On the Runtime Analysis of the Clearing Diversity-Preserving Mechanism

Clearing is a niching method inspired by the principle of assigning the available resources among a niche to a single individual. The clearing procedure supplies these resources only to the best individual of each niche: the winner. So far, its analysis has been focused on experimental approaches that have shown that clearing is a powerful diversity-preserving mechanism. Using rigorous runtime analysis to explain how and why it is a powerful method, we prove that a mutation-based evolutionary algorithm with a large enough population size, and a phenotypic distance function always succeeds in optimising all functions of unitation for small niches in polynomial time, while a genotypic distance function requires exponential time. Finally, we prove that with phenotypic and genotypic distances clearing is able to find both optima for Twomax and several general classes of bimodal functions in polynomial expected time. We use empirical analysis to highlight some of the characteristics that makes it a useful mechanism and to support the theoretical results

A Clearing Procedure as a Niching Method for Genetic Algorithms

The clearing procedure is a niching method inspired by the principle stated by J.H. Holland in 1975: the sharing of limited resources within subpopulations of individuals characterized by some similarities. But, instead of evenly sharing the available resources among the individuals of a subpopulation, the clearing procedure supplies these resources only to the best individuals of each subpopulation. The clearing is naturally adapted to elitist strategies. This can significantly improve the performance of genetic algorithms applied to multimodal optimization. Moreover the clearing procedure allows the GA to efficiently reduce the genetic drift when used with an appropriate selection operator. Some experimental results are presented for a massively multimodal deceptive function optimization

Association of two co-occurring mutations at the AvrMlp7 avirulence locus in poplar rust during the breakdown of RMlp7 resistance gene

International audienceThe deployment of plant varieties carrying resistance (R) genes exerts strong selection pressures towards pathogen populations. Several studiesreported the rapid evolution of avirulence (Avr) genes to escape R-mediated plant immunity and identified a variety of mechanisms leading tovirulence. The poplar rust fungus Melampsora larici-populina is the most damaging pathogen of poplars. A major adaptive event occurred in1994 with the breakdown of RMlp7 resistance gene in poplar in Europe. Population genomics studies identified a locus in the genome of M.larici-populina, which likely corresponds to the AvrMlp7 candidate avirulence gene. We used a population genetics approach combined withdedicated qPCR assays on a comprehensive set of 281 isolates, covering 27 years (encompassing the resistance breakdown event), to validate thecandidate locus and to assess its polymorphism. We found two mechanisms, a point mutation and a deletion, that allowed the pathogen to escapeRMlp7-mediated resistance. Six diploid genotypes were thus characterized at the candidate locus (three avirulent and three virulent). In addition,a temporal analysis revealed that the two virulence alleles pre-existed (harbored as avirulent heterozygous genotypes) since the early samplingsand were found in association (as virulent genotypes) at the time of the resistance breakdown. Our study documented that, in a diploid pathogen,combining virulence determinisms is adaptive