From plant traits to plant communities: a statistical mechanistic approach to biodiversity

How species richness and total abundance constrain the distribution of abundance

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow-curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R(2) values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.

Mechanisms for success after long-term nutrient enrichment in a boreal forest understory

Global levels of reactive nitrogen are predicted to rise in the coming decades as a result of increased deposition from the burning of fossil fuels and the large-scale conversion of nitrogen into a useable form for agriculture. Many plant communities respond strongly to increases in soil nitrogen, particularly in northern ecosystems where nitrogen levels are naturally very low. An experiment in northern Canada that was initiated in 1990 has been investigating the effects of long-term nutrient enrichment (fertilizer added annually) on a boreal forest understory community. We used this experiment to investigate why some species increase in abundance under nutrient enrichment whereas others decline. We focused on four species that differed in their responses to fertilization: Mertensia paniculata and Epilobium angustifolium increased in abundance, Achillea millefolium remained relatively constant and Festuca altaica declined. We hypothesized that the two species that were successful in the new high-nutrient, light-limited environment would be taller, have higher specific leaf area, change phenology by growing earlier in the season and be more morphologically plastic than their less successful counterparts. We compared plant height, specific leaf area, growth spurt date and allocation to leaves in plants grown in control and fertilized plots. We demonstrated that each of the two species that came to dominate fertilized plots has a different combination of traits and responses that likely gave them a competitive advantage; M. paniculata has the highest specific leaf area of the four species whereas E. angustifolium is tallest and exhibits morphological plasticity when fertilized by increasing biomass allocation to leaves. These results indicate that rather than one strategy determining success when nutrients become available, a variety of traits and responses may contribute to a species' ability to persist in a nutrient-enriched boreal forest understory.

Plant trait-species abundance relationships vary with environmental properties in subtropical forests in eastern china

Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests.

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere.

Habitat specialization through germination cueing: a comparative study of herbs from forests and open habitats

BACKGROUND AND AIMS

This study examined the adaptive association between seed germination ecology and specialization to either forest or open habitats across a range of evolutionary lineages of seed plants, in order to test the hypotheses that (1) species' specialization to open vs. shaded habitats is consistently accompanied by specialization in their regeneration niche; and (2) species are thereby adapted to utilize different windows of opportunity in time (season) and space (habitat).

METHODS

Seed germination response to temperature, light and stratification was tested for 17 congeneric pairs, each consisting of one forest species and one open-habitat species. A factorial design was used with temperature levels and diurnal temperature variation (10 °C constant, 15-5 °C fluctuating, 20 °C constant, 25-15 °C fluctuating), and two light levels (light and darkness) and a cold stratification treatment. The congeneric species pair design took phylogenetic dependence into account.

KEY RESULTS

Species from open habitats germinated better at high temperatures, whereas forest species performed equally well at low and high temperatures. Forest species tended to germinate only after a period of cold stratification that could break dormancy, while species from open habitats generally germinated without cold stratification. The empirically derived germination strategies correspond quite well with establishment opportunities for forest and open-habitat plant species in nature.

CONCLUSIONS

Annual changes in temperature and light regime in temperate forest delimit windows of opportunity for germination and establishment. Germination strategies of forest plants are adaptations to utilize such narrow windows in time. Conversely, lack of fit between germination ecology and environment may explain why species of open habitats generally fail to establish in forests. Germination strategy should be considered an important mechanism for habitat specialization in temperate herbs to forest habitats. The findings strongly suggest that phases in the plant life cycle other than the established phase should be considered important in adaptive specialization.

Family of probability distributions derived from maximal entropy principle with scale invariant restrictions

Using statistical thermodynamics, we derive a general expression of the stationary probability distribution for thermodynamic systems driven out of equilibrium by several thermodynamic forces. The local equilibrium is defined by imposing the minimum entropy production and the maximum entropy principle under the scale invariance restrictions. The obtained probability distribution presents a singularity that has immediate physical interpretation in terms of the intermittency models. The derived reference probability distribution function is interpreted as time and ensemble average of the real physical one. A generic family of stochastic processes describing noise-driven intermittency, where the stationary density distribution coincides exactly with the one resulted from entropy maximization, is presented.

