Close encounters of the weird kind: Quick guide to the Neandertal genome

(Apologies to Current Biology).

Something like this probably happened, but with sex, too.  (Photo from Science.)

The genome of Neandertals was just sequenced (reference below).

For those who don’t want to plow through the long (but informative!) explanatory posts about the Neandertal genome that have appeared on several science websites, here’s a quick guide:

  • What’s the deal? A large group of scientists from several countries have determined the DNA sequence of most of the Neandertal genome.
  • Is it “Neandertal” or “Neanderthal”? Either is correct. “Neanderthal” is most common but the new Science paper uses “Neandertal.”   The name is taken from the German “Neander Tal”, or “Neander Valley,” where the first bones of these individuals were found.
  • So who were Neandertals?  They were an extinct group of humans who lived in Europe from about 400,000 years ago until about 30,000 years ago, when they seem to have gone extinct without leaving any descendants.  Their lineage diverged from that of all modern humans several hundred thousand years ago, so they were not our direct ancestors. Our real ancestors appear to have spread out from Africa to Europe and Asia in a migration event beginning about 100,000 years ago. Current Biology published a nice “quick guide” to Neandertals in 2006.
  • Were they members of species different from ours? Neandertals are usually classified as being a subspecies of ours, Homo sapiens neanderthalensis, so they’re usually considered members of our own species. Most biologists regard species as groups that are not capable of exchanging genes with other such groups. Since Neandertals now appear to have hybridized with “modern” H. sapiens and produced fertile offspring, this might suggest that they’re in our species. My own species concept, however, allows for some small amounts of gene flow between species, and given the low level of gene exchange between the two groups and the fact that they appear to have lived side by side in several areas without fusing into one species, I’d say that Neandertals were members of a different species, or at least of an “incipient” species. This is to some extent a semantic issue.  The two groups may have had cultural aversions to cross-mating, which count as “reproductive isolating barriers” similar to those separating species of birds who don’t hybridize because they have different appearances or songs.
  • What about their genome? Sequencing the genome of this group is a stupendous achievement.  The workers took DNA from the bones of three individuals (all females) from a cave in Croatia; these females lived about 40,000 years ago.  Although the DNA extracted from their bones was highly contaminated with bacterial DNA and slightly contaminated with modern human DNA, the researchers managed, with many controls, to sort out the Neandertal DNA and sequence it.  Good sequence was obtained for about 2/3 of the genome, and was compared to sequences from modern humans living in Africa (2 samples), France, China, and Papua New Guinea.
  • What does the DNA show? First, that Neandertals seem to be a bit older than we thought: their lineage diverged from ours about 825,000 years ago (this is a very rough estimate based on a “molecular clock”).  Second, there are some interesting genes that appear to have evolved faster in our lineage than in the Neandertal lineage (we can tell this because we can compare both genomes to that from our closest living relatives, chimps).  These 78 faster-human genes include those involved in skin pigmentation, sweat glands, sperm motility, as well as genes that, in modern humans, carry mutations associated with Down syndrome and schizophrenia.  Perhaps selection leading to modern humans, then, acted on skin traits and cognitive abilities.
  • What else? The finding that has gotten the most attention is that some “old” genes from Neandertals still persist in human populations.  These shared human-Neandertal genes are found in the French, New Guinea, and Asian samples of modern humans but not in the African ones.
  • What does this DNA sharing mean? Most likely that there was some hybridization between Neandertals and “modern” humans after our ancestors left Africa but before they had spread throughout Asia and the Pacific.  In other words, the genome of those modern humans not from Africa carries a trace (about 1%-4%) of DNA that “introgressed” from Neandertals. This is surprising because, based on earlier sequencing work of Neandertal DNA from the cellular organelle mitochrondia, there was no evidence of mixing between H. sapiens and H. sapiens neanderthalensis populations. This led to the idea that Neandertals went extinct without leaving any descendants or DNA. In light of the new findings, that’s probably wrong.
  • Hybridization!  Does that mean that Neandertals interbred with the ancestors of modern humans? Probably!  But there’s one other explanation that we can’t rule out: perhaps the “Neandertal” genes in modern non-African humans are simply genes that are very old and were present in the common ancestors of both modern humans and Neandertals. These then could have been transmitted to Neandertals and non-African humans, while the ancestors of modern Africans simply did not get a sample of those genes. (Note that this does not mean that, evolutionarily speaking, modern non-Africans are more closely related to Neandertals than to modern Africans!) The “differential sorting” scenario seems unlikely to me because it involves special pleading about a non-random distribution of genes between proto-human populations that occurred well before our lineage diverged from that of Neandertals.
  • Why the attention about hybridization? People are fascinated by the possibility that several different species (or subspecies) of humans could have successfully mated with each other.  We already knew that, over our evolutionary history, there have been times when several hominin species lived at the same time and roughly at the same place (as I recall, there could have been as many as three or four species of hominins living at the same time in some parts of Africa).  But in none of these cases do we have evidence for interbreeding.  The new work shows that this probably did occur between two hominin “species”.  This fascinates people for one reason, I think: sex.  It conjures up pictures of hairy, beetle-browed Neandertals shagging individuals that looked much more like us.  And indeed, that’s probably what happened.  This scenario evokes all sorts of primal emotions, and I predict a new genre of internet porn involving human/Neandertal encounters!  But that shouldn’t completely distract us from what is a truly remarkable achievement: our own ability to reconstruct the genome of our extinct relatives by grinding up their bones, extracting the DNA, and using really sophisticated methods to determine the proper sequence of millions and millions of DNA nucleotides.  Think about how amazing that is!
  • Now that we have a Neandertal genome, can we make them by cloning? No.  We don’t have enough DNA, and even if we did we don’t have the technology to package it into chromosomes, or put it in the proper order with the proper surrounding elements. And if we could do those things, we’d still have to inject the Neandertal chromosomes into the egg of a modern human female, and that’s both hard and ethically dubious.
  • Where can I find out more? You’ll find longer but not-too-technical descriptions of the Neandertal work in pieces by Ann Gibbons at Science and Carl Zimmer at The Loom.

