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.
8 comments:
"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".
That admixture is not necessarily from some Denisova-related population in SE Asia previous to the arrival of modern humans. As I have long maintained, that Denisova element may have been carried to the region by the first modern humans. The Denisova element survived strongest where there was less later modern human arrival overlaying that original arrival. Note:
"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".
I suspect a very extended period, possibly from their first appearance. If (and I realise Maju especially is totally opposed to the idea) a Y-DNA C and mt-DNA N population moved east through some region neighbouring the Altai they could easily have picked up the genes along the way. Both haplogroups have a mysterious distribution with C apparently having originated totally in eastern Eurasia, with nothing present anywhere near Africa until being present as downstream branches, and N being split into two regional collections, again with nothing in between until R's expansion.
I'm not sure that I buy that hypothesis any more than Maju does, and you can see my updated post regarding my skepticism of the interpretation of the diverged mtDNA. I've read a couple of papers long ago on the detailed phylogenies of each these uniparental markets and found the conventional explanation to be pretty well supported.
I am much more inclined to see the Denisovans as a relict population.
Another possibility that seems quite plausible in that the Denisovan range more or less coincides with those areas in East Asia where post-Homo Erectus stone tool kits have been found pre-100kya, perhaps due to some biogeographic edge that they had in these regions. But, that is very fuzzy indeed.
I certainly don't disagree that the extreme dilution of Denisovan ancestry in mainland Asia could be due to dilution of first wave-first contact modern humans who exterminated the Denisovans except to the extent that they admixed with them, with the first wave involving the ancestors of the Australian Aborigines and Papuans, even though the 96% dilution of mainlanders relative to Australian Aborigines and Papuans seems a bit extreme for that hypothesis. If so, however, this supports the hypothesis that SE Asia/E Asia were first reached by modern humans only post-Toba, and undermines the accuracy of the dating of the handful of very old modern human remains found in China.
Are there really people whose mtDNA has not mutated for 40 000 years?! It mutates pretty slowly and unevenly but that is extraordinary. The most extreme clock violation I have heard of is an M44 genome which had apparently accumulated only 4 mutations since the root of M, and needless to say this is highly unusual. Behar et al sampled thousands of mitogenomes and found a mean of 57 substitutions from the modern human root, with a standard deviation of 5.9 and a range of 41-77, the vast majority of the distribution being fairly close to the middle.
The putatively older Denisovan had 29 mutations from the root, the younger ones 57. Statistically it seems highly unlikely that of only 3 samples we would happen to find one that had an exceptionally low number of mutations by chance.
The oldest mtDNA clade which is known as A00 or something like that is old indeed.
The range of the Denisovan samples is 18 mutations. The range of modern human variation is 36 mutations per Behar. Naively, the six sigma range spread seen in humans is what would be expected with a sample size of about 330,000 modern humans. I don't know how big Behar's sample is and it was probably not randomly drawn, so its a bit hard to make firm conclusions about what his sample implies for the entire human race. The expectation for everyone living today would be about 12 sigma which would imply a range of 72 mutations - i.e. there would probably be someone alive today with just five or ten from basal mtDNA mutations (if the distribution was truly normal, which it probably isn't in in the extreme tails).
For humans, an 18 mutation spread would be three sigma, which would happen on average one in a hundred comparisons. And, it isn't unreasonable to think that the human standard deviation may be biased to be low, because modern humans have had so many examples of extreme population growth from a small, closely related founding population over short periods of time that would probably be largely absent from the population history of Denisovans.
If the standard deviation of number of mutations in the Denivosans were 9 rather than 5.9, due to its lack of punctuated expansions comparable to that of modern humans, the spread would be only a two sigma spread, which would happen on average on in twenty comparisons.
Thus, the likelihood of this much of a gap solely due to chance is on the order of 1%-5%. My intuition is that the likelihood of mutual deposition in this cave in such close proximity to each other over a 30,000 year period is much lower than that.
Denisovan admixture has also been found with the indigenous peoples of the Americas by the way. So not just confined to East Asia and Oceania.
Also, the indigenous groups with the highest levels of Denisovan ancestry have the lowest levels of affinity to Oceanian populations, which means either there were two different admixture events with Denisovans, or indigenous peoples admixed with two different Oceanian populations, one with Denisovan ancestry, and the other without.
The second scenario isn't impossible. Austronesians would have originally had low levels of Denisovan ancestry as they migrated by sea from Taiwan and only later upon encountering and admixing with Papuans would have had higher levels of Deniosvan admixture.
The second scenario is certainly the case. We know the Austronesians/Polynesians are a mix of 'East Asians' (with immediate origins in Taiwan) and Papuans.
I agree that the second scenario happened. But, the two scenarios aren't necessarily mutually exclusive.
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