Variations of snapshot population genetic indices with rates of clonality and selfing, and ploidy
The principal component analysis on the values of genetic diversity using a snapshot of genetic diversity of a population showed two main non-collinear clusters of genetic indices associated with clonality and selfing (Fig. S2, S3 and S4). Rates of clonality were colinear with clonal heterogeneity and evenness indices (including R, Pareto Beta, the complement of the Simpson index and Shannon-Wienner’s index), with variance of Fis and Fit, and linkage disequilibrium. Increasing rates of clonality increased linkage disequilibrium and variance of Fis among genotyped loci while it decreased clonal evenness. Rates of selfing were colinear with indices based on allele diversity (including gene diversity, probabilities of identity and genetic structure indices) and heterozygosity. Increasing rates of selfing increased mean Fis and Fit, and variances of panmictic probabilities of identity, of the number of alleles per loci, of gene diversity and of pairwise Fst. Conversely, it decreased the mean number of alleles per loci, the mean gene diversity and observed heterozygosity.
The distributions of population genetics indices varied with joint rates of clonality and selfing and with increasing ploidy, except the distribution of rhost values between the two simulated populations (Fig. S5). For a fixed ploidy, changes in the range of expected values with reproductive modes remained quite similar to those observed for diploids.