Denisovans: Ordinary humans with extraordinary genes?

By Carl Zimmer | December 23, 2010 9:52 am

As I report in today’s New York Times, scientists have sequenced the full genome from a 50,000-year-old finger bone from a Siberian cave, and they’ve concluded it belonged to a new lineage of humans they call Denisovans. These Denisovans, they argue, share an ancient common ancestor with us that lived, perhaps, 600,000 years ago–long before our species Homo sapiens arose. A couple hundred thousand years later, their branch of hominin evolution split, with one lineage evolving into Neanderthals, and the other into Denisovans. Much later, the Denisovans mated with Homo sapiens expanding out of Africa into southeast Asia, and today their DNA can still be found in the people of New Guinea and neighboring islands.

When reporting a story like this, it only makes sense to consult with a wide range of experts to get their feel for it. Science is not a democracy, but when a lot of people well-versed in a subject all point to the same problems with a study, their observations are newsworthy. Such was my experience in reporting for Slate on the reactions from the scientific community to claims of arsenic-based life earlier this month. In that case, the responses were generally negative (actually, ranging from wishing it were true to wondering how the paper even got published). But the responses were not uniform, so I ended up reprinting a bunch of them here on the Loom.

In the case of the Denisovans, most reactions I got were of the “my-mind-is-blown” variety. Some people felt that the Denisovan hypothesis now needed to be tested with some new evidence. (Finding another DNA-packed fossil bone won’t be easy, but we living humans have lots of genomes waiting to be analyzed for Denisovan-like DNA.) But Joao Zilhao, an anthropologist at the University of Bristol (and about to take up a post at the University of Barcelona), offered a very provocative response.

Zilhao has been unearthing lots of tantalizing evidence about Neanderthals on the Iberian Peninsula, including painted, drilled shells that they may have used as jewelry. He has also championed the idea that the 24,000-year-old skeleton of a child found in Lagar Velho in Portugal is a human-Neanderthal hybrid. Zilhao has long been at odds with what he sees as an extreme form of the “Out-of-Africa” model of human evolution–that is, that our ancestors expanded out of Africa and mingled not a whit with the hominins they encountered along the way–hominins that not coincidentally became extinct after we showed up in their backyards.

After Zilhao got back to me about the Denisovans, I decided not to include his response in the article. With a limited amount of space to describe the new paper and reactions to it, I felt that I should select a couple quotes that reflected the general reaction I was getting from other scientists. But his response is still worth reading. So here it is (I’ve added a few clarifications in brackets):

1) The authors conclude: “the emerging picture of Upper Pleistocene hominin evolution is one in which gene flow among different hominin groups was common.” Such a picture may be “emerging” for the geneticists, but it has been argued for a long time on the basis of the fossils, namely Lagar Velho 1 and Oase 1 and 2, to mention but three that were found in the last 15 years and in whose excavation and study I was involved. It strikes me that aDNA [ancient DNA] researchers find it so hard to acknowledge the obvious: that their results strongly support Assimilation/Admixture models of modern human emergence and Neandertal/”archaic” demise put forth on the basis of the fossils and the archaeology and which, for a long time, they strongly opposed. The evidence eventually turned them around, and I suppose that’s a good thing. But an honest acknowledgment of the implications of their findings in terms of the history of the debate would be befitting.

2) If the “Denisovans” are eventually shown to be anatomically archaic people indeed, the genetic evidence that they contributed to the Melanesians [people of New Guinea and surronding islands] is an important finding that, as the authors acknowledge, strengthens the case for the spread of modern humans across Eurasia to have featured admixture with local archaics as a rule, not as the exception.

3) But can we confidently assume that the “Denisovans” were indeed anatomically archaic? The two fossils [the finger bone and a molar] are largely undiagnostic, but note that the upper third molar is, in terms of size, identical to those of the Oase 2 cranium [more on Oase 2], which is a “modern human with inherited archaic features.” Moreover, the authors note the exceptional preservation of DNA in the phalanx, which, if anything, is suggestive of the fossil being young rather than old. Add to that the fact that the directly dated items found closest to the phalanx yielded mid-Upper Paleolithic ages and the parsimonious reading of the evidence is, to me, that the “Denisovans” are mid-Upper Paelolithic people that lived in the area somewhere between 30,000 and 15,000 years ago — i.e., I would not be surprised if, when more material is found, they will be shown to be “anatomically modern”, even if “genetically archaic”!