The relationship between species richness and evenness in plant communities along a successional gradient: a study from sub-alpine meadows of the Eastern Qinghai-Tibetan Plateau, China

The relationship between species richness and evenness across communities remains an unsettled issue in ecology from both theoretical and empirical perspectives. As a result, we do not know the mechanisms that could generate a relationship between species richness and evenness, and how this responds to spatial scale. Here we examine the relationship between species richness(S) and evenness (Pielou’s J′ evenness) using a chronosequence of successional sub-alpine meadow communities in the eastern Qinghai-Tibetan Plateau. These meadows range from natural community (never farmed), to those that have been protected from agricultural exploitation for periods ranging from 1 to 10 years. A total of 30 sampling quadrats with size of 0.5 m×0.5 m were laid out along two transects at each meadow. Using correlation analyses we found a consistent negative correlation between S and J′ in these communities along the successional gradient at the sampling scale of 0.5 m×0.5 m. We also explored the relationship between S and J′ at different sampling scales (from 0.5 m×0.5 m to10 m×10 m) using properly measured ramet-mapped data of a10 m×10 m quadrat in the natural community. We found that S was negatively corrected with J′ at the scales of 0.5 m×0.5 m to 2 m×2 m, but such a relationships disappeared at relative larger scales (≥2 m×4 m). When fitting different species abundance models combined with trait-specific methods, we found that niche preemption may be the determining mechanism of species evenness along the succession gradient. Considering all results together, we can conclude that such niche differentiation and spatial scale effects may help to explain the maintenance of high species richness in sub-alpine meadow communities.

Ecological niche structure and rangewide abundance patterns of species

Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance-ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space.

Foundation species influence trait-based community assembly

Here, we incorporate facilitation into trait-based community assembly theory by testing two mutually compatible facilitative mechanisms: changes in the environmental filter, causing either an increase in the range of trait values (i.e. a range expansion effect) and/or a shift in trait distributions (i.e. a range shift effect); and changes in trait spacing, suggesting an effect on niche differentiation. We analyzed the distribution of three functional traits - leaf dry matter content, specific leaf area and lateral spread - of plant communities dominated by a cushion-forming foundation species at four sites differing in elevation and aspect. We found support for environmental filtering and niche differentiation mechanisms by cushions, with filtering effects (in particular range shifts) increasing with environmental severity at higher elevation. The effect size of cushions on trait distribution was similar to that of environmental gradients caused by elevation and aspect. The consideration of intraspecific trait variability improved the detection of cushion effects on trait distributions. Our results highlight the importance of facilitation in the modification of taxonomic and functional diversity of ecological communities, and indicate that facilitation can occur through combined effects on environmental filtering and niche differentiation, with strong environmental context dependence of each mechanism.

Habitat filtering and niche differentiation jointly explain species relative abundance within grassland communities along fertility and disturbance gradients

Deterministic niche-based processes have been proposed to explain species relative abundance within communities but lead to different predictions: habitat filtering (HF) predicts dominant species to exhibit similar traits while niche differentiation (ND) requires that species have dissimilar traits to coexist. Using a multiple trait-based approach, we evaluated the relative roles of HF and ND in determining species abundances in productive grasslands. Four dimensions of the functional niche of 12 co-occurring grass species were identified using 28 plant functional traits. Using this description of the species niche, we investigated patterns of functional similarity and dissimilarity and linked them to abundance in randomly assembled six-species communities subjected to fertilization/disturbance treatments. Our results suggest that HF and ND jointly determined species abundance by acting on contrasting niche dimensions. The effect of HF decreased relative to ND with increasing disturbance and decreasing fertilization. Dominant species exhibited similar traits in communities whereas dissimilarity favored the coexistence of rare species with dominants by decreasing inter-specific competition. This stabilizing effect on diversity was suggested by a negative relationship between species over-yielding and relative abundance. We discuss the importance of considering independent dimensions of functional niche to better understand species abundance and coexistence within communities.

