@article{fdi:010062324,
  title = {{N}ull allele, allelic dropouts or rare sex detection in clonal organisms : simulations and application to real data sets of pathogenic microbes},
  author = {{S}ere, {M}. and {K}abore, {J}. and {J}amonneau, {V}incent and {B}elem, {A}. {M}. {G}. and {A}yala, {F}. {J}. and {D}e {M}eeûs, {T}hierry},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {P}athogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. {H}owever, 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. {T}his is especially critical in clonal organisms in which deviation from panmixia, as measured by {W}right's {F}-{IS}, can, in principle, be used to infer both the extent of clonality and structure in a given population. {I}n particular, null alleles and allelic dropouts are locus specific and likely produce high variance of {W}right's {F}-{IS} across loci, as rare sex is expected to do. {I}n this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. {M}ethods: {W}e have performed various simulations of clonal and partially clonal populations. {W}e introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. {W}e use the narrow relationship that links {W}right's {F}-{IS} 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. {R}esults: {W}e 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. {H}owever, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. {T}he 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. {C}onclusion: {O}ur criterion of superimposing between the {FIS} expected under clonality and the observed {F}-{IS}, is effective when amplification difficulties occur in low to moderate frequencies (20-30%).},
  keywords = {{P}opulation genetics ; {C}lonal reproduction ; {A}llelic dropouts ; {N}ull alleles ; {H}eterozygosity ; {G}enetic diversity ; {Y}easts ; {T}rypanosomes ; {AFRIQUE} {DE} {L}'{OUEST}},
  booktitle = {},
  journal = {{P}arasites and {V}ectors},
  volume = {7},
  numero = {},
  pages = {art. 331},
  ISSN = {1756-3305},
  year = {2014},
  DOI = {10.1186/1756-3305-7-331},
  URL = {https://www.documentation.ird.fr/hor/fdi:010062324},
}