A Draft Sequence of the Neandertal Genome

A Draft Sequence of the Neandertal Genome

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

To cut a long story short…

The authors suggest that non-Africans having about 1-4% Neanderthal ancestry is the most likely explanation for the variation in the DNA they have found. It’s not an absolute. A much less likely but not impossible scenarios is that the variation is due to population structure in Africa prior to the OOA, which may relate with the earlier separation of the ancestors of modern Africans and non-Africans inside Africa, although John Hawkes thinks this is so unlikely he was surprised they gave it space on the paper.

But, considering the number of genes in non Africans that have a time depth that is considerably older than the OOA movement (over 1 million years on one in one study by Hammer et al), and I think there is now decent evidence for Neanderthal ancestry in non-Africans.

I have some issues with the paper. Modern humans were in the near East about 120k ago, keeping company with Neanderthals for many millennia, but the interbreeding date comes out at 80,000 to 50,000 years. What were they doing with the rest of the time?

Such a scenario is compatible with the archaeological record, which shows that modern humans appeared in the Middle East before 100,000 years ago whereas the Neandertals existed in the same region after this time, probably until 50,000 years ago.

  And they observe that modern Europeans don’t seem to have a higher amount of Neanderthal ancestry than anyone else. But then they add:

 This possibility can be addressed by the determination of genome sequences from pre agricultural early modern humans in Europe (85). It is also possible that if the expansion of modern humans occurred differently in Europe than in the Middle East, for example by already large populations interacting with Neandertals, then there may be little or no trace of any gene flow in present-day Europeans even if interbreeding occurred.  

Which is what I suspect is more likely. I’d also like to address the apparent lack of modern human ancestry in the Neanderthals: well a quick look at the dates of the remains sampled; not younger than 38,000 BP. Which is prior to the date modern humans started to move into that part of Europe. Possibly a future investigation of later dated remains would show some AMH ancestry in them, as their appearance suugests they may be hybrids. I think the  Lagar Velho specimen would be a possible source, although it would be a pity to damage the specimen, possibly the Gorham’s Cave bones could yield relevant information.

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8 responses to “A Draft Sequence of the Neandertal Genome

  1. If modern humans mated with Neanderthals in one time and place why would they not do so at other times and places?

    • Beats me Tod. But my observation that no woman is that ugly when you’re desperate seems to have held up.

  2. “when you’re desperate”

    Is there an example of a prey animal hybridizing with a species that it preys on.

    Although Jane Goodall said she saw a chimp male mating with a baboon female, chimps only hunt infant baboons.

    There is evidence that humans preyed on adult Neanderthals who being comparatively slow, clumsy and unable to throw spears were unable to fight back efectively; so they would have been desperately avoiding humans. Neanderthals would be terrified of humans, like a bonobo would be terrified of a chimp in the wild.

    No human could have mated with a ‘wild’ Neanderthal, they’d get parts of their anatomy bitten and twisted off.

    It could be that infant Neanderthals were sometimes kept as a pets after their parents were hunted and occasionaly stayed alive long enough to mate with humans – < 10 years, they matured fast – and that the mating of a non-pet Neanderthal with a human never took place. That would explain why the genes flowed one way; the offspring all were born into a band of humans.



    • Tod, they’ve stated that Nenaderthals were within the range of modern human variation, and that there do appear to be hybrids prior to this paper. This means that they can’t really have been that different.

  3. …i think that’s especially true in the russian
    riverine where kostenkij=kost(rus)=bone
    (mammoth area/moscow time zone)=ko(s)t=
    cotona(N)=pinch/wound=cut(E). 40k bc
    bone sewing needles=naedl(OE)=nettles
    have been found there. fish diet in the riverine
    would produce healthy mothers and babys
    of neander cross. there is really no such thing
    as ugly when it comes to women. if i may be
    allowed to say so, it’s feeling.

  4. Peter Frost and Dienekes are skeptical on the recent findings of Neanderthal-Human copulation. In his anthropology blog, Dienekes writes:

    “…red flags to the tale of Neandertal admixture that has appeared in the media:
    1.The uniformity of alleged Neandertal admixture outside Africa is suspect, given that Neandertals were a West Eurasian species
    2.The observed pattern of Neandertals being closer to non-Africans than to Africans can be well explained by structure in Africa itself, a point which the authors concede (as their Scenario 4), but which has received zero play in the media which -as usual- have jumped on the more easily digestible (“caveman sex”) explanation.
    Now I want to address another major red flag that I hinted at before, namely the direction of gene flow, if gene flow did in fact occur between modern humans and Neandertals.

    The authors reject that gene flow into the Neandertals took place; I immediately got suspicious of this claim because it is not consistent with what we know from historical cases of contact.
    Whether it is Europeans meeting Native Americans, Yayoi meeting Jomon, or Bantu farmers meeting Pygmy hunters, the story is always the same: the dominant intrusive population ends up with admixture from the native one, but admixture goes both ways.
    If modern humans and Neandertals interbred, then there is absolutely no reason to think that “we” got Neandertal genes, but “they” didn’t get ours. To think that requires extra assumptions, e.g., that modern-Neandertal kids were shunned by Neandertal societies, i.e., that Neandertals were a sort of prehistoric Samaritans that practiced strict endogamy. I find that hard to believe.
    There is an alternative explanation for why no modern admixture in Neandertals would be detected, namely the early age of the bones tested in the paper, which are from Europe and date from the Early Upper Paleolithic, when modern humans had not yet arrived in Europe. It is worthwhile to consider this explanation:
    If admixture occurred primarily in Europe itself, then we would expect Neandertal admixture to be higher in modern Europeans or Caucasoids. But we don’t see that at all, so, unless we postulate that Papua New Guinean and Chinese ancestors reached their final destination with a detour through Europe after 40ky or so, we can safely conclude that Neandertal-modern admixture was earlier and occurred in the Middle East.
    So, we have a population of moderns and Neandertals mixing in the Near East. According to the authors’ scenario, episodes of admixture between the two species gave “us” enough Neandertal admixture that was carried by our (modern) ancestors throughout the world, creating a fairly uniform (but small) component of “Neandertal” ancestry.
    But, why wouldn’t the (modern) admixture in Near Eastern Neandertals also be carried a couple of thousand km into Europe? In short: we are supposed to think that Neandertal admixture in modern humans made it to the ends of the earth, but modern admixture in Neandertals could not move a short distance from West Asia into Europe. The explanation of pristine European Neandertals presented in the paper just doesn’t fly in the context of the authors’ broad model.
    It is also worthwhile to consider the actual genetic argument for no modern-to-Neandertal introgression. This goes something like this: we observe closer proximity between modern non-Africans and Neandertals than between modern Africans and Neandertals. This can be explained by either Neandertal-to-non-African gene flow or vice versa.
    The authors observe that modern non-Africans are closer to Yoruba than to San. They argue that if Neandertals had modern non-African admixture, then they would also be closer to Yoruba than to San. But, they observe that they are about equidistant to Yoruba and San. Ergo, they couldn’t have substantial non-African admixture.
    The error in this syllogism is the equation of modern non-Africans (who are closer to Yoruba than to San) with ancient non-Africans for which this was not necessarily the case.
    Perhaps a case could be made that this was true for late Out-of-Africans, as these split off from other moderns after the Yoruba-San split. But, the late Out-of-Africans were not the only anatomically modern humans who left Africa, and we have good evidence of anatomically modern humans outside Africa before the exodus that gave rise to modern Eurasians (at sites like Qafzeh).
    Note that this observation nicely addresses the argument presented by John Hawks on the young coalescence dates between some Neandertal and Eurasian DNA, which supposedly disqualifies the African structure scenario I presented (and which the authors labeled as “Scenario 4″ in their paper). These young coalescence ages can be easily explained as modern-to-Neandertal gene flow within the context of the African structure model.
    Finally, I want to remind readers of a very interesting paper I blogged about last year. Here are the relevant quotes:
    Our data on neighbors and variability is unsupportive of the strict forms of a single-origin model but does not conflict with another approach, the model of ‘‘isolation by distance,’’ which predicts that genetic and phenotypic dissimilarity increases with geographic distance (24, 29–31). The metapopulation framework would predict the same because frequency and magnitude of genetic exchange would follow the likelihood of 2 populations to meet, which declines with geographical distance from the early AMH epicenter in Africa. Our fossil AMH data, however, suggest that before there was isolation by distance from Africa, there already existed (at least temporally) isolation by distance within Africa during the Pleistocene.

    Seemingly ancient contributions to the modern human gene pool (36) have been explained by admixture with archaic forms of Homo, e.g., Neanderthals. Although we cannot rule out such admixture (37), the clear morphological distinction between
    AMH and archaic forms of Homo in the light of the proposed ancestral population structure of early AMH to us suggests another underestimated possibility: the genetic exchange between subdivided populations of early AMH as a potential source for ‘‘ancient’’ contributions to the modern human gene pool (9, 36).

    I won’t present the reasoning behind these conclusions (the paper is open access anyway), but they have an important implication: seemingly “ancient” contributions to modern humans need not have been acquired by either Neandertals or other archaic (pre-sapiens) populations, but they could also have been acquired by admixture with different branches of anatomically modern humans.

    Given that anatomically modern humans appear on the record ~200ky ago, so they probably existed at an even earlier date, while extant sapiens populations trace their earlier split much later (the authors date the Yoruba-San split at most 164ky or as late as 67ky), we can reasonably assume that there were anatomically modern sapiens populations that are not ancestral to any modern humans, and which may have contributed seemingly “ancient” genes to our expanding ancestors.
    There you have it: structure in Africa, modern-to-Neandertal admixture, or even sapiens-to-sapiens admixture, there are plenty of alternatives to the story dominating the media.”

    • Nice comment Insightful, however…

      Since we know Neanderthals are ‘within the range of human variation’ and we know that the standard procedure is to absorb low amounts of routed populations, and understanding the basic sexual behaviour of human males, it’s going to need a REALLY mega strong argument against interbreeding to rescind this paper’s main statement.

      The authors reject that gene flow into the Neandertals took place;

      Well yes, but given that the Neanderthals in the sample didn’t show any evidence of a shared environment with modern humans I’d be surpriesd if they had. At 38k ago I don’t think modern humans were in that area. A different result might be gotten with the later samples.

  5. The interbreeding date of 50,000-80,000 years ago is consistent with the evidence that the earliest modern human-Neanderthal contact ceased ca. 75,000 years ago and than was restored only ca. 50,000 years ago.

    Thus, the any genetic remnant of the first round of modern human-Neanderthal contact either died with that population, or retreated back to Africa, in which case the methodology that distinguished African from non-African genes might not be able to detect it.

    Or, a retreat could have diluted a small Neaderthal component of an already small Near Eastern modern human population further reduced by the factors that forced them to retreat into a much larger East African population to the point where it was undetectable. It you have 2000 modern human in the Near East who are 10% Neanderthal by 75,000 years ago, who have declined to 500 people who successfully manage to retreat, and they are merged into an East African population of 50,000, then the Neaderthal proportion of the population in Out of Africa take two (the one that succeeds in the long run) is only 0.1%. Further, this percentage could fade further because Neaderthal specific traits are likely to be precisely those that have selective advantage outside African, and hence are likely to be neutral or a disadvantage in Africa.

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