As background to a couple previous posts where I made somewhat technical comments about simulations in population genetics, I was in the middle of writing a rather lengthy primer on coalescent theory. Then I saw that RPM has an old post pointing to some of the same material I was planning on hitting. So instead I’ll just say read his post and the links therein. I may get around to finishing what I was writing (there’s a bit of math that most people don’t care to see, so maybe not), but you can essentially boil it down to RPM’s last point:
Without a null model based on the coalescent, there is no way to statistically test hypotheses that are based on DNA data, regarding things like population structure.
Or natural selection.