Admixture between humans and the Others

By Razib Khan | April 20, 2010 9:32 pm

neanderthal-615Mr. Carl Zimmer points me to a new article in Nature, Neanderthals may have interbred with humans. The details within the article are more tantalizing, it seems to me, than the headline would imply.

The topline is this, researchers presented the following at the recent meeting of the American Association of Physical Anthropologists:

* An analysis of 614 highly variant loci, microsatellites, in ~2,000 people from diverse populations imply some variants which seem to be derived from human lineages outside of the mainline which led to the anatomically modern humans who left Africa 50-100,000 years before the present to settle the world. I assume there were “long branches” on the phylogenies of some loci, indicating that some of the alleles were “separated” from others for long periods of time so that recombination wasn’t able to dissolve the differences between distinctive haplotypes (if we’re all descended from a small African populations which expanded demographically less than 100,000 years ago the common ancestor of the variants should have a shallow time depth).

* The data imply two admixture events, one 60,000 years ago in the eastern Mediterranean, the other 45,000 years ago in East Asia. I think of this as a floor to the number of events. The latter one seems particularly clear in Oceanic populations from the reporting.

* African populations do not have the variants for these two admixture events (there hasn’t been that much back migration to Africa aside from north of the Sahara and the Horn of Africa. I assume that’s because Africans are well adapted to their environment, and outsiders are not).

In light of the recent discovery of a Siberian hominin which lived ~30,000 years ago, and was not a H. sapiens sapiens or H. sapiens neanderthalis, as well as the confusing but intriguing Hobbits of Flores, I think we can conclude that the the evolutionary genetic past was much more complicated than we’d assumed 10 years ago. Remember three years ago when there was a spate of research on a few genes which were suggestive of introgression into the human genome from Neandertals? There are other hints here and there which pop up in the literature over the years, some in Asia. But the methods being imperfect, and interpretation being somewhat an art, a consensus of Out-of-Africa + total replacement has been assumed to be a null. So we look at isolated results with some skepticism (I think this is justified).

So is this going to be met with skepticism due to reliance on the orthodox model? This section of the article is intriguing:

A test of the New Mexico team’s proposals may come soon. Svante Pääbo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced early last year that they had finished sequencing a first draft of the Neanderthal genome, and they are expected to publish their work in the near future. Pääbo’s earlier studies on components of Neanderthal genomes largely ruled out interbreeding, but they were not based on more comprehensive analyses of the complete genome.

Linda Vigilant, an anthropologist at the Planck Institute, found Joyce’s talk a convincing answer to “subtle deviations” noticed in genetic variation in the Pacific region.

“This information is really helpful,” says Vigilant. “And it’s cool.”

rupertTrying to glean what results Paabo is going to come out with is like reading tea leaves, but it is notable that a colleague at Max Planck seems to be excited about the results of this study. I do not get the sense that any of these results would reject the model that the overwhelming signal of ancestry in non-African humans is African. There’s a reason that mtDNA, later analysis of classical markers, and finally modern genomics (as well as cladistic analysis of skeletal features) imply that there was an Out of Africa event, whereby anatomically modern humans entered into a period of massive demographic and range expansion from a small ancestral group. But that does not preclude the assimilation of other groups along the way, and there is circumstantial evidence of sex between the Others and modern humans (the time of separation between various hominin lineages is on the low side in relation to various other taxa which can still produce fertile hybrid young).

A final point is that if these results hold up, one might look to Africa itself for other hybridization events. It may be that ancient hominin genetic variation is preserved in modern Africans as H. sapiens sapiens entered its period of expansion within that continent. Those signals may be currently obscured because the archaics in Africa were genetically more similar than those outside of Africa, and the African genome hasn’t been as well characterized as that of other populations in relation to its great diversity (remember the finding of new SNPs in the recent paper on Bushmen).

Image credit: National Geographic, Wikimedia Commons

CATEGORIZED UNDER: Evolution, Science
  • dearieme

    If I’m part Neanderthal, can I claim my ancestral bit of Germany, please? Or Spain.

  • coryy

    Okay. Very interesting. But why Ron Weasley?

  • J.J.E.

    Is the timing and/or location of the MRCA between humans and neanderthals preceding any putative admixture known?

  • dave chamberlin

    I wish and I hope that the pristine and undisturbed limestone caves from around the world have hundreds more pinky bones and molars of ancient peoples, and that the genetic analysis of these tiny fragments continues on it’s expotential growth curve. As of now southest asia is one big blank spot, stay tuned folks because I don’t believe it is going to stay that way. At last count 202 of 206 indentified neanderthal fragments have been discovered in limestone caves. Fact of the matter is except in rare circumstances bones turn to dust and stone tools suck. The experts in human evolution have always overstated their case in response to creationists and simply because they have to in order to make a living at what they love.

  • bioIgnoramus

    Pinkyphobe!

  • Katharine

    Well, Neanderthals are a different subspecies .

  • Billare

    That Neanderthal has some distinctly feline facial features…

  • http://mengbomin.wordpress.com/ Meng Bomin

    But why Ron Weasley?
    Probably the red hair. It’s a feature that Rupert Grint and I share with Neandertals, though if I remember correctly, the Neandertal mutation that led researchers to believe that some had red hair was different than the one that gives modern humans like Rupert and I red hair.

    EDIT: Here is the relevant John Hawks post.

  • MW

    I’ve been looking papers about at whether H. sapiens and H. neanderthalensis interbred recently, just out of interest.

    There’s a pop-sci article about Neandertal genetic sequencing in Science vol 323 pg 866 (13 Feb 2009.)
    A review showing no evidence of introgression: Hodgson & Disotell, Genome Biology, 9, 206 (2008) http://genomebiology.com/2008/9/2/206

    (This covers the ‘Ron Weasley’ question: a Neandertal gene for skin/hair colour has been sequenced and translated into protein, and shown to have similar effect to a modern European light skin/blond-red hair gene. Therefore we have evidence Neandertal were pale and blond/red haired. But interestingly, the mutation from the ancestoral form to achieve this in Neandertal is different from the mutation in Europeans. When the (presumably dark) H. sapiens migrated to Europe, they needed such a gene, and nicking it from the Neandertal by a bit of cross breeding would have been the easy way to get it – yet they got it the hard way instead, by independent mutation.)

    One of the ‘3 years ago’ papers mentioned above, showing evidence of introgression in the microcephalin gene:
    Evans et al, PNAS 103 18178 (2006).

    My, that’s a cute Neandertal in the Nature news story illustration.

  • coryy

    Great link, Meng. Thanks!

  • Eric Johnson

    > nicking it from the Neandertal by a bit of cross breeding would have been the easy way to get it – yet they got it the hard way instead, by independent mutation

    The hard way might not have been so hard, though. I think at least some of the MCR1 alleles involved in this are total loss of function alleles. In general for any gene, there are a vast number of different possible mutations that will yield total loss of function, therefore such mutations are pretty abundant. There are countless different changes you can make in any machine that will completely stop the machine from working.

    If you want something more precise, like you want MCR1 to change so that it functions precisely 34-38% as intensely, or has its expression go up exactly 2.1 to 2.2-fold after exposure to X amount of radiation in Y wavelength band, there will be only a few possible mutations that can do this. And you would probably have to wait around for quite a while, many generations, if you wanted them to crop up in your own (euro-sapiens) population. That’s the kind of allele that’d be more likely to be nicked from neanderthals (or from erectus if you are an early sapiens in Asia, etc).

  • Pingback: Neandertal genomics paper coming? | Gene Expression | Discover Magazine()

  • Pingback: Science in the News! 018 – Naughty with Neanderthals()

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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