Characterizing species abundance distributions across taxa and ecosystems using a simple maximum entropy model

The species abundance distribution (SAD) is one of themost studied patterns in ecology due to its potential insights into commonness and rarity, community assembly, and patterns of biodiversity. It is well established that communities are composed of a few common and many rare species, and numerous theoretical models have been proposed to explain this pattern. However, no attempt has been made to determine how well these theoretical characterizations capture observed taxonomic and global-scale spatial variation in the general form of the distribution. Here, using data of a scope unprecedented in community ecology, we show that a simple maximum entropy model produces a truncated log-series distribution that can predict between 83% and 93% of the observed variation in the rank abundance of species across 15 848 globally distributed communities including birds, mammals, plants, and butterflies. This model requires knowledge of only the species richness and total abundance of the community to predict the full abundance distribution, which suggests that these factors are sufficient to understand the distribution for most purposes. Since geographic patterns in richness and abundance can often be successfully modeled, this approach should allow the distribution of commonness and rarity to be characterized, even in locations where empirical data are unavailable.

Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales

Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R(2): 5.6 × 10(-7) to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2): 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.

A predictive model of community assembly that incorporates intraspecific trait variation

Community assembly involves two antagonistic processes that select functional traits in opposite directions. Environmental filtering tends to increase the functional similarity of species within communities leading to trait convergence, whereas competition tends to limit the functional similarity of species within communities leading to trait divergence. Here, we introduce a new hierarchical Bayesian model that incorporates intraspecific trait variation into a predictive framework to unify classic coexistence theory and evolutionary biology with recent trait-based approaches. Model predictions exhibited a significant positive correlation (r = 0.66) with observed relative abundances along a 10 °C gradient in mean annual temperature. The model predicted the correct dominant species in half of the plots, and accurately reproduced species' temperature optimums. The framework is generalizable to any ecosystem as it can accommodate any species pool, any set of functional traits and multiple environmental gradients, and it eliminates some of the criticisms associated with recent trait-based community assembly models.

When should we expect microbial phenotypic traits to predict microbial abundances?

Species' phenotypic traits may predict their relative abundances. Intuitively, this is because locally abundant species have traits making them well-adapted to local abiotic and biotic conditions, while locally rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn't the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species' relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of “adaptedness” and “niche differences.” Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed toward understanding the link between phenotypic traits and frequency-dependence of demographic rates.

Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly

Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (-9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.

Woody encroachment decreases diversity across North American grasslands and savannas

Woody encroachment is a widespread and acute phenomenon affecting grasslands and savannas worldwide. We performed a meta-analysis of 29 studies from 13 different grassland/savanna communities in North America to determine the consequences of woody encroachment on plant species richness. In all 13 communities, species richness declined with woody plant encroachment (average decline = 45%). Species richness declined more in communities with higher precipitation (r2 = 0.81) and where encroachment was associated with a greater change in annual net primary productivity (ANPP; r2 = 0.69). Based on the strong positive correlation between precipitation and ANPP following encroachment (r2 = 0.87), we hypothesize that these relationships occur because water-limited woody plants experience a greater physiological and demographic release as precipitation increases. The observed relationship between species richness and ANPP provides support for the theoretical expectation that a trade-off occurs between richness and productivity in herbaceous communities. We conclude that woody plant encroachment leads to significant declines in species richness in North American grassland/savanna communities.

Using plant functional traits to explain diversity-productivity relationships

Background

The different hypotheses proposed to explain positive species richness–productivity relationships, i.e. selection effect and complementarity effect, imply that plant functional characteristics are at the core of a mechanistic understanding of biodiversity effects.

