero-sum assumption). Here we focus on the zero-sum assumption. We present a general theory for calculating the probability of observing a particular species-abundance distribution (sampling formula) and show that zero-sum and non-zero-sum formulations of neutral theory have exactly the same sampling formula when the community is in equilibrium. Moreover, for the nonzero-sum community the sampling formula has this same form, even out of equilibrium. Therefore, the term "zero-sum multinomial (ZSM)" to describe species abundance patterns, as coined by Hubbell [2001. The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ], is not really appropriate, as it also applies to non-zero-sum communities. Instead we propose the term "dispersal-limited multinomial (DLM)", thus making explicit one of the most important contributions of neutral community theory, the emphasis on dispersal limitation as a dominant factor in determining species abundances. (C) 2007 Elsevier Ltd. All rights reserved.

Body size of vertebrate herbivores is strongly linked to other life history traits, most notably (1) tolerance of low quality forage and (2) vulnerability to predation, which both impact the composition and dynamics of natural communities. However, no study has thus far explored how the combination of these two body-size related traits affect the long-term composition and dynamics of the herbivore and plant communities.We made a simple model of ordinary differential equations and simulated a grassland system with three herbivore species (small, medium, large) and two predator species (small, large) to investigate how the combination of low-quality tolerance and predation-vulnerability structure the herbivore and plant community. We found that facilitation and competition between different-sized herbivores and predation by especially small predators stimulates coexistence among herbivore species. Furthermore, the interaction between different-sized herbivores and predators generated cyclical succession in the plant community, i.e. alternating periods of short vegetation dominated by high-quality plants, with periods of tall vegetation dominated by low-quality plants. Our results suggest that cyclical succession in plant communities is more likely to occur when a predator predominantly preys on small herbivore species. Large predators also play an important role, as their addition relaxed the set of conditions under which cyclical succession occurred. Consequently, our model predictions suggest that a diverse predator community plays an important role in the long-term dynamics and maintenance of diversity in both the herbivore and plant community.

The allometry of metabolic rate has long been one of the key relationships in ecology. While its existence is generally agreed on, the exact value of the scaling exponent, and the key mechanisms that determine its value, are still hotly debated.The network model of West, Brown & Enquist (Science 276, 122-126, 1997) predicts a value of (3)/4 but, although appealing, this model has not been generally accepted.Here we reconstruct the model and derive the exponent in a clearer and much more straightforward way that requires weaker assumptions than the original model. Specifically, self-similarity of the network is not required. Our formulation can even be used if one or several assumptions of West et al. (1997) are considered invalid.Moreover, we provide a formula for the proportionality constant (i.e. the intercept of the allometric scaling relation) that shows explicitly where factors as temperature and stoichiometry affect metabolism.

Disease models usually assume disease to act independently of other mortality- and morbidity-causing factors. Alternatively, disease may function as a competing risk factor, for example, killing already moribund hosts. Using tuberculosis (TB) in African buffalo as a model system, we explore consequences of competing or independent disease effects for host population dynamics. We include scenarios with density-dependent and density-independent effects of environmental variation, exemplified by variable food availability (driven by rainfall) and catastrophic droughts, respectively. Independent disease effects reduce population size linearly with prevalence, irrespective of the nature of environmental variation. Competing disease risks alter population size only if density-independent variation is present; then, disease reduces population size nonlinearly. Field data indicate that the net effect of TB on buffalo likely falls between the extremes of total independence and competition with other risk factors: TB increases mortality and decreases fecundity in some prime- aged buffalo, suggesting independent disease risks in these individuals, while similar disease effects in senescent buffalo may act as competing risks. Moreover, increased survival and fecundity of TB-negative buffalo may compensate for some disease-related losses. Model assumptions on independent or competing disease risks and environmental variability should be considered explicitly when assessing disease effects on wildlife populations.

The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11¿14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.

The neutral model of biodiversity, proposed by Hubbell (The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ, 2001) to explain the diversity of functionally equivalent species, has been subject of hot debate in community ecology. Whereas Hubbell studied the model mostly by simulations, recently analytical treatments have yielded expressions of the expected number of species of a particular abundance in a local community with dispersal limitation. Moreover, a formula has been offered for the joint likelihood of observing a given species-abundance dataset in a local community with dispersal limitation, but this formula is too complicated to allow practical applications. Here, I present a much simplified expression that can be regarded as an enhanced version of the famous Ewens sampling formula. It can be used in maximum likelihood methods for quick estimation of the model parameters, using all information in the data, and for model comparison. I also show how to rapidly generate examples of species-abundance distributions for a given set of model parameters and how to calculate Simpson's diversity index.

Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species-abundance data that yields a full joint probability distribution of each model's parameters plus a relatively parameter-independent criterion, the posterior Bayes factor, to compare these models. We illustrate our approach by comparing three classical distributions: the zero-sum multinomial (ZSM) distribution, based on Hubbell's neutral model, the multivariate Poisson lognormal distribution (MPLN), based on niche arguments, and the discrete broken stick (DBS) distribution, based on MacArthur's broken stick model. We give explicit formulas for the probability of observing a particular species-abundance data set in each model, and argue that conditioning on both sample size and species count is needed to allow comparisons between the two distributions. We apply our approach to two neotropical communities (trees, fish). We find that DBS is largely inferior to ZSM and MPLN for both communities. The tree data do not allow discrimination between ZSM and MPLN, but for the fish data ZSM (neutral model) overwhelmingly outperforms MPLN (niche model), suggesting that dispersal plays a previously underestimated role in structuring tropical freshwater fish communities. We advocate this approach for identifying the relative importance of dispersal and niche-partitioning in determining diversity of different ecological groups of species under different environmental conditions.

Metapopulation theory teaches that the viability of metapopulations may be enlarged by decreasing the probability of extinction of local populations, or by increasing the colonization probability of empty habitat patches. In a metapopulation model study it has recently been found that reducing the extinction probability of the least extinction-prone patch and increasing the colonization probability between the two least extinction-prone patches are the best options to prolong the expected lifetime of a metapopulation. In this article I examine with a more detailed model whether this translates into enlarging the largest patch and reducing the interpatch distance between the largest patches. Using two measures of metapopulation persistence (longevity and resilience) I found, firstly, that the largest patch should generally be enlarged if the choice is to enlarge a patch by a certain percentage (relative change) and that the smallest patch should generally be enlarged if the choice is to enlarge a patch by a fixed amount of area (absolute change), and secondly that indeed one should reduce the interpatch distance between the two largest patches, if the choice is among all pairs of patches. The strength of these rules of thumb (particularly the second part of the first rule) depends on the parameter values, particularly the amount of clustering of patches, the mean dispersal distance and the number of dispersers. Also, the rules of thumb are less pronounced when resilience is chosen as a measure of metapopulation persistence than when longevity is chosen. (C) 2004 Elsevier B.V. All rights reserved.

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.

Current neutral theory in community ecology views local biodiversity as a result of the interplay between speciation, extinction and immigration. Simulations and a mean-field approximation have been used to study this neutral theory. As simulations have limitations of convergence and the mean-field approximation ignores dependencies between species' abundances when applied to species-abundance data, there is still no final conclusion whether the neutral theory or the traditional lognormal model describes community structure best. We present a novel analytical framework, based on the genealogy of individuals in the local community, to overcome the problems of previous approaches, and show, using Bayesian statistics, that the lognormal model provides a slightly better fit to the species-abundance distribution of a much-discussed tropical tree community. A key feature of our approach is that it shows the tight link between genetic and species diversity, which creates important perspectives to future integration of evolutionary and community ecological theory.

Many organisms experience an Allee effect: their populations do not grow optimally at low densities. In addition, individuals compete with one another at high densities. The Allee effect and competition thus create a lower and an upper bound to local population size. Local populations can, however. be connected through dispersal. By using a spatio-temporal integro-difference simulation model, parameterized for Drosophila melanogaster, we explore the consequences of the Allee effect, scramble competition and dispersal for different combinations of resource distributions, initial adult distributions and densities, modes of dispersal and boundary conditions. We found that the initial distribution and density of adults determines whether a population can establish, while resource availability, the ability to reach resources and heterogeneity are mainly responsible for subsequent population persistence. In our model heterogeneity was introduced by the distribution of resources, the initial adult distribution, and the boundary conditions. Although local population dynamics are inherently unstable, overall stability can be attained by (re)colonization processes. The averaged dynamics of the total population turned out to be reasonably smooth, so apparently upper and lower local population bounds, coupled with dispersal, created an effective stable mean population density for the system as a whole. This suggests that stable mean population densities for spatial populations can be emergent properties appearing at sufficiently large scales, as opposed to inherent properties occurring at all scales. We also found. in agreement with most literature but contrary to some recent literature, that population persistence can be facilitated by a leptokurtic dispersal mode, which has higher probabilities of traveling both short and long distances, but smaller probability of traveling intermediate distances than random dispersal. (C) 2002 Elsevier Science B.V. All rights reserved.

Benedetti-Cecchi [1] argues that 1/f environmental fluctuations can produce the same patterns as neutral theory and, hence, present an alternative explanation for the sort of spatio-temporal variability observed in ecological systems. However, environmental fluctuations are not an alternative to neutral theory, but should instead be embedded in it. Current neutral models use demographic stochasticity, but neutral theory does not exclude other sources of stochasticity. Neutrality does not imply a homogeneous and constant habitat, as is sometimes mistakenly assumed.