“Who We Are: #3 Neanderthals

In Chapter 2, Encounters With Neanderthals, David Reich talks about his work in analyzing the first successfully sequenced Neanderthal genomes, and the discoveries that led to.

Reich’s team, with Nick Patterson making an especially important contribution, found that Neanderthals were about equally [genetically] close to Europeans, East Asians, and people from New Guinea, but closer to all non-Africans than to sub-Saharan Africans. This was what you would expect if the ancestors of non-Africans had interbred with Neanderthals, while sub-Saharan Africans had not.

Even thought these results were statistically very strong, Reich was skeptical because it went against the scientific consensus of the time – that there had been no admixture between anatomically modern humans and archaics such as Neanderthals as AMH expanded out of Africa. This was a question that I and John Hawks were interested in. We had concluded that the “scientific consensus” was based on nothing and put no stock in it. We had predicted that such admixture would be found, and that sometimes Neanderthal alleles would have conferred selective advantages and become common. Our reasoning went as follows:

The evidence for zero mixing was weak. It was clear that modern humans did not carry Neanderthal Y-chromosomes or mtDNA, but that could have occurred because they reduced fitness (a slight reduction have been enough to eliminate them, over tens of thousands of years) or because they were never common and were later lost by chance. Y-chromosomes and mtDNA are only two loci. We had checked what was known about successful hybridization in mammals: it turned out that after two species separated, it usually took a couple of million years for serious genetic incompatibility to develop. But we knew, from the fossil record, the Neanderthals split off around a half million years ago. Hybridization should have been possible. Moreover, if it happened, even at a low level, it would be an efficient means of transmitting new favorable alleles to modern humans, some of which might be common today.

One reason [ we think] for that bogus scientific consensus was a confusion of terms. Paleontologists call two sets of fossils separate species if they look sufficiently different [morphological species] while biologists usually define separate species as populations that can’t interbreed. Those aren’t equivalent definitions: we can distinguish the skeletons of Labrador retrievers and poodles, yet labradoodles happen.

Another reason: Ernst Mayr, a prominent figure in biology had opined that hybridization was an unimportant factor in evolution, as far as I can tell for no particular reason at all. For equally mysterious reasons, people paid attention to him.

Anyhow, Reich’s skepticism led to even better evidence for mixing with Neanderthals, which is the way it’s supposed to work in science. By looking at the average length of Neanderthal-derived segments of the genome, they were able to make a rough estimate of the time of mixing. Later work, using ancient DNA from a modern human that lived and died in Siberia about 45,000 years ago, gave a more accurate of 50-60 thousand years ago for Neanderthal admixture. The fact that the amount of Neanderthal admixture was not very different in widely separated populations in Eurasia suggested that admixture occurred in the Middle East, an inevitable first step in expanding out of Africa.

Later work showed something very interesting: the amount of Neanderthal ancestry ( in regions that actually do anything) has been slowly declining over time. In certain regions you see no Neanderthal ancestry at all – Neanderthal gene deserts – bu the trend is general. Not universal, since some Neanderthal genes appear to have been useful and have become common, but the general trend is the gradual shedding of the minority genome.

There are a couple of explanations under consideration for this genetic rejection. One is that Neanderthals were messed up: because their long-term numbers were lower, particularly at glacial maxima, purifying selection would have been less efficient in Neanderthals, and slightly deleterious mutations would have accumulated to higher levels than in anatomically modern humans. We have more example: it looks as if most of the functional part the Denisovan genome is also being slowly rejected by Melanesians. But there’s more: West Africans seem to have have picked up genes from an archaic group in Africa that are slowly being rejected, while Altai Neanderthals seem to have picked some modern human ancestry ( possibly from the Qafzeh-Shkul population in the middle East around 100,000 years ago) and they were rejecting the modern human genome. I can’t see how Neanderthal genomes could simultaneously be both better than and worse than modern human genomes: I think it more looks like a kind of mild incompatibility, where every subspecies is rejecting minority DNA from any exterior source. If true that would be very interesting. But I could be wrong. Probably am.

