We now have (partial) autosomal DNA from two more Denisovan individuals (the one who was the source of the mtDNA sample and a new individual) and a new set of Densiovan mtDNA (with a different haplogroup than the other two samples) from the same new individual.
This new DNA data confirm that all three teeth comes from individuals of the same Denisovan species of archaic hominin.
Denisovans appear to be a sister clade of archaic hominins to Neanderthals and all three samples come from a single cave in Siberia. But, significant Denisovan admixture (in addition to the ordinary amount of Neanderthal mixture for East Eurasians) is present in modern humans with Australian Aboriginal ancestry or Papuan ancestry. There may also be an independent source of Denisovan admixture in some Asian Negrito populations (e.g. in the Philippines, but not in the Andamanese) and possibly some very slight traces of Denisovan ancestry in modern humans in Southeast Asia and East Asia. The introduction to the paper notes that:
In 2008, a finger phalanx from a child (Denisova 3) was found in Denisova Cave in the Altai Mountains in southern Siberia. The mitochondrial genome shared a common ancestor with presentday human and Neandertal mtDNAs about 1 million years ago, or about twice as long ago as the shared ancestor of present-day human and Neandertal mtDNAs. However, the nuclear genome revealed that this individual belonged to a sister group of Neandertals. This group was named Denisovans after the site where the bone was discovered. Analysis of the Denisovan genome showed that Denisovans have contributed on the order of 5% of the DNA to the genomes of present-day people in Oceania, and about 0.2% to the genomes of Native Americans and mainland Asians.
In 2010, continued archaeological work in Denisova Cave resulted in the discovery of a toe phalanx (Denisova 5), identified on the basis of its genome sequence as Neandertal. The genome sequence allowed detailed analyses of the relationship of Denisovans and Neandertals to each other and to present-day humans. Although divergence times in terms of calendar years are unsure because of uncertainty about the human mutation rate, the bone showed that Denisovan and Neandertal populations split from each other on the order of four times further back in time than the deepest divergence among present-day human populations occurred; the ancestors of the two archaic groups split from the ancestors of present-day humans on the order of six times as long ago as present-day populations. In addition, a minimum of 0.5% of the genome of the Denisova 3 individual was derived from a Neandertal population more closely related to the Neandertal from Denisova Cave than to Neandertals from more western locations .The abstract also notes that:
The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.All of this is pretty much what we would expect from additional Denisovan DNA samples and none of them answer the big unsolved questions we have regarding the Denisovans, but it is still nice to have the additional data.
The one point I would add is that the more basal nature of the mtDNA from Denisovan 8 is used to argue that this tooth is much older and represents a prolonged occupations of the site. This is not a necessary interpretation, or even, in my humble opinion, a likely one.
It is common for particular individuals in modern human populations living at the same time, to have both more basal and less basal mtDNA. For example, in the same village in Nigeria, there might be one individual with mtDNA which most recently mutated 1,000 years ago, and another individual with mtDNA that most recently mutated 40,000 years ago.
This is an elementary inference from the apparent common mitochondrial origin of all hominins, and the fact that mutations happen with a low random frequency at each generation. In any substantial sized population, the mtDNA sequence with the least recent mutation is likely to have last mutated many thousands of years earlier than the mtDNA sequence with the most recent mutation.
Given the archaeological context of the teeth, in similar layers of debris in a single cave, the likelihood that there was mtDNA diversity with both older and younger clades of mtDNA present seems more likely to me than a continuous occupation for thirty thousand or so years that managed to be deposited in such close proximity to each other. One could estimate a predicted population size on this basis and compare it to the estimate using other methods.
The open access PNAS paper is here. John Hawks has an analysis at his blog.