Standards Drift

We now know that the fraction of Neanderthal ancestry in coding regions has been gradually decreasing with time since the origin admixture, and is now something half as large as it was originally. There were some useful Neanderthal alleles that were favored by selection, and others that deleterious enough to have disappeared completely, but we’re talking about the general trend.

A couple of papers argue that Neanderthals had a lot of small-effect genetic load resulting from inefficient purifying selection in a small population. They conclude that Neanderthals must have been pretty screwed-up – tens of percent fitness drop – but that can’t really be the case, since they resisted replacement by modern humans for something like 60,000 years after AMH first left Africa.

Moreover, it now seems that the Altai Neanderthals picked up some AMH ancestry roughly 100,000 years ago, possibly from the Qafzeh-Shkul population – and there too, the fraction of minority ancestry seems to have decreased in coding regions. So this isn’t not caused by low population size, at least primarily: it’s a kind of incompatibility.

I’m thinking of it as standards drift. In a populations, alleles are always being selected for compatibility, for working correctly, conferring high fitness, on a particular average genetic background. Each allele has a spec it needs to meet. That spec doesn’t necessarily stay the same over time: obviously changes in environment will make a difference. Drift should matter too: if a given allele becomes more common, even by chance, the specs will change for other alleles that interact with it. But there’s always a spec.

When two populations split, their specs start to drift apart. There’s no genetic equivalent of that iridium meter bar. Function at the organismal level doesn’t change so much, but there are many slightly different ways of achieving that function.

So: we now know that if two hominid populations have been separated for 600,000 years, their alleles are on average no longer wholly interchangeable. Admixture and adaptive introgression are still possible, but the alien genome is, in general, slowly rejected.

This means that we can expect the same effect in other cases. Melanesians should have been slowly purging their Denisovan ancestry in coding regions – even though the Denisovans apparently had a significantly higher effective population size than Neanderthals. Since the AMH/Neanderhal/Denisovan split is almost a trichotomy, Neanderthals were probably rejecting Denisovan admixture, while Denisovans were slowly rejecting Neanderthal admixture.

While we’re at it, if there are Pygmies whose genomes are majority ancient Pygmy, their Bantu component is probably slightly incompatible: if left to themselves for a hundred thousand years, they’d probably lose a fair amount of it. Of course they will all be eaten long before that happens.

This is a subtle effect, one that takes thousands of generations to play out. I don’t know if anyone has seen it in the lab – wouldn’t think so.

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62 Responses to Standards Drift

  1. John Galt says:

    In the context of communication/computing platforms (and culture), this sounds like “network effect” a/k/a “who’s on first”

  2. et.cetera says:

    That’s a very interesting idea, but it’s even more interesting coming from you, since if true, it gives a lot of weight to the “multilevel” selection paradigm (beyond gene-culture coevolution), by equating different “levels” of selection with different epistatic equilibria / (sub-)specs.

    • gcochran9 says:

      If I could understand what you are saying, I would most likely disagree.

      • et.cetera says:

        I think I’m being clear enough: the genetic “standard” / resulting “average genetic background” / doesntmatterwhatyoucallit can be usefully accounted for as a unit of selection.

        You write —

        “I’m thinking of it as standards drift. In a populations, alleles are always being selected for compatibility, for working correctly, conferring high fitness, on a particular average genetic background. Each allele has a spec it needs to meet. […]

        So: we now know that if two hominid populations have been separated for 600,000 years, their alleles are on average no longer wholly interchangeable. Admixture and adaptive introgression are still possible, but the alien genome is, in general, slowly rejected.”

        So a gene can be selected against by mere virtue of it being from the “wrong” background.

  3. tautology123 says:

    If neanderthals picked up AMH genes, and neanderthal genes were partly responsible for modern humans being as innovative as they are, shouldn’t they also have spiked in creativity? Is there any evidence of such a thing happening?

    • gcochran9 says:

      I once suggested that an in fusion of Neanderthal genes might have increased human smarts/creativity, but it’s not obviously true from what we know today.

  4. Doug Jones says:

    There’s some recent research on rates of speciation in a very wide range of organisms (arthropods, vertebrates, plants) suggesting that the formation of new species happens at a relatively constant, clocklike rate (about 2 million years for fairly pronounced reproductive isolation). This would be consistent with reproductive isolation being a result of a steady process of “standards drift,” and not closely tied to visible adaptive divergence, which happens at widely varying rates. This is pretty preliminary though; as always More Research Needed.

    Here’s a pop version, with links to the original article:
    https://www.quantamagazine.org/20150505-a-surprise-for-evolution-in-giant-tree-of-life/

    Modern Homo sapiens is highly polymorphic with lots of visible adaptive divergence, but different major populations don’t seem show much sign of reproductive isolation (at least in my reading of the literature, and leaving aside cultural constraints on interbreeding). Here’s a discussion on my blog from last year, which I’ll revise a bit when I repost later in the year (August):
    https://logarithmichistory.wordpress.com/2015/08/14/species/

  5. John Hawks over at his weblog has continued to write clear, concise, scientifically accurate updates on this most interesting area of human evolution. Be there or be square. The man has the same gift as Greg Cochran does, he can make cutting edge areas of science understandable to the rest of us. He has a May 25th post up over at John Hawks weblog that talks about Neanderthals that I found especially interesting. It is simply amazing that a total population over the entire time period of Neanderthals existence (he guesstimates a total population of 1.3 billion IF 50,000 were alive at any one time) left such a sparse record.

    Neanderthals happened to frequent limestone caves in frigid locations so their record is vastly more likely to be detected than Denisovans. Anyway, I won’t go on, just go over there and read it if this subject is interesting to you.

    If NeanderthaL genes did have the effect of increasing human smarts/creativity science should be able to prove it one way or the other in the upcoming decades. This assumes that considerable progress will be made in understanding the genetic underpinnings of human intelligence.

    It will be controversial as hell if the badly titled “great leap forward” was due in large part because of our admixture with Neanderthals. But as loyal readers of West Hunter know scientific controversies make this place highly entertaining.

    • FOXP2 says:

      Interesting, but it would be, I guess, completely uncontroversial to state that developmental verbal dispraxia was likely uncommon in Neanderthals. In other words, they had a lot to say to each other, almost every single one of the one or two billion of them. For all we know, Homer and Moses riffed on archaic human linguistic riffs that were, in turn, riffs on even more archaic Neanderthal riffs. Chesterton, if I recall correctly, guessed they were fairly civilized; as an unusually large human, abundantly fond of ancient foods and drinks, his opinion merits respect.

    • Garr says:

      What if Neanderthals were loners who didn’t talk much if at all but liked to space out looking at interesting trees and rocks and sunsets, while Africans were social animals who always chattered together and told each other group-reinforcing stories. Put the two together and you get people who see things from their own solitary perspective and also want to tell other people about it. This would result in lots of new creative activity.

    • gwern says:

      We’ve already seen some studies of the negative effects of Neanderthal admixture like “The phenotypic legacy of admixture between modern humans and Neandertals” http://www.gwern.net/docs/genetics/2016-simonti.pdf , Simonti et al 2016. If the Neanderthal genes were beneficial for cognitive functioning, why hasn’t anyone shown this using GCTA or LD score regression with the education polygenic scores from Rietveld and Davies etc?

      • Thanks for providing the interesting link. The effects of neanderthal admixture on increasing human smarts/creativity are simple not known yet, the paper you link to says as much. What can be stated at this time is merely speculative. What we do have are the following facts. Shortly after there was admixture between anatomically modern humans and neanderthals that small admixed population took over the entire world excluding Sub Saharan Africa. Right about the time this admixture occurred stone tools became far more complex. To me these facts prove nothing BUT I am strongly leaning towards admixture being a key element in humans getting smarter. Fortunately it won’t be very long before a better picture is given to us by advancing science.

        But this knowledge will not rest as just an interesting tidbit of history from our distant past. Oh no. Once we know how one “great leap forward” happened we won’t have to wait another 60,000 years to jump forward again. I hope to live long enough to enjoy the first few episodes of the drama that is bound to follow.

        • gwern says:

          If you’re curious, I think you should be able to find an answer within weeks. LD Hub (http://ldsc.broadinstitute.org/ http://biorxiv.org/content/early/2016/05/03/051094) makes it easy to do LD score regressions for correlation; if you log in, you can see that they already have done a bunch of correlations with ‘Childhood IQ’ / ‘College’ (http://ldsc.broadinstitute.org/lookup/). You can upload your own GWAS polygenic score file (http://ldsc.broadinstitute.org/upload_file/#) to do correlations with ‘Education’/’Personality traits’. I don’t know where one would find a Neanderthal polygenic score, but it must exist since people do papers on schizophrenia and other traits.

        • 34sddfasdfksdsf says:

          I wouldn’t hold out for much, or any of the other bizarre ideas that neanderthals improved our intelligence somehow (but this fetishization of neanderthals probably won’t go away even then). Even aside from your narrow understanding of the “great leap forward”, neanderthal admixture is widely found in SS africans, due to introgression from north africa and east africa. Even primitive hunter-gatherers like the hadza and sandawe have it. Don’t bother falling back on brain size either- neanderthal brain size was typical of humans worldwide back then.

          And it’s not like that people with less neanderthal admixture today aren’t capable of making complex stone tools and more.

          • Everybody has a narrow understanding of how humans got smarter, because we don’t know. It is a real possibility that we hybridized with neanderthals and benefitted from it. It is far from proven but it is also far from bizarre. I don’t want to debate with you on it, believe what you like. goodbye

  6. Henk says:

    I once thought about a similar (but faster-acting) variant of this as a biological explanation for why couples of less than third-level cousin level of consanguinity seem to lose fertility.

  7. Greying Wanderer says:

    I’ve wondered if miscarriage had any similarities to transplanted organs being rejected..

  8. quamuri says:

    Is there some evidence that Neanderthal DNA fraction isn’t dropping in the non-coding regions? Because if an admixed group has such a strong selection advantage that it is able to gain preferential access to the females of pure groups, then the size of the “admixed population” will expand, and the average admixture of the group will drop, but this represents selection for the Neanderthal genes that the admixed group is spreading.

  9. Tommy says:

    [i]Each allele has a spec it needs to meet. That spec doesn’t necessarily stay the same over time: obviously changes in environment will make a difference[/i]

    I roughly grasp what you’re saying and I imagine the mere presence of admixture must change the spec to a certain, ordinarily small, extent.

    What sort of mathematical model of a decline would we really be looking at here? Would it be something linear, logarithmic, or a different model entirely?
    How does the composition of the original mixture tend to impact the decline? You have an inheritance consisting of a mix of positive and negative genes, each gene having it’s own magnitude of impact in one direction or the other and all being spread in (and being diluted within) a population. You have to initially take the whole package of admixture, but in time your descendants will get experience every combination of surviving alien genes at a certain rate of probability. For instance, you might have a mix with a few very positive genes and a great many slightly negative ones, or maybe a moderate number of highly positive genes, many slightly negative genes, and a few very negative ones, or maybe a lot of moderately positive ones, some slightly negative and positive ones, and a few nasty ones, just the right amount needed to confer a slight overall advantage, at least in the first few generations after hybridization. Some of your descendants will ultimately get some lousy mixes while others hit the jackpot, yet others will break even. How does this initial “polarity” of a mix of genes effect what is ultimately left when geneticists examine a population many generations later? Would we expect a different result from hybrids with wider parentage than those whose parentage is more closely related?

  10. Watchin'It says:

    I’m also curious about the non-coding regions. Since many of the control elements are in these regions, seems that incompatibility could lead to wrong levels of transcription – too much or too little. If so, these might be lost quicker than problems in the coding region. I wonder if there is evidence of selection in the non-coding regions of the retained favorable Neanderthal alleles.

  11. 34sddfasdfksdsf says:

    “While we’re at it, if there are Pygmies whose genomes are majority ancient Pygmy, their Bantu component is probably slightly incompatible: if left to themselves for a hundred thousand years, they’d probably lose a fair amount of it. Of course they will all be eaten long before that happens.”

    What is “ancient pygmy” in this context? Pygmies and bantus haven’t been separated quite that long, and they don’t look that different aside from height.

    • Ursiform says:

      They have been separated for a long time, and they don’t look that much alike. Unless you consider them both having dark skin to make them look alike …

      • 34sddfasdfksdsf says:

        Pygmies and bantu really don’t look that different. They’re comparable to europeans vs. some other caucasoid group. Aside from height, pygmies have wider noses, more prominent brows, more squarish faces, and more facial and body hair. They’re also moderately lighter, but if it weren’t for their height, you’d be very hard pressed to consider them a distinct race on appearance alone. But here you’re claiming they really don’t look much alike overall- that’s a first in my experience.

        Hard to say whether mixing has muted any original differences, because there’s still very pronounced ones, like the height and their extreme maturation rates.

        Didn’t know the bushmen were that distinct from bantus. They certainly look more like bantus as compared to navajos and germans.

        Out of curiosity, where do the hadza fit in with all of this? They’re the one isolated african hunter-gatherer group that look virtually identical to bantus.

        • 34sddfasdfksdsf says:

          Actually, a better comparison to the features of pygmies vs. bantus would be something like the japanese compared to the chinese (not talking genetic distance, just appearance). Though fairly different looking, they still look like members of the same race: http://i.imgur.com/sv7h4OE.jpg

          • Tim says:

            You are an idiot. You are probably asking yourself questions like, ‘Why do we spend all this money on genome sequencing when they could just ask me if I think two photos look similar? Brown skin? Check. Wide nose? Check. I think they are closely related.’

            • Garr says:

              Tim, his point is not even slightly idiotic. The author of this blog has repeatedly recommended that we take our ordinary observations (e.g. of the comparative dullness and impetuosity of certain groups) seriously. The fact is, Pygmies look like little Africans. This fact is interesting, given the long-ago split, and requires explanation.

              • Tim says:

                How about… these are ancestral traits that are conserved in many populations living at low latitudes. Also seen in Negritos, Australian Aborigines, and South Asians.

                This requires no explanation at all. It is like requiring an explanation for why nearly all wild mice and rats have agouti coats, while lab rats are often white.

                The question should be why the lab rats are white. And this has a clear explanation, because they were recently selected to have a different color than wild rats.

              • Frank says:

                “The fact is, Pygmies look like little Africans.”

                I could not agree more with this statement. Especially because they actually are little Africans.

            • JayMan says:

              Frank, you beat me to it.

              • 34sddfasdfksdsf says:

                Others did a good job at calling you out (though I think I made it very clear to begin with I wasn’t AT ALL saying that because they look alike, they must be very closely related), but I’ll also address your claim/diversion that they look similar because these traits were selected for in some way relating to their environment. To begin with, some of the populations you described barely resemble eachother aside from skin color. Africans look very different from australian aborigines, as do negritos (who all look different from eachother) compared to australian aborigines. Papuans look quite different from australian aborigines and africans as well. Of course, some of these groups do look quite similar to eachother, like aborigines compared to many south indians, and africans compared to various negritos, but I really doubt much of this is due to natural selection and environmental adaptions. These groups and many others all variously exhibit traits that don’t really match up with conventional explanations given relating to environmental adaptions. There has been a study finding the flat faces of east asians offers no benefit to protection against the cold: https://en.wikipedia.org/wiki/Mongoloid#Cold_adaptation

                Human physical variation is due far more to drift and sexual selection than many people think.

                And as an aside, I don’t think “the comparative dullness and impetuosity of certain groups” has much to do with this subject.

              • gcochran9 says:

                Idiots get to doubt too.

    • gcochran9 says:

      Pygmies and Bantu have mixed a lot in the past couple of thousand years: the ur-Pygmy component seems to been separate for a long time, as much as three hundred thousand years. Possibly complicated by moderately recent admixture with a very diverged (~900,000 years) archaic sapiens group.

      Certainly Bushmen (probably also in the Pygmy branch) are more genetically distant from the Bantu than the Bantu are from Germans or Navajo.

  12. Karl Zimmerman says:

    It seems to me that one could apply the ideas of the gene-centered view of evolution to this “spec” idea. Just as organisms are adapted to their environment, genes are adapted to the environment of the genome they happen to be in. If they jump into a new genome (through admixture or some form of lateral transfer) it is quite likely they will not be well adapted, and thus will face negative selection over time.

  13. Bob says:

    Would this be evidence for Rushton’s Genetic Similarity Theory?

    https://en.wikipedia.org/wiki/JP_Rushton#Genetic_similarity_theory

  14. dux.ie says:

    From Pearce’s data the cranium size of Neanderthal and AMH are
    about the same at 25 kbp. The introgression between them occured
    between 60 kbp and 45 kbp and occured multiple times. For simple
    checking assuming that happened only once at the mid point, i.e.
    52.5 kbp and scales the data accordingly, the respective cramium sizes
    are

    n52 1507.09
    s52 1364.83

    There is a significant difference. The diff was even higher at 60 kbp

    When they interbred, there will be a spectrum of different traits.
    Of interest is when the resulting admixed adult had a neanderthal size
    head and less muscular AMH body.

    A biological equivalent example is when a pitt-bull is crossed with a
    dashhund the resulting pup has pitt-bull head, short snout, long body
    and short legs like this

    https://www.youtube.com/results?search_query=pitbull+dashund+cross&uploaded=a&aq=f

    Thus the above neanderthal-AMH admixed adult with less muscular body
    would had spare brain cells which were plastic and could be deployed
    for other purposes like cognition. Natural selection will do the rest. Whether the
    neanderthal parent was intelligent or not was secondary and might be inmaterial.

