Neandertal genome open thread

By Razib Khan | May 6, 2010 3:21 pm

My thoughts on the topic are pretty disjointed, and I can’t come up with a post that adds anything to what others have already said. And there’s still the primary documents to digest in full. So I’m going to open this post up to stray thoughts/comments (though try to keep it at least at the level of a Neandertal cognitively). Question: what other human evolution story is of the same order of magnitude in terms of significance? I think the last one of this magnitude was the Cann, et. al. “mitochondrial Eve” narrative of the mid-80s. Before that Lucy?

CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Neandertal Genome
  • http://blogs.discovermagazine.com/gnxp Razib Khan

    is it appropriate to refer to “neandertal-human mating” anymore? obviously no definitive “right” answer. but i’m leaning toward re-humanizing neandertals and shying away from using a term like “mating” as if it was a bestial affair.

  • biologist

    Anyone have links to the data and code?

  • http://lablemming.blogspot.com/ Lab Lemming

    I think the big question is whether our Neanderthal heritage is as inbred as our non-Neanderthal heritage. Do the 4% gene come from just a few individuals whose offspring were highly fit, or was interbreeding common throughout the interface of the two populations during the final Neanderthal contraction?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    the study implies that the assimilation seems to have been mostly middle eastern from what i recall. they gather that because all the eurasian groups seem to be of similar proportions, so it wasn’t as if there was dilution of the african signal as it moved into euro-neandertal territory. re: inbred, the african group from which eurasians descend was small, and went through rapid expansion. the neandertals of the middle east (northern mid east) were part of long resident groups, so probably had a greater amount of genetic variance on average than the incoming africans.

  • Konkvistador

    Haven’t Neanderthals “been human” for quite some time? I tought they wher classified as Homo Sapiens neanderthalensis?

    I hope this latest discovery helps us widen the term human to mean more than one species or subspecies instead of expanding the already clutered catogry of Homo Sapiens Sapiens (I’ve heard clasifications that put every hominid in the last 400 000 thousand years as “Homo Sapiens”, crazy).

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Email from friend:

    “Nows the time for a hot Neanderthal / modern romance movie

    Keira Knightley or Megan Fox would make a good Neanderthal.”

  • znz

    Wasn’t there a documentary about this subject?

    (No, not seriously. It’s a link to Clan of the Cave Bear.)

  • Pingback: The Neandertal Draft Genome « Anthropology.net()

  • http://drvitelli.typepad.com Romeo Vitelli

    So why have previous mitochondrial DNA studies ruled out any possibility of human-neanderthal interbreeding?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    john hawks believes that mtDNA of neandertals was subject to negative selection. IOW, mtDNA is not a neutral marker.

  • M-K

    Lines of mitochondrial DNA die out whenever a woman has no daughters, her daughters have no daughters, or die. If one strain of mitochondria contributes a survival advantage, it should eventually replace other, less advantageous variants. With Neandertals, we’re talking about small, scattered populations and tens of thousands of years–plenty of time for both the mtDNA and Y to be replaced, especial if the incoming population is large.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    mtdna is haploid, so it has smaller effec pop size. also lots of mutation in the hypervariable region. convenient in some ways, but not necessarily the best for a clock over a the long haul.

  • MK

    No surprise to those who have seen Nikolai ‘Beast from the East’ Valuev.

    http://www.thesun.co.uk/sol/homepage/features/2712511/Meet-Nikolai-Valuev-The-Beast-from-the-East.html

  • bioIgnoramus
  • MW

    I’m overwhelmed. A normal Science/Nature paper is like an extended abstract of a real paper, where the real paper is the ‘supplementary material’. This paper is 19 extended abstracts concatenated together. The supplementary material is 174 pages long! And that isn’t 150 pages of tables or repetitive graphs and 24 pages of text, it is only slightly more data-table-rich than expected of a scientific paper. (And I’ve only looked at the first paper so far.)

    Someone should have put their foot down and said “No, this should be at least a dozen independent papers.” It is almost enough to make one yearn for the old LPU* days before we started counting citations and impact factors.

    But I’m happy with the result. I was drawn reluctantly into the ‘no interbreeding’ camp by recent papers, but now I can return to my ‘Out of Africa with a little introgression’ happy place.

    * LPU = Least Publishable Unit – the practice of breaking research into as many papers as possible to increase one’s publication count.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    green is on science friday tomorrow
    http://www.sciencefriday.com/program/archives/201005072

  • http://www.rishon-rishon.com David Boxenhorn

    This solves a problem that I’ve long had with the Neanderthal introgression hypothesis: the Neanderthal genes that introgressed must have been advantageous, or at least neutral; so where are the Neanderthal pigmentation genes? Why did Homo sapiens have to re-evolve light pigmentation? Well, if the introgression occurred in the Middle East, maybe Neanderthal pigmentation was disadvantageous!

  • http://www.rishon-rishon.com David Boxenhorn

    OK. Here’s a question: I keep seeing things like, “this pretty much proves”; well, there is no last word in science, so let’s say that at some point in the future we discover that there is no Neanderthal contribution to our genome. What would we have to conclude about the present reports?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    there are less parsimonious explanations.

    http://dienekes.blogspot.com/2010/05/tales-of-neanderthal-admixture-in.html

    i agree that “this pretty much proves” is a touch retarded. though i think it comes close to falsifying out-of-africa + total replacement. the other scenarios are generally more complicated.

