Relationship between species relative abundance and plant traits for an infertile habitat

This study tested whether differences in species abundance at an infertile site could be explained by differences in the species' plant traits. Nine traits were chosen for the analysis based on results of previous studies conducted across soil fertility gradients. The traits were measured for each of seven herbaceous species whose abundance ranged from 5% to 100% of locations occupied in a ridgetop habitat. Using linear regression, significant relationships were found between species relative abundance and each of five traits. In these relationships, a trait explained between 69% and 88% of interspecific variation in abundance. Relatively abundant species had a slower growth rate, smaller shoot mass, higher root to shoot ratio, slower loss of leaf tissue to herbivores and higher infection of roots by mycorrhizal fungi than less abundant species. Using three of these five traits (i.e. shoot mass, mycorrhizal infection and loss of leaf tissue to herbivores) as independent variables in a multiple regression equation explained 99% of interspecific variation in abundance. The latter result indicates that species relative abundance can be explained for a single habitat by choosing traits found to be related to species abundance in previous gradient studies. However, not every trait chosen was significantly related to species abundance. Therefore, a large number of traits may have to be chosen initially to ensure that some subset of these traits can explain species relative abundance.     

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.     

Positive interactions, discontinuous transitions and species coexistence in plant communities

The population and community level consequences of positive interactions between plants remain poorly explored. In this study we incorporate positive resource-mediated interactions in classic resource competition theory and investigate the main consequences for plant population dynamics and species coexistence. We focus on plant communities for which water infiltration rates exhibit positive dependency on plant biomass and where plant responses can be improved by shading, particularly under water limiting conditions. We show that the effects of these two resource-mediated positive interactions are similar and additive. We predict that positive interactions shift the transition points between different species compositions along environmental gradients and that realized niche widths will expand or shrink. Furthermore, continuous transitions between different community compositions can become discontinuous and bistability or tristability can occur. Moreover, increased infiltration rates may give rise to a new potential coexistence mechanism that we call controlled facilitation.     

Phylogeny, traits, environment, and space in cerrado plant communities at Emas National Park (Brazil)

Soil, drought, and fire are abiotic factors that may act as environmental filters in the cerrado, the Brazilian savanna. We used a framework to analyze environmental filtering in geographic and phylogenetic context, sampling woody species in one of the largest cerrado reserves. In 100 quadrats, we measured 10 functional traits on each woody individual. We also measured several soil variables, altitude and slope as a rough surrogate of water availability, interval between fires, and time since last fire. Almost all environmental variables were spatially auto-correlated. We found an overall trait clustering, but not an overall phylogenetic clustering. Nevertheless, we found a phylogenetic signal for some traits. Linking phylogeny, traits, environment, and space, we were able to detect a major dichotomy between two geomorphological units. The flat tableland was positively related with altitude, fire frequency, and nutrient-richer soil. Environmental filtering caused by water availability and fire lead to trait clustering, with smaller shrubs and trees that presented thicker barks, denser woods, sclerophyllous leaves, highlighted by the prevalance of Myrtaceae. The other geomorphological unit, hilly terrain, was positively related with slope, low fire frequency, and nutrient-poorer soil. Environmental filtering was caused especially by nutrient-poor soil that lead to trait clustering, assembling taller trees, with thinner barks, lighter woods, and compound, large, tender, nutrient-richer leaves, distributed across many lineages, including Fabaceae. Hence, the high environmental variability in space with different environmental filters assembled different combination of plant traits and lineages, increasing the overall diversity in cerrado.     

Photophysics of ethidium bromide complexed to ct-DNA: a maximum entropy study

Time-integrated and time-resolved fluorescence spectroscopies have been used to probe the photophysical properties of ethidium bromide (Eb) complexed to calf thymus DNA (ct-DNA). Fluorescence decay profiles are obtained using the technique of time-correlated single photon counting (TCSPC), and subsequently analysed using conventional sum-of-exponential (SOE) routines and also the maximum entropy method (MEM). Through use of these methods and simulated decay data, it is demonstrated that the kinetics of Eb in the presence of ds-DNA are best described by a generic model consisting of three exponential terms. At all DNA:Eb ratios and NaCl concentrations studied, free Eb is detected. Furthermore, Eb is found to interact with ds-DNA through two mechanisms, each distinguishable by its fluorescence decaytime. Eb is shown to interact with DNA through classic intercalation, and also through binding at secondary sites. The component decaytimes are shown to be a function of NaCl concentration but independent of DNA:Eb molar ratio.     

