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nature16544-f3

According to a new paper in Nature, Ancient gene flow from early modern humans into Eastern Neanderthals, a basal population of anatomically modern humans mixed with eastern Neanderthal populations on the order of ~100,000 years ago. The figure above is from the paper, and shows (on the left) the proportions and direction of gene flow across the phylogenetic tree, and (on the right) the dates of divergences and effective population sizes of the various groups. In The New York Times Carl Zimmer has a write-up, Ancient Humans May Have Left a Genetic Mark on Neanderthals (also, see Ewen Callaway in Nature, Evidence mounts for interbreeding bonanza in ancient human species). It’s useful to read, because he reports that some of the researchers assumed their results were in error, so they double-checked, and, other prominent researchers believe that the results are broadly credible. This doesn’t mean the results are correct…though the team that came out with this has people I trust to attend to details, and the results are not implausible on a priori grounds.

51t3ZeiK+vL._SX331_BO1,204,203,200_ Where does this lead us? As observed on Twitter there are some curious results in this paper in terms of the phylogenetic relationships and demographic history of human populations. The modern human lineage which contributed to the Altai individual seems to have done so ~100,000 years ago. This is 40,000 to 50,000 years before the “Out of Africa” event which we know of, and which seems to have resulted in the patterns of human genetic variation outside of Africa, excepting archaic admixture, that we see today. As noted in the paper there have been recent finds in locations such as China of very ancient pre-”Out of Africa” modern human remains, and there has always been the Skhul and Qafzeh hominids in the Near East. So that’s not too much of a problem necessarily. But, if you look closely at the phylogenetic tree above San diverge from other modern lineages ~200,000 years ago, well before the admixture event, but the modern human ancestry in the Altai Neanderthal looks equally related to all modern humans. That seems peculiar, since in the 100,000 intervening years there should have been significant structure to sample. There are a variety of ways to “resolve” this…though as one of the authors stated, there are many reasons why the date of the divergence of the various groups and admixture differ so much (e.g., archaic admixture into the San might push back their divergence from other groups). I need to think about this more and read the supplements. The picture in the details is getting cloudier, not clearer….

But the overall result does clarify and highlight some big picture inferences we can make in generating a framework toward understanding new results. Mait Metspalu’s group is going to publish a paper on low levels of pre-”Out of Africa” modern admixture in Sahul populations (that is, a earlier movement of modern people than the canonical one), and I now judge that their result is a true positive to a higher degree than earlier. These Altai Neanderthals likely did not contribute to modern human Neanderthal ancestry, as the Neanderthal ancestry in modern humans is closer to that of European Neanderthals (who did not have modern human ancestry like the Altai individual). Follow that?

The upshot is that these results should change our prior expectations about the nature of ancient human population structure. Yes, it was complicated, but there’s a pattern. The genetic patterns indicate that there was selection in the genome against the introgressed variants, so Neanderthals and modern humans exhibited hybrid breakdown. In light of no such genomic evidence for admixture of Eurasian ancestry into KhoeSan (I’ve asked, people have looked), that suggests we know that for hominins hybrid incompabilities seem to arise on the scale of between 200,000 and 600,000 years. It also seems that due meta-population dynamics lineage extinctions were very common in hominins. The genetic relatedness of Neanderthals across human swaths of territory indicate that they were subject to this dynamic, where there were massive lineage pruning events over the 600,000 years that this group was a distinct population. With modern humans, we now know that first settlers do not always leave a genetic impact later on because of extinction events. With these facts under our belt it is less surprising if there were “false dawns” of the “triumph of humanity.”

mmXlVoUaP2In-yXZPl_WuZg What these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion, where the hominin-made-man swept all before them. Probably the best illustration of this thesis can be found in Richard Klein’s 2002 book, The Dawn of Human Culture. In it he proposes that 50,000 years ago there was a single mutation which resulted in a pleiotropic cascade, and allowed for the emergence of full elaborated language and ergo the package of features which we associate with behavioral modernity. This model was presaged in the earlier decade with popularizations of “mitochondrial Eve” which implied that all humans were descended from a very small tribe resident in East Africa on the order of ~100,000 years ago. (the date varied as a function of the vicissitudes of mutational rate estimates)

Here’s what we know now that changes this. First, there are populations within Africa, in particular the the San of the far south, who diverged much earlier than 50,000 years ago. The most recent genomic estimates are suggesting divergence dates as early as ~200,000 years before the present. Second, the effective population size of humans outside of Africa is incredibly small, suggesting expansion from a very small founding population, but one should be cautious about generalizing to groups within Africa. That is, the blitzkrieg sweep model of modern human expansion does not hold to within Africa, and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently. And, these lineages may have admixed with modern humans just as they have outside of Africa.

