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The Ancient Scramble for Eurasia
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TestSEAsia.gz..1.out

When I wrote the Pleistocene was humanity’s Hyborian age, I meant humanity. For contingent reasons the new genetic sciences of ancient DNA have elucidated the history of northwest Eurasia first. But prior to the Great Divergence Europe was not quite so exceptional. In fact the historian Victor Lieberman wrote Strange Parallels, his macrohistory of Eurasia, to highlight just how similar the trajectories of Western Europe and mainland Southeast Asia were up until the early modern era, when the West distanced itself from the rest. In short, European prehistory updates our priors for the prehistory of us all.

For various reasons having to do with professional responsibilities I look at TreeMix plots quite often. Like PCA TreeMix is great for exploratory data analysis. You throw a bunch of populations in there, and it searches a bunch of parameters which can fit the model. But often the results are weird.

They’re not weird because they’re “wrong.” They’re weird because we’ll forcing data to give us answers, and the model pops out something which is reasonable with the conditions imposed on it. And often we just don’t have the big picture. Statistical inference was indicating strange connections between Native Americans and Europeans for the past decade…but it took ancient DNA from Siberia to resolve the mystery. Europeans and Amerindians exhibit ancestry from a shared common population. In Europe this ancestry is relatively recent, on the order of the past ~4 to 5 thousand years. Statistical genetic inference can tell us our model is missing something, but it can not always specify clearly just exactly what we’re missing.

The image above from a TreeMix plot is hard to make out; click it. But what it will show you are two things which are strange:

1) Gene flow from between the East African (mostly HapMap Masai for what it’s worth) node and Mbuti (HGDP) to the Papuans (HGDP).

2) Gene flow from near the East African node to the point which defines the whole East Eurasian, Amerindian, and Oceanian, nodes.

I would laugh this off, but I see it all the time in TreeMix. I know I’m not the only one. I have no explanation for it. It’s obviously not recent admixture. Rather, there are affinities between populations which we just don’t have a good model for. Knowing what we know about ancient Europe it is mostly likely that these gene flow edges which seem inexplicable reflect prehistoric events which make sense only in the context of population patterns which have been totally obscured over the last 10,000 years. Ancient DNA from China will probably shed a great deal of light on these topics. I predict that the Chinese will exhibit the same discontinuity with their Paleolithic ancestors that modern Europeans do, and the affinities between East Eurasians and some Africans in these TreeMix plots probably is a shadow of a “ghost population” which has been absorbed in Eurasia, and may have contributed to some of the ancestry of a group which migrated back to Africa.

Notes I set TreeMix to check for covariance across blocks of 1000 SNPs. I had 215,000 total markers in the data set (very high quality ones). I rooted it with Mbuti, set 5 migration edges, and ran it 10 times. They all looked the same. Most of the populations are pooled from public sources.

 
• Category: Science • Tags: Genomics, TreeMix 
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  1. Shaikorth says:

    Does the Mbuti-Papuan edge persist if Denisovan is in the tree?

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    • Replies: @Razib Khan
    will check tonight.
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  2. Pat Casey says:

    stupid guy here, white flag—please don’t mug me for trespassing I’m innumerate. but I don’t even know if Egyptians are East African or NW Asian. it occurs to me that IF Egyptians are counted as East African, you might profit from thinking about megalithic structures. Alot of Razib’s posts seem to basically say the more we know the more we know we don’t know. Well I’ve come to believe you can’t really know anything about so called prehistory until you really digest what comes out in the netflix series The Pyramid Codes. Did you know the Pyramids are not tombs but power plants that harnessed subtle energy? And that megalithic structures the world over are built on subtle energy avenues. Have you ever heard of subtle energy? And don’t get me started on the ionic orbs…

    If the way Egyptians are related to Amerindians is strange, my unstudied intuition would be that it might be time to account for the aliens Amerindians believe that they come from.

    Read More
    • Replies: @Razib Khan
    egyptians have a minor recent african admixture. they are mostly similar to west asians. these samples are masai, as i state din the post.

    the amerindian affinity has to do with *ancient north eurasian* ancestry.

    for readers clueless about what pat is referring to in our history, he offered kung fu movies as evidence for less sex dimorphism in east asians a long time ago. i thought that was pretty stupid.