Reich believes that moderns and Neanderthals were at the edge of biological compatibility, probably with reduced fertility. The evidence is that there is an especially low level of Neanderthal ancestry on the X chromosome, a known hotspot for fertility problems in crosses between related species. And that’s good evidence. But on the other hand, comparisons with other mammalian sister species indicates that it usually takes a considerably longer separation before real fertility problems show up – enough, say, to materially inhibit gene flow.

Probably we need to define terms. I think that a few-percent decrease in fertility in people with large amounts of Neanderthal ancestry might be enough to create those Neanderthal gene deserts on the X chromosome – but at the time, nobody would have noticed it. Smallish effects had something like 2000 generations to play out.

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61 Responses to “Who We Are: #3 Neanderthals

  1. magusjanus says:

    Any speculations as to what specific advantages Neanderthal admixture brought? IQ?

    Also, one thing I’ve never grokked is why the heck we “beat” them. They were around environments with more selection (colder/etc) for much longer than we were. What advantage did we have as we burst forward out of Africa?

    • Tershul says:

      Neanderthals were probably dumber, and used less sophisticated hunting methods. Possibly stabbing spears only. AMH used throwing spears/atlatl.

    • Neanderthals had larger skulls, so that opens a path to higher IQ.

      One reason we beat them was aggression. Genes linked to hyperactivity and aggression in humans are missing from the Neanderthal genome. Another big factor was larger social groups. One theory I’ve seen is that language allows for larger groups sizes by allowing you to scale social grooming; instead of having to take the time to eat lice off one individual at a time you can build social rapport with multiple people at once by shooting the breeze.

      Or more importantly you can induce shared religious experiences around the camp fire by telling the story of your tribes divine origin and the heroes you all try to emulate. Advances in Sape language abilities were a key difference vs Neanderthal brains that seem to have selected for greater visual spatial processing with larger occiputs at the back of their heads.

      Sapes can hold up to around 150 individuals in a group. Neanderthal groups on the other hand were much smaller and isolated, maybe around 12 individuals.

    • sprfls says:

      Not going to venture specific guesses, but here are some general ones… 🙂
      -something immunity-related (now seen as increased risk for allergies, etc.)
      -something cognitive-related (now seen as increased risk for depression, addiction, what else?)
      -something skin-related

      The increased risk for depression that Neanderthal genes supposedly confer is sort of interesting given the sharp contrast in depression rates between Africans and the rest of the world. Lots of confounds there though (and not really sold on the global depression data either).

    • engleberg says:

      @What advantage did we have?

      They were stronger, so they probably needed more food. And they weren’t a huge population; maybe early modern humans had enough numbers to just swamp them.

    • dave chamberlin says:

      “Any speculations as to what specific advantages Neanderthal admixture brought to IQ?”

      One thing that truly stands out is that right around the time anatomically modern man interbred with Neanderthals the horribly named “great leap forward” happened. Evidence of higher intelligence is evident in tool making as well as success in a small population expanding and taking over the entire world excluding Sub Saharan Africa.

      But that isn’t proof that Neanderthal admixture boosted intelligence. It might be that as humans expanded they simply picked up Neanderthal genes. It is an interesting question that we don’t have an answer to yet. I once thought it quite likely Neanderthals hybridization boosted our intelligence but several pieces of evidence have since come out that make this hypothetical less likely.
      1) A Reich paper looking at the first farmers showed that they derived from three population, one of them having no Neanderthal admixture.
      2) The genes that Neanderthals gave us that bestowed an advantage and thereby increased in the interbred population don’t seem to have much if any influence on brain function.

      • Rodep says:

        “One thing that truly stands out is that right around the time anatomically modern man interbred with Neanderthals the horribly named ‘great leap forward’ happened.”

        Unless we can date these very precisely, the opposite ordering seems more likely. The Leap Forward happens, after which we use our newfound brains to overcome the Neanderthals’ brawns.

