Abstract
Polyploidy can have a huge impact on the evolution of species, and is a common occurrence, especially in plants. Two types of polyploids – autopolyploids and allopolyploids – differ in the level of divergence between the genes brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homologous copies of genes within them are as divergent as the parental species that came together to form them. This means that common methods for estimating the timing of polyploidy events fail to correctly date allopolyploidy, and can lead to incorrect inferences about the number of gene duplications and losses. Here we have adapted the standard algorithm for gene-tree reconciliation to work with multi-labeled species trees (MUL-trees). MUL-trees are defined as having identical species labels, which makes them a natural representation of polyploidy events. Using this new reconciliation algorithm we can: accurately date allopolyploidy events on a tree, identify the parental lineages that hybridized to form allopolyploids, distinguish auto-from allopolyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin of this group, but identifies slightly different parental lineages than a previous analysis. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy.
