March 1, 2011

Selective sweeps lacking in human evolutionary history

There is a (quite mainstream) school in Genetics that just loves the idea of small genetic changes being so extremely adaptive that they quickly replace all or most other variants in frequency, clinging to fixation not by founder effect or drift but because of sheer adaptive power.

The followers of this school are plainly wrong. It was common sense before (I really never liked the idea at all: it's plain silly, overly simplistic, sensationalist, irrational) but now it has been reasonably demonstrated: selective sweeps are extremely rare in the human genome, while small, gradual, less important shifts, maybe in dynamic equilibrium... are the norm instead.

Full story at Science Daily.

12 comments:

  1. "Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect"

    So I guess they're talking about 'recent human adaptation'. Selective sweeps may have been important during the change from Australopithecus to Homo, for example.

    "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture."

    That makes sense too.

    "selective sweeps are extremely rare in the human genome"

    As a result we could perhaps assume that where an apparently older haplogroup shares a region with an apparently more recent arrival the disparity in numbers is not a result of replacement. It is the result of the relative sizes of the two (or more) contributing populations.

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  2. I have to agree that while selective sweeps have probably not been very common since the Eurasian population settled in various localized populations, they haven't been very important. But, it seems likely that they were important prior to that point (in Africa and in the proto-Eurasian population).

    It also seems likely that cultural advantages have produced multiple instances in which one population has come close to replacing a prior one, dragging their collective genetic legacy, rather than a particularly favored gene trait, with them.

    The possiblity of that kind of cultural sweep also presents an interesting possibility from a neurodiversity perspective. It is entirely possible the very low frequency genetic traits that confer an advantage in technological innovation or group leadership could produce great evolutionary selective advantage for the entire group, even though most members of the population lack the trait. A group with a 1% frequency of a trait that gives one an edge in military leadership or the organization and management food production, for example, could allow the entire group to predominate over its neighbors.

    Now, there may be no such traits. Perhaps it is all cultural. But, then again, perhaps having that one in a million person who is an Einstein or a militarily successful general does make a huge difference - this could be the reason that rare and usually negative combinations of genes like psychopathy aren't selected against more effectively.

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  3. I have no idea why you claim this, Andrew: "it seems likely that [genetic sweeps] were important prior to that point (in Africa and in the proto-Eurasian population)".

    In particular I see no reason at all to think of any genetic sweep at the OoA. In fact any case of non-African fixation is best explained by default by founder effect in that very migration (maybe enhanced by drift).

    What you suggest for leadership advantages would make some sense as part of dynamic equilibrium. But there are two fundamental errors:

    1. 1% of 20 people is zero. And also leaders were typically irrelevant before Neolithic or later.

    2. The fundamental error of the evolutionist school is to believe that traits are absolutely advantageous or disadvantageous when typically they are both at the same time with a strong tendency towards neutrality and triviality.

    Genetic advantage is almost never B&W but extremely complex and self-neutralizing, not to mention the randomness of circumstances these traits are subject to.

    "perhaps having that one in a million person who is an Einstein or a militarily successful general does make a huge difference"...

    In reality I suspect that, sadly, selection is not so much focused towards raw advantages like intelligence but towards social advantages like submission. As intelligence is naturally opposed to submission, intelligence is to some extent at least non-adaptive. This may explain the alleged reduction in brain size since Neolithic times and is a good example of how selection does not work neither linearly nor, often, in too obvious ways, being more subtle, double-edged and twisted than the evolutionist school believes (in the religious sense of the term "believe").

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  4. Re: 1% of 20 is zero.

    First, even in the earliest hunter-gatherer era, there was some level of social organization beyond the root level band, that probably convened in loose knit gatherings at least annually for seasonal type gatherings like hunts at migration routes and mate exchange.

    Second, there is no reason why the predominant selective benefit of rare alleles could have been Neolithic or in prosperous fishing societies pre-Neolithic that had large populations. Indeed, it very likely was.

    Third, leadership is not the only case of a rare trait that could be an advantage. A combination of genes that together produce a born inventor could be a dramatic advantage to one population over its neighbors even if it came together only once every few generations.

    Re: Fixation.

    My point is that proto-Eurasians were the last point where there could have been selective sweeps with such broad expanse going forward. Pulling off a selective sweep within a population of twenty thousand people who interact with each other on a semi-regular basis is much easier than getting one to impact millions of people from England to Taiwan. Ditto for sweeps within the pre-Bantu-expansion, non-Pygmy, non-Khoisan population.

    Indeed, one interesting pre-history of religion theory suggest that a key evolutionary role of religion was that dietary restrictions and other taboos in early religions (which were highly localized prior to Arab and European colonization in Africa) was precisely to disrupt the flow of selective sweeps, which might have been common before this adaptation, as much as to unify large numbers of people. If somebody in the region didn't eat bushmeat because it was taboo, a pathogen with a bushmeat linked vector couldn't wipe out the human race.

    The absence of any mtDNA L3, or any Y-DNA A or B or most kinds of E, outside Africa is suggestive of the possibility that there may have been selective sweeps in proto-Eurasians (where ever this founding population came to be). Why otherwise wouldn't there be some meaningful global residual of ancestral African uniparental traits as there are in Africa against a predominant haplogroup background in any give area? Founder effects alone could certainly amplify the importance of a rare where it arose founder mutation, but isn't terribly likely to entirely wipe out all competing lineages with effective population sizes as large as that suggested for the Eurasian founder population without some sort of selective sweep. Y-DNA D arguably looks like a much smaller founding population source with a founder effect predominating, but I don't think that this view holds up in the bigger picture.

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  5. BTW, andrew and Andrew Oh-Willeke are one in the same. I have two Google IDs and hadn't switched over.

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  6. "First"...

    That is an assumption you make which is not supported by anthropology. Historical hunter-gatherer groups have no hierarchies: they are totally anarchist and communist (however they are ethnic as well: the Inuit did not mix much with the Tuniit, which they eventually drove to extinction against the Arctic Ocean).

    This is important to understand, both for the purposes of reconstructing/understanding our own prehistory, as for the more political purpose of understanding what is wrong with our societies and civilization in general.


    "Second"...

    Maybe. But the Neolithic circumstances are very recent and therefore we'd see these evolutionary advantages showing up without doubt in the study, something we do not (or almost not). Hence no Neolithic evolutionary sweeps.

    "Third"...

    True (dynamic equilibrium with submission would enhance leadership of few - however the traits are opposed and infighting). But you assume that such traits would be described by a single gene (allele) when in fact they are much more likely to be described by a vast matrix of complementary ones, each of which can have four SNP-states. It's like a huge matrix of states which can range between 0 and 3 (quaternary numeral system) and each combo produces a unique result: an individual.

    Not all quaternary states are available, in fact most are fixated to a single state through the species and upstream taxa, but there is still enough variability in the genetic pool and enough variable positions for each actual result to be invariably unique.

    Maybe Einstein had an AB and his unknown retard cousin had an AA simplified combo. Without the retard cousin Einstein would not exist therefore (no A allele). This is hypothetical and oversimplified but happens often, for example with sickle cell anemia.

    That school of genetics fails to see the whole picture, which can be expressed mathematically in any case, so it's not just matter of empirical consideration but also of failure of preliminary abstract thought and bias induced by animal breeding, which is akin but not the same to what we find in nature (nature does not select for single traits, almost never, but for balanced dynamic genetic pools).

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  7. "My point is that proto-Eurasians were the last point where there could have been selective sweeps with such broad expanse going forward".

    Don't forget Native Americans, their colonization was the last one before modernity.

