We've reported in the past that researchers were attempting to sequence the Neanderthal genome in an attempt to better understand the origin of modern humans. The need for this project might have gotten a boost from a recent report that suggested that at least some of this pre-modern human lineage lives on in our own genomes. So it seems to be a perfect time to provide an update on how that work's going. Conveniently, both Nature and Science have obliged, and they describe different approaches to this attempt to understand our ancestry.
The Nature paper provides an excellent summary of the difficulties posed by the problem of getting an accurate sequence from ancient samples. They describe a detailed survey of Neanderthal remains, in which they examined 70 different bone and tooth samples for DNA content and contamination. After rejecting most as poorly preserved, they screened six for Neanderthal-specific DNA. Most showed high amounts of contamination by human sequences, but a 38,000 year old sample from Croatia provided over 90 percent Neanderthal sequences. All the work was done using this individual.
Using a new sequencing technique that amplifies single molecules for characterization, they obtained over a quarter-million unique sequences. Nearly 80 percent of these came from unknown sources, which is apparently typical of samples of this age. Most of the rest were equally divided between DNA from soil bacteria and primate sequences. Overall, there were nearly 16,000 individual pieces of primate DNA sequenced. One of the things that quickly became clear was that this DNA had suffered some damage over the years. Attempts to estimate its age relative to humans suggested that the Neanderthal lineage was twice as old that of modern humans, which makes very little sense when you consider that we've outlived them.
A different method of sequencing, which examined populations of DNA molecules (instead of single examples) was used to look at the same sequences. In these populations, the damage should average out—sure enough, 14 of the 34 bases that looked different were the products of damage. Eleven of these were the result of known forms of age-related damage, so they provide information that should help in interpreting the rest of the sequences. It's also worth noting that both the human and Neanderthal sequences are so close to the chimps that, should a Neanderthal sequence look different from both the human and chimp version, chances were good that it was an error, rather than a real difference.