"There's been a small glitch"

That's how I approached my boss yesterday with the news that this awesome data set, which I had just finished a second draft of a manuscript for, had something wrong with one of the analyses. Oops. There's a lot to this population genetic stuff, and I discovered an inconsistency when I was going over the results for something else and I have to get it figured out before we can publish the paper.

One of the measurements one makes when doing population genetics is a measure of inbreeding. Big populations of organisms, like mosquitoes in general, should be random with respect to who they are mating with. This more or less absence of mate choice means there should be NO inbreeding in these populations. Small, isolated rare plant populations? Sure, they're expected to have some inbreeding. But big (like 10's or 100's of thousands - geez, maybe more) populations of flying organisms shouldn't have detectable levels of inbreeding.

But mine do. My feeling this is most likely a scoring error. I put the bits of DNA of interest through a DNA sequencer that is able to detect the size of the bits. Sometimes, especially when the bits are close in size, it's hard to tell what they call stutter, from actual data.

So I'm going back over the whole data set today - let's see, that's 10 markers times 247 individuals. I sure hope I can tweak the machine so I don't have to score all of them by hand, but I might have to look at a lot of raw data to get this figured out. *sigh*

To my boss's credit, his main concern was that we didn't put out erroneous data, so he's OK with me re-doing this part. I don't think it's going to change the gist of the data, but if the problem is what I think it is, what I'll do over the next few days will fix this finding of inbreeding that shouldn't be there. If it doesn't, well, I guess we'll have to come up with an explanation, but I'll feel better that that finding is genuine if I go through this exercise first.