Methodology/Principal Findings

We used two community-wide measures of plant functional composition, (1) community-weighted means of trait values (CWM) and (2) functional trait diversity based on Rao’s quadratic diversity (FD_Q) to predict biomass production and measures of biodiversity effects in experimental grasslands (Jena Experiment) with different species richness (2, 4, 8, 16 and 60) and different functional group number and composition (1 to 4; legumes, grasses, small herbs, tall herbs) four years after establishment. Functional trait composition had a larger predictive power for community biomass and measures of biodiversitity effects (40–82% of explained variation) than species richness per se (<1–13% of explained variation). CWM explained a larger amount of variation in community biomass (80%) and net biodiversity effects (70%) than FD_Q (36 and 38% of explained variation respectively). FD_Q explained similar proportions of variation in complementarity effects (24%, positive relationship) and selection effects (28%, negative relationship) as CWM (27% of explained variation for both complementarity and selection effects), but for all response variables the combination of CWM and FD_Q led to significant model improvement compared to a separate consideration of different components of functional trait composition. Effects of FD_Q were mainly attributable to diversity in nutrient acquisition and life-history strategies. The large spectrum of traits contributing to positive effects of CWM on biomass production and net biodiversity effects indicated that effects of dominant species were associated with different trait combinations.

Conclusions/Significance

Our results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production.

Relationship between reproductive allocation and relative abundance among 32 species of a Tibetan alpine meadow: effects of fertilization and grazing

BACKGROUND

Understanding the relationship between species traits and species abundance is an important goal in ecology and biodiversity science. Although theoretical studies predict that traits related to performance (e.g. reproductive allocation) are most directly linked to species abundance within a community, empirical investigations have rarely been done. It also remains unclear how environmental factors such as grazing or fertilizer application affect the predicted relationship.

METHODOLOGY

We conducted a 3-year field experiment in a Tibetan alpine meadow to assess the relationship between plant reproductive allocation (RA) and species relative abundance (SRA) on control, grazed and fertilized plots. Overall, the studied plant community contained 32 common species.

PRINCIPAL FINDINGS

At the treatment level, (i) RA was negatively correlated with SRA on control plots and during the first year on fertilized plots. (ii) No negative RA-SRA correlations were observed on grazed plots and during the second and third year on fertilized plots. (iii) Seed size was positively correlated with SRA on control plots. At the plot level, the correlation between SRA and RA were not affected by treatment, year or species composition.

CONCLUSIONS/SIGNIFICANCE

Our study shows that the performance-related trait RA can negatively affect SRA within communities, which is possibly due to the tradeoffs between clonal growth (for space occupancy) and sexual reproduction. We propose that if different species occupy different positions along these tradeoffs it will contribute to biodiversity maintenance in local communities or even at lager scale.

Top-down determinants of niche structure and adaptation among African Acacias

The role of top-down factors like herbivory and fire in structuring species' niches, even in disturbance-dependent biomes like savanna, remains poorly understood. Interactions between herbivory and fire may set up a potential tradeoff axis, along which unique adaptations contribute to structuring communities and determining species distributions. We examine the role of herbivory and fire in structuring distributions of Acacia saplings in Hluhluwe iMfolozi Park in South Africa, and the relationship of species' niche structure to traits that help them survive herbivory or fire. Results suggest that (1) fire and herbivory form a single trade-off axis, (2) Acacia sapling distributions are constrained by fire and herbivory, and (3) Acacia saplings have adaptations that are structured by the tradeoff axis. Herbivory-adapted species tend to have 'cage'-like architecture, thicker bark, and less starch storage, while fire-adapted species tend to have 'pole'-like architecture, relatively thinner bark, and more starch storage.

Biophysical model of prokaryotic diversity in geothermal hot springs

Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms.

