Update: Hawks responds.
John Hawks has not commented on this feature in Wired titled Code of the Caveman. But I'm sure he will, and when he does, I will point you to it because what he says on this topic is worth listening to. But, until then, here are a few points.
1) This extraction of ancient autosomal DNA, not just the copious mtDNA, from Neandertals by the Paabo group and its associates has been talked about for a year or so now. So within the scientific community this isn't a big surprise.
2) The new bioinformatically flavored techniques offer up the possibility to "learn more about their skin and hair color [Neanderatls], as well as what they ate and even their language," according to the research profiled. What does he mean by this? Well, in modern humans we know some of the genes which are involved in these traits. For example, SLC24A5 and MC1R are important in different ways in determining the complexion of Europeans. Analyses of these loci might tell us if Neandertals were redheads, for instance.
3) Yet, even though the researcher points to the importance of function, he switches back to admixture & ancestry, as if that is the whole ball of wax. The article suggests that Neandertals and our own lineage separated 500,000 years ago (plausible), and that there was no admixture between the two groups. Then, he goes on to assert that "believes offspring of individuals from such divergent groups would probably have been sterile, like mules." Earlier he states "I don't really like cells or anything...I just like data." Well, perhaps it would have helped him if he liked organisms more, because he might have had the intuition that 500,000 years isn't long enough for there to be a slam dunk in regards to obligate sterility. In fact, the primates are a lineage where interspecies (lineage) hybridization is relatively less risky. Lions and tigers seem to have speciated approximately 2 million years ago, but they can still produce fertile offspring!
4) It seems in Eurasia adult lactase persistence (allowing the digestion of milk) rose to high frequency in Northern Europe, and later spread to other regions (i.e., the Northern European variants are ancestral). In Northern India 70% of the population exhibit lactase persistence, but neutral genomic studies show little, if any, admixture with Northern Europeans within the last 10,000 years. Canadian anthropologist Peter Frost has asserted that fair complexions in Europeans are the result of recent sexual selection because the diversity of polymorphism on MC1R is simply too great to have arisen within the last 35,000 years by non-frequency dependent dynamics. In fact, the coalescence (back to the common ancestor) of some of the morphs might go back nearly 1 million years, so some of these fairness inducing alleles seem very ancient indeed...you can connect the dots I hope?
Remember, phylogeny does not imply morphology, and vice versa.
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