The Jermyn Program

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With the detection of Neanderthal admixture in Eurasians (Green et al), evidence for two admixture events in an upcoming paper from Jeffrey Long’s group (probably Neanderthals and erectus), and analysis from Jeffrey Wall and Vincent Plagnol suggesting that some African populations (Pygmies and Bushmen) admixed with other archaic populations, it seems that we are on the verge of a new paradigm.* In the picture, anatomically modern humans arose in East Africa and then spread globally – but mixed (to a degree) with the archaic humans that already already occupied most of the Old World.
Of course this is the surprise-free prediction, much more plausible than total replacement, which would have required an unlikely biological incompatibility.

Admixture at the few-percent level would have given most favorable archaic alleles a good chance of reaching high frequency in modern human populations, and some must have done so – alleles that conferred regional adaptations, and perhaps some that had general advantages. Svante Paabo thinks, or any rate says, that this Neanderthal admixture probably didn’t have any biological significance, but he’s almost certainly wrong.
This pattern has been seen in some other invasive species: the cosmopolitan species assimilates favorable alleles from local sister species. Resistance is futile.

There may be more in the pipeline: The Max Planck people have that strange finger bone from the Altai, and if it’s a good-enough sample, they could run the same general analysis and check for admixture from that archaic population, whoever they were. And there’s a possibly-significant line in their Science paper, concerning Wall and Plagnol’s high estimate (14%) of archaic admixture in Europeans:
“almost an order of magnitude greater than our estimates, suggesting that their observations may
not be entirely explained by gene flow from Neandertals. ” Maybe from somebody else?

*Mike Hammer and others have also been saying this.

22 Comments

  1. from late march:
    http://www.newscientist.com/article/dn18699-meet-xwoman-a-possible-new-species-of-human.html

    Pääbo and his team are hesitant to speculate too much about X-woman’s nature until they obtain DNA sequences from the nuclear genome’s 3.1 billion letters. That project is already under way, and the first results should come within months. Pääbo’s team will likely want X-woman’s genome to answer the same questions they are asking of the Neanderthal genome, which is due for publication soon.

  2. Greg,

    Your still thinking about this in a “multiregional” context. Ironically, the one thing this pattern of admixture is not is multiregional. Remember that Oceanic peoples share as much Neandertal ancestry as Europeans. There is no regional continuity. Consequently you shouldn’t really expect locally adaptive alleles to introgress.

    And for what its worth, none of the locally adaptive genes that we know about introgressed from Neandertals. Europeans and Neandertals both had light skin for example, but modern Europeans went the long way around and evolved it independently. Why didnt it introgress? Well, because the admixture did not happen in Europe where light skin would have been advantageous!

    Microcephalin was thought to be the best candidate (erroneously in my opinion) but it did not introgress from Neandertals. MAPT either.

  3. The ~2% Neanderthal mixture may be the same over Eurasia, but that number applies to the genome as a whole – mostly neutral. The action is in the coding and regulatory area, a small fraction of the overall – there we don’t know the impact of admixture.
    As for none of the skin color genes introgressing from Neanderthals, how do you know?

  4. This is the only science that could support it’s own gossip columnist. Hominid Hints from Heloise.

  5. I seem to recall reading somewhere that Dr. Cochran had speculated about a relict Neanderthal population in Europe, or perhaps had a guess about the population which had the most Neanderthal gene introgression. If I recall correctly, he refused to specify which population, because his Neanderthal interbreeding hypothesis wasn’t even seriously considered at the time. Does anyone remember this? Would the good doctor care to weigh in, now that his hypothesis is moving closer to the mainstream?

  6. Greg,

    Are you referring to this paper by Hammer on Homo Habilis in East Asians, based on Chromosome X analysis?

    Or is there a newer study coming out?!

  7. Yes, that paper, but the candidate source group was homo erectus.

    I suggested that there might be a Neanderthal-derived host cell line infection in humans: more plausible now, since we clearly had intimate contact with Neanderthals.

    On that same note, I would suggest that Chris Stringer’s notion that Neanderthals died out just before anatomically modern humans showed up seems less likely in view of the recent results on admixture, if we discount necrophilia. I am reminded of the paleontologists who have suggested that the dinosaurs died out just before the asteroid hit, and those have argued that the American megafauna died out just before the paleoIndians showed up. There is some common thread to those arguments – and I don’t believe that it’s Occam’s razor.

  8. Occam’s hair extensions, the finest in improbably lush, attractive hair customized so it’s right for you.

  9. Greg,

    Well, we know for certain that MC1R evolved convergently in Neandertals and Europeans. However, the European version isnt clearly selected. It might rather be the absence of purifying selection driving the loss of function.

