MITOCHONDRIAL MISMATCH ANALYSIS IS INSENSITIVE TO THE MUTATIONAL PROCESS

Mismatch distributions are histograms showing the pattern of nucleotid e (or restriction) site differences between pairs of individuals in a sample. They can be used to test hypotheses about the history of popul ation size and subdivision (if selective neutrality is assumed) or abo ut selection (if a constant population size is assumed). Previous work has assumed that mutations never strike the same site twice, an assum ption that is called the model of infinite sites. Fortunately, the res ults are surprisingly robust even when this assumption is violated. We show here that (1) confidence regions inferred using the infinite-sit es model differ little from those inferred using a model of finite sit es with uniform site-specific mutation rates, and (2) even when site-s pecific mutation rates follow a gamma distribution, confidence regions are little changed until the gamma shape parameter falls well below i ts plausible range, to roughly 0.01. In addition, we evaluate and reje ct the proposition that mismatch waves are produced by pooling data fr om several subdivisions of a structured population.