Rachid Senoussi

Estimation of the number of virus particles transmitted by an insect vector

Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two Potato virus Y variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5–3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important.

How does winter pruning affect peach tree–Myzus persicae interactions?

Winter tree pruning is a cultural practice known to modify vegetative growth, which is likely to affect the development of pests. However, it has been poorly addressed as a cultural control method for diminishing the population levels of the green peach aphid, Myzus persicae (Sulzer) (Homoptera: Aphididae), in peach [Prunus persica (L.) Batsch (Rosaceae)] orchards. In this study, we conducted a 2‐year, on‐station experiment to evaluate how winter pruning affects peach–M. persicae interactions, by examining tree vegetative growth, aphid population dynamics, and crop yield and fruit quality. We collected data under an insect‐proof shelter on adult peach trees submitted to various levels of pruning and artificially infested with aphids. Our results showed that pruning enhanced shoot growth due to the proportion of growing shoots, which increased exponentially (10–60%), whereas the growth rate of growing shoots was not affected. The degree of infestation of peach trees increased with increasing pruning intensity. This effect was mainly due to the increase of the proportion of growing shoots, on which aphids developed better than on rosettes. In turn, the higher the aphid infestation, the higher the aphid‐induced shoot‐tip damage, leaf curling, and leaf fall that disturbed the growth of growing shoots. However, aphids did not considerably reduce fruit quality at harvest. They did not affect fresh fruit weight, and the refractometric index (indicator of sugar content) was reduced by only 3–4%. The relevance of winter pruning as a cultural method for pest control in orchards conducted under integrated fruit production guidelines is discussed.

Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts.

An Implicitization Algorithm for Rational Surfaces with no Base Points

We present an implicitization algorithm which is free of extraneous factors if the rational parametric surface has no base points. This algorithm is based on the method of Sylvester for computing the resultant of three homogeneous polynomials in three variables. Some examples and computations illustrate the efficiency and limits of this method.

Should I Stay or Should I Go? A Habitat-Dependent Dispersal Kernel Improves Prediction of Movement

The analysis of animal movement within different landscapes may increase our understanding of how landscape features affect the perceptual range of animals. Perceptual range is linked to movement probability of an animal via a dispersal kernel, the latter being generally considered as spatially invariant but could be spatially affected. We hypothesize that spatial plasticity of an animals dispersal kernel could greatly modify its distribution in time and space. After radio tracking the movements of walking insects (Cosmopolites sordidus) in banana plantations, we considered the movements of individuals as states of a Markov chain whose transition probabilities depended on the habitat characteristics of current and target locations. Combining a likelihood procedure and pattern-oriented modelling, we tested the hypothesis that dispersal kernel depended on habitat features. Our results were consistent with the concept that animal dispersal kernel depends on habitat features. Recognizing the plasticity of animal movement probabilities will provide insight into landscape-level ecological processes.

Narrow bottlenecks affect Pea seedborne mosaic virus populations during vertical seed transmission but not during leaf colonization.

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence.

Nonparametric Identification of Controlled Nonlinear Time Varying Processes

We are interested in the identification of an unknown time varying additive component of a controlled nonlinear autoregressive model, a problem of interest in the modeling and control of uncertain systems, such as those met in biotechnological processes. A kernel-based nonparametric estimator is proposed whose almost sure convergence is studied by means of a Lyapunov stabilizability assumption and laws of large numbers for martingales. We then adapt the general result to several classes of deterministic or random functional model uncertainties.

Estimating virus effective population size and selection without neutral markers

By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation.

Within-Crop Air Temperature and Humidity Outcomes on Spatio-Temporal Distribution of the Key Rose Pest Frankliniella occidentalis

Frankliniella occidentalis (Pergande) is a key pest of various crops worldwide. In this study, we analyse the dependence of the infestation of this pest on spatially distributed micro climatic factors in a rose greenhouse. Despite the importance of this subject, the few existing studies have been realized in laboratory rather than in greenhouse conditions. However, recent progress on greenhouse microclimate characterisation has highlighted the strong indoor climate heterogeneity that may influence the within-crop pest distribution. In this study, both microclimate (air temperature and humidity) and thrips distribution were simultaneously mapped in a rose greenhouse. The measurements were sensed in a horizontal plane situated at mid-height of the rose crop inside the greenhouse. Simultaneously, thrips population dynamics were assessed after an artificial and homogeneous infestation of the rose crop. The spatio-temporal distribution of climate and thrips within the greenhouse were compared, and links between thrips infestation and climatic conditions were investigated. A statistical model was used to define the favourable climate conditions for thrips adults and larvae. Our results showed that (i) the air temperature and air humidity were very heterogeneously distributed within the crop, (ii) pest populations aggregated in the most favourable climatic areas and (iii) the highest population density of thrips adults and larvae were recorded at 27°C and 22°C for temperature and 63% and 86% for humidity, respectively. These findings confirm, in real rose cropping conditions, previous laboratory studies on the F. occidentalis climatic optimum and provide a solid scientific support for climatic-based control methods against this pest.

An Automated MCEM Algorithm for Hierarchical Models with Multivariate and Multitype Response Variables

In this article, we consider a model allowing the analysis of multivariate data, which can contain data attributes of different types (e.g., continuous, discrete, binary). This model is a two-level hierarchical model which supports a wide range of correlation structures and can accommodate overdispersed data. Maximum likelihood estimation of the model parameters is achieved with an automated Monte Carlo expectation maximization algorithm. Our method is tested in a simulation study in the bivariate case and applied to a data set dealing with beehive activity.