Ecometrics: the traits that bind the past and present together

We outline here an approach for understanding the biology of climate change, one that integrates data at multiple spatial and temporal scales. Taxon-free trait analysis, or "ecometrics," is based on the idea that the distribution in a community of ecomorphological traits such as tooth structure, limb proportions, body mass, leaf shape, incubation temperature, claw shape, any aspect of anatomy or physiology can be measured across some subset of the organisms in a community. Regardless of temporal or spatial scale, traits are the means by which organisms interact with their environment, biotic and abiotic. Ecometrics measures these interactions by focusing on traits which are easily measurable, whose structure is closely related to their function, and whose function interacts directly with local environment. Ecometric trait distributions are thus a comparatively universal metric for exploring systems dynamics at all scales. The main challenge now is to move beyond investigating how future climate change will affect the distribution of organisms and how it will impact ecosystem services and to shift the perspective to ask how biotic systems interact with changing climate in general, and how climate change affects the interactions within and between the components of the whole biotic-physical system. We believe that it is possible to provide believable, quantitative answers to these questions. Because of this we have initiated an IUBS program iCCB (integrative Climate Change Biology).

Advances, challenges and a developing synthesis of ecological community assembly theory

Ecological approaches to community assembly have emphasized the interplay between neutral processes, niche-based environmental filtering and niche-based species sorting in an interactive milieu. Recently, progress has been made in terms of aligning our vocabulary with conceptual advances, assessing how trait-based community functional parameters differ from neutral expectation and assessing how traits vary along environmental gradients. Experiments have confirmed the influence of these processes on assembly and have addressed the role of dispersal in shaping local assemblages. Community phylogenetics has forged common ground between ecologists and biogeographers, but it is not a proxy for trait-based approaches. Community assembly theory is in need of a comparative synthesis that addresses how the relative importance of niche and neutral processes varies among taxa, along environmental gradients, and across scales. Towards that goal, we suggest a set of traits that probably confer increasing community neutrality and regionality and review the influences of stress, disturbance and scale on the importance of niche assembly. We advocate increasing the complexity of experiments in order to assess the relative importance of multiple processes. As an example, we provide evidence that dispersal, niche processes and trait interdependencies have about equal influence on trait-based assembly in an experimental grassland.

The statistical mechanics of community assembly and species distribution

• Theoretically, communities at or near their equilibrium species number resist entry of new species. Such 'biotic resistance' recently has been questioned because of successful entry of alien species into diverse natural communities. • Data on 10,409 naturalizations of 5350 plant species over 16 sites dispersed globally show exponential distributions both for species over sites and for sites over number of species shared. These exponentials signal a statistical mechanics of species distribution, assuming two conditions. First, species and sites are equivalent, either identical ('neutral') or so complex that the chance a species is in the right place at the right time is vanishingly small ('idiosyncratic'); the range of species and sites in our data disallows a neutral explanation. Secondly, the total number of naturalizations is fixed in any era by a 'regulator'. • Previous correlation of species naturalization rates with net primary productivity over time suggests that the regulator is related to productivity. • We conclude that biotic resistance is a moving ceiling, with resistance controlled by productivity. The general observation that the majority of species occur naturally at only a few sites, and only a few species occur at many sites, now has a quantitative (exponential) character, offering the study of species' distributions a previously unavailable rigor.

Measurement scale in maximum entropy models of species abundance

The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry with regard to measurement scale. By symmetry, I mean that different ecological processes preserve the same measure of information and lose all other information in the aggregation of various perturbations. I frame these explanations of symmetry, measurement, and aggregation in terms of a recently developed extension to the theory of maximum entropy. I show that the natural measurement scale for the species abundance distribution is log-linear: the information in observations at small population sizes scales logarithmically and, as population size increases, the scaling of information grades from logarithmic to linear. Such log-linear scaling leads naturally to a gamma distribution for species abundance, which matches well with the observed patterns. Much of the variation between samples can be explained by the magnitude at which the measurement scale grades from logarithmic to linear. This measurement approach can be applied to the similar problem of allelic diversity in population genetics and to a wide variety of other patterns in biology.

