Parentage and sibship inference from markers in polyploids

Many plants and some animal species are polyploids. Nondisomically inherited markers (e.g. microsatellites) in such species cannot be analysed directly by standard population genetics methods developed for diploid species. One solution is to transform the polyploid codominant genotypes to pseudodiploid-dominant genotypes, which can then be analysed by standard methods for various purposes such as spatial genetic structure, individual relatedness and relationship. Although this data transformation approach has been used repeatedly in the literature, no systematic study has been conducted to investigate how efficient it is, how much marker information is lost and thus how much analysis accuracy is reduced. More specifically, it is unknown whether or not the transformed data can be used to infer parentage and sibship jointly, and how different sampling schemes (number and polymorphism of markers, number of individuals) and ploidy level affect the inference accuracy. This study analyses both simulated and empirical data to examine the effects of polyploid levels, actual pedigree structures and marker number and polymorphism on the accuracy of joint parentage and sibship assignments in polyploid species. We show that sibship, parentage and selfing rates in polyploids can be inferred accurately from a typical set of microsatellite loci. We also show that inferences can be substantially improved by allowing for a small genotyping error rate to accommodate the distortion in assumed Mendelian inheritance of the converted markers when large sibship groups are involved. The results are discussed in the context of polyploid data analysis in molecular ecology.