without reading your link, and so hoping to not be repetitive, there was some data that suggested massive interbreeding. Such data are generally amplification based, and a couple of my skin cells can go a long ways towards mucking up the result.
Those results were debunked.
Subsequent results have indicated that for those sapien populations derived from the coexistence with neander in Europe, that perhaps some 1-4% of sapien genome from those populations may reflect neander "dna". My understanding it this is not a settled matter, and that obviously what one would like is a DNA sample from sapien just prior to stepping into europe ... the 1-4% similarity may predate cohabitation and go back to the whole issue of just how many independent human populations were there in Africa and how many migrated out of Africa and when.
Having not looked at it closely, we are likely talking SNiP analysis, although retroviral integration or REs could form the basis for similar conclusions affording AFPL type data.
Glossary:
SNiP : single nucleotide polymorphism, the change of a single base of DNA
AFLP : amplification length polymorphism, the distance between two primers used for amplificaiton is observably different, indicating that one or the other has some intervening DNA between the two priming elements.
Dormant/dead retroviral integrations are one means to generate AFLPs.
Repetitive elements are a little more plastic IMO, and I would guess that they are least likely to be used for such things.
I doubt RFLPs would be used in this (restriction fragment length polymorphisms)
AFLPs are typically observed by running amplified fragments on size separating gels.
SNPs are typically observed by sequencing, and while there other means to do so, modern pyrosequencing and such has led more or less towards a 'screw it just sequence the damn thing' approach.
| 