The story of Homo keeps getting weirder and weirder. Just as I was getting used to the idea that Neandertals and more modern Homo sapiens may have made the beast with two backs, somebody calls my attention to yet another lineage of Homo that may have coexisted with both of them. This conclusion comes from DNA extracted from a single bone and described in a paper by Krause et al. (and, of course, Svante Pääbo) in the April 8 issue of Nature.

First, a wee bit of background. We now know (or at least think) that there were three migrations of our relatives out of Africa:

The first migration of Homo erectus from Africa throughout Eurasia (and maybe to Indonesia), beginning 1.9 million years ago. H. erectus seems to have vanished without leaving descendants, though we’re not sure about this. And the “hobbit,” H. floresiensis, which lived in Indonesia until only 12,000 years ago, may have come from this migration. The migration that gave rise to Neandertals, beginning about 500,000 years ago. We now think that these individuals went extinct without leaving descendants, but left a few of their genes by hybridizing with members of the third migration. The final migration that took place about 60,000 years ago, giving rise, so we think, to all modern humans.

But the new paper suggests that there may have been a fourth out-of-Africa migration. The genetic data suggesting this comes from a single finger bone found in a cave in the Altai Mountains in southern Siberia (see circled location in Fig. 1 below). While the cave may have been sporadically occupied by hominins starting 125,000 years ago, the bone comes from a stratum dating between 30,000 and 48,000 years ago.

Fig. 1. Locations of specimens used in DNA analysis. Modern humans in gray, Neandertals in blue, Denisova individual circled in red.

After extracting the DNA from this bone (and again let us remember how remarkable an achievement this is), the authors sequenced the entire mitochondrial genome. They then compared its sequence to that of several modern human populations, some already-sequenced Neanderthal mtDNAs, and a bonobo and a chimp as outgroups. What they found, as seen in Figure 2 below, is that the Denisova sample was an outgroup to Neandertals and modern humans; that is, it diverged from the (Neandertal + modern human) lineage roughly a million years ago, well before the divergence of the Neandertal and modern human lineages from each other.

Fig. 2. Mitochondrial DNA phylogeny of modern humans (gray), Neandertals (blue) and the individual from Denisova (red)

What this means is that this individual could not have been part of either of the last two out-of-Africa migrations, nor could it have been part of the earlier migration 1.9 million years ago, since it diverged from our own lineage well after our lineage diverged from the ancestors of Homo erectus. This tentatively suggests that there was yet another migration out of Africa—a fourth—that gave rise to the Denisova individual and the population to which it belonged.

Further, this “species” could have been a contemporary of Neandertals and modern humans. The authors note that individuals with Neandertal-like mtDNA lived only 100 km away from Denisova at about the same time, and other artifacts suggest that “modern” humans also lived in the region around 40,000 years ago. It’s possible, then, that there could have been three evolutionarily independent species of hominins living in the same area of Asia at about the same time. (We already know a similar situation held for earlier species of hominins in Africa). More opportunities for hybridization!

Now this conclusion is tentative, for it’s based on mitochondrial DNA from a single individual. It’s possible that there was simply an ancient mitochondrial DNA kicking around in the Neandertal genome, and this individual was simply a Neandertal that had it. This can be resolved by looking at both other individuals and at the nuclear DNA of Denisova samples. (I don’t know if there are enough bones to provide this).

And of course we can’t yet tell if this individual was a member of a new species of Homo. That’s hard to tell from mitochondrial DNA, although zoologists often blithely (and, I think, erroneously) diagnose new species of animals based on an observed difference in mtDNA sequences.

Steve Gould once wrote that when he taught human evolution each year, his first job was to throw out all the lecture notes from the preceding year. With our remarkable ability to recover and sequence DNA from our ancestors and relatives, and the use of “phylogeography” to trace human movement using present-day genetic patterns, the field is moving even faster now. I am certain there are big surprises in store.

Fig. 3. Altai Mountains of Siberia, a view from just above the cave at Denisova where the new specimen was found (Photo by J. Krause, from Nature).

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J. Krause, Q. Fu, J. M. Good, B. Viola, M. V. Shunkov, A. P. Derevianko and S. Pääbo. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:838-839