  3. Marcus says:

    to highlight just how similar the trajectories of Western Europe and mainland Southeast Asia were up until the early modern era

    Similar in what ways, and what do you mean by SE Asia? Politically, Western Europe was a patchwork of feudal dependencies with most kings wielding severely limited power, whereas SE Asia saw the rise of numerous and sundry empires, foreign and indigenous. Hinduism and Buddhism had only indirect influence in the West. Culturally I see few, if any, parallels.

    Read More
    • Replies: @Razib Khan
    #3, i stated mainland for a reason. the histories of the mainland and maritime cultures diverge considerably because of their 'exposure' to international geopolitical currents. he labels both SE asia and western europe eurasian 'protected zones' (japan is another case).

    Western Europe was a patchwork of feudal dependencies with most kings wielding severely limited power

    nation-state formation in mainland SE asia went through very similar stages at very similar times. for more details read the book. he lays the case out extensively.

  4. @Marcus

    to highlight just how similar the trajectories of Western Europe and mainland Southeast Asia were up until the early modern era
     
    Similar in what ways, and what do you mean by SE Asia? Politically, Western Europe was a patchwork of feudal dependencies with most kings wielding severely limited power, whereas SE Asia saw the rise of numerous and sundry empires, foreign and indigenous. Hinduism and Buddhism had only indirect influence in the West. Culturally I see few, if any, parallels.

    #3, i stated mainland for a reason. the histories of the mainland and maritime cultures diverge considerably because of their ‘exposure’ to international geopolitical currents. he labels both SE asia and western europe eurasian ‘protected zones’ (japan is another case).

    Western Europe was a patchwork of feudal dependencies with most kings wielding severely limited power

    nation-state formation in mainland SE asia went through very similar stages at very similar times. for more details read the book. he lays the case out extensively.

    Read More
    • Replies: @Marcus
    So basically just Indo-China? The Indian subcontinent was anything but protected historically, from relatively positive interactions with the Greeks to the ravages of the Muslim hordes.
  5. @Pat Casey
    stupid guy here, white flag---please don't mug me for trespassing I'm innumerate. but I don't even know if Egyptians are East African or NW Asian. it occurs to me that IF Egyptians are counted as East African, you might profit from thinking about megalithic structures. Alot of Razib's posts seem to basically say the more we know the more we know we don't know. Well I've come to believe you can't really know anything about so called prehistory until you really digest what comes out in the netflix series The Pyramid Codes. Did you know the Pyramids are not tombs but power plants that harnessed subtle energy? And that megalithic structures the world over are built on subtle energy avenues. Have you ever heard of subtle energy? And don't get me started on the ionic orbs...

    If the way Egyptians are related to Amerindians is strange, my unstudied intuition would be that it might be time to account for the aliens Amerindians believe that they come from.

    egyptians have a minor recent african admixture. they are mostly similar to west asians. these samples are masai, as i state din the post.

    the amerindian affinity has to do with *ancient north eurasian* ancestry.

    for readers clueless about what pat is referring to in our history, he offered kung fu movies as evidence for less sex dimorphism in east asians a long time ago. i thought that was pretty stupid.

    Read More
  6. @Shaikorth
    Does the Mbuti-Papuan edge persist if Denisovan is in the tree?

    will check tonight.

    Read More
    • Replies: @backup
    Could it be that archaics skew the results because Mbuti shares a lot of ancestral with them?
  7. Marcus says:
    @Razib Khan
    #3, i stated mainland for a reason. the histories of the mainland and maritime cultures diverge considerably because of their 'exposure' to international geopolitical currents. he labels both SE asia and western europe eurasian 'protected zones' (japan is another case).

    Western Europe was a patchwork of feudal dependencies with most kings wielding severely limited power

    nation-state formation in mainland SE asia went through very similar stages at very similar times. for more details read the book. he lays the case out extensively.

    So basically just Indo-China? The Indian subcontinent was anything but protected historically, from relatively positive interactions with the Greeks to the ravages of the Muslim hordes.

    Read More
  8. yes. burma, thailand, laos, cambodia, vietnam.

    The Indian subcontinent was anything but protected historically, from relatively positive interactions with the Greeks to the ravages of the Muslim hordes.

    no shit sherlock. the guy is a historian, not a moron. and no one defines the indian subcontinent as southeast asia in american english that i know of.

    Read More
  9. Anonymous says: • Disclaimer

    These fundamental problems of Treemix are equally evident for f3, f4 or D-statistics, and yet no-one mentions anything when they use those. This always drives me mad.