Finally, the emergence of H. sapiens sapiens supremacy seems to have been a process, not a singular event which emerged de novo like a supernovae in the hominin firmament. The Omo remains in Ethiopia were anatomically modern humans. The people who gave rise to Omo lived ~200,000 years ago. The encephalization of the human lineage increased gradually up until around ~200,000 years ago, and Neanderthals were famously the most encephalized of all. Therefore, some form of modern humans were present within Africa for 150,000 years while other lineages were dominant elsewhere. Remains from places like China suggest though that offshoots of African humanity did push into the rest of the world…but they may not have left much of a genetic trace. This may have been part of movements due to climate change during the Pleistocene, or one of the natural migrations which a consequence of Malthusian pressures and inter-deme competition which afflicted humans. But they clearly did not conquer all before them. Why? We don’t know. And we don’t know why the situation was different 50,000 years ago. As a null hypothesis one might entertain the possibility that it was random. That periodically turnovers occur, and it just so happened that an African lineage lucked out in a massive extinction event. But that’s hard to credit when you consider that these modern humans crossed into Sahul and Siberia after sweeping aside other groups, and then eventually crossed over into the New World. There was something different about us. Additionally, the modern humans eventually absorbed or extirpated other lineages within Africa too.

A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.

Addendum: We need to start thinking about Eurasian gene-flow into Africa over the Pleistocene.

 
• Category: Science • Tags: Human Evolution 
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  1. This is a huge surprise, but on the other hand it makes a lot sense because there is no good reason why humans and neanderthals wouldn’t come in contact long before the the interbreeding event that gave rise to modern eurasians.

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  2. Fascinating. If I’m reading this correctly, modern Oceanians may have trace elements of this “basal AMH” component which jumped into their gene pool through two intervening populations (first Altai Neandertals, and then Denisovans).

    I know a few years back I read some bloggers, like Dienekes, who seemed to be suggesting that higher levels archaic admixture in Africa may be the sole reason that Africans seem to be so “basal” compared to non-Africans. That the real origin of AMH may not even be Sub-Saharan Africa at all, but North Africa or even the Near East. This seems to fly against the most basal haplogroups of both mitochondria and Y-DNA being in Africa however. Of course, we’ve misinterpreted haplogroups before (see The Seven Daughters of Eve) but aside from the YAP Y-DNA haplogroups I see a non-African origin as pretty implausible. What are your thoughts?

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    • Replies: @Razib Khan
    Fascinating. If I’m reading this correctly, modern Oceanians may have trace elements of this “basal AMH” component which jumped into their gene pool through two intervening populations (first Altai Neandertals, and then Denisovans).


    hm. probably not, but i'm not sure. i obviously didn't take a pic of mait metspalu's poster, but the basic result was that it looked some of their modern human ancestry is basal to all other non-africans, including basal eurasians. so there was a first wave out of africa...the famous 'southern route.' this got overlain by a dominant second wave in sahul (pretty overwhelming). i don't think they said they got this through denisovans, though the first wave may have had a higher denisovan percentage. the denisovans in this study don't seem to have any of the first wave ancestry btw.

    I know a few years back I read some bloggers, like Dienekes, who seemed to be suggesting that higher levels archaic admixture in Africa may be the sole reason that Africans seem to be so “basal” compared to non-Africans. That the real origin of AMH may not even be Sub-Saharan Africa at all, but North Africa or even the Near East. This seems to fly against the most basal haplogroups of both mitochondria and Y-DNA being in Africa however. Of course, we’ve misinterpreted haplogroups before (see The Seven Daughters of Eve) but aside from the YAP Y-DNA haplogroups I see a non-African origin as pretty implausible. What are your thoughts?


    yeah, still skeptical. most people that i know with whole genomes seem skeptical too. africans have really high diversity, and i don't think that archaic admixture can explain that. it COULD be that the original eurasian population replaced most africans, and this eurasian population was replaced by a second eurasian pop which went through the bottleneck...but that's less parsimonious than the mostly out of africa.
  3. @Karl Zimmerman
    Fascinating. If I'm reading this correctly, modern Oceanians may have trace elements of this "basal AMH" component which jumped into their gene pool through two intervening populations (first Altai Neandertals, and then Denisovans).

    I know a few years back I read some bloggers, like Dienekes, who seemed to be suggesting that higher levels archaic admixture in Africa may be the sole reason that Africans seem to be so "basal" compared to non-Africans. That the real origin of AMH may not even be Sub-Saharan Africa at all, but North Africa or even the Near East. This seems to fly against the most basal haplogroups of both mitochondria and Y-DNA being in Africa however. Of course, we've misinterpreted haplogroups before (see The Seven Daughters of Eve) but aside from the YAP Y-DNA haplogroups I see a non-African origin as pretty implausible. What are your thoughts?

    Fascinating. If I’m reading this correctly, modern Oceanians may have trace elements of this “basal AMH” component which jumped into their gene pool through two intervening populations (first Altai Neandertals, and then Denisovans).

    hm. probably not, but i’m not sure. i obviously didn’t take a pic of mait metspalu’s poster, but the basic result was that it looked some of their modern human ancestry is basal to all other non-africans, including basal eurasians. so there was a first wave out of africa…the famous ‘southern route.’ this got overlain by a dominant second wave in sahul (pretty overwhelming). i don’t think they said they got this through denisovans, though the first wave may have had a higher denisovan percentage. the denisovans in this study don’t seem to have any of the first wave ancestry btw.

    I know a few years back I read some bloggers, like Dienekes, who seemed to be suggesting that higher levels archaic admixture in Africa may be the sole reason that Africans seem to be so “basal” compared to non-Africans. That the real origin of AMH may not even be Sub-Saharan Africa at all, but North Africa or even the Near East. This seems to fly against the most basal haplogroups of both mitochondria and Y-DNA being in Africa however. Of course, we’ve misinterpreted haplogroups before (see The Seven Daughters of Eve) but aside from the YAP Y-DNA haplogroups I see a non-African origin as pretty implausible. What are your thoughts?

    yeah, still skeptical. most people that i know with whole genomes seem skeptical too. africans have really high diversity, and i don’t think that archaic admixture can explain that. it COULD be that the original eurasian population replaced most africans, and this eurasian population was replaced by a second eurasian pop which went through the bottleneck…but that’s less parsimonious than the mostly out of africa.

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  4. Rick says:

    So I read the paper, and it has me wondering something. Because the Altai Neanderthal genome is the best quality, wasn’t it used as the primary reference in determining the ‘official’ percentage of Neanderthal admixture in non-Oceanians Eurasians?

    If I remember right, they filter first for sites where most Africans have the ancestral allele, but the Neanderthal is derived, and then see which allele is in Eurasians.

    But if that specific Neanderthal had>2% African-like admixture, then that would have masked up to that much Neanderthal in modern Eurasians. And this would have also made the western Neanderthals appear to be more closely related to the admixing population in Eurasians, simply because they were less African-like than the Altai Neanderthal.

    I can’t find anywhere in the paper where they discuss re-calculating percentages based on this new knowledge.

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    • Replies: @Razib Khan
    it was vindija. http://science.sciencemag.org/content/328/5979/710.long but a follow up paper used the altai http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072735/
  5. @Rick
    So I read the paper, and it has me wondering something. Because the Altai Neanderthal genome is the best quality, wasn't it used as the primary reference in determining the 'official' percentage of Neanderthal admixture in non-Oceanians Eurasians?

    If I remember right, they filter first for sites where most Africans have the ancestral allele, but the Neanderthal is derived, and then see which allele is in Eurasians.

    But if that specific Neanderthal had>2% African-like admixture, then that would have masked up to that much Neanderthal in modern Eurasians. And this would have also made the western Neanderthals appear to be more closely related to the admixing population in Eurasians, simply because they were less African-like than the Altai Neanderthal.

    I can't find anywhere in the paper where they discuss re-calculating percentages based on this new knowledge.
    Read More
    • Replies: @Rick
    The original paper had estimates as high as 4%, but the later paper using the Altai sequence refined it to ~2.3%. So that is still consistent with a lower estimate coming from African-like admixture in the Altai specimen.
  6. Rick says:
    @Razib Khan
    it was vindija. http://science.sciencemag.org/content/328/5979/710.long but a follow up paper used the altai http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072735/

    The original paper had estimates as high as 4%, but the later paper using the Altai sequence refined it to ~2.3%. So that is still consistent with a lower estimate coming from African-like admixture in the Altai specimen.

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  7. I saw an interview with an evolutionary biologist recently who said the Red Deer Cave people lived in SW China alongside modern humans 14,000 years ago, so there might have been some interbreeding. Whether they can get any DNA to compare with modern DNA remains to be seen. The chinese see themselves as having originated in China so maybe if they have Red Deer Cave people DNA this will turn out to be true.