4) We will not know for sure what the age of these remains is until they are directly dated (and the tooth could be, despite its small size, for instance, the age of the early modern human remains from Mladec, in the Czech Republic, was established by radiocarbon dating of teeth; cf. Wild et al 2005: 332-335; Nature 435), but let me stress that I have myself pointed out in different occasions that the stratigraphy of Denisova was disturbed to the extent that dating by association was unwarranted, and I am happy to see that, at last, the excavators acknowledge that such is indeed the case.

For instance, concerning the personal ornaments in level 11 (the same level where the phalanx was found), I wrote:

“A major discontinuity separates OIS-3 layer 11 of Denisova from the immediately overlying OIS-2 level 9, and the contact between the two is significantly disturbed. Because the range of ornaments from level 11 is identical to that found in both level 9 and the pockets containing level 9 lithics that penetrated deeply into level 11 (Derevianko and Shunkov, 2003, Fig. 7), their association with the IUP is questionable” (Zilhão 1997: 12-13; Journal of Archaeological Research, http://www.springerlink.com/content/tg033r44623u33q5/fulltext.pdf) [pdf link]

And, where the age of the phalanx and its implications for the understanding of the DNA evidence are concerned, I wrote:

“These problems are compounded by the fact that archaeologists, anthropologists and media people (and even many geneticists) often mistakenly equate genetic ‘lineages’ (namely, mtDNA ones) with biological species. Take the recent realisation that the mtDNA extracted from a human phalange recovered in the cave site of Denisova, Siberia, belonged to a lineage that was even more distant from extant humans than the Neanderthals’: this finding was hailed as evidence for yet another ‘species’ of human living some 40,000 years ago! However, the levels whence the Denisova phalanx came are so disturbed that the chances of that phalanx being 20,000 (or even 10,000) years old are as large as its being 40,000; until it is directly dated, we can’t tell. In any case, the fossil simply goes to show the extent to which past human genetic variation was much higher than at present, something for which many clues exist even among the genes of extant humans.” (Zilhão 2010: 6; Radical Anthropology, Issue 4, November 2010, http://www.bris.ac.uk/archanth/staff/zilhao/radicalanthropology.pdf). [pdf link]

So, I suspect the “Denisovans” are in fact “modern humans.” The future will tell, but that should surprise no one, because I see no reason to suppose that genetic lineages (however defined, namely via mtDNA [mitochondrial DNA]) that are very old and cannot be found any more among present day humans did not survive until a very recent past (in evolutionary terms). Until “globalization” events occurring in the last 10,000 years confused everything, that would be the thing to expect under a scenario where, at any given point in paleontological time, all humans belonged to a single biological species but one where, due to strong population structure related to geographical isolation, local extinctions and frequent recolonizations with attendant founder effects, there was a lot more variation in morphology and in genetics than there is today. To me, that’s what the fossils have bee saying for the last 15 years, and the genetic evidence is simply adding further detail and further complexity to that scenario.

Comments (16)

  1. greg Tingey

    Inter/intra-species breeding, huh?

    Anyone here familiar with the term “Rishathra” ??

    Larry-Niven reading SF fans will know.

  2. pconroy

    So, I suspect the “Denisovans” are in fact “modern humans.”

    All I can say is WOW!

    I think he could correct though

  3. johnk

    Fascinating. Not my area but I’d like to read more on this. Some confusions: what is the role of ‘hybids’ in evolution? If two species separate, but can form non-sterile hybrids, why are the ancestral lines considered two species? If the ‘hybrids’ can have evolutionary descendants that mix with either ancestral species, it would seem like a branching mess. Zilhao’s model seems to remove the ‘hybrid’ concept and clean things up.

    [John–Start with James Mallet’s work on hybrids and speciation: http://www.ucl.ac.uk/taxome/jim/jimpubs.html Basically, hybridization can potentially collapse two incipient species back in on each other. Or selection or other factors can keep the two species distinct despite the flow of genes due to fertile hybrids.]

  4. i didn’t add that in my post, but i wonder about the role in holocene framing expansions in washing away a lot of diversity.

