A simple neutral model predicts that the ratio of non-synonymous to sy
nonymous fixed differences between species will be the same as the rat
io of non-synonymous to synonymous polymorphisms within species. This
prediction is tested with existing mitochondrial datasets from 25 anim
al species. In slightly over half of the studies, the ratio of replace
ment to silent polymorphisms within species is significantly greater t
han the ratio of replacement to silent fixed differences between speci
es. These observations are best explained by a substantial number of m
ildly deleterious amino acid mutations that contribute to heterozygosi
ty but rarely become fixed.