Deep dive into the Denisovans

By Razib Khan | August 31, 2012 1:25 am

By now you have probably seen the new Denisovan paper in the media. John Hawks has an excellent overview, as you’d expect. The only thing I will add is to reiterate that I think population movements in near and far prehistory significantly obscure our comprehension of the patterns of past genetic variation. One reason that the Denisova hominin presents conundrums (e.g., how did Australians and Melanesians admix with a population whose only remains are found in Siberia) is that we’re viewing it through the lens of the present. What other lens can we view it through? We’re not time travelers. But we should be perhaps more conscious of the filter which that imposes upon our perception and model of the world. This is probably a time when it is best to have only a modest confidence in any given proposition about the prehistoric past.

Also, I don’t know why, but I much like this tree:

MORE ABOUT: denisovan
  • Tim

    Disregarding the ethics and legality of the issue, with the ability to sequence ancient genomes this accurately, could scientists clone extinct species now, including archaic H. Sapiens?

  • Sandgroper

    I was betting she would have pale skin – wrong!

    I wonder why she died. And how odd that I should care.

  • toto

    (e.g., how did Australians and Melanesians admix with a population whose only remains are found in Siberia)

    Doesn’t it just mean that Denisovan introgression occurred after the divergence between (ancestors of) East Asians and Australians-Papuans?

    Also, I’m not sure the Siberian aspect is relevant – from John Hawks’ comment you get the feeling that Denisovans may well have lived in South Asia too.

  • Chad

    Damn Science Express….

    Anyhow, its not just population movements that obscure our vision, I would think that the Environment’s ability to preserve (or NOT preserve) remains would heavily bias our assumptions of prehistoric distributions.

  • Sandgroper

    @4 – And also not forgetting changes in sea level.

  • Rashid

    Razib pondered ” how did Australians and Melanesians admix with a population whose only remains are found in Siberia”

    Paleolithic club meds?

  • O-town

    I don’t get it. Why couldn’t the admixture have happend on Papua or nearby islands like Flores? Do we know for sure that the Flores pygmies were not Denisovans?

  • ohwilleke

    How did a population that was present in Melanesia leave traces in Siberia without leaving any genetic legacies in between? There are a few ways that could explain this pattern, not necessarily exclusive.

    (1) The Toba eruption may have opened Southeast Asia to modern human migrants by temporarily destroying jungles that had protected them from more fit hominins until then while simultaneously greatly reducing the Denisovan population in the middle of their geographic range, which was the area most powerfully impacted by the mega-eruption. This may also have provided a Denisovan-DNA free zone from which later Asian populations could emerge.

    (2) Denisovans may have fled incoming humans or been slaughtered by them in circumstances where Neanderthals would have stood their ground and co-existed with modern humans long enough to admix. Neanderthals had tools roughly comparable in efficacy to those of the first Mesolithic modern humans they encountered and roughly similar brain size relative to body size; Homo Erectus (from whom Denisovans are likely derived, at least in part) had smaller brains than modern humans and inferior tools. Thus, Denisovans may have been far more clearly outmatched, making either flight or slaughter in the face of mass migrations of modern humans into their territory more likely.

    (3) Exile may not have been an option in Island Southeast Asia because they couldn’t swim long distances or make boats. Denisovans who had undergone island dwarfism in Flores, however, might have escaped slaughter, where their non-pygmy kin did not, because they didn’t seem like as much of a threat to incoming modern humans. Hobbits are cute. Archaic hominins in Flores and modern humans co-existed on that small island for as much as 25,000 years, longer in such close proximity anywhere else in the world ever. So even if fertile hybrids were rare, there might still have been some in Flores.

    (4) Denisovan-modern human couplings may have been less likely to produce fertile offspring than pairing between the more closely related Neanderthals and modern humans as a result of their greater genetic distance, so successful admixture with the Denisovan may have been less common. Perhaps there was just one instance of fertile Denisovan admixture period in all of history, perhaps in Flores where the Denisovan population was cornered, amplified by the extreme population bottle neck in the founding populations of Papua New Guinea and the Sahul that involved an effective population of fewer than a hundred people and could have involved just half a dozen or a dozen women.

