I was finally able to go back to the Nature Genetics story about Icelanders with a genetic inversion . The subscription article is available here . On looking through it, the genomics are just outstanding. To identify such a "small" inversion, they had to clone out small pieces of known chromosone 17 DNA from a lot of people.
Ok, so I looked at their dating methods and it looks just beautiful. Of the 900 K basepairs they focused on a smaller piece which overlaps with a known gene. This is necessary and pretty standard practice. The killer, for me, is a "sliding window" analysis in which the molecular clock method is separately calculated for each 5 K window of this smaller piece. Remarkably, the inverted sequences throughout the window always fall pretty much halfway between modern H. Sapiens and modern chimpanzees-- exactly what you'd expect for indeed a very ancient divergence.
So, how did Europeans get it? The two possibilities were that either it was always there in the European peoples (for 3 million years!) and recently became more common; or that some very divergent hominid contributed DNA to much more recently to the European lineage. This isn't just a question of, ahem, close contact. This means successful interbreeding. Just astonishing.