Short communicationGenetic identities and local inbreeding in pure diploid clones with homoplasic markers: SNPs may be misleading

•This paper deals with population genetics of diploid clones.•Expectations for different parameters with homoplasy are derived.•It is shown that maximum homoplasy can be problematic.•This raises concerns about the use of SNPs in clonal populations.

Expected values for observed heterozygosity, genetic diversity, and inbreeding of individuals relative to inbreeding of the population (FIS) are derived in the case of one locus displaying homoplasy with K possible allelic states (KAM model) in a clonal diploid population. Heterozygosity (HO) and genetic diversity (HS) are substantially affected by homoplasy as long as the number of alleles K ⩽ 10, while FIS remains weakly affected in any case. Simulations suggest that in big populations, or in case of maximum homoplasy (K = 2), expected values can appear far from the observed ones because equilibrium takes too many generations to be reached at homoplasic markers in clonally propagating populations. This raises some concern on the use of SNPs, at least in clonal populations.

Graphical abstract○ Expected values; × average across simulations; − 95% confidence intervals across 20 replicates; FIS remains poorly, if any, affected by homoplasy, except in very big populations.Download full-size image