Gene Expression

Neandertal & humans – introgression

i-46b4a2c5df014325a139097bc9a0db7f-introgression5.jpgI’ve been talking about introgression for a year right now. I’ve been waiting for the papers on this topic to come out, and the first has. If you haven’t, please read the posts from Greg and John Hawks. Another paper is on the way, and Hawks promises something within this week. I strongly suspect that the Paabo group also has something up their sleeves. As I noted earlier the paper from Lahn et. al. is open access, free to the public. Read it, it’s an elegant and compact piece of work, and I think they make a compelling case for introgression of an allele implicated in brain development from archaic non-African populations into the expanding proto-modern Out-of-Africa groups. The papers, and the commentary from Hawks and Cochran are pretty good, so I won’t make this long. To the left is a graphic that I yanked out the Lahn paper. Two issues:

1) the phylogeny of the gene, MCPH1, shows that the modal allele, D, in modern human populations seem to be a long branch with a deep coalescence with the non-D alleles. It seems to have “jumped” and “swept” through human (mostly Eurasian) populations 30-50 K BP after our primary ancestors left Africa.

2) The longer schematic shows a rough representation of the demographic dynamic at work. What you see are two operationally distinct populations which meet, and there was a crossover event (hybridization) and the allele slipped from the Neandertals (or other archaics) into the expanding populations from Africa which constitutes the overwhelming preponderance of our ancestry as evidenced by neutral markers and most of the autosomal genome.

And this is where 2s comes in. I mentioned last week that most beneficial alleles will go extinct, so multiple introductions are necessary. If you had an allele, say the D variant, within Neandertals, then each breeding event can be conceived of us a separate mutational event. The mathematical logic is clear: if the probability of fixation is 2s, then the probability of non-fixation is (1-2s), and if you conceive of the breeding events as isolated and distinct in time then the probability of non-fixation is (1-2s)n, where n = number of breeding events. To make it concrete, if you assume that the selection coefficient favoring a D variant was 1%, that is, 0.01, then the probability of non-fixation drops below 1% with 230 successful breedings. In other words, even with minimal levels of interbreeding beneficial alleles will spread. Neandertals were a highly successful human ecotype, in hindsight it should surprise us if there possessed many alleles which might come in handy for the soon to be Europeans who just arrived from Africa (MC1R?). But, the interesting possibility with MCPH1 is that archaic human populations outside of the main trunk of our ancestry might have been indispensible in shaping our own species!

Comments

  1. #1 Agnostic
    November 8, 2006

    The 2 John Hawks links aren’t clearly 2 separate links, since they are split by the row break. If you added a word or something to the line with “John” in it…

  2. #2 Mustafa Mond, FCD
    November 8, 2006

    I am reminded of the novel Dance of the Tiger by Bjorn Kurten, in which sapiens – Neandertal hybrids are smarter and more capable than either species. However, in the novel the hybrids are sterile.

  3. #3 razib
    November 8, 2006

    i read that too. i was skeptical about hybridization at the time, but i was a kid who didn’t know biology :)

  4. #4 Will Baird
    November 8, 2006

    Well, in some ways I am unsurprised by this. My aunt, Frances Borella, a PhD in physical anthro, iirc, did a protein study back in the early 1990s of the Basque population and found unique protiens in the blood that she attributed to interbreeding with Neanderthals. This was her dissertation at UC Riverside, iirc. She’s 150% a Wolpoffian.

    On the other hand, color me skeptical. There might be a good test. What about populations of H sapiens that were isolated prior to contact with the Neanderthals? And populations that were isolated afterwards but not a regular part of the Eurasian gene pool. The former might be the Aboriginals of Australia. The latter might be the NorAm Indians. Do these have the same genetic bits?

    Is this a good test of the theories of the origin of those genes? Or am I so completely off base that this might be a case of humiliating myself in public?

  5. #5 razib
    November 8, 2006

    And populations that were isolated afterwards but not a regular part of the Eurasian gene pool. The former might be the Aboriginals of Australia. The latter might be the NorAm Indians. Do these have the same genetic bits?

    yes. at least for the north am. the ozzies had to come through eurasia, though they might have swung by so fast that they missed ‘em.

    Is this a good test of the theories of the origin of those genes?

    look at the locus in ancient neandertal DNA. a better picture will emerge once we get a better conception of the genome in a few years….

  6. #6 Will Baird
    November 8, 2006

    yes. at least for the north am. the ozzies had to come through eurasia, though they might have swung by so fast that they missed ‘em.

    If the genes aren’t there, that gives us data too, ja? However, if they do have the genes, doesn’t that hint that the idea that they originated with the Neanderthals needs to be, perhaps, revisited?

