Neanderthals are us– More evidence

by Greg Mayer

Alert reader daveau has drawn my attention to a  manuscript (abstract only; BBC story here) posted on Science’s website by Laurent Abi-Rached and others on the genetic evidence for interbreeding between anatomically modern Homo sapiens and earlier Eurasian Homo (Neanderthal man, and a related group, the Denisovans.) Jerry and I have addressed this issue earlier here at WEIT here and here.

The story so far is that study of ancient DNA has shown that Neanderthals contributed a few percent to the nuclear genome of modern Eurasian populations (but not African), and that a previously unknown population of archaic humans, the Denisovans from Siberia, has contributed a slightly higher percentage of the genome of Melanesians. There are two new developments, both discussed by Ann Gibbons in a news article (abstract only) in Science, in which she reports on a conference hosted by Russian researchers held at the fossil sites (including Denisova) in southern Siberia. First, Australian Aborigines, like Melanesians, derive about 5% of their genome from the Denisovans. Second, Abi-Rached and colleagues have looked at three loci involved in the immune response (HLA loci), and found a much higher proportion of Neanderthal/Denisovan contribution at these loci. Over half the alleles had an archaic origin, and they reached frequencies of over 50% in some modern populations.

Tree showing interbreeding, via BBC

Abi-Rached et al. attribute this to interbreeding between anatomically modern humans coming from Africa, and the resident archaic populations (Neanderthals/Denisovans) of Eurasia. Why would the immune loci show much stronger influence than the genome as a whole? Immune loci are highly functional, and subject to strong selection. Diversity of alleles is selectively advantageous at immune loci, so that heterozygotes resulting from interbreeding would be favored, and the particular alleles of archaic humans, who had been in the Eurasian environment for a long time, might also be favored.

John Hawks of the University of Wisconsin, Madison, finds this a plausible interpretation, and favors it himself. But he does raise some cautions. Because these loci are subject to strong selection, some of the alleles may have been maintained in human populations for a long time, without any need for interbreeding to introduce them into anatomically modern humans. And one of the alleles that Abi-Rached et al. think shows archaic influence, HLA-B*73, wasn’t actually found in any of the archaic individuals studied. (This is not as bad as it sounds– HLA-B*73 is closely associated with linked alleles that are in the Denisovan.) He has some other cautions, and his full account is well worth reading.

So where does this leave us? Mostly wanting more data, especially from more archaic individuals, but the conclusion Jerry and I (and John Hawks) came to still stands, and is in fact now slightly firmer: Neanderthals, and Denisovans, are us.

(As an aside, it is unclear to me if the posting by Abi-Rached will eventually appear as a paper in Science or not. It is not one of the posted-just-before-publishing posts, since it has not been formatted for publication, and at nine pages it’s longer than what Science usually publishes. There are also 45 pages of supplemental text, with 26 extra figures– if they think they have a monograph, they should publish a monograph! As John Hawks dryly put it, “bibliographic information not yet available“. Science has had some bad experience lately with posting things they intended to publish, but then things didn’t work out as well as they hoped. I’m not suggesting there’s anything wrong here, just that this odd state of not knowing if or when a manuscript will be published is not something to be encouraged.)

20 Comments

  1. Posted August 29, 2011 at 7:01 am | Permalink

    Fascinating! Thanks!

  2. Darth Dog
    Posted August 29, 2011 at 8:34 am | Permalink

    So Adam was a Neanterthal and Eve was a modern human. My wife would say that explains a lot.

    • Orlando
      Posted August 29, 2011 at 2:14 pm | Permalink

      I would say that there is extant evidence of neanderthals: it just that they now call themselves Republicans.

      • Dominic
        Posted August 30, 2011 at 1:13 am | Permalink

        How dare you insult Neanderthals!

  3. Margaret
    Posted August 29, 2011 at 8:49 am | Permalink

    So where does this leave us? Mostly wanting more data, especially from more archaic individuals…

    Ken Ham? Tea Partiers? There are lots of archaic individuals here in the USA to choose from.

  4. Tom Mankins
    Posted August 29, 2011 at 8:51 am | Permalink

    Finally, this explains my bulbous nose, gnarly teeth and desire to club small animals to death.

  5. Sidd
    Posted August 29, 2011 at 9:09 am | Permalink

    Perhaps I am being paranoid, but I fear the social implications of Neanderthals. There have always been racist theories saying that such-and-such race possesses “special” genes which make it superior. Thus I am a little disappointed that the “We are all Africans” response to racism (I love that T-shirt) becomes less forceful in light of this evidence, since we are not all Africans to quite the same degree as previously thought.

    • Chris Granger
      Posted August 29, 2011 at 9:26 am | Permalink

      One would have to determine what all of the
      ‘special’ genes do, and decide if they made one superior, or merely different. It’s all about adaptation to an ecological niche anyhow, so ‘superior’ depends on a lot of factors that might have been relevant then but not so much today.