    Sound improbable? What if the small extended family and a few other friends of the only fertile Denisovan-modern human hybrid child ever born made the do or die decision to sail off into the horizon where they could see no destination that put them in Sahul (the only part of the trip to Australia and Papua New Guinea that couldn’t be made by navigation to a visible destination), so that they could flee persecutors who would probably have killed them precisely because they were tied to the hybrid Denisovan child, by going someplace that they could be sure that no one would ever follow them, when the only reason they had to believe they would find land was faith in providence. Why shouldn’t the most amazing interracial love story in the history of the world be romantic?

    (5) First wave modern humans who were admixed with Denisovans could have been profoundly diluted by later waves of modern humans originating in the Denisovan “dead zone” where they were nearly wiped out by the Toba explosion. Paleolithic carriers of Y-DNA haplogroup O with poor maritime capabilities could have expanded, for example, into Western Indonesia when it was part of a Sundland pennisula connected to mainland Asia, and this dilution could have been further enhanced by later waves of Asian Neolithic migrants. Something similar could have unfolded in mainland Asia, but with more of an Asian Neolithic impact. How could Paleolithic hunter-gatherers with Y-DNA halogroup O so powerfully diluted prior Paleolithic hunter-gatherer populations (in some place like Western Indonesia with only a minority Austronesian ancestry)? One plausible possibility is that the Y-DNA haplogroup O rich population that diluted first wave modern human populations (and perhaps Y-DNA haplogroup D rich populations as well), had domesticated dogs that gave them a decisive advantage, while the previous Paleolithic hominin populations did not.

  • Mike

    I read one study claiming up to 60 percent of the genome is of Denisovan origin in some modern Papuan populations and most others claiming between 1 and 6 percent? Which is it?
    I wouldn’t be surprised if scientists wanted to keep something like that under wraps to try and prevent any type of discrimination or worse. After all following tragic events like the holocaust and Darfur I could understand why people may have reasons for wanting to withhold this type of information. Personally I would argue that the type of people who take such actions will come up with reasons to take such actions regardless, and that in this particular circumstance the Papuans are a very homogenous nation.

  • Razib Khan

    #9, cite the study. you can play with the genome yourself to see if scientists are hiding anything.

  • Eurologist

    It’s going to be difficult to unravel, but – as ohwilleke said – there are clear signs of waves of migrations and bottlenecks (e.g., associated with the Toba eruption and subsequent harsh climatic environment).

    For example, y-DNA haplogroup D displays such an extreme relict distribution that it could be a good candidate for the first migration out of the green Sahara/ Arabia. And given the initial lack of new technologies, I wouldn’t be surprised if such people focused on environments that most resembled where they came from and thus were only sparsely represented in SE Asia, pre-Toba. C and K also have “weird” distributions: perhaps C entered the area also relatively early, and K was the first representative of the “UP revolution.”

    There is a significant number of middle paleolithic sites in Pakistan/India in the ~45,000 to 100,000 ya time frame, with upper paleolithic starting ~45,000 ya. Given the distribution and ages of haplogroups, to me that indicates a lot went on in the area for ~50,000 years before the “UP revolution,” and unlike Europe, it involved to a good part AMHs.

    There are many possible areas and times of Denisovan admixture, but to me it seems it would have been easier in the MP and in regions climatically similar to where the people initially came from – i.e., in parts of Pakistan and Northern India, which is much closer to the Altai than SE Asia. Any such group with admixture would then later be marginalized not only due to Toba and its consequences, but due to the waves of the technologically much advanced UP people (and later neolithic, such as associated with haplogroup O). Even Neanderthal admixture may have happened relatively late, because these waves of people would have marginalized all non-admixed modern humans.

    However, I am somewhat optimistic that with new genetic and statistical advances more details of this story will unfold, pretty soon.


Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


See More


RSS Razib’s Pinboard

Edifying books

Collapse bottom bar