Lifting degeneracy

Some time ago I discussed the idea that Neanderthals were fucked-up because their low effective population size led to inefficient purifying selection. But the usual harmonic-mean effective population size is not quite right: for salvage mutations, things that somewhat correct the wrongness caused by increased genetic load, the effective population size is closer to the average.  In other words, there were probably a lot more Neanderthals during interglacial periods, and these genetic consequences of those population booms ameliorated their genetic problems.

Second, Neanderthal Y chromosomes and mtdNA have even smaller effective population sizes, 1/4th as big as the autosomal effective size, and thus were even more likely to be messed up. which is why, maybe the Neanderthals seem to have picked up mtDNA from some African group closer to modern humans around a quarter of a million years ago: they needed it.

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43 Responses to Lifting degeneracy

  1. dearieme says:

    When will the People’s Republic of China send forth an army of Neanderthals carefully bred using ancient DNA? Perhaps they could be equipped with the right pinch of Tibetan so that they can fight effectively at high altitudes. And also have a dash of whatever lets some other mob thrive on long dives underwater.

    What other little bits of modern human diversity might they usefully have added to them? Or, indeed, little bits of ancient DNA diversity, if available?

    • Frau Katze says:

      That Chinese doctor who genetically altered two embryos (to make them resistant to HIV, that mother apparently had) has had the book thrown at him. There’s no indication that the Chinese leadership is in interested modifying embryos.

      Note 1: How does he how to make one resistant to HIV? I recall reading that there (very rare) cases of people being resistant. The hemophiliac son of Robert Massey (who the book on the Tsar Nicholas and his family, including a hemophiliac son) said he is a rare case of resistance.

      Note 2: the technique, that requires implanting embryos is too expensive and resource consuming for large scale use.

      • Bonner Tal says:

        The mutation He induced occurs naturally in Europeans. Those individuals with two copies are immune to HIV. I think something like 1% of Europeans, especially Northern Europeans. Not all that rare, really.

        In Denmark almost 10% of all kids are IVF-kids. That sounds like large scale use of embryo implanting to me.

        • Frau Katze says:

          OK, I was just reading up on the mutation. A single gene affected.

          So it would be a good test case. If it works, the babies will be fine despite the mother having HIV.

          What do people here think?

          The doctor was surprised at being attacked. He was foreseeing praise.

          I suppose he could have made a mistake and the embryos would not survive.

          But that can’t be the concern as people are blasé about survival of embryos (unfortunately for the anti-abortion crowd).

  2. Lior says:

    We got more mtDNA than Y chromosomes from Neanderthals, right?
    Is this becasuse we conquered and dominated them or because of selection against their messed up Y chromosome?

    • gcochran9 says:

      No Neanderthal Y chromosomes, no Neanderthal mtDNA. as far as we know.

      • TWS says:

        Is it possible we did get some but the differences have disappeared over time?

        • Neanderthal Y and Mt says:

          AMH must have got some of one or those if they interbred, but none survives today (or in the fossil record of N admixed HS).

          AMH could simply have lost N y / mtdna by being on the “wrong” side of two episodes of sex biased admixture.

          Assume an initial mating of human males with Neanderthal females, picking up 6% Neanderthal ancestry and 12% Neanderthal mtdna, no Neanderthal y.

          If that population then has male sex biased mating back into AMH, then you end up with 3% Neanderthal autosome, but all the Neanderthal mtdna will be gone, and so will the Neanderthal y.

          Sex biased mating seems common, and reversals of fortune on sex biased mating do too (e.g. X males mate with Y females to produce Z…. then Z males mate with X females. Pretty common and even the Americas has some examples).

    • DRA says:

      If If we (researchers) found both mtDNA or Y chromosomes in Neanderthal bones, we would likely have found more mtDNA, as there are many copies of the latter per cell.

      This is different than we, modern humanity, having inherited either from them.

