The 1%

We don’t see people today with Neanderthal Y chromosomes or mtDNA. I keep hearing people argue that this means that mating between Neanderthal males and AMH females must have produced sterile males, or that matings between AMH men and Neanderthal women were all sterile, or whatever.

That is not necessarily the case. A slight disadvantage is all that would be required to totally eliminate Neanderthal Y-chromosomes or mtDNA.

Imagine that a Neanderthal Y-chromosome reduces the bearer’s fitness by 1%, and that the original frequency of Neanderthal Y chromosomes (after admixture) was 2%.

It’s been something like 1500 generations. The expected frequency is 5.67 x 10-9. In real life it would probably have fluctuated to zero, and of course stayed there.

Understand and remember.

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41 Responses to The 1%

  1. epoch2013 says:

    Y-DNA of El Sidron male. Also hint at reduced fertility due to some genes on Y-DNA.
    http://www.cell.com/ajhg/fulltext/S0002-9297%2816%2930033-7

  2. MawBTS says:

    A slight disadvantage is all that would be required to totally eliminate Neanderthal Y-chromosomes or mtDNA.

    This might be too basic a question, but are there any circumstances where this would not happen? Any circumstances where a gene with a net fitness disadvantage would stay around, or increase in frequency (other than chance)?

    I’m not talking stuff like the African sickle cell mutation. Presumably the people who die from sickle cell are fewer than the people who would have died from malaria. On net, it’s not really deleterious.

    PZ Myers is on record as saying that deleterious genes can rise to fixation in a population. I’m trying to understand why he thinks this.

    • rkr says:

      Genes and particularly something like a Y-chromosome can be spread through ethno-patriarchal domination independently of its fitness(as long as it somewhat works).

    • RCB says:

      “(other than chance)”
      No… not that I know of

    • gcochran9 says:

      In a small population, slightly deleterious genes ( whose disadvantage is on the order of or smaller than 1/Ne) fluctuate pretty much randomly in frequency and can drift to fixation.

      A gene with meiotic drive can go to fixation even if it is deleterious.

      PZ Myers is of course an idiot.

      • RCB says:

        Meiotic drive… of course. My mind has gone soft…

        See Genes in Conflict, by Burt and Trivers, for more examples like this. My favorite is cytoplasmic male sterility.

        Of course, it gets weird at this point. If you define “deleterious” as something that hurts an individual’s ability to survive and reproduce, than all these are good examples. But, at the end of the day, if the allele is leaving more descendants for systematic (not chance) reasons, I tend to think of that as “positive selection”, and so the term deleterious seems strange to me. The purpose of the fitness construct is to help us predict evolutionary dynamics; if you call an allele deleterious even as it is systematically spreading, I’d question the usefulness of the term. (All semantics, admittedly.)

    • ohwilleke says:

      In the baseline of selectively neutral haplogroups, you very rapidly lose lots of all but the most common lineages during periods of declining population. In times of stable population, it is far less unusual to lose a low frequency lineage than you would intuitively expect and you lose quite a few low frequency lineages every few generations. But, in a period of sustained population growth you lose very few lineages, and the lineages that you do lose you tend to lose in the very early generations because of the founder effects that amplify and fix the proportions that are established in the first few generations of rapid growth.

      Slight selective fitness disadvantages make it significantly less likely that low frequency lineages that were at high risk already disappear over a large number of generations in the declining and stable population histories, but in the rapidly growing population history scenario, the overall fitness of the population that is causing rapidly population growth competes with the slight lack of fitness of the deleterious allele and so lineages that are less than the best can still ride the wave of population expansion to reach a point where it becomes far more difficult for the slightly deleterious allele to be purged from the population entirely as a result of the slight fitness disadvantage that it places on its bearers even over lots of generations.

      In application to archaic admixture, if it happens before a major populations bottleneck, it is entirely plausible that archaic Y-DNA and mtDNA lineages would be purged from the population via drift. But, if instead archaic admixture happens at the very bottom of a bottleneck, perhaps encourages because there was a shortage of same species mates, and is followed by a long, sustained period of population growth because whatever conditions lead to the bottleneck abate, then lineage loss looks less attractive.

      Still, discounting Haldane’s law (which the paper specifically states is consistent with the fitness reducing protein coding portions of the Neanderthal Y-DNA) doesn’t make lots of sense when we have direct evidence of functional aspects of real Neanderthal Y-DNA that could give rise to exactly that effect.

      • gcochran9 says:

        Well, we happen to know the interfertility of a number of mammalian sister species that have been separated for various amounts of time: and I can’t think of a case that shows significant sterility problems that hasn’t been separated a good deal longer than AMH and archaics were.

        That’s why discounting Haldane’s law – for this degree of time separation – makes sense.

  3. RCB says:

    “We don’t see people today with Neanderthal Y chromosomes or mtDNA. I keep hearing people argue that this means that mating between Neanderthal males and AMH females must have produced sterile males, or that matings between AMH men and Neanderthal women were all sterile, or whatever.”

    What people? Population geneticists?

    “The expected frequency is 5.67 x 10-9. In real life it would probably have fluctuated to zero, and of course stayed there.”

