The challenges associated with inferring evolutionary process from patterns of genetic variation apply to any historical inference. The manuscript discusses those inferences particular to phylogeography and provides a specific framework of considerations that need to be addressed in this field given the dramatic increase in the variety and types of methodological approaches now available.

With the increase in sophisticated and powerful methods for statistical phylogeographic study, the gap between those developing the methods and the novice applying such methods is increasing. This gap needs to be bridged. Otherwise, more researchers will continue to apply methods in which there is no way no to assess the statistical confidence of any inference or distinguish among alternative hypotheses. The continued use of such methods not only limits the utility of phylogeographic studies, but in some cases, can produce positively misleading results.

The manuscript addresses some fundamental issues about how inferences about evolutionary process can be made from patterns of genetic variation. With recent methodological advances and careful consideration of the challenges associated with studying events in the past, the field of statistical phylogeography is poised to make critical insights into the processes underlying patterns of genetic variation, as well those contributing to the formation of new species.