Croatoan

There is a new article out on the genome of the Altai Neanderthal, found in the same cave as the Denisovan. The authors find clear signs that this population of Neanderthals had some admixture with modern humans, roughly 100k years ago, or perhaps a bit more. That’s a twist, especially considering that the main migration of modern humans out of Africa is thought to have occurred roughly 65-70k years ago.

There was an earlier expansion of anatomically modern human out of Africa: the Qafzef-Shkul skeletons, around 125-90 k years ago, in Israel – probably this occurred during the last interglacial. As the climate cooled, Neanderthals returned to the area. Humans didn’t yet have the moxie required to beat out archaic humans on their own territory, and the Qafzeh-Shkul population is usually thought to be a dead end.

Maybe it’s not as simple as that. Those Altai Neanderthals had to pick up those genes from someone – maybe it was from the lost colony, Qafzeh-Shkul. Apparently there is another paper coming out suggesting that there’s a touch of ancestry from a separate human expansion, roughly that old, in New Guinea

Another point: in that Altai Neanderthal genome, there seems to be some adaptive introgression of modern human variants (FOXP2, for example), while at the same time, you see a lower amount of human introgression in regions of the genome under strong purifying selection – much the same pattern as we see with Neanderthal introgression in modern humans. This is strong evidence that this purging effect is mostly due to incompatibility between very different groups (dawning species), rather than genetic load in the smaller populations. Which we knew couldn’t have had the nasty effects suggested in those earlier papers, since archaic humans like Neanderthals and Denisovans didn’t lose rapidly when they first encountered modern humans.

Meta: a high-quality ancient genome contains an enormous amount of information (billions and billions !): it’s not like any other kind of fossil. You can figure out interesting properties of a population, including a lot about its history, from the genome of a single individual. Although there have to be limits: the Chinese have more Neanderthal admixture than Europeans (about 1.2 times as much) – and maybe they picked up the extra from a different Neanderthal population – maybe those Altai Neanderthals. So they might carry a tiny amount of genetic material from those Qafzef-Shkul types: but this way lies madness.

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55 Responses to Croatoan

  1. MawBTS says:

    You just reminded me of that Harlan Ellison story where he chases an aborted fetus flushed down a commode.

    Aren’t the Qafzeh-Skhul remains thought to be part Neanderthal? They have the brow ridges and facial profiles, plus there’s confirmed Neanderthal remains in nearby caves dating from around 120,000-90,000 years ago.

  2. Fascinating, and probably totally incomprehensible to 80% of social scientists who, if they think about these findings at all, must regard them as impermissible. THAT is the way that madness lies.

    • AnonymousCoward says:

      I suspect that they wouldn’t mind that much, if it was just the Chinese. Othering the Chinese is somehow not equally triggering.

  3. IC says:

    With advance of scientific technology, more and more evidences (data) can be found. After all, science is hypothesis modification until all evidences fit.

    It has been my intuitive feeling based on the modern world: Human migration is multidirectional, bidirectional, but asymmetric. Thus human gene flow should be similar pattern in the past. Long-term asymmetric gene flow will result in introgression change (or even total replacement) in one of two population with bidirectional exchange.

    This concept of human genes flow also fits Fisher evolutional idea. Constant reshuffling of human genes through admixture and introgression would create most adaptive combination for various human environment. Let nature environmental (or social like agriculture development) selection pressure choose the most fit combination (or admixture) for particular region or condition.

    • IC says:

      Science is hypothesis modification until all evidences fit.

      This concept of science also fit other area. Early human believed geocentric universe basic on simple personal experience or evidence by looking at sky. Copernicus heliocentrism is hypothesis modification due to some unfit evidences. Galileo scope provided confirming evidences for heliocentrism. Newton theory (hypothesis) provide explanation for how heliocentric system work until new evidences demanding for its modification. Then you have Einstein new hypothesis trying to explain things that Newton theory could not. Seeking new evidences to confirm Einstein crazy ideas lead to new research effort. Last one is the discovery of gravitational wave in recent report, which confirmed all hypothesis of Einstein. Advance of technology is critical factor in the whole process.

      With new discoveries and evidences of human ancestors and our own genes, the picture of human evolution will be far more complicated than originally concepted.

    • IC says:

      When people still stubbornly embrace a hypothesis that is proven wrong with new evidences, this hypothesis has become a faith(or religion).

    • IC says:

      To further clarify my thought on gene flow.