Methods for detecting non-randomness in species co-occurrences: a contribution

Summary Comparison of co-occurrences between species on a group of islands with those expected from a randombased null model could provide evidence on community structure. However, it is difficult to decide on the appropriate null model. Gilpin and Diamond proposed a model and a test for departure from it, but this test is shown to indicate significant structure even when applied to a matrix of random numbers. An alternative method is suggested, using the distribution of Gilpin and Diamond's deviation as test statistic, but determining the expected distribution by Monto Carlo simulation, and using many such simulations as a randomisation test of significance. The null model used accepts the observed totals of occurrences for islands and species; it therefore offers a somewhat conservative test. Applied to the Vanuatu bird data that Gilpin and Diamond used, significant departure from a null model is seen, but with an excess of extreme negative associations, the opposite result from that given by Gilpin and Diamond's method. It is not possible to tell whether the negative associations are due to autecology, biogeography, or to interactions between species.     

Heterogeneous communities with lognormal species abundance distribution: Species-area curves and sustainability

Heterogeneous species abundance models are models in which the dynamics differ between species, described by variation among parameters defining the dynamics. Using a dynamic and heterogeneous species abundance model generating the lognormal species abundance distribution it is first shown that different degrees of heterogeneity may result in equivalent species abundance distributions. An alternative to Preston's canonical lognormal model is defined by assuming that reduction in resources, for example reduction in available area, increases the density regulation of each species. This leads to species-individual curves and species-area curves that are approximately linear in a double logarithmic plot. Preston's canonical parameter gamma varies little along these curves and takes values in the neighborhood of one. Quite remarkably, the curves, which define the sensitivity of the community to area reductions, are independent of the heterogeneity among species for this model. As a consequence, the curves can be estimated from a single sample from the community using the Poisson lognormal distribution. It is shown how to perform sensitivity analysis with respect to over-dispersion in sampling relative to the Poisson distribution as well as sampling intensity, that is, the fraction of the community sampled. The method is exemplified by analyzing three simulated data sets.     

Investigation of a two-point maximum entropy regularization method for signal enhancement applied to magnetoencephalography data

A two-point maximum entropy method (TPMEM) was investigated for post-acquisition signal recovery in magnetoencephalography (MEG) data, as a potential replacement of a low-pass (LP) filtering technique currently in use. We first applied TPMEM and the LP filter for signal recovery of synthetically noise corrupted MEG “phantom” data sets in which the true underlying signal was known. Results were quantified with the use of visual plots, percent error histograms, and the statistical parameters root mean squared error and Pearson’s correlation coefficient. Synthetically noise corrupted data from a simulated magnetic dipole was used to quantify the improvements gained in using TPMEM over LP filters in reconstructing known dipole parameters such as position, orientation, and magnitude. Finally, we applied TPMEM and LP filters to a sample MEG patient data set. Our results show that TPMEM has improved noise-reduction and signal recovery capabilities than those of the LP filter, and furthermore data processed with TPMEM shows less error in the reconstructed dipole parameters. We propose that TPMEM can be used for MEG signal processing, resulting in improved MEG source characterization.     

Processes regulating the community composition and relative abundance of taxa in the diatom communities of the Malili Lakes, Sulawesi Island, Indonesia

Although high levels of endemism have been reported on Sulawesi Island for almost 150 years, the aquatic systems of the island have received little attention until recently. The diatoms of the ancient Malili Lakes, located on central Sulawesi, exhibit levels of endemism unequaled elsewhere in the world. Interestingly, the diatom community of the lakes is taxonomically impoverished, and the entire order Centrales is conspicuous by its absence. In this article we review the mechanisms contributing to the development and maintenance of community composition and relative abundance of taxa within the system, at within-lake and system-wide scales. Our findings demonstrate that stochastic processes related to biogeography and colonization have had little influence on the diatom flora of the lakes, and deterministic processes related to competition, selection, speciation, and adaptive radiation, functioning on very small spatial scales, have contributed greatly to the diversity, community structure, and endemism of the system.     

Temporal niche dynamics, relative abundance and phylogenetic signal of coexisting species

The coexistence of similar species accounts for some 30% of diversity within communities, yet the coexistence and relative abundance of similar species is a continuing ecological conundrum. Using close phylogenetic relatedness as a measure of similarity, we previously demonstrated that neither classic niche theory nor neutral theory can explain the relative abundances of co-occurring pairs of similar tree species in a diverse tropical forest. Here, we show that the stable, focused competition of a temporal niche dynamic fits the distribution of observed fractional abundances (pairwise relative abundances). Previously published, independent evidence of temporal dynamics in this community supports our results; our model identifies additional criteria for field tests of differential sensitivity (DS) temporal dynamics. The success of temporal dynamics at explaining the observed distribution—and the failure of alternative hypotheses to do so—indicates that current diagnostics of community structure and assembly needs general re-examination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Prediction of species composition of plant communities in a rural landscape based on species traits