  15. Fourth doorman of the apocalypse says:

    One of my interlocutors suggested that drift could reduce the variance in trait a population, but it seemed to me only likely if they went through a bottleneck, and that it is the bottleneck that causes the reduction in variance.

    Am I full of shit or what?

    • Frank says:

      Drift is stronger in small populations. This is often called a ‘bottleneck’. The effect depends on several factors, such as the time (number of generations) spent within the small effective population, the initial pool of genetic variation, and the selection during the bottleneck.

      You are both talking about the same thing.

  16. IC says:

    “alleles are always being selected for compatibility”

    This has been what I always believed regarding natural selection/evolution at gene level. At genetic level, natural selection is like game of poker cards. An allele is good or bad depending on others genes drawn together with for each organism. A lucky card is depending on other cards in hand.

    Genes (or mutation) responsible for myopia or pale skin might be bad for survival. But if these genes come in package with genes giving high mental ability, such `bad’ genes would not subject to high selection pressure due to sheltered life style which does not demand 20/20 vision and strong skin.

    • Frank says:

      Except that there is zero evidence for, and lots of evidence against, the fact that myopia and skin pigmentation and intelligence are all genetically linked. This is the theory of a 12 year old who doesn’t have internet access.

      • IC says:

        Indeed, 12 year old.

        • j says:

          Do we need to re-discover the wheel every generation? H. von Moers-Messmer (in 1940) proved the existence of intelligence-myopia correlation, which as eyeball and brain originate both from the neural ectoderm. Big eyeballs – big brain.

          Skin pigmentation is unrelated to intelligence and related to sexual attractiveness, which is how it should be.

          • Bob says:

            I believe myopia has to do with the shape of the eyeball, not size.

            There is a correlation between myopia and intelligence, but most intelligent people are exposed to significant, chronic near work.

      • dux.ie says:

        Well, at least in Cambodia, Pol Pot executed all intellectuals and those wearing glasses,

        https://en.wikipedia.org/wiki/Khmer_Rouge#Life_under_the_Khmer_Rouge

        “People who they perceived as intellectuals or even those who had stereotypical signs of learning, such as glasses, would also be killed.”

  17. Withywindle says:

    Is there work being done on ancient DNA of other partially interbred species–wolves and coyotes, dogs and wolves–to see if there’s also a gene-purging effect there?

  18. dux.ie says:

    Current zika epidemic which results to microcephaly is a sad occurance.
    However, many other causes during pregnancy like alcohol abuse, rubella,
    etc can also produce microcephaly. Thus it is probable that it is the lost
    of brain cells that causes the various observed symptoms.

    On the other hand, with a possible increase of brain (stem) cells
    from the interbreeding of neanderthal and AMH, and because
    neuro-plasticity could better organized the connections, those
    are also the possible areas where the functions can be enhanced,
    e.g. cognition, motor functions, speech, visual, etc. Natural
    selection will determine the best for each environments.

    Some interpolation from Pearce’s data,

          76kbp  60kbp  52.5kbp  45kbp   25kbp
       measured  calc    calc    calc  measured
    

    Neander 1535.5 1516.2 1507.1 1498.0 1473.8

    AMH 1272.0 1335.2 1364.8 1394.5 1473.5

    diff 263.5 181.0 142.3 103.6 0.4
    %dif 20.7 13.6 10.4 7.4 0.0

    However an abnormally large brain can also cause problem like
    megalencephaly. Therefore only a certain range and rate of increases
    could be advantageous.

    Although the exact mechanisms are not known, the various cognitive
    performances plotted with respect to %introgression, %ASPM
    hint that the relationships could be inverted V shapes because of the above
    effects and they are observed from some data points.

    Various studies only reported results on mega population groups and some
    mega population groups were left out, the detail of the compositions were
    not disclosed. Because of the possible inverted V shape relationships,
    different compositions of the mega population groups could exhibit increasing,
    flat or decreasing results.

    It is interesting to speculate that after 25 kbp (and the disappearance of neanderthal)
    wrt brain size there was nothing to gain from introgression and as reported from John
    Hawk the sapien’s brain size started slowly shrinking from about that period. Is the
    sudden stop of increasing AMH brain size due to approaching that of the neanderthal
    and the extinction of them?

  19. melendwyr says:

    If some of the Neanderthal genes have negative effects and are selected against, the genes with positive effects must be quite valuable. Eventually a few genes would be very widely distributed and the rest deleted.

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