      Human genes flow is certainly dependent on human migration. But quantity of gene flow is not equal to quantity of migrants. Human migration might brought new genes into new place. If most new genes are not very adaptive fit for new environment. These genes are unlikely to stay long and remains in population.

      On the other hand, if small number migrants carrying new genes far more adaptive in new environment, (example farmers colonization vs native hunter-gatherers in fertile land), these more adaptive new genes can quickly spread and take roots.

      Survival of the fittest (genes) is the rule.

  4. et.cetera says:

    The way I’m reading these findings, claiming that there live among us members of at least 2 human subspecies is a lot less preposterous than before. But that’s preposterous in itself so, where am I going off track here?

    • peppermint says:

      a subspecies is a population that you think has sufficient behavioral or physical differences from another population to be called a subspecies. The word has no technical significance, so there’s no reason to breathlessly italicize

  5. Flinders Petrie says:

    It sure makes sense that there would have been early gene flow from AMH’s to Neanderthals, given the Levantine fossil record. The folks at Qafzeh at 100 kya seem to be very similar to the South African Klaises River Mouth folks around the same time, both physically (anatomically modern), and culturally. Although there has been much effort to pin ‘behavioral modernity’ on these early AMHs, their material culture was nearly indistinguishable from Neanderthals. The folks at Klaises were making some interesting backed microliths, but this tradition was lost and afterwards there was nothing in Africa that screamed “modern” until well after Neanderthals were genocided in Europe.

    Besides beads and ochre (which Neanderthals also used), the lithic assemblage at Qafzeh at 100 kya was the same Levallois industry that Neanderthals were using. So like you said, these early AMH’s didn’t seem to have the moxie to replace Neanderthals yet, who ran-off the AMHs from the Levant at 60 kya, taking back their territory.

    But suddenly there was a whole new breed of AMHs at ~45 kya. They traveled in large groups and knew how to party: they left huge trash piles in caves, had feasts, played music, and liked to carve images of dangerous animals and naked ladies. They basically flash-mobbed the Neanderthals out of existence.

    The big question is where the groups of AMH 2.0 came from. There’s not a trace of them in Africa. The earliest evidence is possibly at Ksar Akil in Lebanon at around 45 kya, but the excavations were problematic (early 20th-century methodology). It’s clear that they entered Germany (at Geissenklosterle) just before 40 kya. But from where? The best clues are in material culture, and all of the lithic industries that show a local, organic transition from the Middle Paleolithic (Neanderthals) to the Upper Paleolithic (AMH) from 50-40 kya in Central Europe, Eastern Europe, and the Levant.

    It seems to me that things will become real interesting when we stop considering Neanderthals and Anatomically Modern Humans as homogenous groups. Clearly, the AMHs at 40 kya were very different than the Klaises-Qafzeh-Skul people over 50,000 years prior. Behaviorally for sure, and probably genetically. Also, the French Neanderthals were maybe quite different than those in Siberia.

  6. IC says:

    To make this topic fun for everybody (except morally correct people), did STDs help the mating with Neanderthals?
    In last topic, I speculated that STDs might make infected sluttier (reduced pickiness or standard for sex mate). Infected Sapiens might found Neanderthals very sexy. Vise versa. If so, STDs contributed to human evolution. Maybe infected people even likely to make out with animals. Who knows.

    Is there any chance to find the evidence of STDs in human fossils? Retrovirus can imbedded in human genomes. HIV is retrovirus and STD. But Herpes virus is not. Certain strains of HPV can incorporated into human genomes also. If DNA can be recovered in fossil tissue other than bones, there is chance of discovery.

    Have fun:)

    • sprfls says:

      I really don’t think you need anything extra to explain males having sex with females.

    • IC says:

      The two unnamed (German) individuals say they are sexually attracted to animals.
      http://www.bbc.com/news/world-europe-35611906
      I wonder whether they have STD infections. Gay germs (proposed by Greg Cochran) might be just different (variant) expression with standard STDs. As we know, same germ can cause different expression or symptoms in different individuals. This infection might be direct or congenital through mother. Sluttyness (reduced threshoold) and promiscuity are the outcome of infection for mind-control STDs. For some, the threshold for sex is so low that they can mate with anything including animals. Just hypothesis here. Evidences (data) are needed to prove or disprove this hypothesis.

      But infected people are fearless ones who might change the history as brave warriors or slutty sex with unthinkable. Human history or evolution is shaped by bugs. Free will might not free at all. We might not be better than poor zombie (arthropods lost their mind to parasites infection.)

