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Clonal reproduction and linkage disequilibrium in diploids: a simulation study.

Abstract

Estimating the rate of clonal reproduction in natural population of diploid organisms is recognised as being problematic and even the detection of strictly clonal populations is often controversial. One well-acknowledged signature of clonal reproduction is the generation of non-random associations between loci. Linkage disequilibrium (LD) is thus often used for estimating the amount of clonal reproduction. Here we explore with computer simulations the effect of the rate of clonal reproduction on LD estimates obtained from different estimators within a comprehensive parameter range. None of the LD estimators studied is able to accurately measure the proportion of clonal (or sexual) reproduction on its own, due to strong bias, incoherent behaviour, or huge variances. The joint use of several statistics is thus recommended for the estimation rates of clonal reproduction in natural populations. We hope that our work will provide useful tools for the study of clonal diploids, many of which can only be studied with molecular markers, as it is the case for medically important parasites.

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  • Authors+Show Affiliations

    ,

    Génétique et Evolution des Maladies Infectieuses, Equipe Evolution des Systèmes Symbiotiques, UMR 2724 CNRS-IRD, BP 64501, 911 Av. Agropolis, 34394 Montpellier Cedex 5, France. demeeus@mpl.ird.fr

    Source

    MeSH

    Clone Cells
    Computer Simulation
    Diploidy
    Genetic Variation
    Genetics, Population
    Heterozygote
    Kinetics
    Linkage Disequilibrium
    Reproduction, Asexual

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    15374532

    Citation

    TY - JOUR T1 - Clonal reproduction and linkage disequilibrium in diploids: a simulation study. AU - de Mee슩s,Thierry, AU - Balloux,François, PY - 2004/02/04/received PY - 2004/04/30/revised PY - 2004/05/03/accepted PY - 2004/9/18/pubmed PY - 2004/12/16/medline PY - 2004/9/18/entrez SP - 345 EP - 51 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect. Genet. Evol. VL - 4 IS - 4 N2 - Estimating the rate of clonal reproduction in natural population of diploid organisms is recognised as being problematic and even the detection of strictly clonal populations is often controversial. One well-acknowledged signature of clonal reproduction is the generation of non-random associations between loci. Linkage disequilibrium (LD) is thus often used for estimating the amount of clonal reproduction. Here we explore with computer simulations the effect of the rate of clonal reproduction on LD estimates obtained from different estimators within a comprehensive parameter range. None of the LD estimators studied is able to accurately measure the proportion of clonal (or sexual) reproduction on its own, due to strong bias, incoherent behaviour, or huge variances. The joint use of several statistics is thus recommended for the estimation rates of clonal reproduction in natural populations. We hope that our work will provide useful tools for the study of clonal diploids, many of which can only be studied with molecular markers, as it is the case for medically important parasites. SN - 1567-1348 UR - https://www.unboundmedicine.com/medline/citation/15374532/Clonal_reproduction_and_linkage_disequilibrium_in_diploids:_a_simulation_study_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567134804000528 ER -