Monthly Archive for December, 2010

From John Timmer, Nobel Intent

It’s been a busy year in research on recent human ancestry. Back in the spring, scientists completed a draft of the Neanderthal genome, which provided clear evidence that these now-extinct humans left some of their genes behind by interbreeding with some human ancestors. A bit earlier in the year, DNA sequencing revealed an even larger surprise: there seems to have been another population of premodern humans present in Asia that were genetically distinct from modern humans and Neanderthals. Now, the team behind both of these discoveries is back with a draft genome of this population that suggests it was genetically distinct from both humans and Neanderthals, and a single tooth that suggests it was physically distinct. And that it also interbred with the ancestors of a modern human population.

The new population was identified based on sequence from a single bone found in a cave called Denisova. Sequencing the genome of its mitochondria indicated it had branched off from the ancestor of both humans and Neanderthals roughly a million years ago, making it a relatively archaic lineage. But mitochondrial DNA is prone to rapid sequence changes as well as founder and bottleneck effects, which could exaggerate the divergence. The bone it came from didn’t differ significantly from either of these human populations, meaning there was no physical indication that the Denisova remains represented a new population.

In the new paper, which will be published in Nature, the researchers have gone back and corrected both of these issues.

They’ve used a new technique to limit the errors in the sequencing of ancient DNA. These arise primarily from sites where a base has been either lost or chemically modified so that it base pairs improperly. The authors treated their DNA with an enzyme that recognizes the modified base and chops it off, turning it into the equivalent of a missing base. They then used a second enzyme that cuts the DNA backbone wherever there are bases missing. Combined, these two treatments significantly cut down on the errors.

Despite the single source, the authors were able to obtain nearly two-fold coverage of the Denisova genome, meaning that, on average, each base was sequenced twice. Over the billions of base pairs in a human genome, however, that average means we’ll have both areas that are well sequenced and gaps that don’t appear at all.

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