      (Parasites That Mind-Control Their Hosts)
      http://news.nationalgeographic.com/news/2014/10/141031-zombies-parasites-animals-science-halloween/

      • peppermint says:

        yes, bugs have an incentive to cause slutty behavior that harms the ability to have children survive to reproduce

        no, bugs do not have a chance at making children survive to reproduce more

      • IC says:

        On sex drive
        “Gay men tend to have more sex than straight men,”

        http://www.thedailybeast.com/articles/2010/07/20/sex-statistics-who-does-it-the-most.html

        On promiscuity
        “28% of homosexual men had more than 1000 partners:”
        https://carm.org/statistics-homosexual-promiscuity

        Both evidences support the hypothesis (not truth yet) of STD-controlled behavior to increased sex drive and reduce sexual discrimination in gays. It would be interesting find out about statistics of men who are sexually attracted to animals.

        I am not saying STD infection always produce gays. Majority of infected only exhibit increased sex drive and reduced standard for heterosex (less picky). Only small percentage of infected become gays. Even less become bestials. Just like physical disease: Only small percentage women developed cervical cancer in HPV infection. But HPV is true cause of cervical cancer. Before HPV etiology understood, all kind crazy ideas or hypotheses existed for cervical cancer like hygiene or men’s foreskin ect due to simple associations.

        • peppermint says:

          Yes, gays have sex with more women than straights.

          This is totally consistent with gays being caused by an STD trying to infect more people, but it is also consistent with being a “beta” strategy of men who believe that they would be better served by that reproductive strategy than trying to compete to get married and raise children like an “alpha”.

      • IC says:

        Most gays are actually bisexual. So watching out those women claiming:”He is just a friend and gay”

        Well, he might be a friend of benefit also.

  7. Ilya says:

    Dr Cochran, I assume you meant “purging” instead of “urging”?

  8. sprfls says:

    ‘Moxie’ is such a great term; completely underutilized today.

    I wonder if this concept could be measured psychometrically, or modeled as a combination of existing personality and other constructs.

  9. epoch2013 says:

    Nice explanation of Lake Mungo man’s mtDNA.

  10. This one friend of mine, owing to a complicated series of events, finds himself with just two choices for a wife. One is a Neanderthal woman. (I know, I know, Neanderthals are supposedly extinct. But it turns out – long story – that the space-time continuum is more permeable than you might think.) The other is his first cousin. Which of these is a worse bet genetically? In other words is outbreeding depression with a Neanderthal worse than inbreeding depression with a cousin? With a niece? Or don’t we know the numbers that well yet?

    My friend is a regular anatomically modern Homo sapiens, just like me.

    • Flinders Petrie says:

      The cousin would probably be a safer bet. Some recent studies suggest that modern humans and Neanderthals had evolved separately so much that their offspring were almost not viable. They suspect that the male offspring were infertile.

      So you’d have to get to the level of Tutankhamun’s inbreeding (brother and sister, or generations of first cousins) before approaching that kind of genetic risk.

      • gcochran9 says:

        I doubt if the male offspring were infertile. Slightly reduced fertility, maybe – and, if that’s caused in part by their different Y chromosome, that’s enough to explain why we don’t see any of their Y chromosomes today.

        • TWS says:

          They have trouble finding bison that don’t have some hybridization with domestic cattle. If those two can wind up genetically mixed anything can.

        • jamesd127 says:

          “I doubt if the male offspring were infertile” Coastal Australian aboriginals (the same species as Tasmanian aboriginals and Mungo Man) remained separate and distinct from mainland aboriginals despite inhabiting the same continent for tens of thousands of years indicating severely reduced fertility when crossbreeding with mainlanders. They became extinct in part because of near zero fertility when crossbreeding with whites.

          Neanderthal/early modern crossbreeding was probably even worse than white/tasmanian crossbreeding or mainlander/Mungo Man crossbreeding.

        • jamesd127 says:

          PC truth, based on two selected paintings, is that tasmanian aboriginals were gracile. They were not. Their skulls were similar to Mungo man, and their interfertility with modern type humans, while sufficient allow for some gene flow, was near zero. This likely provides us with a model of human/neanderthal gene flow.

          • gcochran9 says:

            “was near zero.” Nonsense.

          • jamesd127 says:

            James Bonwick was there, saw what was in front of his face, saw the Tasmanians disappearing, and wrote a book about it “The lost Tasmanian race.” He tells us it was rare for half caste children to be born “even under the most favorable circumstances”, indicating dramatically reduced, but non zero, fertility.

            So, according to a contemporary eyewitness who studied the matter, near zero interfertility.

            Everyone who claims descent from a Tasmanian aboriginal and has genealogical evidence for it claims descent from an aboriginal woman who was clearly a mainlander, not a Tasmanian, which suggests that the native Tasmanian population had precisely zero introgression into the white population – certainly mighty close to zero. While there are vague claims of descent from the sealer hybrid population, no one has any real evidence of descent from the sealer hybrid population, which while it existed reproduced at far below replacement.

            Also, Tasmanian aboriginal skulls simply do not look human. They look pretty similar to Mungo Man. http://blog.jim.com/science/tasmanian-aboriginal-skull/ Just looking at images of female Tasmanians, my genitals do not think that is something I could breed with.

            • gcochran9 says:

              None of this is true.

              VD can run rampant in virgin populations and is quite efficient at causing infertilty. Fertility crashed in Hawaii, after contact.

              It would be easy enough to tell if any given person was descended from the Tasmanian natives: they would have chunks of DNA with a unique signature, at least somewhat different from mainland aboriginals.

              As for their skulls looking nonhuman, I know a physical anthropologist who was looking at a Tasmanian skull last time I gave him a call: funny that he has never noticed this. It’s a lie.

              You might want to be more careful about your facts.

          • AnonymousCoward says:

            James: sauce or it didn’t happen.

        • Flinders Petrie says:

          Interesting, thanks for your input. Do you think that Reich is stretching when he says that Neanderthals and AMH were at the edge of biological compatibility?

          Also, it’s my impression that we know a lot more about the Neanderthal genome and we do about ancient AMH genomes (>40kya). Am I off-base here? If this is the case, is there any suspicion that humans today are a lot different genetically than, say, the AMH burials at Qafzeh? Maybe even nearly as different as we are to Neanderthals?

          • gcochran9 says:

            I would say that Neanderthals and AMH were just starting to be biologically incompatible, from what I know. Small incompatibility disadvantages have had 2000 generations to play out.

            At last report, we don’t have any really ancient DNA from Africa. We have lots more Neanderthal skeletons, and Europe is cooler than Africa, which seems to help with DNA preservation.

            Those Qafzeh skeletons differ from contemporary humans, but then everything that old does. They certainly don’t look as different as Neanderthals. As for how genetically different, we don’t know. I believe that people have tried to get aDNA from them, but at last report, no joy.

        • Flinders Petrie says:

          Part of me suspects that the physical anthropologists make a judgement call about a skeleton, based on where the measurements fall within a range of (overlapping) variability, and then whatever category they choose (AMH, Neanderthal) is taken for granted by the geneticists, and everyone else for that matter.

          Have you heard of Manot cave? A sealed cave only recently opened in Israel with a MP to UP sequence, and an AMH cranium dating to 55 kya. Exciting! Svaante must be chomping at the bit to get his hands on it, if he hasn’t already.

        • epoch2013 says:

          On what grounds do you doubt that the male offspring was infertile?

    • dearieme says:

      Depends partly on whether his first cousin is a woman.

    • Flinders Petrie says:

      Plus, Neanderthals were very precocious, so she’s going to look just like her mom by the time she’s 16.

      • TWS says:

        Just how often will she need a full body wax too? I’ve heard that they were rather hairy. I’d go with the cousin. More chance your kid won’t need special classes and mom can help them learn to read.

    • IC says:

      “My friend is a regular anatomically modern Homo sapiens, just like me.”

      Pure homo sapiens are Africans. Everybody else are hybrid with neanderthals. Do you imply you and your friend are African?

      To preserve racial purity of Sapien stock (ideological reason), yes marry other Africans. To follow biological instinct without ideological motivation, marry whoever he feels right.

      Got feeling that you might not be african. But when you refer others as neanderthal, you imply yourself as pure Sapiens (Africans).

  11. Question says:

    Dr. Cochran,

    An off-topic question: you have said that if GWAS find 100 genetic variants affecting IQ and their distribution is well correlated with phenotypic IQ between populations in similar environments, then they should provide rock-solid evidence of genotypic differences.

    A reviewer of a manuscript making that argument gave the objections below. Do the objections hold up or modify your earlier take?

    “Reviewer #1: I recommend the rejection of this manuscript without opportunity for revision. It does not meet the very high standards for demonstrations of natural selection acting to differentiate modern human populations that have been set by recent publications (Turchin et al., 2012; Robinson et al., 2015). Here I will only detail a few of the manuscript’s shortcomings.