  10. Multiregional origin of modern humans has always been appealing. Instead of total replacement theory like out of Africa, constant gene flow with local adaptation actually is more reasonable.

  11. “Multiregional origin of modern humans has always been appealing. Instead of total replacement theory like out of Africa, constant gene flow with local adaptation actually is more reasonable.”

    It may be more reasonable but it doesn’t appear to be what happened. Multiregional evolution has always been about regional continuity. There is no regional continuity with this pattern of admixture. Europeans are surprisingly not particularly closely related to Neandertals.

  12. Greg

    Bruce Lahn went looking for genes that 1)exress themselves in fetal and infant brain development
    and 2) have spread very quickly throughout the human population. This seems to me to be a fascinating scientific angle to pursue. Unfotunately in science it would seem the meek have inherited the earth.I would love to hear your opinions on this matter.

  13. gcochran asks: “As for none of the skin color genes introgressing from Neanderthals, how do you know?”

    For example, there’s this paper: “A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals”
    http://www.sciencemag.org/cgi/content/abstract/1147417

    Given that we know many of the alleles affecting pigmentation in modern humans, and we have the genome of some Neanderthals, it should be easy to look for matches. If there’s a pigmentation allele present in both Neanderthals and non-African humans (but rare/absent in Africa) it would seem likely that we got it from the Neanderthals or they got it from us.

    Different mutations for the same phenotype (e.g. red hair) would suggest convergent evolution, rather than gene flow.

  14. Multiregional evolution has always been about regional continuity. There is no regional continuity with this pattern of admixture. Europeans are surprisingly not particularly closely related to Neandertals.

    The apparent skeletal continuity in Europe is predominantly with early Upper Paleolithic Europeans, not later populations. We don’t know whether Upper Paleolithic Europeans had more Neandertal than later people, but given the evidence of substantial mtDNA replacement in Europe since the Mesolithic, I think it is a reasonable hypothesis.

    As to East Asia, we don’t yet know how much contribution the recent populations may have had from the prior inhabitants. Yet.

    After the last week, I think that an attitude of less certainty might be in order…

  15. “The apparent skeletal continuity in Europe is predominantly with early Upper Paleolithic Europeans, not later populations.”

    So then these early Upper Paleolithic folks were completely replaced or at least contributed no genes to later Europeans (at least not the fraction of the genome containing the Neandertal admixture)? Where is the continuity in that scenario? I can’t see any reasonable scenario that looks like regional continuity in Europe. As you point out, East Asia is more suspect.

    “given the evidence of substantial mtDNA replacement in Europe since the Mesolithic, I think it is a reasonable hypothesis.”

    I think it a reasonable hypothesis too (but I note the irony of you basing it on mtDNA).

    “After the last week, I think that an attitude of less certainty might be in order…”

    I fully agree.

  16. What are the prospects for estimating admixture in populations in regions of the world where archaic fossils would not be well preserved, or preserved at all (e.g. the tropics…)? Are there ways to ferret out evidence of admixture without having the genome of an archaic population to refer to?

  17. Evan, you asked: I seem to recall reading somewhere that Dr. Cochran had speculated about a relict Neanderthal population in Europe, or perhaps had a guess about the population which had the most Neanderthal gene introgression.

    My guess would be he meant the Basques.

    The live close to the last known site of Neanderhtal occupation in Europe, they have unusally high levels of RH negative and Type O blood. Some have linked this to Neanderthals who aslo lack a Rhesus factor as well as type A or B blood.

    I’m not convinced and I don’t think their facial features do not resemble Neadnerthals any more than other modern Europeans.

  18. My guess is that he never said anything about a relict Neanderthal population in Europe – but what would I know?

  19. I think he eventually revealed that by “surviving Neandertals” he was referring to this.

  20. “What are the prospects for estimating admixture in populations in regions of the world where archaic fossils would not be well preserved, or preserved at all (e.g. the tropics…)?”

    The prospects are very poor. Attempts have been made in Sri Lanka to retrieve DNA from remains that are only a few thousand years old. No luck. DNA degrades rapidly in tropical environments.

    “Are there ways to ferret out evidence of admixture without having the genome of an archaic population to refer to?”

    There are indirect ways, but they all involve assumptions that are open to criticism. Ironically, the best assumption is to use the reconstructed Neanderthal genome as a proxy for the genomes of other archaic populations in Asia and Oceania. These other archaic groups were probably more similar to the Neanderthals than to modern humans.

  21. at cold harbor it was reported that they said that the denisova hominin is closer to neandertals than modern humans
    http://en.wikipedia.org/wiki/Denisova_hominin

  22. Of course some populations might have been descended from the first erectus expansion, about 2 million years ago, and thus genetically distant from both AMH and Neanderthals.

    As for the technical difficulties with degraded ancient DNA, we’re getting somewhat better at it.

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