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A new study of Neanderthal and Denisovan mTdna, reveals that Denisovans and Neanderthal split far earlier than was though, on the order of one million years ago
Even more surprising is the fact that the studies show the contribution of a previously unknown human ancestor.
From John Hawks' weblog,
and from the original article,
From the detailed genomes of both Neandertals and Denisovans, Pääbo and Montgomery Slatkin of the University of California, Berkeley, estimated that 17% of the Denisovan DNA was from the local Neandertals. And the comparison revealed another surprise: Four percent of the Denisovan genome comes from yet another, more ancient, human —"something unknown," Pääbo reported. "Getting better coverage and more genomes, you can start to see the networks of interactions in a world long ago," says David Kingsley, an evolutionary biologist at Stanford University in Palo Alto, California.
Meanwhile, the article sheds light on two interesting contradictions in the Denisova data. The analysis of the high-coverage data last fall  noted that the pinky bone genome is consistent with a very small long-term effective size, because of its limited genetic variation ("Denisova at high coverage". These results included a "drastic decline in size" around the time the Denisovans were estimated to have separated their population from the ancestors of living sub-Saharan Africans.
That result was curious in comparison with the mtDNA evidence. The Denisovan mtDNA is substantially more divergent from living human and Neandertal mtDNA, with an estimated time for the last common ancestor of mtDNA among these groups a bit more than a million years ago.
Now, we may be learning that the Denisovan genome itself represents different ancestral groups -- not only a more ancient "something unknown" population, but substantially the local Neandertals. That kind of mixture is not the population history described by papers on the Denisova genome so far. And a third Denisovan mtDNA from one of the third molars at the site is substantially different from the other two, pointing to greater mtDNA diversity within the Denisovan population than now known from either Neandertals or living people.
So Demisovans split off from the rest of us a million years ago, and they are the product of an unknown human ancestor, and they carried 17% local neanderthal DNA, fascinating stuff.