This is a very late post, but I just stumbled upon this thread and have some meager info to add. The "ginger gene" in humans causes the red hair and freckles found in some caucasian populations. I believe researchers at Oxford determined that the gene was indiginous to northern Europe and 50,000-100,000 years old (tending toward the higher figure). This would imply that the gene evolved in neanderthal populations as it predates Homo sapiens in Europe (at least those believed to have contributed to modern human genome).
I don't have time to search for this source, but I remember it was a peer-reviewed journal article. Dr. Milfred Wolpolf discussed this at a talk I went to several years ago. As I recall there was mention of another bit of evidence that supported this, but I don't know what that one was.
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