    Unless the population growth rate was >1%, in which case the number of Neanderthal Y chromosomes would increase even as their frequency decreased. Evidently not.

    • gcochran9 says:

      Come on, you know that long-term population growth was way less than 1% a generation.

      “Population geneticists?” Well, my comment sprang from Ann Gibbons’ comments on a current article in AJHG, lead author Fernando Mendez. He does mention Haldane’s rule, which is a first generation sterility thing.

      • RCB says:

        It was more a theoretical nitpicking than an actual suggestion. I find that I often entertain the theoretical merits of obviously-false-for-empirical-reasons hypotheses, for fun. A major drag on my productivity…

  4. IC says:

    Power of compound interest at 1%.

    • Anonymous says:

      An initial population of two people increasing at a steady 1% per year would result in a popuulation with total mass equal to the mass of the earth in roughly 5,000 years.

  5. Guy says:

    Is there another explanation? I’ve read that it was common for polygynous prehistoric societies to kill off the males of rival groups, and mate with the captured or remaining women.

    In an encounter between AMHs and Neanderthals, it seems reasonable to assume that often the AMHs would have the upper hand numerically. Neanderthal males would be a threat, whereas Neanderthal females could help with passing on a lineage. Poof, no more Neanderthal Y chromosome.

    • gcochran9 says:

      Polygynous societies worked especially well back in Ice Age Eurasia, because every woman you captured could go out and catch enough mammoths to feed herself and her children. That and food stamps.

      • IC says:

        Recently I have been thinking about association among IQ, personality and geographic regions.

        Tropical region can sustain higher density and diversity of living beings for both plant and animals.
        North cold region is opposite and has lower density of living beings. Certainly this applies to human population. Thus lower density, more personal space, less social interaction should be the case for northern population in ice cold region.

        In tropic, you really do not need to be very smart if you have good social/communication skill. One smart person is enough for every body due to strong social interaction. On top of that, multiple linked thinking brains can figure out thing that single brain could not.

        In place near artic, your next door neighbor could be several days distance away. Consulting others for difficult problems is not very practical. Your brain is better to figure out every thing on your own. You can not survive if you can not figure out stuff alone. This kind of environment force individual to have mental power multiple times than those living in higher density. Due to lack of other human neighbors around, autism or introversion due to social isolation become default personality. Thus they naturally prefer less people around. Extreme quiet, introvert personality of Finns might be due to such environment. Individualism is social norm.

        Certainly this is about prehistorical human condition. Then there is positive association among north latitude, introversion, intelligence.

        • IC says:

          In recent human history of civilizations, additional factors were thrown into the pictures.

          Poor people of lower intelligence can survive by helping (depending) each other through strong social bonding. Social bonding need strong social verbal skills.

          Upper noble class people of higher intelligence are more or less achieving success through self-efficacy. As result, more personal space can be achieved due to possession of more personal wealth (larger property, individual bedroom, living room, personal office ). More personal space facilitate introversion due to reduced social interaction. On top of that, top 1% mental ability reduce available people who can be communicate with. Genius just can not have `common sense’ like average folk. Very likely, noble class had northern ancestors who enjoy social isolation in the first place.

        • Jim says:

          Your next door neighbor wouldn’t be several days away. People lived in bands not isolated families but in the arctic or tundra bands would have often consisted of 10-20 people or so.

          • st says:

            Jim, as much as I admire your reasoning you’ve been off target here. Read Tacitus, not the contemporary anthropologist’s accounts or text books. Tacitus describes in certain depth the life of northern europeans. They do not “live in bands”. Each family lives in willful isolation, as far away from its inevitable neighbour as it can possibly be, which shocks Tacitus – what kind of people do not want to meet each other regularly? They put privacy above all – says Tacitus – and are so individualistic – that they get angry when somebody tresspasses the forest where their single villa is located in – the preferred distance from the neighbour’s family is the flight of an arrow. Or more. They get in bands only in war. But then again they even do not have king – they elect one only for the war duration and then dismiss him, going back to their individualistic isolation. But even then they are so slow in electing a king for the war party, until they come to an agreement the war is usually over. What kind of society is this, asks Tacitus. The answer he gives to the last question might surprise you.

          • Difference Maker says:

            Swedish bus stop

          • Jim says:

            I don’t think the areas Tacitus describes were arctic or tundra, Germany isn’t arctic or tundra. Arctic or tundra bands were small but not isolated nuclear families.

        • IC says:

          “I am a Finn and I agree on introversion. In our culture hard working in solitude is respected and showing your feelings is suppressed; both good for classroom study. In sports this culture shows too: we do generally very bad in team sports.”

          https://news.ycombinator.com/item?id=126608

          Chinese are pretty bad with team sports too. But good with individual types of sports like table tennis.

          • Jim says:

            Northeast Asians have quicker decision times according to Jensen no doubt very important in competitive table tennis.

        • Greying Wanderer says:

          I think those sort of factors are likely critical.

          • Greying Wanderer says:

            nesting makes unclear that was a reply to

            “Recently I have been thinking about association among IQ, personality and geographic regions.”

