A new high-coverage Neandertal genome

Today, Svante Pääbo’s group at the Max Planck Institute for Evolutionary Anthropology released high-coverage sequence data from a toe bone from Denisova Cave. The new genome comes a year after the same group released the high-coverage genome of the Denisova finger bone, several months before they published the first high-coverage analysis of this ancient genome Meyer:Denisova:2012 . Today’s announcement is here: “A high-quality Neandertal genome sequence”. It adds a second high-coverage genome from Denisova Cave, this one from a toe bone. Unlike the first finger bone genome, this toe has produced a genome very much like Neandertal specimens from much further west, including the Vindija Neandertals.

Something interesting in these data: the presence of a Y chromosome.

There’s not so terribly much we can say about a toe. This particular bone was first reported in 2011 by Mednikova Mednikova:2011 , who described the specimen’s anatomy. She found the toe similar in some respects to equivalent Neandertal toe bones, but also like recent humans in a couple of details. Still, the anatomy wouldn’t be enough to conclude that the bone is a Neandertal, because we don’t know much about the toes of other ancient human populations.

The genetics are fairly clear about the level of similarity of this new genome to other Neandertals. From the announcement:

The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Denisova Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.

This is a cluster diagram based on genome-wide similarity, which doesn’t tell us about possible mixture among the populations. But it does show the high degree of similarity among the known Neandertals. This new specimen from Denisova (labeled “Altai”) is a bit further from them than they are to each other, but not much. It will be interesting to assess this degree of similarity in comparison with the within-population similarity of more living human populations.

I’m reluctant to accept a dichotomy of “Denisovan” versus “Neandertal”. Distinguishing the samples in that way invites a typological assumption about the ancient people, giving an impression of distinctness that I’m not yet convinced about. It remains to seriously investigate the hypothesis that one or both of these putative samples represents some amount of gene flow from each other, or from yet more ancient populations. But I suppose we’re stuck with the “Neandertal from Denisova” and the “Denisovan from Denisova”.

Unless we go for “manual genome” versus “pedal genome”, which is admittedly unappealing.

There’s not much meat in this announcement, that will wait for the full published analysis that we can expect later this year. The most important aspect of this, like the Denisova data availability from last year, is that we can now start working with the high-quality data. As someone who works with sequences, I cannot overstate the importance of having the best high-coverage data available for our work.

I have a paper in preparation where I make a relevant analogy, in this case noting last year’s high-coverage Denisovan genome in comparison to the history of ancient DNA sequencing:

To put this into context: the original 360bp sequence from Feldhofer 1 has been memorialized on a cross-shaped plaque at the site outside Mettmann, Germany. This plaque is approximately 1 square meter in size. A similar monument to contain the Denisova high-coverage data would need to be more than 14 kilometers across. Compared to the first sequencing effort in 1997, todays state of the art involves the generation of more than 200 million times more data.

It’s a pretty awesome time for those of us exploring human evolution!