Although the role of lateral gene transfer is well recognized in the evolution ofbacteria, it is generally assumed that it has had less influence among eukaryotes.To explore this hypothesis, we compare the dynamics of genome evolution intwo groups of organisms: cyanobacteria and fungi. Ancestral genomes areinferred in both clades using two types of methods: first, Count, a gene tree unawaremethod that models gene duplications, gains and losses to explain theobserved numbers of genes present in a genome; second, ALE, a more recentgene tree-aware method that reconciles gene trees with a species tree using amodel of gene duplication, loss and transfer. We compare their merits andtheir ability to quantify the role of transfers, and assess the impact of taxonomicsampling on their inferences. We present what we believe is compellingevidence that gene transfer plays a significant role in the evolution of fungi.