Clonal reproduction and linkage disequilibrium in diploids: a simulation study

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.