Figure 3.

Classification of novel and expanded ortholog clusters based on phylogenetic profiles. Ortholog clusters were predicted using OrthoMCL [32] and species phylogeny was constructed from a matrix of presence and absence of ortholog clusters using maximum parsimony. The clade given as “crown group apicomplexa” is taxonomically not defined but comprises the Apicomplexa under exclusion of Cryptosporidium. Numbers in the upper half of the boxes present the total number of genes, of E. falciformis genes and of ortholog clusters novel in a given clade. Numbers are not given cumulative, and the listed lower level genes/clusters are not contained within the higher levels. Novelty was inferred from the taxonomic range of constitutive member genes for each cluster. The lower half of boxes gives numbers for E. falciformis genes and ortholog clusters expanded at a given node. Expansion was inferred from reconciliation of individual gene trees (see Methods) with the species tree. Gene families with at least one gene duplication event at a given node were considered expanded. We limited these analyses to the branches leading to E. falciformis.