    The biologist also said that since Melanesians share 4-6% of their DNA with Denisovans, the Denisovans may well have originated in Oceania rather than Siberia.

    So is the Multi-Regional theory gaining ground or, as so often is the case, is a third theory, taking aspects from Out of Africa and Multi-Regionalism, emerging?

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    • Replies: @ohwilleke
    Even if there was introgression of Red Dear Cave genetics into the Chinese, it would be on the order of 1% or less of their ancestry. This is not by any stretch of the imagination consistent with the Chinese originating in China.

    Multi-regional theory, in the conventional sense, is not gaining ground. Out of Africa with almost total replacement, as opposed to Out of Africa with total replacement, might be the best description of the modern theory.
  8. AG says:

    If introgression into Neanderthals was real, there should be degrees of admixture related to time and location. Maybe.

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  9. Razib, Is “pleiotropic cascade” an existing term or something you made up? Nothing returns when I google it. I assume it means in this case, “one gene changes and then interacts with other genes causing a lot of other things to change.”

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  10. AG says:

    I read some news article about this new finding yesterday. As diagram indicated, human genes admixture/introgression might be mutual and multidirectional. I predict that more complicated pattern might emerge in future with increasing evidences and discoveries.

    During discovery of Homo naledi in south Africa, many scientists had since believed that human evolution would be like glacier with numerous branching and merging or fishnet like process( instead of trees like structure with many dead ends).

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  11. I wonder if it would be possible to recover DNA from the ambiguously Neanderthal-AMH remains from Obi-Rakhmat Grotto in Uzbekistan?

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  12. Anonymous says: • Disclaimer

    A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.

    Thank you for stating this so plainly. When I entered the field many a decade ago, it occurred to my atheist self that the then-dominant “Out of Africa-Total Replacement” paradigm bore a disquieting resemblance to the Genesis creation myth. However, the self-professed “secular” scientists I broached it with vehemently denied any such relationship, and the genetic evidence, such as it was, appeared to support them. Amazing how entrenched cultural myths are, even among people who purport not to believe in them.

    Read More
  13. ohwilleke says: • Website
    @John Johns
    I saw an interview with an evolutionary biologist recently who said the Red Deer Cave people lived in SW China alongside modern humans 14,000 years ago, so there might have been some interbreeding. Whether they can get any DNA to compare with modern DNA remains to be seen. The chinese see themselves as having originated in China so maybe if they have Red Deer Cave people DNA this will turn out to be true.

    The biologist also said that since Melanesians share 4-6% of their DNA with Denisovans, the Denisovans may well have originated in Oceania rather than Siberia.

    So is the Multi-Regional theory gaining ground or, as so often is the case, is a third theory, taking aspects from Out of Africa and Multi-Regionalism, emerging?

    Even if there was introgression of Red Dear Cave genetics into the Chinese, it would be on the order of 1% or less of their ancestry. This is not by any stretch of the imagination consistent with the Chinese originating in China.

    Multi-regional theory, in the conventional sense, is not gaining ground. Out of Africa with almost total replacement, as opposed to Out of Africa with total replacement, might be the best description of the modern theory.

    Read More
  14. Jm8 says:

    “…and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently…”

    And perhaps also in (parts of ) Asia.

    “A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China”

    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143332

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  15. Today we know that that’s wrong. We just don’t know what’s right.

    I’d think culture is becoming a stronger and stronger candidate, no? Just look at the demographic turnover between relatively closely related populations of modern humans since the Upper Paleolithic – if small differences in culture could so completely marginalize members of our own species, what chance did other sub-species have to leave behind a greater genetic legacy, especially with their issues of hybrid incompatibility?

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  16. notanon says:

    Even if there was introgression of Red Dear Cave genetics into the Chinese, it would be on the order of 1% or less of their ancestry. This is not by any stretch of the imagination consistent with the Chinese originating in China.

    Doesn’t that depend how important/distinctive that 1% is/was.

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  17. What these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion

    . . . and the final expiration of Chomsky’s linguistic paradigm, which, of course, won’t stop it from being the standard American linguistics education paradigm for the next fifty years.

    Language has structure independent of meaning, but the entire point of generative grammar is that understanding its structure is supposed to tell us something about universal human psychology, predicated upon the assumption that a single genetic mutation gave rise to said psychology. I’m not sure if Chomsky has ever said this directly, but he has always implied that his theory is that this mutation happened during some brief and punctual “human explosion.”

    But if humanity’s emergence were more of a long, slow whimper than a bang? Where does that leave the bedrock assumption of universal grammar?

    In my view, giving up that assumption makes the study of universal structure even more interesting.

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