___

Green, R. E. et al.  A draft sequence of the Neandertal genome.  Science 328:710-722.

40 Comments

  1. artikcat
    Posted May 7, 2010 at 7:39 am | Permalink

    Sex between those two guys? Scary and loud, probably

    • mk
      Posted May 7, 2010 at 1:32 pm | Permalink

      And failing miserably in passing on the genes just discovered! ;^}

      • Sili
        Posted May 7, 2010 at 5:22 pm | Permalink

        But lossy fun, I’m sure.

  2. Posted May 7, 2010 at 7:40 am | Permalink

    The ‘thal’ vs. ‘tal’ comes from a German spelling reform. When the first Neanderthal was discovered in the 19th century, the proper spelling of the German word for ‘valley’ was ‘thal’; the spelling was later changed to ‘tal’.

    • Torbjörn Larsson, OM
      Posted May 7, 2010 at 8:55 am | Permalink

      Yes, that explain the confusion but not “the name”, which you seldom change due to a spelling reform. At least not without asking the owner. 😀

      So it is not really a name, but a convenient handle.

    • Posted May 7, 2010 at 8:59 am | Permalink

      Right. The English cognate is “dale”.

      Unlike in English, older works of German literature (Goethe etc) tend to be printed in modern spelling, thus the transformation from Neanderthal to Neandertal is expected, (interesting: the spell checker in this blog doesn’t like the spelling without the “h”) even though these days even in Germany and probably even in the Neandertal itself (which is in the western part of Germany in the big urban conglomeration of Essen, Düsseldorf, Dortmund etc) it is probably more used as a proper noun referring to the cavemen than to the valley itself.

