Determining species tree topologies from clade probabilities under the coalescent

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy consensus algorithm, which consecutively accepts the most probable clades compatible with previously accepted clades, can be used for this second stage, this method is known to be statistically inconsistent under the multispecies coalescent model. This raises the question of whether it is theoretically possible to reconstruct the species tree from known probabilities of clades on gene trees. We investigate clade probabilities arising from the multispecies coalescent model, with an eye toward identifying features of the species tree. Clades on gene trees with probability greater than 1/3 are shown to reflect clades on the species tree, while those with smaller probabilities may not. Linear invariants of clade probabilities are studied both computationally and theoretically, with certain linear invariants giving insight into the clade structure of the species tree. For species trees with generic edge lengths, these invariants can be used to identify the species tree topology. These theoretical results both confirm that clade probabilities contain full information on the species tree topology and suggest future directions of study for developing statistically consistent inference methods from clade frequencies on gene trees.Comment: 25 pages, 2 figure

Reference prior for Bayesian estimation of seismic fragility curves

One of the crucial quantities of probabilistic seismic risk assessment studies is the fragility curve, which represents the probability of failure of a mechanical structure conditional to a scalar measure derived from the seismic ground motion. Estimating such curves is a difficult task because for most structures of interest, few data are available, whether they come from complex numerical simulations or experimental campaigns. For this reason, a wide range of the methods of the literature rely on a parametric log-normal model. Bayesian approaches allow for efficient learning of the model parameters. However, for small data set sizes, the choice of the prior distribution has a non-negligible influence on the posterior distribution, and therefore on any resulting estimate. We propose a thorough study of this parametric Bayesian estimation problem when the data are binary (i.e. data indicate the state of the structure, failure or non-failure). Using the reference prior theory as a support, we suggest an objective approach for the prior choice to simulate a posteriori fragility curves. This approach leads to the Jeffreys prior and we prove that this prior depends only of the ground motion characteristics, making its calculation suitable for any equipment in an industrial installation subjected to the same seismic hazard. Our proposal is theoretically and numerically compared to those classically proposed in the literature by considering three different case studies. The results show the robustness and advantages of the Jeffreys prior in terms of regularization (no degenerate estimations) and stability (no outliers of the parameters) for fragility curves estimation

Cartographie des systèmes rizicoles du Lac Alaotra (Madagascar)

La cuvette du Lac Alaotra est le «grenier à riz» de Madagascar. Le milieu physique y est très diversifié, naturellement et par suite de l'intervention humaine. Une cartographie des types d'exploitation de ce milieu a été entreprise à l'aide de scènes SPOT. Elle vient en appui aux actions menées en commun par la recherche agronomique et les acteurs du développement

Experimental and numerical investigation of the earthquake response of crane bridges

© 2014 Elsevier Ltd. The experimental and numerical response of crane bridges is studied in this work. To this end, an experimental campaign on a scale model of an overhead crane bridge was carried out on the shaking table of CEA/Saclay in France. A special similarity law has been used which preserves the ratios of seismic forces to friction forces and of seismic forces to gravity forces, without added masses. A numerical model, composed of beam elements, which takes into account non-linear effects, especially impact and friction, and simulates the earthquake response of the crane bridge, is presented. The comparison of experimental and analytical results gives an overall satisfactory agreement. Finally, a simplified model of the crane bridge, with only a few degrees of freedom is proposed

Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus.

Tetrachaetum elegans Ingold is a saprobic aquatic hyphomycete for which no sexual stage has yet been described. It occurs most commonly during the initial decay of tree leaves in temperate freshwater habitats and typically sporulates under water. Dispersal of the aquatic fungus takes place primarily in the water column and has a large passive component. Differences in substrate composition (e.g. quality of leaf litter) may also play a role in the distribution of different species or genotypes. The population genetic structure of T. elegans was studied using amplified fragment length polymorphism (AFLP) multilocus fingerprints. The populations were isolated from the leaf litter of three different tree genera, sampled in nine streams distributed throughout a mixed deciduous forest. Molecular markers were developed for 97 monosporic isolates using four selective primer pairs. A total of 247 fragments were scored, of which only 32 were polymorphic. Significant stream differentiation was detected for the isolates considered in this study. Analysis of molecular variance revealed that 20% of the genetic variation observed was the result of differences between streams. No correlation between genetic and geographical distances was found but a few multilocus genotypes were observed in different locations. Altogether these results suggest that environmental barriers play a role in the population structure of this aquatic fungus. No clear-cut effect of leaf litter composition on genetic variation could be demonstrated. Finally, tests of linkage disequilibrium between the 32 polymorphic AFLP loci as well as simulations did not provide a final answer regarding clonality in T. elegans. Indeed, it was possible to reject linkage equilibrium at different sampling levels and show that full linkage was unlikely

