Choosing mutation models in population genetics

Several mutation models are available to population genetic applications, and are widely used in evolutionary biology, conservation genetics and ecology. Typically, they are used to estimate demographic parameters of the current and past population and to estimate genetic structure, and how it came about. The correct use of these different mutation models in specific genetic questions relies on a number of implicit and explicit assumptions. Typically, a mutation model is chosen based on the marker type, not on the underlying biological question. Using the wrong mutation model may lead, however, to erroneous conclusions. Here I show in more detail the known and hidden assumptions of such mutation models, and how to choose mutation models in population genetics appropriately with regards to commonly tested hypotheses, especially population bottlenecks and expansions.