  3. David Chamberlin says:

    Who in the hell lived in Southeast Asia prior to the rapid expansion of modern humans approximately 50,000 years ago? It looks like it should have supported the biggest hominid population on earth. If it wasn’t the Neanderthals, and Denisovans had a much smaller population than the Neanderthals, who was it?

    What intellectual benefits, if any any, did breeding with Neanderthals give modern humans?

    • gcochran9 says:

      Denisovans likely had a considerably bigger population than Neanderthals.

      • TWS says:

        Don’t modern Oriental teeth have similar characteristics as prehuman teeth?

        • John Massey says:

          No, but East Asians exhibit shovel shaped incisors like Neanderthals had. Neanderthals were not ‘pre-human’ – if you want something pre-human, you need to go back to the Australopithecines.

    • Bonner Tal says:

      Neanderthals had a higher copy number of Duf1220. Which has been linked to IQ and brain size. Whether the link to IQ is real is unclear, but the brain size correlation holds over many species and Neanderthals did have bigger brains.

      I did an analysis whether Duf1220 copy number variation explains global variation in IQ, but there didn’t seem to be much there: https://halfassed.science.blog/2019/01/13/does-duf1220-copy-number-variation-explain-global-variation-in-iq/

      • David Chamberlin says:

        Interbreeding between archaic and modern humans occurred several times. https://en.wikipedia.org/wiki/Interbreeding_between_archaic_and_modern_humans . A small population of modern humans that had recently interbred with neanderthals gained evolutionary advantages that basically gave them a leg up on all their hominid competition and they then made short work of expanding their territory to be the entire world excluding sub Saharan Africa. There is not proof that our present day genes that we inherited from neanderthals give us higher intelligence. What we do have proof of is that neanderthal genes can screw us up, like giving us greater tendencies for autism and schizophrenia as this DUF1220 copy does.
        Introgression events between neanderthals and modern humans happened 47,000 to 65,000 years ago. That population took over the world. That population at that time started making more complex stone tools, basically a tool kit. They expanded rapidly and all their competition disappeared. Why.

        • David Chamberlin says:

          That is the pro argument that the infusion of neanderthal genes made us more intelligent, I should also for accuracies sake put out the con argument. It is perfectly conceivable that as modern humans expanded through neanderthal territory they picked up some neanderthal genes through interbreeding. That populations were incredibly spread out so the temptation to interbreed would have been very strong. This paper https://www.biorxiv.org/content/10.1101/059311v1 from the David Reich Lab looks at the genetic structure of first farmers and finds that “the earliest populations of the near east derived around half their ancestry from a Basal European lineage that had little if any neanderthal admixture.” Amazing paper that catches a glimpse of what the original populations were coming out of the last ice age that contributed to the first farmer gene pool that later thoroughly intermixed. That population with little to no percentage neanderthal would not have contributed 50% to the first farmers genes if that neanderthal gene contribution was crucial to a big increase in intelligence.

          I think the truth lies somewhere in between these two arguments. The infusion of all those neanderthal mutations that had collected for hundreds of thousands of years and increased because of they gave cognitive advantages were thrown into the human population. Their impact could have been tiny but small nudges in average IQ makes for a many multiple increase in the percentage of high IQ people in the overall population. Average IQ in the early hybridized modern human population could quite conceivably have gone down because of the adverse effects of neanderthal genes, but if some of those hybridized ATM/neanderthal mixes were geniuses for their time, making better tools and weapons than that population would then do what they did, take over the world.

      • Yudi says:

        They didn’t have bigger brains than modern humans alive in their time. Human skull size has shrunk in the last 20,000 years.

  4. Gord Marsden says:

    Intellectual benefits? Like now , no one breeds for brains

  5. Greying Wanderer says:

    higher metabolism for warmth becoming a burden as the earth warmed?

  6. LOADED says:

    Enough with the bullshit, we all know that race has become a critical part of how we look at things now. We’ve become so engrossed by race and superficial aspects of a person we’ve forgotten that humans are conditioned to behave the way they do. It’s all group-think nowadays, no individualism. People do not think for themselves if that makes sense. The mind is polluted.

