Studying ecological communities from a neutral standpoint: A review of models’ structure and parameter estimation

Neutral models provide an alternative to niche-based assembly rules of ecological communities by assuming that communities’ properties are shaped by the stochastic interplay between ecological drift, migration and speciation. The recent and ongoing interest about neutral assumptions has produced many developments on the theoretical side, with nevertheless limited echoes in terms of analyses of real-world data. The present review paper aims to help bridge the widening gap between modellers and field ecologists through two objectives. First, to provide a multi-criteria typology of the main neutral models, including those from population genetics that have not yet been transposed to ecology, by considering how the fundamental processes of ecological drift, speciation and migration are modelled and, specifically, how space is taken into account. Second, to review methods recently proposed to estimate models parameters from field data, a point that should be mastered to allow for broader applications.     

Distance-based eigenvector maps (DBEM) to analyse metapopulation structure with irregular sampling

Characterizing spatial patterns due to ecological processes is a major issue for analysing and predicting species distributions. Grasping the non-linear nature of population dynamics over networks of discrete suitable sites is here central, as very specific signatures are expected. In the line of promising results from Fourier analysis of metapopulation maps, we found distance-based eigenvector maps (DBEM) to help disentangle the respective signatures of habitat and metapopulation structuring, with the great advantage of being applicable to irregular sampling schemes, a common feature of ecological surveys. A smoothing procedure was required to obtain the distinguishable signatures, and this may be a critical issue for investigating non-contingent and reliable patterns in spatial ecology.     

An individual-based model to study the reproduction of egg bearing copepods: Application to Eurytemora affinis (Copepoda Calanoida) from the Seine estuary,France

Limited empirical studies have elucidated the daily egg production and associated reproductive processes of egg bearing copepod. Herein, we present an individual-based model which constitutes a realistic representation of the reproduction in egg bearing copepods. The model has been parameterized using an extensive set of experimental data obtained from the literature and from the laboratory and field experiments on the estuarine copepod Eurytemora affinis. The proposed model takes into account the adult female longevity, the clutch size and interclutch duration, which is a function of egg maturation time and latency time required by the female after egg hatching to produce a new clutch. The embryonic development time and hatching success are also taken into account. The effect of temperature on the means and variances of above-mentioned reproductive parameters has been also incorporated. A multi agent system based generic platform “Mobidyc” has been used to generate and calibrate the model. The model demonstrates the reproductive parameters of females of E. affinis which is validated through individual based experiments. Temperature specific simulations provide a dynamical explanation of temperature effect on the cumulative egg production. The daily survival principally affects the number of clutches produced per female during its life span. The results obtained in the present study by combining temperature and survival effects reveal the relatively greater importance of the first factor on the daily egg production of egg-carrying copepods. The present model is generic and hence easily applicable to other animals with comparable reproductive strategy.     

Teachers' conceptions of nature and environment in 16 countries

By using an original framework involving complementary statistical approaches, we investigated the environmental attitudes of 6379 pre-service and in-service teachers in 16 countries of Europe and its neighbourhood. To test hypotheses about the nature of environmental attitudes, we examined the variation across groups of individuals (between-class analysis), investigated the independent effects of several candidate explanatory factors (orthogonal analysis), and finally inspected potential relationships between conceptions on a variety of topics (co-inertia analysis).     

PM2.5 and PM10 air pollution peaks are associated with emergency department visits for psychotic and mood disorders

Environmental Science and Pollution Research - Particulate matters with a diameter of less than 10 µm (PM10) or less than 2.5 µm (PM2.5) are major air pollutants. Their...     

Biological Air Quality Monitoring: a Review

Air quality monitoring is currently ensured by captors measuring few physicochemical parameters, then they cannot evaluate unforeseen compounds and the interaction effects of pollutants. On the contrary, the use of bioindicators can answer these problems. Among them, plants are used in two ways:1) Passive bioindicators: trees, lichens and mosses are used to determine the distribution and even the contaminants long-term effects on vast zones and, possibly, the concentrations of pollutants to which they were exposed.2) Active bioindicators: tobacco and mosses make available the defective zones in plants and enable determination of deposition fluxes.Moreover, techniques based on biomarkers identification should increase the answer's sensitivity. However, the plants present the disadvantage of being unable to provide a response in a time lapse comparable with that of the on-line analysers. Lastly, the development of tools using animal cells should allow, in the near future, to measure the total polluting load under conditions close to those of the routine techniques. Then, the real impact of the contaminant on public health could be approached.     

Estimating parameters of neutral communities: from one single large to several small samples

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

Application of next-generation sequencing technologies to conservation of wood-inhabiting fungi

Next-generation sequencing (NGS) has significantly increased knowledge of microbial communities and their distribution. However, it is still not common to apply NGS technology to microbial conservation. We sought to use NGS technologies to evaluate conservation strategies for wood-inhabiting fungi. Evaluating a deadwood experiment 3 years after it was established, we specifically examined which tree species combinations promoted the highest richness of wood-inhabiting fungi. Deadwood enrichment was an effective strategy and logs of 6 tree species, either those with the highest wood-inhabiting fungal α and γ diversity or those with the highest β diversity, maintained >1,000 operational taxonomic units (OTUs) spread over a wide range of taxonomic groups. In comparison, a conservation strategy based only on the results of sporocarp surveys yielded 591 OTUs. This result highlights the need to use NGS approaches to inform microbial conservation strategies. We also determined that 5 tree species with the highest saproxylic beetle γ diversity simultaneously conserved wood-inhabiting fungi. Apart from deadwood volume, we suggest data on deadwood quality and species also be included as indicators, especially for wood-inhabiting fungal diversity, and incorporated quickly in forest assessment and monitoring systems in Central Europe.     

Impact of the mixing boundary layer on the relationship between PM2.5 and aerosol optical thickness

The purpose of this paper is to study the relationship between columnar aerosol optical thickness and ground-level aerosol mass. A set of Sun photometer, elastic backscattering lidar and TEOM measurements were acquired during April 2007 in Lille, France. The PM2.5 in the mixed boundary layer is estimated using the lidar signal, aerosol optical thickness, or columnar integrated Sun photometer size distribution and compared to the ground-level station measurements. The lidar signal recorded in the lowest level (240 m) is well correlated to the PM2.5 (R² = 0.84). We also show that the correlation between AOT-derived and measured PM2.5 is significantly improved when considering the mixed boundary layer height derived from the lidar. The use of the Sun photometer aerosol fine fraction volume does not improve the correlation.