Draft genome of the oomycete pathogen <i>Phytophthora cactorum</i> strain LV007 isolated from European beech (<i>Fagus sylvatica</i>)

Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malmö, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81 Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000

Genome sequences of six Phytophthora species threatening forest ecosystems

AbstractThe Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth.com/), we sequenced the genomes of six important Phytophthora species that are important invasive pathogens of trees and a serious threat to the international trade of forest products. This genomic data was used to develop highly sensitive and specific detection assays and for genome comparisons and to make evolutionary inferences and will be useful to the broader plant and tree health community. These WGS data have been deposited in the International Nucleotide Sequence Database Collaboration (DDBJ/ENA/GenBank) under the accession numbers AUPN01000000, AUVH01000000, AUWJ02000000, AUUF02000000, AWVV02000000 and AWVW02000000

MAPPING CULTIVATED AREA IN WEST AFRICA USING MODIS IMAGERY AND AGROECOLOGICAL STRATIFICATION

ABSTRACT The northern fringe of sub-Saharan Africa is a region that is considered particularly vulnerable to climate variability and change, and food security remained there a major challenge. To address this issue, major international research efforts are being deployed, coordinated by the ongoing project AMMA (African Monsoon Multidisciplinary Analyses). Its aim is to better understand the West African Monsoon and its variability, and to improve the predictions of the impacts of this variability on West African societies. One of the preliminary stages necessary for analysing such impacts on agriculture and food security is a reliable estimation of the cultivated domain at national level, a scale compatible with climate change studies. The opportunity of using satellite remote sensing for agricultural statistics has been explored by the research community as well as by national departments of agriculture during the last few decades In this study, we develop a methodology for extracting cultivated areas based on their temporal behaviour as captured in time-series of moderate resolution remote sensing images. We tested this methodology in Senegal and Mali at national scale. -First, 46 MODIS 16-days composite NDVI images (MOD13Q1/V04 product, 250 m spatial resolution) were acquired for 2004 and 2005 and NDVI time series were generated. These products include a NDVI quality band (QB). Although MODIS images have already been radiometrically corrected, we noticed some radiometric defects and noises. For dates with a Vegetation Indices Usefulness Index value in the QB data set lower than &quot;good&quot; quality, NDVI values were replaced by linearly interpolated values from the two closest surrounding dates with &quot;good&quot;, &quot;high&quot;, or &quot;perfect&quot; quality. The required set of tools was developed with ID

Stronger diversity effects with increased environmental stress : a study of multitrophic interactions between oak, powdery mildew and ladybirds

Recent research has suggested that increasing neighbourhood tree species diversity may mitigate the impact of pests or pathogens by supporting the activities of their natural enemies and/or reducing the density of available hosts. In this study, we attempted to assess these mechanisms in a multitrophic study system of young oak (Quercus), oak powdery mildew (PM, caused by Erysiphe spp.) and a mycophagous ladybird (Psyllobora vigintiduo-punctata). We assessed ladybird mycophagy on oak PM in function of different neighbourhood tree species compositions. We also evaluated whether these species interactions were modulated by environmental conditions as suggested by the Stress Gradient Hypothesis. We adopted a complementary approach of a field experiment where we monitored oak saplings subjected to a reduced rainfall gradient in a young planted forest consisting of different tree species mixtures, as well as a lab experiment where we independently evaluated the effect of different watering treatments on PM infections and ladybird mycophagy. In the field experiment, we found effects of neighbourhood tree species richness on ladybird mycophagy becoming more positive as the target trees received less water. This effect was only found as weather conditions grew drier. In the lab experiment, we found a preference of ladybirds to graze on infected leaves from trees that received less water. We discuss potential mechanisms that might explain this preference, such as emissions of volatile leaf chemicals. Our results are in line with the expectations of the Natural Enemies Hypothesis and support the hypothesis that biodiversity effects become stronger with increased environmental stress

Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR