Neandertal genome

Does it seem like a lot of anthropology stuff has been making the news lately? Ardipithecus, sediba, the Denisova hominin, and now the Neandertal genome. It's kind of exciting.

Green et al.'s paper in the latest science describes their efforts to sequence the Neandertal nuclear genome (note that Neandertal mitochondrial genomes have been sequenced multiple times). They generated a 1.3x rough draft from three bone samples from Vindija, with an estimated less than 1% contamination from modern human sequences. Interesting findings:

1. Looking at nonsynonymous substitutions, they suggested that skin morphology or physiology might have been different in Neandertals.
2. They found evidence of 111 Neandertal-specific segmental duplications, totaling 1.9 Mb.
3. Found 212 regions with evidence of positive selection sweeps. The top twenty include a gene associated with type II diabetes and three genes associated with cognitive function.
4. The big result is that Neandertal nuclear genes appear to be more similar to modern non-Africans than to Africans. They found this by looking at polymorphisms in modern humans where the Neandertals had a sequence that did not match chimpanzees. Neandertals matched non-Africans significantly more often than Africans. This result was robust no matter how the subdivided the sequences (by chromosome, by sequence length, by sequencing platform, etc.), and it was not likely to be the result of contamination (which would have to be 10% to explain the findings). According to Green et al., "A parsimonious explanation for these observations is that Neandertals exchanged genes iwth the ancestors of non-Africans." Based on the divergence of different African lineages, they also argued that the gene flow was primarily from Neandertals to modern humans. That means I'm carrying 1-4% Neandertal DNA. I'm a living fossil!

Some creationist thoughts: It might be tempting from these results to argue that Neandertals were just aberrant Europeans or Asians, but there's still the mtDNA, which is quite distinct from modern humans. I still think Neandertals are a separate species of the human holobaramin, but the gene flow is very intriguing. I'm wondering whether they went extinct or merely got absorbed by the growing Homo sapiens population. The one-way gene flow would make sense if the Neandertals were significantly outnumbered by sapiens.

I do think these results bode poorly for Reasons to Believe, but I'm sure they'll come up with some kind of spin to explain why these results do not support their idea of Neandertals as non-human animals. That should be entertaining.

And finally, I hate to keep tooting my own horn, but these results are consistent with my own take on the human genome in Answers magazine. In case you're interested, I'm currently working on a technical followup to that work that will examine human mitochondrial DNA diversity from a creationist perspective. I might follow that up with an examination of the nuclear genomes, but don't hold your breath. I've got too many projects going now as it is.

Feedback? Email me at toddcharleswood [at] gmail [dot] com.

Green et al. 2010. A draft sequence of the Neandertal genome. Science 328:710-722.