The complete mitochondrial DNA genome of an unknown hominin from southern Siberia : Nature.
Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans.
Hobbit version 2.0: the undiscovered hominin
As my students have heard me say many, many times, gene trees are not species trees. The different genetic loci within a population have diverse genealogies. Often, when two populations diverge from each other, their gene genealogies will show similar patterns of divergence. But not always.
When we look within a single population, gene genealogies are likewise diverse. but within a single population, there is no population divergence. There must be an oldest branch point in the genealogy of any single gene. Here’s a question: how many individuals do you have to sample so that you are sure you will find this deepest branch point? The answer to that question depends on the frequencies of the lineages on either side of that branch. If one of them happens to be rare, you’re unlikely to find it unless you sample lots and lots of individuals.
And if the population is spread across a substantial amount of space, it is very likely that one of the clades will be geographically limited compared to the other.
Put these two things together, and apply them to a widespread population like the Neandertals. It is pretty likely that if we sample a dozen Neandertals across a subset of their range, that we will miss the deepest divergence in the genealogy of a single gene. That may be what has happened here. By extending the known mitochondrial sample of Neandertals even further to the east, this study may have discovered a deeper branch point than was previously known within the Neandertal population.
Indeed, a million-year-old clade divergence would be entirely normal for a large mammal. That’s what we see in chimpanzees, and as I pointed out yesterday, it’s smaller than the clade divergence we see among mammoth mtDNA across a similar time range and geographic extent.