Abstract
Polyploids are traditionally classified into allopolyploids and autopolyploids, based on their evolutionary origin and their disomic or multisomic mode of inheritance. Over the past decade it has become increasingly clear that there is a continuum between disomic and multisomic inheritance, with the rate of tetrasomy differing among species and among chromosomes within species. Here, we use a simple population genetic model to study the impact of the mode of inheritance on the genetic diversity and population divergence of tetraploids. We found that under almost strict disomic inheritance the tetraploid genome is divided into two separate subgenomes, such as found in classical allopolyploids. In those cases, assuming full tetrasomy in the analysis of polyploid genetic data will lead to an important bias in estimates of genetic diversity and population divergence. However, we found that even a low rate of allele exchange between the two subgenomes, at about one event per generation, is sufficient to homogenise the allele frequencies over the subgenomes, and the estimates become essentially unbiased. The inbreeding coefficient F(IS) can then be used to detect whether the estimates of diversity and divergence will be biased when full multisomy is assumed. Finally, we found that different summary statistics for measuring the strength of population differentiation are differentially affected by a deviation from full tetrasomy. Our model results provide several useful guidelines for the analysis of polyploid data, helping researchers to determine when their inferences are biased and which summary statistics to use.