Phylogenetic distribution of orthologous gene clusters. The numbers after species name abbreviation (see Table 1) indicate the total number of annotated protein coding genes in the genome. The numbers above a branch and proceeded by a '+' sign indicate the number of orthologous gene clusters that are uniquely present in all daughter lineages; the numbers below a branch and proceeded by a '-' sign indicate the number of orthologous gene clusters that are uniquely absent. For example, on the internal branch that leads to the two Plasmodium species, 1,645 gene clusters contain sequences from both Pf and Pv but not any other species present on the tree. Similarly, there are 22 gene clusters that contain sequences from all species except Pf and Pv. Note that a gene cluster may contain more than one sequence from a species if paralogs are present in the genome. The levels refer to the degree of lineage specificity; genes in level 1 are shared by all species on the tree and genes in level 6 are species-specific.