sequencing the neandertal genome

I’ve had this one in my ‘must write about’ file for a little while: in the May 7th edition of Science, a large research team announced that they’d produced a draft sequence of Neandertal DNA (Green et al. 2010). Using DNA from 3 individual Neadertals, the multi-institutional team managed to decipher more than 4 billion nucleotides from the Neandertal genome. Considering that Neandertals disappeared 30,000 years ago, this is a stunning achievement.

Stunning, because DNA so old is always going to be highly degraded, & in this case the researchers were recovering fragments averaging only 200 base pairs long. What’s more, when you die the decomposers take over, & the team was faced with the challenge of distinguishing between Homo neandertalensis DNA & that from the microbes involved in decomposition. This was done by comparing the various DNA fragments with chimpanzee & modern human genomes. (Up until now just 4 fragmentary sequences of Neandertal DNA had been decoded, from loci involved in skin colour, blood groups, speech, & taste. Again, the nature of these fragments was determined by comparing them with modern human DNA sequences. The results of the Human Genome Project are not restricted to modern humans but have allowed us to look far into our past.)

Neandertals first appear in the European fossil record around 400,000 years ago & subsequently spread into Asia, as far as southern Siberia & the MIddle East. They’re regarded as the sister species of Homo sapiens. Anatomically-modern humans moved into the Middle East around 80,000 years ago & it’s long been assumed that the two species would have come into contact, then & later when sapiens moved west into Europe & also into Asia. And a question that’s often asked when I’m talking with school students is, could Neandertals & modern humans have interbred?

Up until now it hasn’t been possible to rule out the possibility. This is because, while the available Neandertal mitochondrial DNA (mtDNA) sequences fall outside the range of modern human mtDNA, this doesn’t rule out interbreeding. (If you can’t see why not, remember that mtDNA is almost always passed down along the maternal line. The absence of any mtDNA apparently belonging to Neandertals may simply mean that no female Neandertal lineages have survived to the present day.)

Green et al. extracted their DNA samples from bones from 3 different individuals, found in a cave in Croatia. (They used mtDNA comparisons to confirm that the remains were indeed from 3 different people.) And they found that yes, there probably was a certain amount of interbreeding between resident Neandertals and the new, younger species moving in from Africa. How much, is hard to say, but it appears that modern human populations from Europe, Asia & the South Pacific have 1-4% ‘Neandertal’ DNA. (But not Africa: only modern human populations moving out of Africa would have had the opportunity to meet up with Neandertals.) The authors also note that any gene flow between the 2 species probably occurred before the divergence of those modern human populations.

There’s much more to the story, though, than simply cataloguing early inter-species matings. There’s enough information in the draft Neandertal sequence to look for variants of genes that are shared by both neandertalensissapiens & those that are unique to one or the other. And it turns out that there are just 78 genes where a ‘novel’ variant has become fixed (either by positive selection or by drift) in the human population (although there are rather more novel non-coding sequences in the modern genome as well). Some of these are implicated in brain development & functioning in modern humans. Mutations in another gene affect the cranium, shoulder girdle & ribcage – all features where sapiensneandertalensis skeletons differ. This is really exciting stuff, where palaeontology and genetics come together to unravel the details of a fascinating time in our past.

You can read much more about this on John Hawks’ weblogPharyngula (of course!), & in Carl Zimmer’s piece in Discover magazine, & there’s a video interview here on the Dolan DNA Learning Centre page.

R.E.Green, J.Krause, A.W.Briggs, T.Maricic, U.Stenzel, M.Kircher, N.Patterson, H.Li, W.Zhai, M.H.Fritz, N.F.Hansen, E.Y.Durand, A-S.Malaspinas, J.D.Jensen, T.Marques-Bonet, C.Alkan, K.Prufer, M.Meyer, H.A.Burbano, J.M.Good, R.Schultz, A.Aximu-Petri, A.Butthof, B.Hober, B.Hoffner, M.Siegemund, A.Weihmann, C.Nusbaum, E.S.Lander, C.Russ, N.Novod, J.Affourtit, M.Egholm, C.Verna, P.Rudan, D.Brajkovic, Z.Kucan, I.Gusic, V.B.Doronichev, L.V.Golovanova C.Lalueza-Fox, la Rasilla, J.Fortea, A.Rosas, R.W.Schmitz, P.L.F.Johnson, E.E.Eichler, D.Falush, E.Birney, J.C.Mullikin, M.Slatkin, R.Nielsen, J.Kelso,, M.Lachmann, D.Reich & S.Paabo (2010) A draft sequence of the Neandertal genome. Science 328: 710-722 doi:10.1126/science.1188021