Search

Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic repositioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic repositioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic repositioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (

Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease.

Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease.

1. Neutral community models are derived from the proposition that basic probabilities of species loss (extinction, emigration) and gain (immigration, speciation) explain biological community structure, such that species with many individuals are very likely to be widespread. Niche models on the other hand assume that interactions between species and differential resource use mediate species coexistence, thus invoking environmental factors to explain community patterns. 2. In this study, we compared neutral and niche models to test how much of the spatial variability of assemblages of heterotrophic bacteria and phytoplankton in 13 lakes they could explain. Analysis of phytoplankton was restricted to cyanobacteria, so that they could be studied with the same molecular fingerprinting method, automated ribosomal intergenic spaces analysis (ARISA), as heterotrophic bacteria. We determined local biotic and abiotic lake variables as well as lake age, glacial history and distance between sites. 3. The neutral community model had a good fit to the community composition of heterotrophic bacteria (R-2 = 0.69), whereas it could not produce a significant model for the community composition of cyanobacteria. 4. The community composition of cyanobacteria was instead correlated to environmental variables. The best model, a combination of total organic carbon, biomass of eukaryotic phytoplankton, pH and conductivity, could explain 8% of the variation. In contrast, variation in the community composition of heterotrophic bacteria was not predicted by any of the environmental variables. Historical and spatial variables were not correlated to the community composition of either group. 5. The pattern found for heterotrophic bacteria suggests that stochastic processes are important. The correlation of cyanobacteria with local environmental variables alone is consistent with the niche model. We suggest that cyanobacteria, a group of organisms containing bloom-forming species, may be less l

1. Neutral community models are derived from the proposition that basic probabilities ofspecies loss (extinction, emigration) and gain (immigration, speciation) explain biologicalcommunity structure, such that species with many individuals are very likely to bewidespread. Niche models on the other hand assume that interactions between species anddifferential resource use mediate species coexistence, thus invoking environmental factorsto explain community patterns.2. In this study, we compared neutral and niche models to test how much of the spatialvariability of assemblages of heterotrophic bacteria and phytoplankton in 13 lakes theycould explain. Analysis of phytoplankton was restricted to cyanobacteria, so that theycould be studied with the same molecular fingerprinting method, automated ribosomalintergenic spaces analysis (ARISA), as heterotrophic bacteria. We determined local bioticand abiotic lake variables as well as lake age, glacial history and distance between sites.3. The neutral community model had a good fit to the community composition ofheterotrophic bacteria (R2 = 0.69), whereas it could not produce a significant model for thecommunity composition of cyanobacteria.4. The community composition of cyanobacteria was instead correlated to environmentalvariables. The best model, a combination of total organic carbon, biomass of eukaryoticphytoplankton, pH and conductivity, could explain 8% of the variation. In contrast,variation in the community composition of heterotrophic bacteria was not predicted byany of the environmental variables. Historical and spatial variables were not correlated tothe community composition of either group.5. The pattern found for heterotrophic bacteria suggests that stochastic processes areimportant. The correlation of cyanobacteria with local environmental variables alone isconsistent with the niche model. We suggest that cyanobacteria, a group of organismscontaining bloom-forming species, may be less likely to fit a neutral co

Cultural evolutionary models that relate spatial and temporal patterning in artifact sequences to human social learning processes and history have made many recent advances. Specifically, these models connect evolutionary forces and social leaning mechanisms along cultural pathways with expectations that can be assessed using material culture. In this dissertation, I use an historical archaeology case study of carved New England gravestones to evaluate three different aspects of cultural transmission and artifact patterns. First, I study the role of social network structure in the transmission of cultural information among carvers organized in workshops that were principally comprised of a carver and his apprentices. The results of this study suggest that the motifs reflect widespread similarity that transcends workshop organization. However, the finer grained decorative elements that make up these motifs correspond with cultural lineages of gravestone carvers. Second, I examine the relationship between the diffusion of innovations and cultural transmission mechanisms that result in spatiotemporal patterning. The spatial patterning suggests that social contagion among consumers created brief instances of wave-like diffusion from a distinct workshop, highlighting the role of consumer choice. A review of probate payments shows that gravestones were rarely purchased from distance sources, as transport costs could be prohibitive. The spatial patterning and historic record suggest that carvers also learned from other carvers creating a hierarchical diffusion process. These two populations created a feedback mechanism that leads to complex emergent phenomena, as illustrated by the rapid and widespread adoption of the cherub motif. Third, the neutral model of stylistic variation is applied to gravestone data to examine the ways that increased consumption and an expanding carving industry led to dominant decorative motifs. This study shows that neutrality can be a fleeting

1. Analyzing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species. For instance, an association between species co-occurrence in local communities and their phylogenetic proximity may reveal the action of habitat filtering, niche conservatism and/or competitive exclusion. 2. Different methods were recently proposed to test such community-wide phylogenetic patterns, based on the phylogenetic clustering or overdispersion of the species in a local community. This provides a much needed framework for addressing long standing questions in community ecology as well as the recent debate on community neutrality. The testing procedures are based on (i) a metric measuring the association between phylogenetic distance and species co-occurrence, and (ii) a data set randomization algorithm providing the distribution of the metric under a given `null model'. However, the statistical properties of these approaches are not well-established and their reliability must be tested against simulated data sets. 3. This paper reviews metrics and null models used in previous studies. A `locally neutral' subdivided community model is simulated to produce data sets devoid of phylogenetic structure in the spatial distribution of species. Using these data sets, the consistency of Type I error rates of tests based on 10 metrics combined with nine null models is examined. 4. This study shows that most tests can become liberal (i.e. tests rejecting too often the null hypothesis that only neutral processes structured spatially the local community) when the randomization algorithm breaks down a structure in the original data set unrelated to the null hypothesis to test. Hence, when overall species abundances are distributed non-randomly across the phylogeny or when local abundances are spatially autocorrelated, better statistical performances were achieved by randomization algorithms preserving these structural features. The, FLWIN, info:eu-repo/semantics/published

