Chimpanzee, as the closest relative of human, has long been a focus of molecular evolution. In this article, we review recent findings of five major categories of human–chimpanzee genomic divergence, namely nucleotide substitution, insertion/deletion, duplication, pseudogenization and rearrangement. It is demonstrated that nonsubstitution variations greatly increase the complexity and play a critical role in human–chimpanzee genome evolution. These genetic changes may provide some clues to the evolutionary origins of human-specific traits.
