We've recently added the ability to model polyploidy and infer rates of exchange between subgenomes to dadi. A preprint describing and applying the method is now posted. To avoid some bioinformatic biases, in our approach we collapse the data from across the subgenomes into a single site frequency spectrum. In this collapsed spectrum, fixed differences between the subgenomes create a spike at 50% frequency. Allelic exchange between the subgenomes generates distinctive shoulders to the spike. Consequently, we can precisely infer model parameters describing the events after the formation of the polyploid. Justin Conover will be building on this work when he joins us to model DFEs in polyploids.
