Statistical approaches to reconstructing genome evolution: beyond the Eukaryote-Prokaryote dichotomy

Although the role of gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less inuence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in two groups of organisms: Cyanobacteria and Fungi. Ancestral genomes are inferred in both clades using two types of methods. First, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome. Second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss, and transfer. We compare their merits and their ability to quantify the role of transfers, and the impact of taxonomic sampling. We present what we believe is compelling evidence that gene transfer plays a signicant role in the evolution of Fungi.