Found this interesting article from Instapundit, which followed through to this, more detailed description of research that shows evidence of inbreeding between modern humans and other proto-human species:
“Our work is different from the research that led to the breakthroughs in Neanderthal genetics,” he explained. “We couldn’t look directly for ancient DNA that is 40,000 years old and make a direct comparison.”
To get past this hindrance, Hammer’s team followed a computational and statistical approach.
“Instead, we looked at DNA from modern humans belonging to African populations and searched for unusual regions in the genome.”
Because nobody knows the DNA sequences of those now extinct archaic forms, Hammer’s team first had to figure out what features of modern DNA might represent fragments that were brought in from archaic forms.
“What we do know is that the sequences of those forms, even the Neanderthals, are not that different from modern humans,” he said. “They have certain characteristics that make them different from modern DNA.”
The researchers used simulations to predict what ancient DNA sequences would look like had they survived within the DNA of our own cells.
“You could say we simulated interbreeding and exchange of genetic material in silico,” Hammer said. “We can simulate a model of hybridization between anatomically modern humans and some archaic form. In that sense, we simulate history so that we can see what we would expect the pattern to look like if it did occur.”
It’s an interesting theory, but any time someone tries to tell me they can successfully model complex systems with a computer program, I get very very skeptical. From my previous job, I know the difficulties in doing this with protein-ligand interactions, which we have a lot of experience modeling in-silico, and even that’s daunting. We’re also, still, not that remarkably good at it.
I would imagine to model something like this, you’d have to make a rather large number of assumptions. Since we also do not have African proto-human DNA, in contrast to what’s available for Neanderthals, I don’t see any way you could invalidate this model. One way I can think of is to see if it can successfully tag DNA sequences from known inter-species hybrids, where we do have the DNA for both parent species available. If it can do that, I might have some faith in it. I’d want to see it work on more than just Neanderthal cross-breeding with modern humans.
I should note, that the theory sounds plausible, and the evidence that it happened with Neanderthals is pretty strong, but my bullshit alarm goes off when computer models are employed to model complex systems with a lot of unknowns.