1. Analyzing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species. For instance, an association between species co-occurrence in local communities and their phylogenetic proximity may reveal the action of habitat filtering, niche conservatism and/or competitive exclusion. 2. Different methods were recently proposed to test such community-wide phylogenetic patterns, based on the phylogenetic clustering or overdispersion of the species in a local community. This provides a much needed framework for addressing long standing questions in community ecology as well as the recent debate on community neutrality. The testing procedures are based on (i) a metric measuring the association between phylogenetic distance and species co-occurrence, and (ii) a data set randomization algorithm providing the distribution of the metric under a given `null model'. However, the statistical properties of these approaches are not well-established and their reliability must be tested against simulated data sets. 3. This paper reviews metrics and null models used in previous studies. A `locally neutral' subdivided community model is simulated to produce data sets devoid of phylogenetic structure in the spatial distribution of species. Using these data sets, the consistency of Type I error rates of tests based on 10 metrics combined with nine null models is examined. 4. This study shows that most tests can become liberal (i.e. tests rejecting too often the null hypothesis that only neutral processes structured spatially the local community) when the randomization algorithm breaks down a structure in the original data set unrelated to the null hypothesis to test. Hence, when overall species abundances are distributed non-randomly across the phylogeny or when local abundances are spatially autocorrelated, better statistical performances were achieved by randomization algorithms preserving these structural features. The, FLWIN, info:eu-repo/semantics/published

In this study, we ask if instead of being fundamentally opposed, niche and neutral theories could simply be located at the extremes of a continuum. First, we present a model of recruitment probabilities that combines both niche and neutral processes. From this model, we predict and test whether the relative importance of niche vs. neutral processes in controlling community dynamics will vary depending on community species richness, niche overlap and dispersal capabilities of species (both local and long distance). Results demonstrate that niche and neutrality form ends of a continuum from competitive to stochastic exclusion. In the absence of immigration, competitive exclusion tends to create a regular spacing of niches. However, immigration prevents the establishment of a limiting similarity. The equilibrium community consists of a set of complementary and redundant species, with their abundance determined, respectively, by the distribution of environmental conditions and the amount of immigration.

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 de. ning 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.

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 de. ning 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.

Tree species distribution has been investigated along 45 km of line transects in the tropical rain forest of the Dja Fauna Reserve in Cameroon. The spatial patterns were expressed by the probabilities that two trees are conspecific according to the distance separating them, providing information on the degree of species clumping as well as on alpha- and beta-diversity. Our objective was to assess the relative importance of habitat heterogeneity and limited dispersal in determining these patterns by: (1) comparing the patterns observed within and across major habitats; (2) comparing the patterns with the ones expected under a neutral hypothesis where limited dispersal is the sole factor. Although, habitat heterogeneity affected the distribution of many species, our results suggest that limited dispersal was the major factor affecting the degree of species clumping. The pattern observed was similar to the one found in Amazonia by Condit et al. [Science 295 (2002) 666]. We discuss the relevance of neutral models of tree communities to study the dispersal abilities of tree species. (C) 2004 Elsevier B.V. All rights reserved., info:eu-repo/semantics/published

Tree species distribution has been investigated along 45 km of line transects in the tropical rain forest of the Dja Fauna Reserve in Cameroon. The spatial patterns were expressed by the probabilities that two trees are conspecific according to the distance separating them, providing information on the degree of species clumping as well as on alpha- and beta-diversity. Our objective was to assess the relative importance of habitat heterogeneity and limited dispersal in determining these patterns by: (1) comparing the patterns observed within and across major habitats; (2) comparing the patterns with the ones expected under a neutral hypothesis where limited dispersal is the sole factor. Although, habitat heterogeneity affected the distribution of many species, our results suggest that limited dispersal was the major factor affecting the degree of species clumping. The pattern observed was similar to the one found in Amazonia by Condit et al. [Science 295 (2002) 666]. We discuss the relevance of neutral models of tree communities to study the dispersal abilities of tree species. (C) 2004 Elsevier B.V. All rights reserved., info:eu-repo/semantics/published

In this study, we ask if instead of being fundamentally opposed, niche and neutral theories could simply be located at the extremes of a continuum. First, we present a model of recruitment probabilities that combines both niche and neutral processes. From this model, we predict and test whether the relative importance of niche vs. neutral processes in controlling community dynamics will vary depending on community species richness, niche overlap and dispersal capabilities of species (both local and long distance). Results demonstrate that niche and neutrality form ends of a continuum from competitive to stochastic exclusion. In the absence of immigration, competitive exclusion tends to create a regular spacing of niches. However, immigration prevents the establishment of a limiting similarity. The equilibrium community consists of a set of complementary and redundant species, with their abundance determined, respectively, by the distribution of environmental conditions and the amount of immigration.