    If the genes are not there for the NorAm native populations, what does that mean too? Speak in small words, I only work in HPC. ;)

  7. #7 razib
    November 8, 2006

    If the genes are not there for the NorAm native populations, what does that mean too? Speak in small words, I only work in HPC. ;)

    they’re there will. that’s what i remember off the top of my head. the only place they aren’t there that we’ve surveyed is sub-saharan africa :) re-read the original posts on the original papers.

  8. #8 Agnostic
    November 8, 2006

    Re: NorAm Indians, they’re my guess for the “living Neanderthals,” if you’ve been following Greg’s teases at GNXP to this effect. From the GNXP archive on Bruce Lahn:
    http://www.gnxp.com/blog/uploaded_images/MCPH1-37,000-722163.JPG

    The D-haplotype (the Neanderthal one) is at highest frequency in the indigenous American groups and Siberia (and, surprisingly, New Guineans). So, either one of the waves of Amerindians from Siberia were Neanderthal (Kenniwick Man), or maybe there’s something to the legends of Europeans sailing the Atlantic to the New World — if a Neanderthal allele helped spark the cultural revolution of cave painting, why not also in bold, cooperative exploration?

  9. #9 Bob3732
    November 8, 2006

    I read the paper from Lahn, et al, and I’ll apologize in advance for this scientifically illiterate question:

    How are we able to date the divergence of haplogroup D at 1.1 mya and the subsequent introgression at 37K years ago? Is there a direct method for this dating (ie, we can isolate & detect the haplogroup from the fossils themselves)? Or is it an indirect method (ie, haplogroup D produces the following measurable characteristics in skulls…they are present in fossil group A but not fossil group B)? I guess the better question is: What is the “interhaplogroup divergence test” the authors speak of? Where can I read more about it? And where do babies come from? (just kidding)

    As a layman, I’m fascinated by claims such as “Haplogroup D rose from a single copy approximately 37,000 years ago.” I just want to understand how the authors can pinpoint such a precise date.

    Thanks!

  10. #10 Bob3732
    November 8, 2006

    Disregard my earlier post…I found most of the answers to my question from John Hawks’ FAQ: http://johnhawks.net/weblog/2006/11/08#introgression_faq_2006

  11. #11 Melisande
    November 8, 2006

    I don’t see the requisite similarities between Native Americans and Neanderthals to make any sort of statement like “Native Americans” are the living Neanderthals.

    It isn’t surprising, given the various other challenges that molecular anthropologists are throwing up to the strictly Out of Africa theory, that an N-gene would pop up on our tree.

    I wonder how long it’s going to take for these “new” concepts to trickle into the consciousness of various academic participants. It’s great to have processes described succinctly by words like “introgression” (great word, great concept – needs a lot more P.R. for itself). I also like the clarity that I’m seeing in various blogs (and articles)about species and subspecies boundaries being more about relative isolation than about “can’t have sex with each other” or “do not produce viable offspring.” I very much like, and can make sense of, this view of species/subspecies (taxa in general).

    I sent the Hawks link to an older colleague (even older than me, and I’m pretty old) in the physical science, and he is going nutso on me, with the phrase:

    “Introgression is the transfer of alleles across species or subspecies boundaries.”

    It makes no sense to him, he’s outraged, how can that be, he says.

    It’s about time some bright people found a way to address this issue. I still haven’t heard from friends (to whom I sent the link) who are dyed in the wool “mtDNA uber alles” people. I think maybe this will get their attention.

    Anyway, what fun. The last three or five years almost make a person like myself (who is interested in the history of physical anthropology and its ideas) want to claim something like a paradigm shift, but it’s not neat and tidy enough to apply those kinds of Kuhnsian terms. These are interesting and exciting times.

  12. #12 razib
    November 8, 2006

    i like your name melisande…“winter is coming.”

  13. #13 Ed Harrison
    February 24, 2007

    Due to the geographics of Europe, & the highest % of Micro Encephlin gene integression in that population, I’ve developed the personal hypothisis that the Neandertal was a light skinned, red haired, blue eyed Humanoid. Other Homo Sapiens living in simular environments for more than 20,000 yrs did not develop these characteristics… take the Alutes as an example, or any northeast Asian population.
    Hawks, Trinkus & Lhan offer some intresting thoughts on interbreeding of the Neandertal, or Neandertal Sapien gene introgression.
    Obviously the 1.1 million old gene that appeared in Haplogroup D, 35-37,000 yrs ago in the mid east, and is almost non existant below North Africa, did not drop out of the sky.

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