What's It Got in Its Genes Pocketses?

I'm already in danger of overworking this rhetorical refrain, but, is it just me? Neanderthal genome got sequenced. Great! Not long, really, after the first gene map of us. So, evolutionary biologists of the world, if I sequence the Neanderthal genome and it shares a novel nucleotide sequence with modern humans, what's the first thing that comes to your mind? NO! It's not that the Neanderthals must have bred with humans. And it's not that they didn't. It's just that on the evidence the only thing we can say is that, in all likelihood, the common ancestor of Neanderthals and modern humans carried the same novel sequence. It's possible that we got it from the Neanderthals, and the genetic evidence could be seen to support that hypothesis. However, an untestable hypothesis it will remain. To say otherwise is to be, at best, mistaken, and at worst, disingenuous.