Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases : the predominant clonal evolution model of pathogenic microorganisms

International audienceThe predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions ("near-clades"). These units of analysis can be used for clinical and epidemiological studies, vaccine and drug design, species description, and evolutionary studies on natural and experimental populations. In this review, the evolutionary and population genetics background of the model will be only briefly mentioned, while considerable emphasis will be given to its practical significance for the study and control of neglected tropical diseases. The goal of the paper is to make this practical usefulness accessible to a broad audience of readers, including scientists who are not evolution specialists, such as epidemiologists, field scientists, and clinicians. For extensive developments about the evolutionary background of the model, see our previous papers [1-9]. Citations of these former articles lead to the many references quoted in them, which cannot be listed again here. Methods: Brief recall of the PCE model and how it has been designed The PCE model of pathogenic microorganisms explores the population structure and evolution of whole, presently described species in their complete ecogeographical range in the long term. It aims at evaluating to what extent genetic recombination is inhibited in the species PLOS Neglected Tropical Diseases | https://doi