Phylogenetics of Allopolyploids

Abstract

We give an overview of recently developed methods to reconstruct phylog-enies of taxa that include allopolyploids that have originated in relatively recent times—in other words, taxa for which at least some of the parental lineages of lower ploidy levels are not extinct and for which ploidy information is clearly shown by variation in chromosome counts. We review how these methods have been applied to empirical data, discuss challenges, and outline prospects for future research. In the absence of recombination between parental subgenomes, the allopolyploid phylogenetic histories can in principle be treated as genome tree inference. However, without whole genome or whole chromosome data, sequences must be assigned from genes sampled to parental subgenomes. The new version of the AlloppNET method, which now can handle any number of species at the diploid and tetraploid level and any number of hybridizations, is a promising attempt that can also treat gene tree discordance due to the coalescent process. The ongoing development of models that take migration, paralogy, and uncertainties in species delimitations into account offers exciting opportunities for the future of inference of species networks.