Ivan Sache

Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans

Outcomes of host-pathogen coevolution are influenced by migration rates of the interacting species. Reduced gene flow with increasing spatial distance between populations leads to spatial genetic structure, as predicted by the isolation by distance (IBD) model. In wind-dispersed plant-pathogenic fungi, a significant spatial genetic structure is theoretically expected if local spore dispersal is more frequent than long-distance dispersal, but this remains to be documented by empirical data. For 29 populations of the oilseed rape fungus Leptosphaeria maculans sampled from two French regions, genetic structure was determined using eight minisatellite markers. Gene diversity (H = 0.62-0.70) and haplotypic richness (R = 0.96-1) were high in all populations. No linkage disequilibrium was detected between loci, suggesting the prevalence of panmictic sexual reproduction. Analysis of molecular variance showed that > 97% of genetic diversity was observed within populations. Genetic differentiation was low among populations (F(st) < 0.05). Although direct methods previously revealed short-distance dispersal for L. maculans, our findings of no correlation between genetic and geographic distances among populations illustrate that the IBD model does not account for dispersal of the fungus at the spatial scale we examined. These results indicate high gene flow among French populations of L. maculans, suggesting high dispersal rates and/or large effective population sizes, two characteristics giving the pathogen high evolutionary potential against the deployment of resistant oilseed rape cultivars.

Influence of host resistance and phenology on South American leaf blight of the rubber tree with special consideration of temporal dynamics

South American leaf blight (SALB), the most dangerous disease of the rubber tree, is responsible for the lack of significant natural rubber production in South America and is a major threat to rubber tree plantations in Asia and Africa. Although the selection of resistant clones is the preferred disease control method, greater knowledge is required of the relationship between host and pathogen, in order to construct more durable resistance. Based on small-scale trials, this study set out to compare the dynamics of SALB on two highly susceptible and one moderately susceptible clone and to analyse the effect of host phenology on disease severity, at leaflet and flush scales. Clonal resistance was found to have a noticeable effect on disease severity, asexual sporulation and stromatal density at both leaflet and flush levels, and on disease dynamics at a leaflet level; time for symptom and sporulation appearance were longer on the moderately susceptible clone than on the susceptible clones. On the moderately susceptible clone, the stromatal density was largely dependent on disease severity. The phenology did not differ among the three clones and could not be considered as a factor in genetic resistance to SALB. However, for the three clones, the position of the leaflet in the flush affected the duration of the immature stages and the disease: the shorter the duration of leaflet development, the lower the disease severity, the sporulation intensity and the stromatal density.

Seasonal Changes Drive Short-Term Selection for Fitness Traits in the Wheat Pathogen Zymoseptoria tritici

ABSTRACT In a cross-infection experiment, we investigated how seasonal changes can affect adaptation patterns in a Zymoseptoria tritici population. The fitness of isolates sampled on wheat leaves at the beginning and at the end of a field epidemic was assessed under environmental conditions (temperature and host stage) to which the local pathogen population was successively exposed. Isolates of the final population were more aggressive, and showed greater sporulation intensity under winter conditions and a shorter latency period (earlier sporulation) under spring conditions, than isolates of the initial population. These differences, complemented by lower between-genotype variability in the final population, exhibited an adaptation pattern with three striking features: (i) the pathogen responded synchronously to temperature and host stage conditions; (ii) the adaptation concerned two key fitness traits; (iii) adaptation to one trait (greater sporulation intensity) was expressed under winter conditions while, subsequently, adaptation to the other trait (shorter latency period) was expressed under spring conditions. This can be interpreted as the result of short-term selection, driven by abiotic and biotic factors. This case study cannot yet be generalized but suggests that seasonality may play an important role in shaping the variability of fitness traits. These results further raise the question of possible counterselection during the interepidemic period. While we did not find any trade-off between clonal multiplication on leaves during the epidemic period and clonal spore production on debris, we suggest that final populations could be counterselected by an Allee effect, mitigating the potential impact of seasonal selection on long-term dynamics.

