On the choice of genetic distance in spatial-genetic studies

We look at how to choose genetic distance so as to maximize the power of detecting spatial structure. We answer this question through analyzing two population genetic models that allow for a spatially structured population in a continuous habitat. These models, like most that incorporate spatial structure, can be characterized by a separation of timescales: the history of the sample can be split into a scattering and a collecting phase, and it is only during the scattering phase that the spatial locations of the sample affect the coalescence times. Our results suggest that the optimal choice of genetic distance is based upon splitting a DNA sequence into segments and counting the number of segments at which two sequences differ. The size of these segments depends on the length of the scattering phase for the population genetic model.