Ceci n'est pas un pothole

In 2005 I wrote this:

"Unusual compared to the rest of the genome" is a phrase you should expect to hear a lot of in the next few years.

I was looking back at that old post today, as I’m writing new stuff about bottlenecks. It’s about the ability to detect selection using the HapMap data – written just as I was starting to think about recent selection:

Suppose we wanted to use a detailed topographic survey of a road to find the potholes. But for everyday roads, there is a problem -- there are lots of bumps and grooves that aren't potholes. And different parts of the road are more or less bumpy. It would help a lot if we could use the empirical distribution of bumps to simulate a section of road -- then we could figure out whether anomalies in the real road were likely to be potholes or not.
Now suppose that the road isn't just pocked with the occasional pothole -- it has a pothole every three or four feet. Remember why we're using simulations -- not only do we not know where the potholes are, we don't know how common they are. So our simulations based on the pothole-rich road will find that pothole-sized bumps are normal. If pothole-sized bumps are not unusual, then our simulation can have only one result: a pothole is not a pothole.

So I’ve been writing about the same problem for over three years – the problem of ignoring history and archaeology when applying models of population history, and how they skew simulations of genetic drift. Time to do something about it, I guess.