The Neanderthal FAQ, by John Hawks, describes the recent DNA analyses as presented in Nature (lots of references and links).
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This page contains a single entry by PvM published on November 19, 2006 10:41 PM.
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The article got into a lot of genetics stuff that is a bit over my head, so I’m unclear on a point. If Neanderthal DNA is chosen for having fewer possible human contaminants, and that is done on the basis of looking for human DNA in the sequence of the Neanderthal bone DNA, then won’t this lead to an inherent bias against the possibility of a close relationship between us and Neanderthals? It seems that the bones that are chosen are those that have less human DNA, however it got there, and therefore will apriori support the hypothesis that we diverged from them a long time ago, and that they disappeared through war/competition rather than sex.
Update