Mitochondrial mismatch analysis is insensitive to the mutational process

Mismatch distributions are histograms showing the pattern of nucleotide (orrestriction) site differences between pairs of individuals in a sample.They can be used to test hypotheses about the history of population sizeand subdivision (if selective neutrality is assumed) or about selection (ifa constant population size is assumed). Previous work has assumed thatmutations never strike the same site twice, an assumption that is calledthe model of infinite sites. Fortunately, the results are surprisinglyrobust even when this assumption is violated. We show here that (1)confidence regions inferred using the infinite- sites model differ littlefrom those inferred using a model of finite sites with uniformsite-specific mutation rates, and (2) even when site- specific mutationrates follow a gamma distribution, confidence regions are little changeduntil the gamma shape parameter falls well below its plausible range, toroughly 0.01. In addition, we evaluate and reject the proposition thatmismatch waves are produced by pooling data from several subdivisions of astructured population.