      • Posted May 7, 2010 at 9:02 am | Permalink

        I added my reply before I saw the previous one (i.e. we were writing at the same time). The “Right” applies to the original comment. However, my explanation, by good luck, addresses the second comment!

      • artikcat
        Posted May 7, 2010 at 10:17 am | Permalink

        Curious I checkedthe status of the spelling in situ, this is what I got regarding driving there;
        Autobahn A 46
        Wuppertal-Düsseldorf, take the exit towards Haan-West, drive on until you reach Hochdahl, and then follow the signs “Neandertal” and “Neanderthal Museum” respectively.

        Autobahn A 3
        Köln-Oberhausen, take the exit towards Mettmann, drive on until you reach Mettmann-Zentrum, and then follow the signs “Neanderthal Museum”.

    • artikcat
      Posted May 7, 2010 at 7:48 am | Permalink

      that is a different species

    • whyevolutionistrue
      Posted May 7, 2010 at 7:52 am | Permalink

      Ha! I didn’t remember that, but I’ve now linked to it above. In return, would you dudes at Current Biology please get some good book reviews? Your current book review section is thin and lame! 🙂

  3. artikcat
    Posted May 7, 2010 at 8:16 am | Permalink

    In “La guerre du feu” (1981, Jean-Jacques Annaud: also, The Bear, Black and white in color)a Neanderthal Ulam tribe man- and pressumably a sapiens girl -engage in “surprising” and advanced sexual divertementos-I mean the guys are having modern sex 80,000 years ago. The movie is based on the 1911 novel by J-H Rosny aine. Some prescient vision.

    • artikcat
      Posted May 7, 2010 at 8:20 am | Permalink

      I forgot to mention,in the same movie, another Neanderthal tribe ate roasted sapiens (those were the bad guys-I mean the neandies- still dont know why).

    • Posted May 7, 2010 at 9:12 am | Permalink

      In English, the film is called “Quest for Fire” (the original French title would be “The War of the Fire”). It is actually quite good (as a film, though keep in mind that it is based on the science of 100 years ago). Their is now understandable dialogue. The female lead role is played by Rae Dawn Chong (nude for most of the film), daughter of comedian Tommy Chong (of Cheech and Chong fame).

      • Posted May 7, 2010 at 9:13 am | Permalink

        “no understandable dialogue”, of course (at least to most viewers)

        • Posted May 7, 2010 at 9:15 am | Permalink

          Aarrgh! “There is no understandable dialogue” is correct. 😐

      • artikcat
        Posted May 7, 2010 at 9:23 am | Permalink

        Quite accurate dont you think? Considering. (well the roasting and other details aside)

  4. NewEnglandBob
    Posted May 7, 2010 at 8:19 am | Permalink

    I do hope that there will be more DNA sequencing of Neanderthal bones beyond the three individuals that were sequenced for this study.

    We may never be able “to package it into chromosomes, or put it in the proper order with the proper surrounding elements”, but we can learn more about differences and similarities and it could help us determine the path of Homo sapiens sapiens.

    • artikcat
      Posted May 7, 2010 at 9:40 am | Permalink

      Is DNA full complement packaged in chromosomes needed for cloning?

  5. Tim
    Posted May 7, 2010 at 8:31 am | Permalink

    Their lineage diverged from that of all modern humans several hundred thousand years ago, so they were our direct ancestors.

    you mean, “so they were NOT our direct ancestors”, right?

    • whyevolutionistrue
      Posted May 7, 2010 at 8:35 am | Permalink

      Good catch! I’ve corrected the typo. Thanks.

  6. Steve
    Posted May 7, 2010 at 8:31 am | Permalink

    “Their lineage diverged from that of all modern humans several hundred thousand years ago, so they were our direct ancestors.” If they “diverged”, how can they be direct ancestors? Small point maybe, but…..