  7. erasmuse says:

    Please clean up your language. The world is full of enough ugliness as it is. Your blog has good substance; have good style too.

  8. teageegeepea says:

    Off-topic, but I’m wondering if Greg has read this:
    https://slate.com/human-interest/2019/06/gay-genetic-research-dna-screening-risks.html
    I believe you discussed Yoder’s review of “A Troublesome Inheritance” recently (which he links to in the above). I’m actually somewhat disappointed that Cochran’s pathogenic theory hasn’t reached the Emmanuel Goldstein status of something like The Bell Curve.

  9. Glengarry says:

    This might be the right place to ask: have the coefficients of relatedness been characterized (e.g., expected values, distributions) for the various peoples of the world? Any links or even tables?

  10. Interested Layman says:

    I am not a geneticist so my questions maybe a little simple. Why would they have needed a large population size? What about the Andamanese islanders? They look healthy and they have been on small islands for thousands of years, with a low effective population size. It is also interesting to me that they have lived there so long with out defoliating the place. They must have come to some type of equilibrium.

  11. TWS says:

    An unrelated question I was looking at fossils of earlier Australians and they were gracile. Is there any other occasions of people going from gracile to robust?

    • John Massey says:

      I question whether they did. I am pretty familiar with Aboriginal people (I mean people of 100% Aboriginal ancestry) in different regions of Australia. In the far north of Western Australia (a region called the Kimberley), the people are really gracile – tall and very slender. In some other regions they are much more robust. It looks to me like a regional variation thing, maybe something that happened after different regional groups became semi-isolated from one another due to climate change.

      I applaud the research that Eske Willerslev and his group did, getting a lot of Aboriginal people to buy in and give DNA samples, when they had previously been very resistant to doing it, but this is a question that research did not answer, because they did not succeed in getting samples from the far north of the country. Another question that was not really answered, to my satisfaction anyway, stems from the fact that they did not succeed in getting samples from speakers of non-Pama-Nyungan languages in the far north. They didn’t say that they failed to get samples from these groups, but it is obvious to me from the results that they reported in their findings – two big gaps which would have answered questions I have had for a large part of my life.

      That’s a research project in waiting for anyone who can go to those areas and persuade people to buy in and give samples. Good luck with that.

      A thought, though – modern humans had arrived in substantial numbers in Australia by at least 47,000 years ago, and probably a lot longer (there is pretty convincing archaeological evidence of a modern human presence in the north dated to 60,000 – 65,000 years ago), but Willerslev’s team found that the ancestors of the people they sampled had not become genetically isolated until 37,000 years ago – after that they seem to have taken a dislike to the neighbours. The land bridge between Australia and New Guinea was not submerged until 8,000 – 10,000 years ago. A lot could have happened over that time span that is waiting to be unpacked. I suspect that there is a lot more genetic variation that has not yet been documented.

  12. Henry Scrope says:

    https://www.nature.com/articles/s41586-019-1335-8

    Is there low hanging fruit here?

  13. Dave Chamberlin says:

    Another question for Cochran while we are close to the subject. Why did those very intriguing Homo Naledi have two interesting characteristics and how are they neatly combined into one answer. Those small brained guys had numerous chips in their teeth and they didn’t experience nutritional hard times like Neanderthals did.

    • John Massey says:

      Easy – they ate dried Vicia faba. Or very nutritious rocks.

      • Dave Chamberlin says:

        Some guys somewhere sometime got the bright idea to leave the small tubers until they were bigger tubers and pound the bigger ones with rocks to a paste to make them more digestible. Maybe it was these guys, maybe it wasn’t, you folks ain’t no fun, I’m going elsewhere,

  14. Dividualist says:

    What’s your opinion about Danny Vendramini’s idea that human evolution was driven by Neanderthal predation on our ancestors? That we got (mostly) hairless so that they could easily tell who is a hairy (cold climate) Neanderthal man-eater and who is a fairly harmless pre-Cro-Magnon?

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