Phylogenetic relationships inferred using three subsets of proteins with varying evolutionary rates. The proteins used for the initial phylogenetic inference were categorized into three subsets each comprising 65 proteins: (A) Slow-evolving proteins (tree lengths of less than two expected substitutions per site); 13,670 aa of 50,332 aa (51%) were used for ML inference. (B) Proteins evolving at an intermediate speed (tree lengths of two or more but less than four expected substitutions per site); 14,967 aa of 27,063 aa (30%) were used for ML inference. (C) Fast-evolving-proteins (tree lengths of four or more expected substitutions per site); 12,021 aa of 96,774 aa (12%) were used for ML inference. T. gondii, C. parvum, T. annulata, and B. bovis were used to root the trees. Numbers at the nodes denote bootstrap support values; scale bars are equal to 0.05 expected substitutions per site.