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.     

Ontogenetic trait variation and metacommunity effects influence species relative abundances during tree community assembly

Predicting species abundance is one of the most fundamental pursuits of ecology. Combining the information encoded in functional traits and metacommunities provides a new perspective to predict the abundance of species in communities. We applied a community assembly via trait selection model to predict quadrat-scale species abundances using functional trait variation on ontogenetic stages and metacommunity information for over 490 plant species in a subtropical forest and a lowland tropical forest in Yunnan, China. The relative importance of trait-based selection, mass effects, and stochasticity in shaping local species abundances is evaluated using different null models. We found both mass effects and trait selection contribute to local abundance patterns. Trait selection was detectable at all studied spatial scales (0.04–1 ha), with its strength stronger at larger scales and in the subtropical forest. In contrast, the importance of stochasticity decreased with spatial scale. A significant mass effect of the metacommunity was observed at small spatial scales. Our results indicate that tree community assembly is primarily driven by ontogenetic traits and metacommunity effects. Our findings also demonstrate that including ontogenetic trait variation into predictive frameworks allows ecologists to infer ecological mechanisms operating in community assembly at the individual level.     

Filtering processes in the assembly of plant communities: Are species presence and abundance driven by the same traits?

Question: Is the response of plant traits to environment at the community level similar when considering species abundance and when considering species presence only? Location: Mountain grasslands, central Argentina. Methods: We used data from 57 floristic samples, ordinated through DCCA along moisture and grazing gradients combined with trait values from 85 species (plant height, leaf area, leaf thickness leaf toughness and SLA). For each sample, we calculated the weighted average (considering species abundance) and the simple average (considering only species presence). Through multiple regressions we analysed how each average (dependent variable) responded to moisture and grazing (DCCA scores along Axes 1 and 2, respectively, as independent variables). Results: Weighted averages of all traits were significantly associated to both gradients, while simple averages did not always respond. In some cases the responses followed similar but weaker trends than the responses of weighted averages, but in other cases these responses were qualitatively different. Traits more associated with size (plant height, leaf area, leaf thickness) responded more consistently (similar trends for both averages) to grazing than to moisture, while traits more associated with plant resource acquisition (SLA, leaf toughness) responded more consistently to moisture than to grazing. Conclusion: The trait values and combinations which determine the probability of species presence are not necessary the same as those which determine their probability of becoming abundant. To understand community assembly rules, both species presence and species abundance should be taken into account as the result of different, although closely linked, filtering processes.     

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.     

Global warming will affect the maximum potential abundance of boreal plant species

Forecasting the impact of future global warming on biodiversity requires understanding how temperature limits the distribution of species. Here we rely on Liebig's Law of Minimum to estimate the effect of temperature on the maximum potential abundance that a species can attain at a certain location. We develop 95%-quantile regressions to model the influence of effective temperature sum on the maximum potential abundance of 25 common understory plant species of Finland, along 868 nationwide plots sampled in 1985. Fifteen of these species showed a significant response to temperature sum that was consistent in temperature-only models and in all-predictors models, which also included cumulative precipitation, soil texture, soil fertility, tree species and stand maturity as predictors. For species with significant and consistent responses to temperature, we forecasted potential shifts in abundance for the period 2041–2070 under the IPCC A1B emission scenario using temperature-only models. We predict major potential changes in abundance and average northward distribution shifts of 6–8 km yr⁻¹. Our results emphasize inter-specific differences in the impact of global warming on the understory layer of boreal forests. Species in all functional groups from dwarf shrubs, herbs and grasses to bryophytes and lichens showed significant responses to temperature, while temperature did not limit the abundance of 10 species. We discuss the interest of modelling the ‘maximum potential abundance’ to deal with the uncertainty in the predictions of realized abundances associated to the effect of environmental factors not accounted for and to dispersal limitations of species, among others. We believe this concept has a promising and unexplored potential to forecast the impact of specific drivers of global change under future scenarios.     

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.     

Grazing alters species relative abundance by affecting plant functional traits in a Tibetan subalpine meadow

Domestic livestock grazing has caused dramatic changes in plant community composition across the globe. However, the response of plant species abundance in communities subject to grazing has not often been investigated through a functional lens, especially for belowground traits. Grazing directly impacts aboveground plant tissues, but the relationships between above‐ and belowground traits, and their influence on species abundance are also not well known. We collected plant trait and species relative abundance data in the grazed and nongrazed meadow plant communities in a species‐rich subalpine ecosystem of the Qinghai–Tibet Plateau. We measured three aboveground traits (leaf photosynthesis rate, specific leaf area, and maximum height) and five belowground traits (root average diameter, root biomass, specific root length, root tissue density, and specific root area). We tested for shifts in the relationship between species relative abundance and among all measured traits under grazing compared with the nongrazed meadow. We also compared the power of above‐ and belowground traits to predict species relative abundance. We observed a significant shift from a resource conservation strategy to a resource acquisition strategy. Moreover, this resource conservation versus resource acquisition trade‐off can also determine species relative abundance in the grazed and nongrazed plant communities. Specifically, abundant species in the nongrazed meadow had aboveground and belowground traits that are associated with high resource conservation, whereas aboveground and belowground traits that are correlated with high resource acquisition determined species relative abundance in the grazed meadow. However, belowground traits were found to explain more variances in species relative abundance than aboveground traits in the nongrazed meadow, while aboveground and belowground traits had comparable predictive power in the grazed meadow. We show that species relative abundance in both the grazed and the nongrazed meadows can be predicted by both aboveground traits and belowground traits associated with a resource acquisition versus conservation trade‐off. More importantly, we show that belowground traits have higher predictive power of species relative abundance than aboveground traits in the nongrazed meadow, whereas in the grazed meadows, above‐ and belowground traits had comparable high predictive power.     