    But your assumption seems wrong to me: the expansiveness of the moment actually allowed nearly any genetic combo to survive, what surely helped to re-diversify an otherwise narrow genetic pool (founder effect, small initial population), not selective sweeps. Selection works best when most die, not when most survive and reproduce happily.

    "Pulling off a selective sweep within a population of twenty thousand people who interact with each other on a semi-regular basis is much easier than getting one to impact millions of people from England to Taiwan".

    Ok, now I see your point. For example people living in Arabia (many less than 20,000 for sure) at the OoA prelude would be pressed to evolve mechanisms against dehydration, such as sweating less or a camel-like water reserve. But this does not seem to have happened (humans are more adaptive through culture than you seem to think) and soon the population was expanding wildly in other ecosystems.

    We know that a few genetic sweeps happened, notably white skin (almost necessary adaption to low UV latitudes). But these happened in specific subregions of Eurasia and do not have single genes responsible for them, but probably complex arrays of them.

    If you want to understand fitness sweeps, I'd recommend to focus not on hypothetical intellectual variants (a fetish rather than any clear reality) but on skin color and how it coalesced. This happened indeed rather early on (but not too early) in the history of Eurasian colonization and maybe to some extent because of the reasons you mention: small founder population, with the right conditions (rather low UV input) for such a fitness trait to become valuable once and again, generation after generation.

    "If somebody in the region didn't eat bushmeat because it was taboo, a pathogen with a bushmeat linked vector couldn't wipe out the human race".

    Pathogens never wiped any population. Not alone, much less local pathogens (i.e. without a bacterial shock scenario, which requires sudden immigration from far away).

    Another fetish.

    Religions and taboos anyhow are cultural elements with no adaptive value other than wiping off their opponents by means of institutional murder, forced assimilation or other forms of genocide.

    "The absence of any mtDNA L3... outside Africa"...

    ... is false: nearly all mtDNA outside Africa is L3, mostly of the M and N subclades.

    "... is suggestive of the possibility that there may have been selective sweeps in proto-Eurasians"...

    No, it only means founder effect. Inserting the phrase "genetic sweep" here is fundamentally wrong, totally absurd.

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  8. "It also seems likely that cultural advantages have produced multiple instances in which one population has come close to replacing a prior one, dragging their collective genetic legacy, rather than a particularly favored gene trait, with them. The possiblity of that kind of cultural sweep also presents an interesting possibility from a neurodiversity perspective".

    I doubt that such phenomena have a genetic basis. Technological advantage is a matter of who thought of it first. For example the Australian Aborigines hardly had an 'Upper Paleolithic' technology when Europeans first arrived but that was simply because it had never soread as far as Australia. But no-one (well, nearly no-one) claims Aborigines are in any way intellectually inferior to those whose ancestors possessed Upper Paleolithic technology.

    "In particular I see no reason at all to think of any genetic sweep at the OoA".

    If we're prepared to grant that neanderthals were the same species their dissappearance certainly suggests some sort of 'selective sweep'.

    "in fact they are much more likely to be described by a vast matrix of complementary ones, each of which can have four SNP-states. It's like a huge matrix of states which can range between 0 and 3 (quaternary numeral system) and each combo produces a unique result: an individual"

    Very true.

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  9. The Neanderthal extinction did not happen at the OoA but much later in the colonization of West Eurasia.

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  10. "The Neanderthal extinction did not happen at the OoA but much later in the colonization of West Eurasia".

    So it's a relatively recent selective sweep. So it's not consistent with the articles claim:

    "Selective sweeps lacking in human evolutionary history"

    We know of at least one major one.

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  11. The article does not deny some selective sweeps (just that they are rare, much rarer than mainstream theories used to claim - on no grounds other than belief) but Neanderthals are clearly not in the radar because they are a different species. They are researching modern human DNA only.

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  12. "Neanderthals are clearly not in the radar because they are a different species".

    That claim dosesn't hold up to any examination. surely it's now generally accepted the two 'species' could form fertile hybrids.

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