    • whyevolutionistrue
      Posted May 7, 2010 at 8:35 am | Permalink

      it was a type (see above).

  7. Posted May 7, 2010 at 8:32 am | Permalink

    I think Gene Simmons has already cornered the dot com market concerning Neandertal porn. Sahelanthropus objectification is next.

  8. Gingerbaker
    Posted May 7, 2010 at 8:45 am | Permalink

    Does science have the technology to be able to discriminate between a Neandertal and a three-weeks-without-a-shave Mel Brooks?

    • NewEnglandBob
      Posted May 7, 2010 at 9:14 am | Permalink

      Yes, a ruler. Mel Brooks is short. 😉

      • Sili
        Posted May 7, 2010 at 5:25 pm | Permalink

        And I don’t think Neandertals speak much Yiddish.

  9. Torbjörn Larsson, OM
    Posted May 7, 2010 at 9:09 am | Permalink

    their lineage diverged from ours about 825,000 years ago (this is a very rough estimate based on a “molecular clock”).

    Now I’m weirded out.

    First, both papers seem to give a separation age of “between 270,000 and 440,000 years ago”. The first paper supplement describes this as the “Neandertal-Yoruba population divergence time”. That would be the lowest bound on lineage divergence, wouldn’t it?

    Second, the same supplement section gives the “Neandertal-Yoruba genetic divergence time” as between 734,000 and 1,087,000 years ago.

    Nowhere do I find a lineage diversion time of 825 000 years. The mean time, FWIW, seems to be 910 000 years ago. The same supplement also gives mtDNA lineage divergence between 250,000 and 650,000 years ago.

    So what gives the rough estimate? And why isn’t the population divergence the more interesting event/measure?

    • whyevolutionistrue
      Posted May 7, 2010 at 9:16 am | Permalink

      P. 713 of paper in section called “Average DNA divergence between Neandertals and humans.” To wit: “Assuming an average DNA divergence of 6.5 million years between the human and chimpanzee genomes, this results in a point estimate for the average divergence of Neandertal and modern human autosomal DNA sequences of 825,000 years.”
      I may not be understanding things here, but the words seem pretty clear.

  10. Sven DiMilo
    Posted May 7, 2010 at 10:24 am | Permalink

    mutations associated with Down syndrome

    ? Does this mean alleles that cause gene-dosage problems from trisomy?

  11. oldfuzz
    Posted May 7, 2010 at 11:25 am | Permalink

    “Most biologists regard species as groups that are not capable of exchanging genes with other such groups. Since Neandertals now appear to have hybridized with “modern” H. sapiens and produced fertile offspring, this might suggest that they’re in our species.”

    This tidbit is part of the fundamentalist Christians problem, unwittingly reinforced by the partially informed evolution adherents, myself included. My conclusion w.r.t the term species has been one of whether it is a classification system, a definition or both. I now see it as both with room for modification as new information is discovered.

    The few creationists I know view species as distinctly separate biological entities, hence evolution is impossible.

    My challenge is to remember that biology is an evolving science with much to be discovered and many current ideas to be altered.

    Thanks for this post.

    • artikcat
      Posted May 7, 2010 at 11:37 am | Permalink

      It has been a long time since species is considered a “reproductively closed” population: humans with humans, horses with horsas, with room to wiggle. Blue whales with humpbacks for example.

  12. Posted May 7, 2010 at 11:41 am | Permalink

    I know this is a gross oversimplification but I’m glad our ancestors “Made Love Not War.” The prospect of a genocide in our distant past always saddened me. Assimilation of a population by a somehow dominant population of humans is somehow easier to understand.

    I know you’ve said that the mitochondria acts like a single gene in that it is inherited as a single unit. So the non-neandertal miochondria some how had a selective advantage? Is this common in other species that have introgressed genes?

  13. mk
    Posted May 7, 2010 at 1:25 pm | Permalink

    So the relationship of “modern” humans and Neandertals was more like bonobos and chimpanzees… or wolves and coyotes… or like great danes and chihuahuas?

