Maximum parsimony tree indicating the minimum number of chromosomal rearrangements and restriction site changes (presence/absence matrix is given in Additional file2: Table S1) necessary to connect the different genotypes exhibited by the S. cerevisiae × S. kudriavzevii hybrids to a putative hybrid ancestor. This putative ancestor is not necessarily the same for all lineages, it just corresponds to an ancestral state containing the complete S. cerevisiae and S. kudriavzevii genomes, but it could be generated several times from different parental strains, as discussed in the main text. Genotypes are represented by white and gray circles for wine and brewing hybrids, respectively. Rearrangements are indicated by arrows giving the direction of the irreversible change and were treated under the Camin-Sokal criterion. Rearrangements were assumed to be caused by nonreciprocal recombination (rec) among homoeologous chromosomes (roman numbers) and whole chromosome losses (loss) of one of the parental chromosomes (kud, S. kudriavzevii). Restriction site changes can be reversible (gains/losses represented by diamonds) and were treated under the Wagner criterion. The gene region and the restriction patterns involved are also indicated (for a description see references  and ).