Fascinatin’ rhythm

At the recent SMBE meeting in Dublin, there was an interesting talk (judging from the abstract) about archaic genes in modern humans.  The  authors were Sriram Sankararaman, Nick Patterson, Swapan Mallick,, Svante Paabo, and David Reich. They believe that they can identify regions of the genome that are of Neanderthal origin and are at high frequency today, enough so that they were almost certainly favored by natural selection.  They say that they have found over 100 such regions.   They mention one in particular – a Neanderthal-derived segment that overlaps CLOCK, a key gene in regulating circadian rhythms.  That segment has a frequency of 85% in Europeans.

This was predictable, in that Henry and I (and John Hawks) predicted it.  To be exact, in our book, Henry and I predicted that at least some people today would turn out to have Neanderthal admixture,  that some Neanderthal alleles would be favored by selection and be common, and that genes in involved in circadian rhythm would be particularly likely to experience such selection, since the Neanderthals had spent hundred of thousands of  years in Europe, where the length of day varies a lot, while anatomically modern humans (AMH) had spent that time much closer to the equator, where the length of day varies little.

It should be interesting to see what the function of those other selected, Neanderthal-derived alleles will be.  So far, the only other published discussion of this topic has concerned Neanderthal-derived HLA alleles – involved in disease defense, which we also thought a likely category . A couple of (probably) Denisovan-derived HLA alleles have also been found, as well as Denisovan versions of a couple of genes in the innate immune system.

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11 Responses to Fascinatin’ rhythm

  1. dearieme says:

    To take an extreme example, do Eskimos have it?

  2. SwampOwl says:

    You must feel a bit like Mr. Higgs right now. Congrats.
    Hmm…And then my lineage went to live back near the Tropic of Cancer. Not much use for the circadian one.

  3. random mutation says:

    Perhaps I am not thinking about this carefully enough, but it seems to me that there would be more diseases closer to the equator than further away, but that things changed with the introduction of civilization and lots of people trying to live together in much smaller spaces.

  4. dave chamberlin says:

    When I heard the announcement made several years back by the group led by Svante Paabo that we are 1% to 3% neanderthal I along with a lot of other people made the quick calculations that out of 30,000 genes 300 to 900 came from this archaic population. It is my opinion that this infussion of genes caused a hybridization event that made us modern. Mutation is oversold as the only means to cause evolution, far more often evolution occurs from hybridization events between long seperated sub species. It stands to reason that there was enormous benefit to be derived from Neanderthals since they had gone on their own evolutionary path for some 700,00 thousand years to become highly intellingent in their own way. It is also my opinion that this would be accepted thinking because it is so logical except that there appears to a much lower neanderthal percentage in that human poulation that lives south of the Sahara. Hopefully through the work of Cochran and others this kind of wishful thinking that the human brain is excluded from the rules of evolution will just go away.

  5. SwampOwl says:

    From the abstract they used data from the 1000 genome project, which includes sub-Saharan and American Indian samples. However they only report having identified 35k and 21k Neandertal derived alleles for Europeans and East Asians respectively. If most of the mixing occurred before the separation of European and Asian lineages as the data suggests, then it can be expected that American Indians too would show such admixture. Not finding it would likely have implications for the current model of human expansion routes.
    I think they simply focused in Eurasian populations, that should explain it.

  6. john says:

    One thing that is made possible by living in the cold climate is a larger brain. There is not as much problem with heat dissipation and more planning is required for harsher climates. I think that we may owe the neanderthals for the size of our brain today.

    • Matt says:

      With reference to this, the fossil early modern homo sapiens populations of the Middle East, the Skhul-Qafzeh population, appear to have the largest endo-cranial volumes of any population of humans (including Neanderthals, especially contemporaneous rather than later Neanderthals and including arctic present day modern humans).

      http://tinyurl.com/cgobt5w

      “Even the early modern Europeans, despite their later dates and more northerly provenence (than the SQ population) have smaller braincases on the average. Intriguingly we see the same difference among Neanderthals, the Near Eastern ones have braincases about 5% larger than the late (Wurm) Neanderthals from Europe (Table 79) – the opposite of what we might expect on the basis of latitudinal effects”

      In context of this, I’m actually pretty sceptical that heat dissipation is even a significant selection pressure.

  7. whatever says:

    I am curious of the nature of the encounter between humans and neanderthals. Was it a strictly sexual exchange or was there more – say, lexical borrowings similar in amount to genetic borrowings? As a newcomer to the Eurasian environment, HS would have benefited from both genetic and cultural borrowings. The lexemes for unknown phenomena – like river ice, snow storms and aurora borealis, among others – would come in handy. Are 1 to 3% of contemporary human lexemes based on neanderthal borrowings, similarly to our genomes?
    It has been known for decades that evolution of human languages, unlike natural evolution, is like a river – it flows only downward; which is ,towards sounds/vowel/consonant reduction; all of a sudden, some sounds have become just too hard to pronounce, for some reason.
    Like laryngeals in IE languages, for example; which is not to say that we inherited laryngeal sounds from neanderthals – we did not have to. Yet, did we borrowed from neanderthals not only a bunch of genes, but a bunch of words as well?

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  9. Joel says:

    If you’re right, then I think 2 more predictions follow
    1. Recent migrants to northern latitudes (eg African Americans) should show a fitness deficiency of some kind connected to circadian rhythms
    2. There should be evidence of ongoing selective pressure on the region, which should be observable in African Americans with European ancestry (not sure of the number but assume it’s well north of 75%)

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