Variation and change in mitochondrial DNA (mtDNA) is often assumed to
conform to a constant mutation rate equilibrium neutral model of molec
ular evolution. Recent evidence, however, indicates that the assumptio
ns underlying this model are frequently violated. The mitochondrial ge
nome may be subject to the same suite of forces known to be acting in
the nuclear genome, including hitchhiking and selection, as well as fo
rces that do not affect nuclear variation. Wherever possible, evolutio
nary studies involving mtDNA should incorporate statistical tests to i
nvestigate the forces shaping sequence variation and evolution.