Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).     

Assessing aboveground tropical forest biomass using Google Earth canopy images

Reducing Emissions from Deforestation and Forest Degradation (REDD) in efforts to combat climate change requires participating countries to periodically assess their forest resources on a national scale. Such a process is particularly challenging in the tropics because of technical difficulties related to large aboveground forest biomass stocks, restricted availability of affordable, appropriate remote-sensing images, and a lack of accurate forest inventory data. In this paper, we apply the Fourier-based FOTO method of canopy texture analysis to Google Earth's very-high-resolution images of the wet evergreen forests in the Western Ghats of India in order to (1) assess the predictive power of the method on aboveground biomass of tropical forests, (2) test the merits of free Google Earth images relative to their native commercial IKONOS counterparts and (3) highlight further research needs for affordable, accurate regional aboveground biomass estimations. We used the FOTO method to ordinate Fourier spectra of 1436 square canopy images (125 x 125 m) with respect to a canopy grain texture gradient (i.e., a combination of size distribution and spatial pattern of tree crowns), benchmarked against virtual canopy scenes simulated from a set of known forest structure parameters and a 3-D light interception model. We then used 15 1-ha ground plots to demonstrate that both texture gradients provided by Google Earth and IKONOS images strongly correlated with field-observed stand structure parameters such as the density of large trees, total basal area, and aboveground biomass estimated from a regional allometric model. Our results highlight the great potential of the FOTO method applied to Google Earth data for biomass retrieval because the texture-biomass relationship is only subject to 15% relative error, on average, and does not show obvious saturation trends at large biomass values. We also provide the first reliable map of tropical forest aboveground biomass predicted from free Google Earth images.     

A physical-microbial food web coupled model to study the evolution of the ecological functioning of a new reservoir after its flooding (Sep,Puy de Dôme)

The aim of this paper is to understand the temporal changes in planktonic populations and to highlight some important factors that control the biological functioning and evolution of a recently flooded reservoir, the Sep reservoir (Massif Central, France). To achieve this objective, a 1D vertical coupled physical–biological model was used and developed. It couples relevant physical processes (dispersion, advection and convection) with biological processes taking into account the complexity of interactions within the microbial food web, including the conventional grazing food chain with a microbial loop.     

Quantifying the dynamics of marine invertebrate metacommunities: What processes can maintain high diversity with low densities in the Mediterranean Sea?

The Mediterranean Sea hosts 5.6% of the world benthic invertebrate species on 0.82% of the ocean surface. Mediterranean ecosystems are also characterized by low densities (and biomasses) compared to other oceanic ecosystems, a feature often attributed to their oligotrophic environment. Oligotrophic conditions can induce lower growth rates and higher mortality rates, and a stronger competition for food between individuals. A theoretical model was developed in order to study the diversity vs. density patterns in coastal benthic invertebrate species. This model describes their minimal population dynamics including basic processes (growth, mortality, reproduction and effects of competitive interactions between individuals) and incorporating fluxes of larvae (finally recruited as juveniles) between a mosaic of local habitats. Populations are therefore structured in a metacommunity. The connectivity between local communities is ensured by passive pelagic larval dispersal. In the Mediterranean Sea, because of the microtidal regime, the connectivity between coastal habitats is lower and more variable than in macrotidal basins. Mathematical properties of the model revealed that competitive interactions (intra- and interspecific competitions) have a stabilizing effect on interacting organisms when gains by recruitment are higher than losses by mortality. In addition, low mortality rates and low connectivity which decreases negative local interactions maintains high regional species diversity with low local densities. This property suggested that oligotrophy cannot be the only factor leading to the high diversity–low density pattern observed in the Mediterranean Sea.     

Bird disturbance on conservation sites in Brittany (France): the standpoint of geographers

Bird disturbance by human activities is one of the impacts related to human presence at conservation sites in Brittany (France). This paper is an attempt at reviewing this relatively unknown problem through the results of an international bibliographical review and of a regional inquiry conducted in close collaboration with managers of the conservation areas in Brittany. These two approaches will help to demonstrate the extent and complexity of the human / fauna interactions, as well as to take stock of the state of research in this field and, last but not least, to highlight the difficulties managers of conservation sites are facing to deal with this new issue. For the managers, bird disturbance is indeed the most important impact related to human attendance on conservation sites in Brittany.     

