A generalized framework of AMOVA with any number of hierarchies and any level of ploidies

The analysis of molecular variance (AMOVA) is a widely used statistical model in the studies of population genetics and molecular ecology. The classical framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in contemporary species. The ploidy level may even vary within the same species, even within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for the multilocus genotypic and allelic phenotypic data. We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a software, polygene, which is freely available at https://github.com/huangkang1987/.