Testing population genetic structure using parametric bootstrapping and MIGRATE-N

We present a method for investigating genetic population structure using sequence data. Our hypothesis states that the parameters most responsible for the formation of genetic structure among different populations are the relative rates of mutation (mu) and migration (M). The evolution of genetic structure among different populations requires rates of M << mu because this allows population-specific mutation to accumulate. Rates of mu << M will result in populations that are effectively panmictic because genetic differentiation will not develop among demes. Our test is implemented by using a parametric bootstrap to create the null distribution of the likelihood of the data having been produced under an appropriate model of sequence evolution and a migration rate sufficient to approximate panmixia. We describe this test, then apply it to mtDNA data from 243 plethodontid salamanders. We are able to reject the null hypothesis of no population structure on all but smallest geographic scales, a result consistent with the apparent lack of migration in Plethodon idahoensis. This approach represents a new method of investigating population structure with haploid DNA, and as such may be particularly useful for preliminary investigation of non-model organisms in which multi-locus nuclear data are not available.