[NukeMan]

IIRC, one of the objections in comparing 'ancient' Neanderthal mDNA (mitochondrial DNA) to CURRENT human mDNA was that it was an apples-to-oranges comparison. In other words, if you had ancient human mDNA it would not compare well with current human mDNA, either (never mind any possible Neanderthal comparisons: a straight humnan-to-human comparison would not look right). Lo and behold, an ancient Aboriginal (Lake Mungo man?) mDNA was extracted and amplified and it showed his mDNA looks rather far off the beaten path compared with latter-day man. Gimme awhile and maybe I can locate the reference...

[NukeMan]

Here is one ref:
http://www.sciam.com/explorations/2001/012901human/

It's from Scientific American (and I know some of you can't stand that mag)...

They also make the point that even if Neanderthal mDNA is not in our current genetic makeup, other DNA might well be.

Here is another ref:
http://www.neanderthal-modern.com/genetic2.htm