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Different biological sequences within an organism may obey different clocks. The amino acid sequence of a protein encoded by a gene changes more slowly than the DNA sequence of the underlying gene because many amino acid changes may be selectively disadvantageous (because they disrupt function). On the other hand, a significant proportion of DNA changes may be selectively neutral because they create a synonymous codon (that is, one that specifies the same amino acid). Similarly, DNA regions within genes change at a slower rate than the DNA sequences located between genes. Accordingly, evolutionary studies of distant species are often carried out by examining amino acid sequences of proteins, while evolutionary comparisons among more closely related species are better done by examining DNA sequences within or between genes.

To study evolution within a single species such as the human, it is often useful to study DNA sequences that change at especially rapid rates. The mitochondrial genome provides an ideal substrate for such studies. The mitochondrion is an organelle found in the cytoplasm of eukaryotic cells, whose primary role is to generate high-energy compounds that the cell uses to drive chemical reactions. Although the mitochondria use many proteins that are encoded by genes in the cell nucleus, each mitochondrion has its own small circular chromosome that encodes a few dozen genes essential for its function.

In the human, the mitochondrial genome consists of 16,569 base pairs whose DNA sequence has been completely determined (Anderson et al., 1981). Human mitochondria are inherited only from the mother, and so their genealogy is considerably simpler to follow than for genes encoded in the nucleus (which are inherited from both parents and are subject to recombination between the two homologous copies in the cell). Conveniently for evolutionary studies, mitochondrial DNA (mtDNA) has an increased rate of nucleotide substitution compared to nuclear genes, owing to the presumed absence of certain DNA repair mechanisms. Moreover, the mitochondrial genome contains certain regions that are particularly tolerant of mutation, that is, appear to be subject to little selective pressure (Avise, 1986) and thus show a great deal of variation. In all, the mitochondrial genome may be evolving 10 times faster than the nuclear genome.

For these reasons, molecular population geneticists have carried out many studies of the DNA sequences of mitochondrial variable regions in many human populations (Di Rienzo and Wilson, 1991; Horai and