Hybridization or Contamination?

I'm starting a new project at work today. It's the one that my coworker, out on medical leave, was to start and it got passed to me. The work isn't technically difficult, consisting of cloning and sequencing a region of ribosomal DNA, but I haven't done much of it yet, so will be well-versed in that by the time I'm done.

We're looking for evidence of hybridization between two species, P and R, that aren't supposed to hybridize.

Although we are starting with a region of ribosomal DNA, my feeling is that we'll need to look at other markers as well. Some specimens, morphologically, have looked "funny" to my boss, but he ID'd those as R. I can remember when he made his comment a couple of years ago, and of course my first question was, "do P and R ever hybridize?" At the time, he said, emphatically, "no". Then we found several instances, then several instances more once we started looking for them, of individuals who showed both diagnostic bands for both species on our species-level screening PCR.

So the plan is to sequence the ribosomal DNA of 5 individuals that showed both bands and that had their morphology examined by an expert (my boss). 3 were ID'd morphologically as P, and 2 as R. We'll run our panel of microsatellite markers on them as well. I did a small sample (1 per family, 48 families) of R, just to see what their microsatellite profiles would look like. I got about 20% with P profiles.

It's a cool conundrum. Stay tuned.