    Thanks.

    Also,I liked John Hawks post on all this: http://johnhawks.net/weblog/

  14. Posted May 7, 2010 at 2:27 pm | Permalink

    The difference between nuclear and mitochrondial DNA results suggests that Neandertal males had sex with human females, but human males did not have sex with Neandertal females… or at least the results of such couplings are not represented in the modern human population for some reason.

    Why that might be so is a lovely subject for fact-free speculation, which is another reason why people find this stuff interesting.

    In any case, thanks for the excellent summary of the findings.

    • artikcat
      Posted May 7, 2010 at 4:11 pm | Permalink

      where did you get this from?

      • Posted May 7, 2010 at 4:46 pm | Permalink

        Where did I get which from? I’m just reasoning about the data.

        Specifically, the difference between mitochondrial and nuclear DNA results is in the blog post above: “In other words, the genome of those modern humans not from Africa carries a trace (about 1%-4%) of DNA that “introgressed” from Neandertals. This is surprising because, based on earlier sequencing work of Neandertal DNA from the cellular organelle mitochrondia, there was no evidence of mixing between H. sapiens and H. sapiens neanderthalensis populations.”

        But mitochondrial DNA is only passed on from the female line. Eggs have mitochodria, sperm do not. Google “mitochondrial eve” if you want some background and references on this. All of your mitochondrial DNA is from your mother. None is from your father.

        Ergo, one explanation of the absence of introgressed mitochondrial genes in the face of introgressed nuclear genes is that Neaderthal males had viable offspring with human females, but not the other way around. Therefore humans today would have no female Neanderthal ancestors, and thus no Neanderthal mitochondrial DNA, while at the same time having male Neanderthal ancestors, and therefore Neanderthal nuclear DNA.

        Furthermore, this hypothesis is testable, maybe, by looking at the differences in frequency of Neanderthal genes on the X and Y chromosomes, versus both each other and the non-sex chromosomes, although exactly what those differences would be I’d have to think about a good deal more.

        • artikcat
          Posted May 7, 2010 at 6:59 pm | Permalink

          I think you read too much unto the scant data. Gret imagination though.

  15. Dar McWheeler
    Posted May 9, 2010 at 8:50 am | Permalink

    I suspect that they will find Neantertal genes in people of the Far Right

  16. Rick
    Posted May 19, 2010 at 4:56 am | Permalink

    Is it Neandertal or Neanderthal?

    I was curious about this many years ago and came up with this: It’s Neanderthal and pronounced “tall” because there is no “th” phoneme in German.


7 Trackbacks/Pingbacks

  1. […] https://whyevolutionistrue.wordpress.com/2010/05/07/quick-guide-to-the-neandertal-genome/ […]

  2. […] share Neanderthal genes was announced. Jerry Coyne talks about the initial announcement here and provides us with a rough guide here. From the second link: Were they members of species different from ours? Neandertals are usually […]

  3. […] https://whyevolutionistrue.wordpress.com/2010/05/07/quick-guide-to-the-neandertal-genome/ […]

  4. […] […]

  5. […] Tomorrow’s Science will have a series of freely available papers on the Neanderthal genome. One claim is that that between 1% and 4% of the DNA of certain modern groups is attributable to hybridization between Homo sapiens and Neanderthals. Carl Zimmer, John Hawks & Jerry Coyne have more. (Update: Coyne has a handy-dandy guide to the paper here.) […]

  6. […] the end of his piece Carroll cites the recent discovery that the genome of modern humans carries a small amount of DNA from Neanderthals.  This suggests (although there is dissent) that humans coming out of Africa in our most recent […]

  7. […] and by the way, remember: the «as much as 4% of our genes» coming from Neandertals is only true for people of European & Asian descent. If you’re African, you should be pure Homo sapiens. […]

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