        • dave chamberlin says:

          I really don’t think there was a great leap forward. It might seem so from todays standpoint but far more likely there was a very very slow progression in mankind getting smarter that extends right up to modern times. It is frustrating how little we know about the early stages of anatomically modern man. There weren’t many of them and they didn’t leave very much. It seems to me awfully damned coincidental that ATM’s took off both in creativity and population after they interbred with Neanderthals. I would be surprised if the Neanderthals contribution to modern mans gene pool did not have some kind of mental benefits. It may not have been a big one, we don’t know, but look at the numbers. Neanderthals had a minimum population of 20,000 for 500,000 years. Make an average generation 20 years long and that means 20,000 times 25,000 neanderthals lived and reproduced. Half a billion neanderthals couldn’t come up with any mutations that benefitted ATM’s intelligence when they interbred? I doubt this, especially in the light of a tiny interbred population of ATM’s and neanderthals damn near taking over the entire world, pushing all other hominids to to extinction.We are at the very beginning of understanding how the human intelligence is influenced by genes. That we haven’t found any proof that Neanderthals contributed to our intelligence doesn’t mean very much at this stage.

          We should keep our mind’s open that Neanderthals gave us some intellectual benefits, doesn’t mean they did, but it is very definitely possible.

    • RCB says:

      Any neanderthal gene that would have conferred an advantage would have been positively selected for, once recombination allowed it to evolve mostly independently of the rest of the neanderthal genotype (i.e. a handful of generations). So it literally could be any good allele that the neanderthals happened to have that we didn’t. For example, Neanderthals might have had an IQ boosting gene that we appropriated, even if on the whole they were dumber.

      • gcochran9 says:

        I think it’s harder to get a new variant that is favorable in both single and double dose than just in single dose. Not many of those fairly common, clearly advantageous Neanderthal alleles look like they’re going to fixation. A consequence of Fisher’s geometric argument.

    • a says:

      “Any speculations as to what specific advantages Neanderthal admixture brought? IQ?”

      lol the obsession with iq and you guys is so funny

      anyways, there was a new paper that showed more neanderthal cranial and (possibly) brain similarity with eurasians than sub-saharan africans

      though the selection appeared to be weak, and mediated through demographic events

      • IQ is measurable. You will note a similar “obsession” with easily-measurable physicals like height and skulls, or evidences that can be attested from archaeology, like farming, or weapons. Musical, artistic, and other creative abilities, or social groupings and attitudes are clearly important, but hard to measure across millennia and continents. Those get mentioned here in the context of speculative fiction, which a lot of folks here have a side interest in.

        Also, IQ also has lots of modern correlates, so the thought is that has been true for a long time.

    • DRA says:

      Speculations are cheap:

      Average food productivity per land area was perhaps lower in the climate of ice age times, so Neanderthals might have been selected for lower population density, and/or smaller tribes or family groups. Extreme case, Orangoutangs rather than Chimpanzees.

      Perhaps Neanderthals hunkered down during the winters, not hibernation but reduced activity. Perhaps similar to depression or seasonal effective disorder.

      If it is possible to determine what Neanderthal characteristics we selected against most strongly, rather than just biological incompatibility, it might give hints as to what advantages AMH had as the environment changed. Undoubtedly more insights to come from further research!

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  3. How did everybody in each of these modern populations end up with this few percent of archaic genes, if they’re slowly being rejected?

    Would it be that, in each case, they must have been useful at the time (e.g. Neanderthal cold weather adaptations) but not later on?

    • Leonard says:

      Not all genes are being rejected. As Dr. Cochran says, “some Neanderthal genes appear to have been useful and have become common”. Everyone eventually got these genes because they increase fitness. However, people did not get individual genes but the whole package: half a Neanderthal genome. Some of the Neanderthal genes were adaptive or the hybrids would not have prospered. But most would be neutral or maladaptive. The maladaptive genes would be rejected. However the rate depends on (a) how malaptive they are, and (b) how far they are on their chromosome from adaptive genes. A gene that is only slightly negative can persist a long time particularly if it is sited close to an adaptive gene.