The species composition of a community is a subset of the regional species pool, and predicting the species composition of a community from ecological traits of organisms is an important objective in ecology. If such a prediction can be made feasible, we could assess the risk of invasion of locally new species (alien species and genetically modified species) into natural communities. We developed and tested statistical models to predict a community’s species composition from ecological traits of the species pool. Various types of communities (forest, meadow, and weed communities) exist in a small area of traditional rural landscape in Japan, and have been maintained by human activities. These communities and the tracheophytes species pool in the 1-km² research area were considered. We used logistic regression and decision-tree analysis to construct predictive models of community species composition based on plant traits, using the presence or absence of species in a community as the dependent variable and ecological traits as independent variables. Plant traits were grouped by cluster analysis, and the average in each trait group was used for model building to avoid multiple collinearity. Statistical prediction models were significant in all communities. About 60–75% of species composition could be predicted from the measured plant traits in forest communities, but 33–56% in the meadow and weed communities. Our results showed the possibility of predicting the species composition of plant communities from the ecological traits of the plant species together with the information on local species pool.     

Network properties, species abundance and evolution in a model of evolutionary ecology

We study the evolution of the network properties of a populated network embedded in a genotype space characterized by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution produces two distinct types of network. When a specific genotype is only able to influence a few other genotypes, the ecosystem consists of separate non-interacting clusters (i.e. isolated compartments) in genotype space. When different types may influence a large number of other sites, the network becomes one large interconnected cluster. The distribution of interaction strengths--but not the number of connections--changes significantly with time. We find that the species abundance is only realistic for a high level of species connectivity. This suggests that real ecosystems form one interconnected whole in which selection leads to stronger interactions between the different types. Analogies with niche and neutral theory and assembly models are also considered.     

Competition, traits and resource depletion in plant communities

Although of primary importance to explain plant community structure, general relationships between plant traits, resource depletion and competitive outcomes remain to be quantified across species. Here, we used a comparative approach to test whether instantaneous measurements of plant traits can capture both the amount of resources depleted under plant cover over time (competitive effect) and the way competitors perceived this resource depletion (competitive response). We performed a large competition experiment in which phytometers from a single grass species were transplanted within 18 different monocultures grown in a common-garden experiment, with a time-integrative quantification of light and water depletion over the phytometers’ growing season. Resource-capturing traits were measured on both phytometers (competitive response traits) and monocultures (competitive effect traits). The total amounts of depleted light and water availabilities over the season strongly differed among monocultures; they were best estimated by instantaneous measurements of height and rooting depth, respectively, performed when either light or water became limiting. Specific leaf area and leaf water potential, two competitive response traits measured at the leaf level, were good predictors of changes in phytometer performance under competition, and reflected the amount of light and water, respectively, perceived by plants throughout their lifespan. Our results demonstrated the relevance of instantaneous measures of plant traits as indicators of resource depletion over time, validating the trait-based approach for competition ecology. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dynamical entropy via entropy of non-random matrices: Application to stability and complexity in modelling ecosystems

In the present paper we have first introduced a measure of dynamical entropy of an ecosystem on the basis of the dynamical model of the system. The dynamical entropy which depends on the eigenvalues of the community matrix of the system leads to a consistent measure of complexity of the ecosystem to characterize the dynamical behaviours such as the stability, instability and periodicity around the stationary states of the system. We have illustrated the theory with some model ecosystems.     

Leaf miner and plant galler species richness on Acacia: relative importance of plant traits and climate

Diversity patterns of herbivores have been related to climate, host plant traits, host plant distribution and evolutionary relationships individually. However, few studies have assessed the relative contributions of a range of variables to explain these diversity patterns across large geographical and host plant species gradients. Here we assess the relative influence that climate and host plant traits have on endophagous species (leaf miners and plant gallers) diversity across a suite of host species from a genus that is widely distributed and morphologically variable. Forty-six species of Acacia were sampled to encapsulate the diversity of species across four taxonomic sections and a range of habitats along a 950 km climatic gradient: from subtropical forest habitats to semi-arid habitats. Plant traits, climatic variables, leaf miner and plant galler diversity were all quantified on each plant species. In total, 97 leaf mining species and 84 plant galling species were recorded from all host plants. Factors that best explained leaf miner richness across the climatic gradient (using AIC model selection) included specific leaf area (SLA), foliage thickness and mean annual rainfall. The factor that best explained plant galler richness across the climatic gradient was C:N ratio. In terms of the influence of plant and climatic traits on species composition, leaf miner assemblages were best explained by SLA, foliage thickness, mean minimum temperature and mean annual rainfall, whilst plant gall assemblages were explained by C:N ratio, %P, foliage thickness, mean minimum temperature and mean annual rainfall. This work is the first to assess diversity and structure across a broad environmental gradient and a wide range of potential key climatic and plant trait determinants simultaneously. Such methods provide key insights into endophage diversity and provide a solid basis for assessing their responses to a changing climate.     

Ecological effects of cell-level processes: genome size,functional traits and regional abundance of herbaceous plant species

Background and Aims

Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate.

Methods

Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis.

Key Results

Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R² = 0·145) than for perennials (R² = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance.

Conclusions

The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes.