Correcting for Replicated Genotypes May Introduce More Problems Than it Solves

Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual-based simulations to study the effect of clone correction on the estimation of the genetic summary statistics H_O, H_S, F_IS, F_ST, F′′_ST and D_est. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For H_S and F_IS, this deviation can be informative about the process of asexual reproduction, but for F_ST, F′′_ST and D_est, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented.