Clustered mutations in the human lineage. (A) Phylogenetic tree of the species used for computing the human-chimpanzee ancestral state (dashed arrow). (B) Multiple sequence alignment demonstrating an incidence of a C-coordinated cluster in which the ancestral state harbors closely located cytosine residues that were mutated in the human lineage. (C) An example of an N-coordinated cluster where the mismatches originated from different ancestral nucleotides. Alignment matches are represented by dots; omitted parts of the sequence are indicated by tildes (∼). Red letters and arrows indicate mismatches in the cluster. Positions in which an outgroup does not agree with the other outgroups are marked in blue, and positions in which the ancestral state could not be inferred are marked in gray. The boundaries of clusters are highlighted in gray.