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.John Hawks: New Denisova and Neandertal DNA results reported
With all the interbreeding, "it's more a network than a tree," points out Carles Lalueza-Fox, a paleogeneticist from the Institute of Evolutionary Biology in Barcelona, Spain. Pääbo hesitates to call Denisovans a distinct species, and the picture is getting more complicated with each new genome.
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.Related posts:
What does it mean? I don't think there's a contradiction here in the data. What this shows is that the methods applied to the data have been too simplistic. The methods will come to a result, but that result may not fit the data as well as a population model with more complexity. Looking only at one kind of comparison -- as the Li and Durbin model applied to the Denisova genome by Meyer and colleagues last year  -- will probably not give a result that describes the true population history. We need to keep our minds open to more complex population histories that may be more consistent with other sources of data, including archaeological and fossil information.