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

Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species

Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping

Background The widespread adoption of high-throughput sequencing technologies by genetic diagnostic laboratories has enabled significant expansion of their testing portfolios. Rare autosomal recessive conditions have been a particular focus of many new services. Here we report a cohort of 26 patients referred for genetic analysis of Joubert (JBTS) and Meckel-Gruber (MKS) syndromes, two clinically and genetically heterogeneous neurodevelopmental conditions that define a phenotypic spectrum, with MKS at the severe end. Methods Exome sequencing was performed for all cases, using Agilent SureSelect v5 reagents and Illumina paired-end sequencing. For two cases medium-coverage (9×) whole genome sequencing was subsequently undertaken. Results Using a standard analysis pipeline for the detection of single nucleotide and small insertion or deletion variants, molecular diagnoses were confirmed in 12 cases (4 %). Seeking to determine whether our cohort harboured pathogenic copy number variants (CNV), in JBTS- or MKS-associated genes, targeted comparative read-depth analysis was performed using FishingCNV. These analyses identified a putative intragenic AHI1 deletion that included three exons spanning at least 3.4 kb and an intergenic MPP4 to TMEM237 deletion that included exons spanning at least 21.5 kb. Whole genome sequencing enabled confirmation of the deletion-containing alleles and precise characterisation of the mutation breakpoints at nucleotide resolution. These data were validated following development of PCR-based assays that could be subsequently used for “cascade” screening and/or prenatal diagnosis. Conclusions Our investigations expand the AHI1 and TMEM237 mutation spectrum and highlight the importance of performing CNV screening of disease-associated genes. We demonstrate a robust increasingly cost-effective CNV detection workflow that is applicable to all MKS/JBTS referrals

Potential impact of climate change on durum wheat cropping in Tunisia

The potential effect of climate change on durum wheat in Tunisia is assessed using a simple crop simulation model and a climate projection for the 2071-2100 period, obtained from the M,t,o-France ARPEGE-Climate atmospheric model run under the IPCC (International Panel on Climate Change) scenario A1B. In the process-oriented crop model, phenology is estimated through thermal time. Water balance is calculated on a daily basis by means of a simple modelling of actual evapotranspiration involving reference evapotranspiration, crop coefficients and some basic soil characteristics. The impact of crop water deficit on yield is accounted for through the linear crop-water production function developed by the FAO (Food and Agriculture Organization of the United Nations). Two stations are chosen to study the climate change effect. They are representative of the main areas where cereals are grown in Tunisia: Jendouba in the northern region and Kairouan in the central region. In the future scenario, temperature systematically increases, whereas precipitation increases or decreases depending on the location and the period of the year. Mean annual precipitation declines in Jendouba and raises in Kairouan. Under climate change, the water conditions needed for sowing occur earlier and cycle lengths are reduced in both locations. Crop water deficit and the corresponding deficit in crop yield happen to be slightly lower in Kairouan; conversely, they become higher in Jendouba

Towards adaptation of agriculture to climate change in the Mediterranean

This study links climate change impacts to the development of adaptation strategies for agriculture on the Mediterranean region. Climate change is expected to intensify the existing risks, particularly in regions with current water scarcity, and create new opportunities for improving land and water management. These risks and opportunities are characterised and interpreted across Mediterranean areas by analysing water scarcity pressures and potential impacts on crop productivity over the next decades. The need to respond to these risks and opportunities is addressed by evaluating an adaptive capacity index that represents the ability of Mediterranean agriculture to respond to climate change. We propose an adaptive capacity index with three major components that characterise the economic capacity, human and civic resources, and agricultural innovation. These results aim to assist stakeholders as they take up the adaptation challenge and develop measures to reduce the vulnerability of the sector to climate change

Assessing the consistency of eddy covariance measurements under conditions of sloping topography within a hilly agricultural catchment

The current current study addressed the consistency of eddy covariance (EC) measurements collected in sloping conditions within a hilly agricultural catchment. In the context of operational monitoring and modelling devoted to decision support, it is important to increase the knowledge of surface fluxes under conditions of hilly topography. The two-metre-high EC measurements were collected at the field scale within the two opposite rims of a V-shaped catchment located in northeastern Tunisia on the southern shore of the Mediterranean Basin. Measurements were collected under bare soil conditions to enhance the effects of the slopes. The data pre-processing and quality control measures were conducted using standard procedures. In assessing the consistency of the EC measurements we first compared the airflow inclinations captured by the EC measurements against the topographical slopes captured by a Digital Elevation Model; we then assessed the energy balance closure. The analysis of the micrometeorological data indicated specific regimes: externally driven winds; forced convection; and stability conditions close to neutrality or low instability. The two dominant wind directions induced upward and downward flows on the two opposite rims. For the upward flows, the airflow inclinations followed the topographical slopes on both fields. For the downward flows, the flows followed the topographical slopes on the southern rim and were almost horizontal on the other rim. In all cases, and especially for the upward flows, the energy balance closure was similar to that reported in the literature. Overall, the behaviour observed for upward flows was close to that reported in the literature for flat conditions, whereas the downward flows exhibited different trends. The different trends we observed for the downward flows were ascribed to the bubble separation zone that implies streamline dilatation, turbulence and reverse flows. Future investigations should address the vegetation conditions. The expected outcomes are of importance for revisiting the operational methods devoted to the estimation of evapotranspiration