title: Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes.
abstract: BACKGROUND
  Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright's FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright's FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex.
  
  
  METHODS
  We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright's FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles.
  
  
  RESULTS
  We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents.
  
  
  CONCLUSIONS
  Our criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%).
authors.affiliation: Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES), 01 BP 454 Bobo-Dioulasso 01, Burkina-Faso. hamihrou_nviendee@yahoo.com.
authors.forename: Modou
authors.initials: M
authors.lastname: Séré
authors.forename: Jacques
authors.initials: J
authors.lastname: Kaboré
authors.forename: Vincent
authors.initials: V
authors.lastname: Jamonneau
authors.forename: Adrien Marie Gaston
authors.initials: AM
authors.lastname: Belem
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ayala
authors.forename: Thierry
authors.initials: T
authors.lastname: De Meeûs
mesh_terms: D000483:Alleles; D000818:Animals; D002175:Candida / Q000235:genetics*; D003198:Computer Simulation; D018895:Microsatellite Repeats; D008954:Models, Biological; D009154:Mutation; D013045:Species Specificity; D014345:Trypanosoma / Q000235:genetics*