  6. James says:

    Considering what things which sexes do or have done to them in population replacement situations, in general, is there some reason the obvious alternative hypotheses is less likely than this one? (I mean, they can both be true at the same time, but.)

  7. krakonos says:

    Once I watched a documentary about pygmies – from sixties, or even older. There was a passage about them crossing a river full of crocodiles.
    What they did, they built something (from lianas) what resembled a suspension bridge. Pretty impressive for people with that low IQ.

  8. We can recruit basketball players from a few african tribes where 5% of their population is over 6 feet 8 inches tall. Kenya and Ethiopia dominate in the marathon. Samoans are designed for football. We need a feel good movie where a small time gymnast coach goes over to Africa and recruits pygmies for his team and wins the championship. Every time I watch gymnastics in the olympics it just looks like a bunch of flipping midgets to me.

  9. Space Ghost says:

    Great point. An equivalent way of formulating it: for there to be a 1% expected frequency of extant Neanderthal mtDNA or Y Chromosomes today, there would have to be a fitness reduction of 0.04% or less (given a starting frequency of 2% and 1500 generations)

    • Rick says:

      “there would have to be a fitness reduction of 0.04% or less (given a starting frequency of 2% and 1500 generations)”

      But there were actually several admixtue events, and not at the same time.

      The most likely places for an archaic Y or mtDNA haplogroup to exist in a human population would be in Australia or New Zealand. They probably only maintained such a high Denisovan % because of a massive founder effect.

      If they have ~5% autosomal ancestry from Denisovans, and were only subjected to 50-100 generations before isolation, how deleterious must the Y chromosome and mtDNA have been? Much worse than 0.04% I think.

      I guess it depends on the size of the bottlenecked population.

  10. All of our human mtDNA/Y DNA samples dating 30,000-40,000 years old are extinct today. They have close relatives living today, but no direct descendants. Does this mean humans are not human 🙂 ? Of course not. What it is, is direct maternal and paternal lines usually become extinct after 1,000s of years, while their ancestry contribution remains.

    We all didn’t just pop up out of no where, humans who lived 40,000 years ago were our ancestors, however most of our ancestor’s direct maternal(mtDNA) and paternal(Y DNA) are extinct today. Only a handful of lucky men and women’s direct lines survived. Considering Neanderthals represent a mere 1-4% of ancestry of Eurasian’s ancestry, we shouldn’t expect to see any Neaderthal mtDNA/Y DNA in modern Eurasians.

  11. TWS says:

    Ok two questions. Forgive my ignorance, is it possible for there to be more archaic admixture we just don’t recognize? Is it possible for more Neandertal or archaic yet to be found.

    • Rick says:

      “Ok two questions. Forgive my ignorance, is it possible for there to be more archaic admixture we just don’t recognize? Is it possible for more Neandertal or archaic yet to be found.”

      Yes. The main reason is that we assume that Neanderthal and Denisovan admixture is zero within some African groups.

      If all Africans had admixture from an archaic group(s) related to Neanderthals and/or Denisovans, then we would be unable to really sort it all out without ancient genomes from at least one of the populations involved.

      We can estimate non-Neanderthal/Denisovan archaic admixture based on unusual differences in the SNP distribution within African populations. This has resulted in some interesting leads. But, it is really hard to sort it out without clear outgroup genotypes.

      They could be just very rare autosomal haplotypes that came from a common ancestor of all modern humans, and maintained because of drift, or because these populations had a large effective population size throughout their history.

  12. albatross says:

    An intact Neanderthal Y chromosome would require that someone (who has been sequenced) has an unbroken male line of descent from a Neanderthal dad. How would I work out the probability of no such person existing now, given the times and an estimated fraction of human Neanderthal ancestors? I guess we should be thinking in terms of prehistoric population sizes (by the time populations expanded from agriculture, Neanderthals were long gone). I can think of ways to approach the question, but I imagine there’s a formula already worked out somewhere….

    • gcochran9 says:

      If you have a model for the population history, easy enough to write a small sim and run it a million times. There’s a fair chance that you could lose the Neanderthal Y chromosome (or Neanderthal mtDNA) by drift alone: Eurasian populations could be pretty small back in the Ice Age, and the effective pop size for the Y chromosome is one-fourth that for autosomal genes.

  13. Greying Wanderer says:

    @Jim

    “I don’t think the areas Tacitus describes were arctic or tundra, Germany isn’t arctic or tundra. Arctic or tundra bands were small but not isolated nuclear families.”

    True but did part of their ancestry come from there?

  14. Greying Wanderer says:

    on-topic

    Although going by the equation we might find some surviving Neanderthal ydna in ancient samples?

    (my guess northern Himalayas would be most recent / least ancient – somewhere near where Yeti legends are common)

  15. Brandon Berg says:

    We don’t see people today with Neanderthal Y chromosomes or mtDNA.

    What’s the sample size? That is, how many people have been examined for Neanderthal Y chromosomes or mtDNA? Can we rule out the possibility that even 1 in 10,000 humans have one or the other? 1 in 100,000?

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