If you are plotting a tree on a map, the ancestral nodes of the tree are plotted on the map as well. Ideally, the placement of the ancestral nodes would be done with an inference procedure that considered geographic and biological factors. However, for the moment, Cartographer simply plots the ancestral nodes at an arbitrary position in the window. The exact algorithm that is used involves squared-change parsimony based upon screen coordinates. As it is not based upon biology or geography, no conclusions should be drawn based upon the ancestral node positions.
Our hope is that someone will add new modules to Mesquite that will reconstruct ancestral locations using more biologically and geographically appropriate methods.