Phylogeny and protein-coding repertoire of Saccharomycetaceae and outgroups. (A) The phylogenetic tree results from the alignment of 180 proteins (66,709 amino acids), selected from all universal one-member families having a homolog in S. pombe, using the MAFFT algorithm (Katoh et al. 2005), cleaned with Gblocks (Castresana 2000) before concatenation. Only families for which the ratio between the cleaned blocks and the initial alignment was higher than 75% were considered. The tree was constructed by maximum likelihood using PhyML (Guindon and Gascuel 2003) with a JTT substitution model corrected for heterogeneity among sites by a gamma-law distribution using four different categories of evolution rates. The proportion of invariable sites and the alpha-parameter of the gamma-law distribution were optimized according to the data. Branch length is indicated above or next to each branch, and bootstrap values (in bold) next to each node. S. pombe was used as an anchoring outgroup. Clades number and designation for Saccharomycetaceae are according to Kurtzman (2003) and Kurtzman and Robnett (2003). Protoploid species are highlighted (bold blue names). (B) Figures represent the total number of protein families in each species or node (pan-proteome, defined as the sum of all families present in all species posterior to the node). Pie charts indicate the proportion of families classified as “ubiquitous” (core-proteome, common to all species posterior to the node), “species-specific” (present in only one of the species posterior to the node), or other combinations. In orange, the proportion of families shared by all five protoploid species. Note the similar pie charts for the Saccharomycetaceae species, compared to the different pie charts of the outgroup.