  • bioIgnoramus

    “there are less parsimonious explanations”: as my chum the biochemist likes to say “Nature does not shave with Occam’s razor”.

  • http://www.rishon-rishon.com David Boxenhorn

    I have a better explanation than Dienekes: When sapiens reached Eurasia it had a very small population size in comparison to neanderthals, so there was a significant degree of intermixture. By the time sapiens reached Europe, it had a large population size in comparison to neanderthals, so the additional intermixture was not significant. This is compounded by the fact that archaic humans, genetically similar to neanderthals, lived throughout Eurasia, further minimizing genetic differences between east and west.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    When sapiens reached Eurasia it had a very small population size in comparison to neanderthals, so there was a significant degree of intermixture. By the time sapiens reached Europe, it had a large population size in comparison to neanderthals, so the additional intermixture was not significant.

    this seems like a very parsimonious model, and it’s what i believe occurred too. or at least it’s what i believe to be the most likely model. from what little i know about paleoanthropology it seems that anatomically modern humans tarried for tens of thousands of years in the middle east in close proximity with neandertal groups. whatever advantage the moderns had, it wasn’t enough to break out of their biogeographic range, which moved north and south with the climatic regime. at some point ~50,000 years ago the pattern shifted. it is now that behaviorally modern humans, with some neandertal admixture, may have entered in a period of more rapid population expansion to europe and east into asia, finally marginalizing all the other archaic groups.

  • http://dienekes.blogspot.com Dienekes

    When sapiens reached Eurasia it had a very small population size in comparison to neanderthals, so there was a significant degree of intermixture. By the time sapiens reached Europe, it had a large population size in comparison to neanderthals, so the additional intermixture was not significant.

    If by the time they reached Europe they dominated Neandertals demographically, then there would have been substantial introgression of “modern” genes into European Neandertals, especially late ones as the ones DNA tested here. However, the authors reject this: “Thus, all or almost all of the gene flow detected was from Neandertals into modern humans.”

    Consider the analogy of Europeans demographically swamping North America. Sure, they picked up some Native American DNA, and their demographic dominance meant that admixture episodes barely changed the basically European character of North American whites. However, this demographic dominance also resulted in substantial European admixture in the natives (Amerindians).

    So, while you can postulate low late Neandertal->Modern introgression due to a numbers’ advantage, that’s a double-edged sword, because it would also result in high Modern->Neandertal introgression.

  • M-K

    Our DNA sample comes from Neandertals who did not share a range with HSS. (Some article or other said as much.) When we get samples from late western Neandertals we’ll be in a better position to tell if Neandertals eventually picked up HSS genes.

  • Sagat

    Does anyone know if there are any plans to sequence the DNA of Java man or any other ancient remains found in Asia and Oceania? I’ve read that there is some evidence pointing to a second interspecies mating in Asia. This would seem to account for some of the morphological variation in humans, especially in Australian Aborigines.

  • diana

    Let’s say this does bear out. What about the racial implications?

    “: “Those of us who live outside Africa carry a little Neanderthal DNA in us,” he said. Good to know.”

    Says the NY Times. Is it really “good to know”? Because if true then it’s Africans and “those of us who live outside Africa.”

    It’s naive to say that there are no racial implications. We should face them.

  • kcm

    Admittedly, it’s been some years since I studied Human Origins and Osteology, but if modern humans and Neanderthals produced fertile offspring than by definition they would have to be the have been the same species–however, morphologically, the differences between even upper paleolithic Moderns and Neanderthals is profound–Neanderthals even had thicker tooth enamel.

    There just seems to be too many practical problems with the mating scenario for it to have been likely, even if we were the same species–the widths of the modern female pelvis and the Neanderthal female pelvis, not the least among them (producing the same problems that face the cross breeding of lions and tigers–which can only succeed one way, lion father, tiger mother, producing a sterile liger); and the fact that females of any species tend to be highly selective in choosing mates. It seems improbable that modern females would willingly opt to breed with mates that would seem so “wrong” to them (and vice versa for Neanderthal females, who would presumably would place great store in physically strong mates, and unlikely be attracted to a puny, weakling modern male).

    Considering how strong the Neanderthal was in comparison to moderns, overpowering and rape by modern males of Neanderthal females seems unlikely to have been very successful on a widespread basis; whereas rape of modern females by Neanderthal males seems likely to have resulted in childbirth death due the aforementioned narrowness of modern female pelvises. Either way, interbreeding implies we acquired these genes–if in fact the they really are there– forcibly one way or another, which is hardly something to rejoice about.

    One thing I remember quite clearly from my studies in the early 1990s was how entrenched the two camps (the inter-breeders and the separatists) were–I would like to know which camp the authors of these studies where in. I will be far more willing to consider their results objectively, if I learn that they were anti-inter-breeders, as opposed to die hard Walpovians, before they interpreted their results.

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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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