Mixing layer in open-channel junction flows

When two open-channel flows merge in a three-branch subcritical junction, a mixing layer appears at the interface between the two inflows. If the width of the downstream channel is equal to the width of each inlet channel, this mixing layer is accelerated and is curved due to the junction geometry. The present work is dedicated to simplified geometries, considering a flat bed and a \(90^{\circ }\) angle where two configurations with different momentum ratios are tested. Due to the complex flow pattern in the junction, the so-called Serret–Frenet frame-axis based on the local direction of the velocity must be employed to characterize the flow pattern and the mixing layer as Cartesian and cylindrical frame-axes are not adapted. The analysis reveals that the centerline of the mixing layer, defined as the location of maximum Reynolds stress and velocity gradient, fairly fits the streamline separating at the upstream corner, even though a slight shift of the mixing layer towards the center of curvature is observed. The shape of the mixing layer appears to be strongly affected by the streamwise acceleration and the complex lateral confinement due to the side walls and the corners of the junction, leading to a streamwise increase of the mean velocity along the centerline and a decrease of the velocity difference. This results in a specific streamwise evolution of the mixing layer width, which reaches a plateau in the downstream region of the junction. Finally, the evaluation of the terms in the Reynolds-Averaged-Navier–Stokes equations reveals that the streamwise and normal acceleration and the pressure gradient remain dominant, which is typical of accelerated and rotational flows.     

Choosing classes for size projection matrix models

Projection matrix models are intensely used in ecology to model the dynamics of structured populations. When dealing with size-structured populations, there is no satisfactory algorithm to partition size into discrete classes. We show that the Vandermeer-Moloney algorithm for choosing classes is inconsistent with the Usher model, and systematically selects the finest classes. Considering that the matrix model is a discrete approximation of a continuous model, we define an approximation error as the sum of a distribution error (the difference between the discrete distribution and its continuous counterpart), and a sample error. The optimal partition of size into classes is the one that minimizes the approximation error. This method for choosing classes also shows that the choice of the class width cannot be disconnected from the choice of the time step. When applied to 520 trees of Dicorynia guianensis in French Guiana, this algorithm identified 8 classes of 11.4 cm in width, which is in agreement with the empirical choice of foresters.     

Intra-sex vocal interactions in two hybridizing seabird species (Puffinus sp.)

Hybridization between two closely related species breeding in sympatry depends on the effectiveness of both inter-sex (sexual attraction) and intra-sex (competitors’ repulsion) components of communication. As birds primarily communicate acoustically, several studies have investigated interspecific vocal interactions between the sexes and their consequences on sympatric zones with a focus on songbird species. Here, we investigate these issues on intra-sex vocal interactions occurring during incubation in two non-songbird sister species, the Yelkouan Puffinus yelkouan and the Balearic Puffinus mauretanicus shearwaters. We compared the acoustical structure of calls and the behaviors obtained in response to same-sex Yelkouan and Balearic calls across allopatric parental populations from each species and a sympatric-hybridized population. Acoustic analyses showed that, for both sexes, calls have species-specific characteristics while hybrids have intermediate acoustic features compared to their parental species. Playback experiments showed that despite their vocal differences, both species interact and reply to each other. Remarkably, incubating Yelkouan and hybrid individuals resulted in equal intra-sex responses to either species while incubating Balearic birds led to lower territorial responses to Yelkouan than to conspecific calls. Moreover, incubating Balearic males less readily responded to same-sex Yelkouan calls than Balearic females. These results may have fitness consequences: Yelkouan birds, and especially males, would be more likely to win same-sex disputes against Balearic incubating birds than against Yelkouan incubating birds.     

Laboratory scale tests for the assessment of solid explosive blast effects. Part I: Free-field test campaign

The definition of blast loads applying on a complex geometry structure is still nowadays a hard task when numerical simulations are used, essentially because of the different scales involved: as a matter of fact, modelling the detonation of a charge and its resulting load on a structure requires to model the charge itself, the structure and air surrounding, which rapidly leads to large size models on which parametrical studies become unaffordable. So, on the basis of the Crank–Hopkinson’s law, an experimental set-up has been developed to support reduced scale structures as well as reduced scale detonating solid charges. As a final objective, the set-up must be used to produce the entry data for numerical assessments of the structure resistance.This set-up is composed of a modular table, sensors and targets and has been designed to conduct non-destructive studies. In the context of security, the general aim is to study the effects of detonation shock waves in the vicinity of facility buildings and to test various shock wave mitigation means that could be implemented for the protection of facilities in sensitive locations. Especially, the set-up offers the possibility to measure the loading in terms of pressure-time curves, even for very complex situations like multiple reflections, combination and diffraction.The present paper summarizes the development of the set-up as well as the first tests performed. The main features of the table, the instrumentation and the pyrotechnics are given. Also the paper summarizes a first qualification tests campaign that has been conducted. In this campaign, free-field blast tests (i.e. blast tests performed without structures) have been conducted. Overpressure maxima, arrival time of the shock wave and impulse are presented as non-dimensional characteristics of the pressure-time history. The results obtained have been found in good agreement with reference curves available from the open literature and numerical model results.