    The authors do not address the possibility that the GWAS results of Rietveld et al. (2013) are contaminated by confounding (cognition- or education-affecting environmental variables that happen to be correlated with genetic variation). Although the original publications of the SSGAC deal with this issue to some extent, they do not come up to the standards set in the papers that I have cited in the previous paragraph. Furthermore, one research group with control of an extremely large family cohort is currently working on a manuscript documenting that years of education is subject to a very peculiar form of confounding. Until these results are published and well absorbed, any naive inferences regarding the basis of racial differences should be regarded with skepticism.

    The authors also do not address the issue of ascertainment bias. A GWAS of Europeans is more likely to detect SNPs with high minor allele frequencies. The minor allele is usually the derived allele, and thus the use of SNPs ascertained to have low p-values in a GWAS of Europeans will lead to an overrepresentation of SNPs with high derived allele frequencies specifically in Europeans. If the derived allele tends to have a positive effect (as the authors claim), this is certainly an issue that needs to be carefully addressed.

    True, it may be that ascertainment bias is less of an issue when all SNPs regardless of p-value are used to construct a polygenic score. But the extrapolation to non-European populations is still problematic because the accuracy of the polygenic score declines in such populations as a result of differing LD patterns (Scutari et al., 2015). An example will make this clear. Suppose that two SNPs in perfect LD in Europeans have quantitatively close positive reference betas. Now suppose that in a different population the SNPs are uncorrelated, the reference allele at the causal SNP has a somewhat higher frequency, and the reference allele at the tag SNP has a much lower frequency. Then the inference made from comparing the polygenic scores of the two populations is exactly the opposite of the truth. We can conclude from this that the use of polygenic scores to infer the causes of intercontinental differences requires much more care than given to it here.

    Because stabilizing selection (favoring the “golden mean,” as the authors put it) also eliminates genetic variation, higher dispersion of allele frequencies across populations is by itself not diagnostic of directional selection.

    The fact that a large fraction of the enhancing alleles reported by Rietveld et al. (2014) SNPs are derived does not mean very much. First, as it is likely that many of the SNPs are not causal, the relationship between derived alleles at different polymorphic sites must be addressed. Second, even if it be assumed that these are the causal SNPs, it is not necessarily the case that an association between derived status and a positive effect points toward selection increasing the mean of the trait. Such selection can actually lead to the opposite association (between derived status and a negative effect) at certain allele frequencies.

    A general comment is that the appropriateness of much of the hypothesis testing in this paper is difficult to judge. The stochastic model justifying a particular statistical test is usually unclear. Is the source of randomness inaccuracy in the GWAS estimates? The inherent stochasticity of evolution?

    Robinson, M. R., Hemani, G., Medina-Gomez, C., et al. (2015). Population differentiation of height and body mass index across Europe. Nature Genetics, 47, 1357-1362.

    Scutari, M., Mackay, I., & Balding, D. J. Using genetic distance to infer the accuracy of genomic prediction. arXiv:1509.00415.

    Turchin, M. C., Chiang, C. W. K., Palmer, C. D., Sankararaman, S., Reich, D., GIANT Consortiu, & Hirschhorn, J. N. (2012). Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nature Genetics, 44, 1015-1019.”

  12. Matt says:

    There’s a hint of a puzzle to me, here, as to why Sap introgression to Neanderthal should make it in the Altai, and not in European Neanderthal.

    Paleoclimate? Central Asia prior to 100,000BC is somehow an environment with relatively higher fitness for AMH vs Europe. Or possibly the interbreeding happened somewhere else, where Sapiens actually was more competitive with Neanderthal (West Asia?), and worked its way into Central Asia via deme-deme flow that excluded European Neanderthal (http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/fabre-2009-population-structure-mtdna-neandertals.html).

  13. I love to speculate on the Neanderthals but what we really need is more freezing cold caves that hold tiny fragments of hominid bones. This Denisovan cave has a year round temperature of 1 degree above freezing. It is a refrigerator. The genetic preservation of the few bones from there place is simply amazing. We know that the Tibetans have a gene from the Denisovans so there must have been a large population of them up yonder in the high elevations in Asia where there are plenty of frigid caves waiting for careful and thorough excavation. We only have one piece out of 500 in the puzzle of who lived in Asia before the moderns got there and cleaned the place out. I never bought the “out of Africa” theory, although I know it is mostly true because there is more genetic diversity in Africa. But it seems likely that when hominids gained enough smarts to go everywhere they went everywhere and I would place that out of Africa event way way back in time, more like 2 and a half million years ago. After that it was a braided stream party where diverse populations moved hither and yon and were nearly as obsessed with sex as we are.

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