      Even so, we do all share common ancestry, even if the “we are all Africans” response ultimately gets binned like the Adam & Eve fairy tale has been.

      • Orlando
        Posted August 30, 2011 at 6:41 am | Permalink

        Well, 50% of Americans have an IQ below 100; put differently, a below average intelligence. And polls indicate roughly 50% of Americans consider themselves conservative. Coincidence? Perhaps.

    • Margaret
      Posted August 29, 2011 at 9:47 am | Permalink

      The Neanderthals would have been the result of an earlier migration out of Africa, so we are still all African in ancestry.

      • Sidd
        Posted August 29, 2011 at 11:10 am | Permalink

        Some of us have a lesser proportion of ancient ancestors who lived in the geographic location of Africa. I don’t see how you could interpret “not all Africans to quite the same degree” as “not all Africans”.

  6. daveau
    Posted August 29, 2011 at 9:32 am | Permalink

    I hadn’t realized that Denisovians had been covered here before. I guess it takes a couple of passes to sink in. I’m intrigued by these archaic populations, and how nothing in our evolution is as straight-forward or as simple as I once thought.

  7. Joe Dickinson
    Posted August 29, 2011 at 10:58 am | Permalink

    Even if there is no doubt that modern humans share alleles with an archaic population like the Denisovians, it seem risky to say we inherited those alleles from that population. Isn’t it at least as likely that we and Denisovians simply have some common ancestors, very possibly at a very different time and place than the known Denisovian population?

    • Posted August 29, 2011 at 2:01 pm | Permalink

      Well, sort of. Merely sharing particular traits with anything doesn’t necessarily mean we came FROM them, as much as it proves we at least are related. However, this is easily determined as a matter of degree. For instance, one could compare the DNA of a child to a father, and if it were summed up by saying that they merely share DNA, then all that would be proven is that the child and father are related somehow. However, by comparative analysis, it’s very easy to tell the difference between a child and a father, compared to, say, a child and a cousin or any other distant or removed relative. It’s merely a matter of degree. I do, however, respect your skepticism, and it’s never a bad thing to question anything. More research certainly needs to be done, but the research that is done is most certainly conclusive.

      • Joe Dickinson
        Posted August 29, 2011 at 10:10 pm | Permalink

        I’m thinking of an analogy with the fossil record where, I believe, it is generally accepted that it is problematic to claim that any given ancient species is ancestral to any particular extant species. It is safer to say that the ancient specimen is related to the ancestral lineage rather than asserting that it is in the direct line. After all, most lineages ultimately go extinct.

        • whyevolutionistrue
          Posted August 30, 2011 at 7:52 am | Permalink

          Deeper in the fossil record this is a reasonable precautionary interpretation (although one that can be oversold). But in this instance, the history is so recent, and the genetic evidence so rich, we should be able to distinguish between interbreeding ca. 40K years ago vs. descent from an ancestral polymorphism 100K plus years ago. These are some of the alternatives John Hawks discusses in his post on the matter.

          GCM

    • Alice Wonder
      Posted November 14, 2013 at 7:22 pm | Permalink

      Old old thread, I know, but there is a good argument for it coming from introgression rather than common ancestor.

      Namely, these alleles do not exist in the sub-saharan population of Homo sapiens.

      When an exit from Africa happened, only a subset of the gene pool went with them, so populations farther away have less genetic diversity.

      Given that these populations with less diversity have alleles not present in their ancestral population but that are present in other homonids, the most likely explanation is that they entered via introgression.

  8. Scott
    Posted August 29, 2011 at 2:02 pm | Permalink

    I think we are even more wonderful than we once thought. Whatever the allels, we survived to mate. We are all africans,and we all can act like neanderthals. We are now a Neanderthal and Human mixture. How awesome is that!

    • whyevolutionistrue
      Posted August 30, 2011 at 7:45 am | Permalink

      We’re a mixture, but it’s a human and human mixture– Neanderthals are people, too.

      GCM

  9. Torbjörn Larsson, OM
    Posted August 29, 2011 at 2:06 pm | Permalink

    Thanks for the update!

    A well balanced post. Since more diseases stems from within a population than from without, at least for humans AFAIK, I am suspicious of portraying is as a one-sided benefit: “getting these genes by mating would have given an advantage to populations that acquired them.” [BBC]

    Who knows if no association at all would have been more beneficial? Along those lines bloggers note that humans are coping with a lot of autoimmune disease, and wonders if the introgressed genes were less suited to integration with the previous genome. What would WEIT readers say?

    But post facto, more evidence for crossbreeding is good.


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  1. [...] recent data indicates that modern man interbreed with other species – such as Neanderthal (about 100 thousand years ago) or even earlier African species (about 700 thousand years ago) – [...]

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