Phylogenetics of Allopolyploids

Abstract

We give an overview of recently developed methods to reconstruct phylogenies of taxa that includes allopolyploids which have originated in relatively recent times, i.e., such that at least some of the parental lineages of lower ploidy levels are not extinct, and that there is clear ploidy information shown by variation in chromosome counts. We review how these methods have been applied to empirical data. The challenges are discussed and prospects for the future are outlined. The review includes a description of a new version of the AlloppNET method, which now can handle any number of species at the diploid and tetraploid level, and any num,ber of hybridisations. AlloppNET is an extension of the *BEAST model which can handle allotetraploids.