Relative abundance distributions in plant communities: effects of species richness and of spatial scale

Abstract. Relative abundance distributions (RADs) are an important feature of community structure, but little is known of the factors affecting which type of RAD is observed in a particular community. We examined the influences of species richness and of spatial scale on the RAD of plant communities. The effect of species richness was examined by analysing simulated communities generated under the Broken stick model, the Sequential breakage model, and a randomized version of Niche pre-emption model. In all cases, when there were few species in the community the data only occasionally gave the best fit to the model that was used to generate it. With 40–65 species, a best fit was obtained for the correct model in about 75 % of cases, almost irrespective of the model. Effects of spatial scale were examined in data from four dune slacks and from two semi-arid grasslands, by analysing biomass values at a range of sample sizes. The model that best fitted the whole sample differed between the four slacks and between the slacks and the semi-arid grasslands. The change in which model of RAD fitted best, as sample size was reduced, varied between sites and between habitat types. At the smallest sample sizes, the Zipf-Mandelbrot model often fitted, and in the slack sites the Broken stick also, though neither fitted (in the vegetation examined) at larger spatial scales. It is concluded the RAD is affected by species richness and by spatial scale, in ways that currently do not enable simple prediction. RADs can theoretically give information on the processes such as resource partitioning, immigration and competition that have structured the community, but they are a blunt tool for this purpose.     

Mycorrhizal traits and plant communities: perspectives for integration

Plant functional type‐ and trait‐based approaches to understanding vegetation dynamics are gradually gaining popularity. However, plant mycorrhizal traits are rarely considered in plant trait databases and are almost totally neglected in trait‐based plant community studies, despite more than 90% of the land flora being mycorrhizal. In this paper I describe and define the mycorrhizal traits of plant species, notably mycorrhizal type, mycorrhizal status, mycorrhizal flexibility and mycorrhizal dependency, which potentially influence plant distribution and community structure. I propose ways of using these traits for large‐scale synthetic studies for understanding the role of mycorrhizal symbiosis in vegetation dynamics. I suggest considering plant community mycorrhization – community means of mycorrhizal traits weighted by plant species abundances – and suggest an index of mycorrhization to describe the mycorrhizal trait composition of plant communities.     

Plant traits as predictors of woody species dominance in climax forest communities

Abstract. The dominance of a given tree or shrub species in a particular forest community may be determined by many ecological traits of the target species, as well as those of the surrounding species as its potential competitors. The present study was conducted to evaluate the possibility of predicting community status (species composition and dominance) on the basis of traits of local flora using statistical methods, and to visualize the mathematical function which determines species dominance. A general linear model and logistic regression were used for the statistical analysis. Dependent variables were designated as dominance and presence/absence of species in climax forest, with independent variables as vegetative and reproductive traits. Subalpine, cool‐temperate, warm‐temperate and subtropical climax rain forests in East Asia were studied. Quantitative prediction of climax community status could readily be made based on easily measured traits of local flora. Species composition and 74.6% of the total variance of species dominance were predicted based on two traits; maximum height and shade tolerance. Through application of this method, the capacity of an alien species to invade a climax forest community could possibly be predicted prior to introduction of the alien 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.     

Sampling beetle communities: Trap design interacts with weather and species traits to bias capture rates

Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long‐term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels, standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large‐bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well‐known but likely common phenomenon—an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long‐term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.     

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.     

Plant traits and regeneration of urban plant communities after disturbance: Does the bud bank play any role?

Questions: What is the relative role of the bud bank, seed and various species traits in the regeneration of urban plant communities after severe disturbances? Do invasive and exotic species, highly abundant in disturbed communities, regenerate better than native species after disturbance? Methods: Hand tilling was applied to three urban plant communities with and without additional herbicide treatment to exclude regeneration from the bud bank. Plant traits were determined from the literature and databases. Species responses to the treatments were evaluated with RDA analyses in CANOCO. Linear models were applied to identify traits that could predict the responses of species to disturbance. Results: The bud bank played a key role in regeneration in the plots without herbicide. In the plots with herbicide treatment, the seed bank was important in re‐establishing vegetation after disturbance. Exclusion of the bud bank by using herbicide allowed the establishment of small annuals, whereas biennials and perennials were successful in plots where the bud bank was not inhibited by herbicide. Exotic species with a long residence time in the local flora were successful in plots where regeneration from the bud bank was excluded, whereas species with short residence times or that were invasive were suppressed by both types of disturbance. Conclusion: In response to various types of disturbance, species with different regeneration strategies (either seeds or bud bank) were promoted. Exotic species were suppressed primarily by disturbance, which suggests that factors other than just regenerative capability contributed to the high abundance of exotics in urban communities.