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In the past, evolutionary studies of species have depended soley on anatomical changes observed in fossil records and on carbon dating. More recently, these studies are being suported by the molecular analysis of the sequence and size of selected genes or whole DNA molecules. Evolutionary altertions of a selected DNA molecule from different species can rapidly be assessed by restriction endonuclease mapping. Generation of restriction endonuclease maps requires a pure preparation of DNA. Mammalian mitochondria contain a covalently closed circular DNA molecule of 16,569 base pair that can rapidly be purified from cells. The mitochondrial DNA can be employed directly for the study of evolutionary changes in DNA without the need of cloning a specific gene.

Mitochondrial DNA has been purified from the Guinea baboon, rhesus macaque, guenon, and human and cleaved with 11 diferent restriction endonucleases. Restriction maps were constructed for each species. The maps were all aligned relative to the direction and the nucleotide site where DNA replication is initiated. A comparison of restriction endonuclease sites allowed for the calculation of the degree of divergence in nucleotide sequence between species. The rate of base substitution has been about tenfold greater than changes in the nuclear genome. This high rate of mutation of the readily purified mitochondrial DNA molecule makes it an excellent model to study evolutionary relationships between species.

The analysis of mitochondrial DNA can also be used to assess the migration patterns of people who settled in diverse geographic regions but possess the same restriction-enzyme-generated patterns. Native Americans have been grouped into four major haplogroups based on their mitochondrial DNA restriction patterns. These groups appear to have migrated from Asia and Siberia some 18,000 years ago, just before the major ice age period.