Segmentation applied to weather-disease relationships in South American leaf blight of the rubber tree.

South American leaf blight (SALB) is a severe threat to world rubber production. One way of controlling it is to set up plantations in zones not conducive to the disease. Such zones are known once a plantation has been set up, but few data are available on how climate affects the disease, especially in the Amazon region. With better knowledge of conditions that are favourable to SALB epidemics it would be possible to more accurately identify risk zones in Asia and Africa, continents that are still SALB-free. Based on a trial design involving detailed and frequent observations, and with a method rarely used in plant epidemiology, the segmentation method, the results presented in this article make it possible to list, in order of importance, climatic factors that influence disease severity under conditions where the climate varies little over the year.

Evolution of dispersal in asexual populations: to be independent, clumped or grouped?

AbstractnThe question Why to disperse? has been extensively investigated from an evolutionary perspective, and the strategy to disperse can be explained by several proximate and ultimate factors. The amazing diversity of dispersal mechanisms that animals, plants, fungi, peat mosses and other organisms have developed leads to the following question: How to disperse? In this article, we introduce an original modeling framework to study the evolution of dispersal in asexual populations where reproducing individuals release propagules and can adopt (by mutation) three strategies: independent movements of all propagules, clump dispersal (i.e. clumps of propagules attached together and settling at the same location), or group dispersal (i.e. groups of propagules simultaneously released and settling at different but positively correlated locations). We show how the spatial limits and fragmentation of the species’ habitat shape the frequencies of the three strategies in the population and the sizes of groups and clumps. The co-existence of the independent, clump and group dispersal strategies at the stationary state of the population dynamics is of particular note. However, group dispersal never appeared as a dominant strategy, whereas independent and clump dispersal were both dominant for different parameter ranges (essentially because dispersal is either adaptive or maladaptive)n.

Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population

The efficiency of plant resistance to fungal pathogen populations is expected to decrease over time, due to their evolution with an increase in the frequency of virulent or highly aggressive strains. This dynamics may differ depending on the scale investigated (annual or pluriannual), particularly for annual crop pathogens with both sexual and asexual reproduction cycles. We assessed this time‐scale effect, by comparing aggressiveness changes in a local Zymoseptoria tritici population over an 8‐month cropping season and a 6‐year period of wheat monoculture. We collected two pairs of subpopulations to represent the annual and pluriannual scales: from leaf lesions at the beginning and end of a single annual epidemic and from crop debris at the beginning and end of a 6‐year period. We assessed two aggressiveness traits—latent period and lesion size—on sympatric and allopatric host varieties. A trend toward decreased latent period concomitant with a significant loss of variability was established during the course of the annual epidemic, but not over the 6‐year period. Furthermore, a significant cultivar effect (sympatric vs. allopatric) on the average aggressiveness of the isolates revealed host adaptation, arguing that the observed patterns could result from selection. We thus provide an experimental body of evidence of an epidemiological trade‐off between the intra‐ and interannual scales in the evolution of aggressiveness in a local plant pathogen population. More aggressive isolates were collected from upper leaves, on which disease severity is usually lower than on the lower part of the plants left in the field as crop debris after harvest. We suggest that these isolates play little role in sexual reproduction, due to an Allee effect (difficulty finding mates at low pathogen densities), particularly as the upper parts of the plant are removed from the field, explaining the lack of transmission of increases in aggressiveness between epidemics.

Trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100039). The efficiency of plant resistance to fungal pathogen populations is expected to decrease over time, due to its evolution with an increase in the frequency of virulent or highly aggressive strains. This dynamics may differ depending on the scale investigated (annual or pluriannual), particularly for annual crop pathogens with both sexual and asexual reproduction cycles. We assessed this time-scale effect, by comparing aggressiveness changes in a local Zymoseptoria tritici population over an eight-month cropping season and a six-year period of wheat monoculture. We collected two pairs of subpopulations to represent the annual and pluriannual scales: from leaf lesions at the beginning and end of a single annual epidemic, and from crop debris at the beginning and end of a six-year period. We assessed two aggressiveness traits – latent period and lesion size – on sympatric and allopatric host varieties. A trend toward decreased latent period concomitant with a significant loss of variability was established during the course of the annual epidemic, but not over the six-year period. Furthermore, a significant cultivar effect (sympatric vs. allopatric) on the average aggressiveness of the isolates revealed host adaptation, arguing that the observed patterns could result from selection. We thus provide an experimental body of evidence of an epidemiological trade-off between the intra- and inter-annual scales in the evolution of aggressiveness in a local plant pathogen population. More aggressive isolates were collected from upper leaves, on which disease severity is usually lower than on the lower part of the plants left in the field as crop debris after harvest. We suggest that these isolates play little role in sexual reproduction, due to an Allee effect (difficulty finding mates at low pathogen densities), particularly as the upper parts of the plant are removed from the field, explaining the lack of transmission of increases in aggressiveness between epidemics.

Stability in the genetic structure of a Zymoseptoria tritici population from epidemic to interepidemic stages at a small spatial scale

Subpopulations of the wheat pathogen Zymoseptoria tritici (26 sample groups composed of 794 pure strains) were collected in two nearby wheat fields, during both epidemic and interepidemic periods of three successive years (2009–2013). The alternative presence of wheat debris allowed taking into account different forms (ascospores vs. pycnidiospores) of inoculum and, thus, its putative origin (local vs. distant). We used a molecular epidemiology approach, based on population genetic indices derived from SSR marker analysis. The aim was to describe putative changes in the neutral genetic structure and diversity of these subpopulations over the time-course of several epidemics, in two close fields, i.e. at a spatiotemporal scale consistent with epidemiological observations, and to determine the possible structuring factors. Genetic structure was stable over time (within and between years) and between fields. All subpopulations displayed very high levels of gene and genotypic diversity. The low levels of linkage disequilibrium and the low clonal fraction, and the similar frequencies of the two mating types in most subpopulations were consistent with the regular occurrence of sexual reproduction in the two fields over the epidemic and interepidemic stages. In conclusion, at this fine spatiotemporal scale, we found that the period, the nature of inoculum and its putative origin had little effect on the short term evolution of the local population, with population size and diversity apparently large enough to prevent genetic drift, and with a major contribution of migration between and within plots to the stabilization of genetic diversity.

IPSIM-Web, An Online Resource for Promoting Qualitative Aggregative Hierarchical Network Models to Predict Plant Disease Risk: Application to Brown Rust on Wheat

A qualitative pest modeling platform, named Injury Profile Simulator (IPSIM), provides a tool to design aggregative hierarchical network models to predict the risk of pest injuries, including diseases, on a given crop based on variables related to cropping practices as well as soil and weather environment at the field level. The IPSIM platform enables modelers to combine data from various sources (literature, survey, experiments, and so on), expert knowledge, and simulation to build a network-based model. The overall structure of the platform is fully described at the IPSIM-Web website ( www6.inra.fr/ipsim ). A new module called IPSIM-Wheat-brown rust is reported in this article as an example of how to use the system to build and test the predictive quality of a prediction model. Model performance was evaluated for a dataset comprising 1,788 disease observations at 13 French cereal-growing regions over 15 years. Accuracy of the predictions was 85% and the agreement with actual values was 0.66 based on Cohens κ. The new model provides risk information for farmers and agronomists to make scientifically sound tactical (within-season) decisions. In addition, the model may be of use for ex post diagnoses of diseases in commercial fields. The limitations of the model such as low precision and threshold effects as well as the benefits, including the integration of different sources of information, transparency, flexibility, and a user-friendly interface, are discussed.