Predicting the post-fire responses of animal assemblages: testing a trait-based approach using spiders

1. Developing a predictive understanding of how species assemblages respond to fire is a key conservation goal. In moving from solely describing patterns following fire to predicting changes, plant ecologists have successfully elucidated generalizations based on functional traits. Using species traits might also allow better predictions for fauna, but there are few empirical tests of this approach. 2. We examined whether species traits changed with post-fire age for spiders in 27 sites, representing a chronosequence of 0-20 years post-fire. We predicted a priori whether spiders with ten traits associated with survival, dispersal, reproduction, resource-utilization and microhabitat occupation would increase or decrease with post-fire age. We then tested these predictions using a direct (fourth-corner on individual traits and composite traits) and an indirect (emergent groups) approach, comparing the benefits of each and also examining the degree to which traits were intercorrelated. 3. For the seven individual traits that were significant, three followed predictions (body size, abundance of burrow ambushers and burrowers was greater in recently burnt sites); two were opposite (species with heavy sclerotisation of the cephalothorax and longer time to maturity were in greater abundance in long unburnt and recently burnt sites respectively); and two displayed response patterns more complex than predicted (abdominal scutes displayed a U-shaped response and dispersal ability a hump shaped curve). However, within a given trait, there were few significant differences among post-fire ages. 4. Several traits were intercorrelated and scores based on composite traits used in a fourth-corner analysis found significant patterns, but slightly different to those using individual traits. Changes in abundance with post-fire age were significant for three of the five emergent groups. The fourth-corner analysis yielded more detailed results, but overall we consider the two approaches complementary. 5. While we found significant differences in traits with post-fire age, our results suggest that a trait-based approach may not increase predictive power, at least for the assemblages of spiders we studied. That said, there are many refinements to faunal traits that could increase predictive power.

Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes

All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the 'assembly rules' concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant-fungal interactions, and (iii) investigation of microbe-microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host-fungus interactions and mechanisms of fungal-fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies.

Conceptual synthesis in community ecology

Community ecology is often perceived as a "mess, "given the seemingly vast number of processes that can underlie the many patterns of interest, and the apparent uniqueness of each study system. However, at the most general level, patterns in the composition and diversity of species--the subject matter of community ecology--are influenced by only four classes of process: selection, drift, speciation, and dispersal. Selection represents deterministic fitness differences among species, drift represents stochastic changes in species abundance, speciation creates new species, and dispersal is the movement of organisms across space. All theoretical and conceptual models in community ecology can be understood with respect to their emphasis on these four processes. Empirical evidence exists for all of these processes and many of their interactions, with a predominance of studies on selection. Organizing the material of community ecology according to this framework can clarify the essential similarities and differences among the many conceptual and theoretical approaches to the discipline, and it can also allow for the articulation of a very general theory of community dynamics: species are added to communities via speciation and dispersal, and the relative abundances of these species are then shaped by drift and selection, as well as ongoing dispersal to drive community dynamics.

A structured and dynamic framework to advance traits-based theory and prediction in ecology

Predicting changes in community composition and ecosystem function in a rapidly changing world is a major research challenge in ecology. Traits-based approaches have elicited much recent interest, yet individual studies are not advancing a more general, predictive ecology. Significant progress will be facilitated by adopting a coherent theoretical framework comprised of three elements: an underlying trait distribution, a performance filter defining the fitness of traits in different environments, and a dynamic projection of the performance filter along some environmental gradient. This framework allows changes in the trait distribution and associated modifications to community composition or ecosystem function to be predicted across time or space. The structure and dynamics of the performance filter specify two key criteria by which we judge appropriate quantitative methods for testing traits-based hypotheses. Bayesian multilevel models, dynamical systems models and hybrid approaches meet both these criteria and have the potential to meaningfully advance traits-based ecology.

Bacterial chemotaxis and entropy production

Entropy production is calculated for bacterial chemotaxis in the case of a migrating band of bacteria in a capillary tube. It is found that the speed of the migrating band is a decreasing function of the starting concentration of the metabolizable attractant. The experimentally found dependence of speed on the starting concentration of galactose, glucose and oxygen is fitted with power-law functions. It is found that the corresponding exponents lie within the theoretically predicted interval. The effect of the reproduction of bacteria on band speed is considered, too. The acceleration of the band is predicted due to the reproduction rate of bacteria. The relationship between chemotaxis, the maximum entropy production principle and the formation of self-organizing structure is discussed.