    • Eponymous says:

      Founder effects + mixing I would think? If a reasonably small population of AMH left Africa, interbred enough that their gene pool became X% Neanderthal, then stayed together long enough that this share became evenly distributed before heading their separate ways, then you would expect to see the pattern observed. Even if the Neanderthal genes are (slightly) deleterious on average.

      It is a bit strange though that the populations that subsequently lived in Neanderthal-inhabited regions didn’t interbreed further and therefore end up with a higher share.

  4. Which is worse, genetically, having a kid with a Neanderthal or having a kid with a cousin? (I’m talking specifically here about outbreeding/inbreeding depression from having a kid who is depressed below the midpoint of the parents on traits like fertility, height, or IQ.) Just asking for a friend.

    • Toddy Cat says:

      Seeing as how our ancestors seemed to thrive after interbreeding with Neanderthals, I’d guess a cousin is worse, but we’ll see what Dr. Cochran says…

      • gcochran9 says:

        Depends on the cousin, I would think.

        • Smithie says:

          Surely, the royal houses of Europe could have used a healthy infusion of Neanderthal blood at some stage.

          • Is there any evidence the royalty was more inbred than general population? There’s large bias to ignore any inbreeding in peasantry (who did not have biographers).

            • Smithie says:

              Egyptian and Incan dynasties (god-kings) were severely inbred. Often brother-sister pairings. I think the same reasoning (wanting to show you are a class apart) in a more restrained form, led to a lot of inbreeding among royalty in Europe.

              It seems like royalty could exert pressure for exemptions or were given more leeway. There was even a brother-sister pairing among the Inca which was sanctioned by the Church, as a diplomatic move, even though the Inca had lost their empire.

              With peasants, I think that it was very useful to have large kin networks. Lots of 2nd and 3rd cousins to act as an information and support network. So, you could marry your 2nd or 3rd cousin, without collapsing the network too much or suffering greatly deleterious health consequences.

              Of course, I’m speculating a lot here. Was this really the case in early Middle Ages? And why do they marry their first cousins so often in some places? I have no idea whether it was just the influence of the Church or not. But then wasn’t Sicily Christian?

    • RCB says:

      I’m going to take this somewhat seriously…

      What is the additional relative loss of fitness (load) of the offspring of two cousins? If you assume N loci with deleterious recessives at equilibrium, you can show (approximately)

      added relative load = 1/8 * (sqrt(s/mu) – 1)

      where s is the selection coefficient of each locus, and mu is the per-locus mutation rate. The formula assumes s >> mu, so the term is potentially big. If there are lot of lethals segregating in the population this can be pretty high.

      This fitness cost only lasts for one generation. If your inbred kid can manage to survive and breed with a non-relative, then your grandkids will be fully outbred and therefore totally normal.

      For a neanderthal… no such formula. There will be additive fitness loss in your offspring, since neanderthals are surely not as adapted to human society as the average human. The sky is the limit for how big this cost is. Might be sex dependent: a half-neanderthal daughter might have more trouble finding a mate, for example. Then there is any hybrid incompatibility to throw on top. Worse still, your grandchildren will be 1/4th neanderthal, and so on… so the costs last more than one generation.

      I’d go for the cousin. Darwin pulled it off.

  5. pyrrhus says:

    Thank you for some great science, Dr. Cochran! Anecdotally, Neanderthal DNA doesn’t seem to going away very fast in my group of relatives on 23AndMe..My segments are almost 4% Neanderthal, and there are a couple slightly higher, out of 1200 or so. I won a bet on this….

  6. another fred says:

    I have a question for Dr. Cochran, or anyone who feels they know, how much of the Neanderthal and Modern Human genomes are indistinguishable, i.e how much overlap?.

    If a person has 4% Neanderthal, how much can be declared to be certainly NON-Neanderthal?

    • another fred says:

      I do understand that we are talking about a different kind of statistic that the kind that says we share 98% of our genome with Chimps.

      • dearieme says:

        And yet another kind from the sort of tests that can conclude that the Scots and English are about 30% German and 70% Welsh. (Oh, all right: 30% Anglo-Saxon and 70% Ancient British.) Speaking as an ignorant layman, how should I grasp these different scales of scrutiny?

        • MawBTS says:

          When people say we share 98% of our DNA with chimps, they’re talking about genes (which could be likened to words in a sentence), and when they say you’re 30% German they’re talking about alleles, variants of the same gene (which could be likened to grammatical variants of the same word – jumped/jumping/did jump/will jump, etc).

          All humans, in theory, have the same genes at the same places, otherwise sexual reproduction wouldn’t work. But these genes come in different forms. British DNA might go “we scream for ice-cream” while German DNA might go “we screamed for ice-cream”. All the words are there, but the meaning has changed a bit.

          But look at the same locus on a lettuce’s DNA, you’d might see “my hovercraft is full of eels”. There’s a totally different gene there, which is why we can’t reproduce with lettuce.

          • RCB says:

            “All humans, in theory, have the same genes at the same places, otherwise sexual reproduction wouldn’t work.”

            Is that so? Doesn’t evolution sometimes occur via gene duplication and deletion happen? If so, then presumably a deletion/duplication mutant can still reproduce… otherwise such chromosome changes would never make it into the next generation.

            E.g. if I have two copies of a gene where everyone else has one, then no problem: I just have two places on my chromosome where transcription of that gene can occur. During meiosis, presumably one gene “loops out” while the other aligns with the copy on the other chromosome for recombination. I vaguely remember all sorts of loopy stuff like that from genetics class…

            More generally, “small” differences here and there across the chromosome wouldn’t interfere too much when the two chromosomes come together to cross over (whatever that’s called), so meiosis still mostly works. Someone correct me if I’m getting this wrong.

            • MawBTS says:

              Yeah, I wasn’t thinking. So long as the genes are there, meiosis will occur. It isn’t necessary that the chromatin strands perfectly match up like a zipper – they end up broken and jumbled out of sequence anyway.

              More generally, “small” differences here and there across the chromosome wouldn’t interfere too much when the two chromosomes come together to cross over (whatever that’s called), so meiosis still mostly works. Someone correct me if I’m getting this wrong.

              There’s such a thing as a speciation gene, whose presence immediately results in sterile offspring. Not sure how common they are.

              And different chromosome counts usually cause problems. Horses have 64 chromosomes and donkeys have 62 – when they breed, they produce an infertile offspring with 63. But that’s a problem that only shows up in the gametes of the next generation: the actual sexual reproduction process works fine.

              • athEIst says:

                Since you probably know, people don’t breed mules with mules for obvious reason, but are mules sexually normal other than infertile.

          • dearieme says:

            Thank you for that constructive and helpful reply.

        • A prehistoric super scientist (either sub-Saharan Egyptian/Wakandan or a Melonhead, I speculate) was trying to breed a more efficient danger to sheep.

          The best laid plans, and all that.

  7. bob sykes says:

    As an aside, in “The Clan of the Cave Bear,” Jean Auel speculated that Neandertal and human interbreeding did occur, and that hybrids occurred. The Clan in question were, in fact, Neandertals, although Ayla, their adopted human orphan, eventually rejoined other humans.

    Considering this was published in 1980, Auel was prescient. Of course, she, herself, was a pervert, and her books contains all sorts of perversions presented as normal behavior.

    • Toddy Cat says:

      So how is she a pervert? La Wik says that she’s married and has five kids. That of course doesn’t rule out being a pervert, but it’s not the usual kind of pervert at any rate.

      “her books contains all sorts of perversions presented as normal behavior.”

      Care to elaborate? I’ve never read them, although my wife read and loved them – maybe I need to check up on that woman…

      • Anuseed says:

        I read the first book and there’s some rape and kid fucking. I think Ayla was 11 when she had her virginity taken. One of the women explains how she’d gladly get into position if some men came over from another tribe “wanting to relieve themselves.”

        Jean Auel knows how it went down back in those days.

      • MawBTS says:

        One of her books won the Bad Sex Award.

    • Pincher Martin says:

      Human/Neanderthal admixture, like the existence of races, was once considered de rigueur by scholars in the early 20th century. Madison Grant wrote about it matter-of-factly in his popular book a century ago. The idea became lost (or neglected) knowledge until Greg and others revived it.

  8. Smithie says:

    I’d guess this purifying selection must have just about stopped.by now. The more detrimental variants have likely already been eliminated, and there’s pretty low childhood mortality and generally low average fertility.

    BTW, looking back, it seems funny that some assumed that lack of alleles on the X-chromosome must have meant male Neanderthals mating with female humans.

  9. dux.ie says:

    With neandertal-sapien there could be generally 4 type of hybrids, 1) large head and body, 2) small head and body, 3) large head small body, and 4) small head large body. Evolution determines which is better. Neandertal had large head could be to better control the large body or more muscles. Type 3 hybrids might have more spare brain cells for other functions like better cognition. Type 4 might be too dumb and too poor muscle coordination to be competitive.

    Pearce’s paper with the cranial capacities of Neandertal and Anatomically Modern Human AMH through history (kbp KYears before present) provided an interesting comparison, though only with two and a half set of data points,

            76kbp  25kbp present

    Neandertal 1535.5 1473.8 –

    AMH 1272.0 1473.5 1365.17(Pearce12avg)

    diff 263.5 0.4

    At 76kbp there was large cranial capacitiy diff between neandertal and AMH. Before the extinction of the neandertal, there was little difference in the cranial capacities of neandertal and AMH. One possibility is that because of introgression in both direction, the cranial capacities converged to the same value. After the extinction of the neandertal, the cranial of AMH reversed the increasing trend and have gradually shrunk to the present size.

    Sankararaman has the neandertal introgression data in sapien. Until the exact genetic mechanism can be determined, the following could be a motivating example, at the population level the correlation of PctNeand with OECD PISA maths score,

    PISAMath = +108.33*NeandPct +355.42; #n=27; Rsq=0.2923; p=0.003593 ** (V Significant)

  10. Yeyo says:

    Fascinating post, thanks Greg

    On the slow rejection of neanderthal DNA in modern humans and the reverse in neanderthals, morphological differences points to possibly quite large differences in methods of sustenance and survival strategies between the two (sub?)species. If that’s the case shouldn’t we expect an overall slow rejection of minority DNA with a few minor exceptions?

  11. deuce says:

    “Ernst Mayr, a prominent figure in biology had opined that hybridization was an unimportant factor in evolution, as far as I can tell for no particular reason at all. For equally mysterious reasons, people paid attention to him.”

    A typical Cochran killshot. One reason I keep coming back.

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  14. jovien says:

    One says simultaneously :
    1° There is a Neandertal admixture in every Eurasian population, so the admixture must have occurred before the AMH expansion out of the Middle-East.
    2° Neandertal admixture was adaptative to the different environments where AMH expanded.

    Is there not a latent contradiction in that ?
    Especially if one reads David Reich and sees the percentages of Neandertal admixtures : it is especially low in Europe (about 0,5%), and especially high in India, China (not far from 2%), SE Asia, with its peaks in New-Guinea and Australia (2%).

  15. jovien says:

    I got the numbers from David Reich book, fig.10, page 58, which gives Neandertal ancestry by percentages of 2% (the maximum for any present day population). New Guinea is almost 100% of these 2%, and Salomon Islands are 100% of these 2%, whereas European populations are at about one fourth of these 2%.

  16. jovien says:

    Excuse me.
    I have been misreading the figure for months…

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