    Some confusions: what is the role of ‘hybids’ in evolution? If two species separate, but can form non-sterile hybrids, why are the ancestral lines considered two species? If the ‘hybrids’ can have evolutionary descendants that mix with either ancestral species, it would seem like a branching mess. Zilhao’s model seems to remove the ‘hybrid’ concept and clean things up.

    look up ‘species concept.’ it’s not cut & dried. some different bird species can hybridize after 30 million years of evolutionary distinctiveness.

  5. DK

    In what way then may Denisovans be “modern”? If they have archaic genes (and they do; no need to concentrate that much attention on mtDNA when most of the nuclear geneome is available), then it would be extraordinary strange if they had at the same time modern anatomy. So the answer to “can we confidently assume that the “Denisovans” were indeed anatomically archaic?” is almost certainly yes. That they may have lived recently does not make them anatomically modern. If the main point is about systematics (single species or not), then it’s arbitrary anyway. The usual splitters vs lumpers apply.

  6. Miley Cyrax

    Derived variants point to Denisovan-Neanderthal clade with “us” as the outgroup. Are you arguing for the possible Human-Denisovan parallel evolution where they both developed convergent adaptations, or for the possibility that the modern human phenotype was largely established in the ancestral population of Denisovan, Neanderthal, and humans where the humans and Denisovans retained primitive features and the Neanderthals evolved derived traits?

    Both of these scenarios seem unlikely to me, but these seem to me the only way “archaic” genes could remain in the Denisovans but with “modern” (i.e., similar to “us”) anatomical features.

  7. AH

    I guess I understand why Zilhao come’s off a bit angry since he has been proven right about the refutation of the out of Africa dogma, but I don’t really understand what he is advocating for here.

    Separating Neanderthals, Denisovans and moder humans into seperate species certainly doesn’t make sense, but neither does lumping them all into one big group called “modern humans”. They may be all one species, but they are clearly significantly different from each other. What is interesting is to see what the differences in these populations are ecologically and genetically and how they interacted.

    This sentence seems particularly strange to me, “I would not be surprised if, when more material is found, they will be shown to be “anatomically modern”, even if “genetically archaic”!”

    Why would we expect them to be “anatomically modern,” Wouldn’t we expect them to be “anatomically Neanderthal,” since Neanderthal’s are their closest relative? Furthermore it seems to me that the genetic evidence for a separate archaic population is much more biologically interesting than if the Denisovans are coincidentally anatomically modern.

    Lastly, though I agree that mtDNA is often misused as a marker for genetic lineages. The Denisovan study used nuclear DNA which is much better measure. Harping on about mtDNA in this case is a bit misleading on Zilhao’s part.

  8. dave chamberlin

    What makes this all so exciting is additional evidence will keep pouring in. If the hypothesis that “human genetic variation was much higher than at present” up to the agricultural revolution is true, then it shouldn’t be long before it is further confirmed with the DNA in bones already in museum collections.

  9. Monkey

    Textbooks should, from here forward, be made with eraseable ink. Or in a three ring binder o we can simply remove the offending material in insert the new-found material!! Its all coming so fast…

    Cool stuff, cant wait to hear the follow up on this in a few months time when the dust has settled and many lines are able to convene on one strong hypothesis. Juicy stuff, though.

    Nature always has a few (million) tricks waiting for us to discover, eh?

  10. David B. Benson

    If it were flowers being considered, there would be one genus, one species and then either subspecies or varieties. I guess that makes me a grand lumper.

  11. Alyson Irvin

    I wonder if they will find any admixture of Homo floresiensis in any group of humans.

    I personally suspect that in our mythologies that we tend to think of as pure fiction are some real if adulterated and diluted accounts of our encounters with other homonids. For instance the leprechaun and the menehune could well be Homo floresiensis, and “trolls” could be Neanderthals.

    I think some of our oral traditions may be a lot older than we currently suspect. But who knows. I am curious to see what else got mixed into the modern human. I’m so glad we have the science to actually prove some of this. I had always believed that we must have interbred with Neanderthals, but its nice to have data to back it up.

  12. David B. Benson

    Homo floresiensis — First need a DNA analysis.

    The wee folk of Keltish traditions were, IMHO, the earlier Neolithic settlers in Scotland and, I suppose, Ireland. The Kelts largely displaced them, but with the possibility of some surviving genes in the outermost Outer Hebrides and just possibly also northwest Ireland.

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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