Sleeping like a Neandertal

By Razib Khan | June 25, 2012 9:36 am

Forgot to highlight one of the coolest abstracts from SMBE 2012, A genomewide map of Neandertal ancestry in modern humans:

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow

One of the predictions of assimilation of a large intrusive population with a small but long endemic population is that there will be biased representation of adaptive alleles from the latter into the former. In other words, if genome-wide admixture is on the order of 5% from the latter into the former, alleles which confer local fitness benefits will be present in the descendants of the asymmetric admixture in proportions of out sync with the expected frequencies. In this case the Neandertal admixture is < 5%, but the Neandertal variant may be as high as ~85%. Not only that, the authors have found an excellent and plausible candidate for Neandertal-specific adaptive alleles: we know that this H. sapiens lineage was present at high latitudes for hundreds of thousands of years!

But some cautions. First, there is going to be variation around expected values of admixture of any given genomic region. There will be many segments where the descendant populations don’t have any signature of Neandertal admixture, and a few segments where the Neandertal allele predominates, through random chance. Second, we need to be careful of being too eager to find what we’re looking for. If, for example, you find a genomic region enriched for Neandertal ancestry one of the first things you’ll no doubt do is pull up all the genes in that region, and identify plausible candidates for selection. But given a large enough genomic region, you are guaranteed to find a “plausible” candidate.

This is why a “map” of the Neandertal genome is essential. To assess the probabilities you need prior expectations pegged in. Hopefully these caveats will be rendered moot in the near future as many more researchers start digging into the data. What I do find somewhat confusing is how adamant some of the original authors of the first Neandertal ancient genome paper were about the lack of evidence of adaptation.

MORE ABOUT: Human Evolution

Comments (8)

  1. gcochran

    To most of the people working the problem, for example Svante Paabo, your comment about the predictions of assimilation would have been totally meaningless.

    Henry and I mentioned adaptation to big swings in day length as a good candidate for introgressive Neanderthal genes, but we were probably just lucky. Or something.

  2. Do we know of any corresponding differences in phenotype between Europeans and East Asians?

  3. Dwight E. Howell

    It is commonly stated that ~3% to ~5% of the genome of non Africans is Hsn but not exactly the same genes. Has anyone tried to figure out exactly how much of the Hsn genome is still actually around in living people?

    The next issue is just as interesting to me. It is pretty obvious that when people are talking about Hsn genes they are only talking about those segments of the genome that were obviously different than Hs however most of it is the same in the encoding material. Has anyone actually bothered to find out how much of this so called “same” material may have been inherited from Hsn ancestors? I don’t think this is going to just jump out and slap a researcher in the face. They are going to have to seriously look at so called junk genes. The assumptions seems to be non of it but I have grave reservations about that being a valid assumption.

  4. pconroy

    I’m very interested in this research, as I read somewhere of a link to CLOCK and Autism Spectrum Disorder…

    In any case, I have strange circadian rhythms, in that I get by on about 4/5 hours of sleep most nights, and on nights where it rains or even will rain, get about 2 hours sleep.

  5. #3, your comment is almost impossible to decipher. you need to get more familiar with the technical issues to ask a pointed question. but the short answer is yeah, the estimate takes into account genome-wide averages. they’re comparing whole modern genomes to composite whole neandertal genomes. the neandertal genome isn’t the best, but good enough for this.

  6. I applaud the duly caution exercised, Razib.

    Something I immediately missed when I first read this conference note is any mention of South Asians or other non-African populations. A Europe-China contrast may be suggestive of something but when I looked at SNPedia for noticeable difference in allele frequency between Indians and Europeans at CLOCK SNPs, I found none. Not sure if this quick look (mini-sample) is representative but to me suggests that the real difference may well be in the bottleneck at the origin of East Asian specificities rather than excess admixture in Europe.

    In any case, I’d ask researchers to use also samples from at least these three other key regions: South Asia, West Asia and Native Australasians (Papuans for example). That should give a more clear view of the real geography underlying these findings.

    For example it’s tentative to imagine that some of the plausible (well said) selective pressure on said region is because it favors depigmentation (maybe because CLOCK interacts with SIRT1, which is an epigenetic regulator, apparently), the most obvious adaptive pressure north of certain latitude (c. 40º). But if the same apportions exist in South Asians, then (1) it’s West Eurasian specific admixture but some other origin and (2) whatever possible selective pressures have nothing to do with latitude or pigmentation most likely.

  7. Bahr Kaniz

    What if most of the important introgressed material is CNV?

  8. Justin Giancola

    night owl gene anyone? 😉


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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