Phylogeographic methods enable inference of the geographical history of genetic lineages. Recent examples successfully explore the patterns of human migration and the origins and spread of viral pandemics. Nevertheless, longstanding disagreement exists over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally how we view the relationship between the inferred history of the sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely side-step inference about the history of the population will eventually help the field toward this goal.
展开▼
