Denisovans: Ordinary humans with extraordinary genes?

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.