I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures of genetic distance, such as Nei's DA, DS, and Edwards Chord distance. The answers I get between these measures are conflicting, but each explained by a sound hypothesis, and so I must carefully and objectively choose which measure of genetic distance is to be most trusted given my data. So my question to the community is not, "which should I choose?" but "how should I choose?" I am interested in an answer or (ideally) resource that describes what factors I should take into account and that may bias my result.