    Read More
  10. @Anonymous
    These fundamental problems of Treemix are equally evident for f3, f4 or D-statistics, and yet no-one mentions anything when they use those. This always drives me mad.

    list them please.

    Read More
  11. Pat Casey says:
    @Razib Khan
    egyptians have a minor recent african admixture. they are mostly similar to west asians. these samples are masai, as i state din the post.

    the amerindian affinity has to do with *ancient north eurasian* ancestry.

    for readers clueless about what pat is referring to in our history, he offered kung fu movies as evidence for less sex dimorphism in east asians a long time ago. i thought that was pretty stupid.

    lol

    Read More
  12. Matt_ says:

    Without reading Strange Parallels, if you consider over the past 1000 years of post Migration Era Europe that’s really Lieberman’s focus (per the link) then it seems probable for parallels to be there in relation to isolation from the Central Asian dynamic, and building up from quite a basic level of settled culture (eliding over the fact that it wasn’t always quite so basic in much of Western Europe), plus a maritime littoral is all plausible.

    It’s more over the long scale of the thousands of years before that in the dynamics of relatively early neolithic colonisation of Europe by the first neolithic farmers in the world (with little admixture from the mesolithic people), then later shift to a much more nomadic pastoralist style with Indo-European migration (inhibiting sophisticated settled culture?), then to the highly advanced Roman Empire, that Europe (particularly West Europe) is really quite divergent from mainland Southeast Asia. And this seems to me quite likely to be what makes a lot of the difference between premodern states in Europe versus mainland Southeast Asia with in some ways quite similar basic dynamics of state building from a baseline of no states.

    But Strange Parallels is not really the focus of the post, other than to illustrate the idea of parallelism of dynamics that are cross applicable! (Not that I wouldn’t appreciate a Razib Khan post on the ideas of Strange Parallels)

    Re: treemix, this may be obvious, I think the most useful way to think of these tends to me to be along the lines of what the edges functionally tend to do, e.g. the edge from East Africa here is making the whole “ENA” clade closer to East Africa, and more distant from West Africa, South India and West Eurasia, than it would be under the simple tree divergence. That could be reflective of a wave of ancestry related to East Africa and not to West Africa and West Eurasia, that survived in East Asia, or to gene flow between West Eurasia, India and West Africa that didn’t include East Asia.

    Read More
    • Replies: @RK
    Lieberman didn't just make the case for Southeast Asia and West Europe as 'protected zones'; Japan was included as well, and the parallels between historical processes in Japan and Western Europe are too many to count. Other than the belt of 'protected zones', Lieberman also makes the case that the 'exposed zones', where agricultural peoples come to the edge of the steppes, are another group united via parallels, with China, N India, Russia, and the Middle East under e.g. the Ottomans. Comparing adjacent exposed and protected societies brings us another level pregnant with parallels, such as Japan vs China, NW Europe vs Russia, and so on.

    I really recommend the book by the way. It has shaped my view of state-society interaction greatly, and, while it talks about 'parallels', it makes you realise just how deep and how different are the institutional histories in different places.
  13. RK says:
    @Matt_
    Without reading Strange Parallels, if you consider over the past 1000 years of post Migration Era Europe that's really Lieberman's focus (per the link) then it seems probable for parallels to be there in relation to isolation from the Central Asian dynamic, and building up from quite a basic level of settled culture (eliding over the fact that it wasn't always quite so basic in much of Western Europe), plus a maritime littoral is all plausible.

    It's more over the long scale of the thousands of years before that in the dynamics of relatively early neolithic colonisation of Europe by the first neolithic farmers in the world (with little admixture from the mesolithic people), then later shift to a much more nomadic pastoralist style with Indo-European migration (inhibiting sophisticated settled culture?), then to the highly advanced Roman Empire, that Europe (particularly West Europe) is really quite divergent from mainland Southeast Asia. And this seems to me quite likely to be what makes a lot of the difference between premodern states in Europe versus mainland Southeast Asia with in some ways quite similar basic dynamics of state building from a baseline of no states.

    But Strange Parallels is not really the focus of the post, other than to illustrate the idea of parallelism of dynamics that are cross applicable! (Not that I wouldn't appreciate a Razib Khan post on the ideas of Strange Parallels)

    Re: treemix, this may be obvious, I think the most useful way to think of these tends to me to be along the lines of what the edges functionally tend to do, e.g. the edge from East Africa here is making the whole "ENA" clade closer to East Africa, and more distant from West Africa, South India and West Eurasia, than it would be under the simple tree divergence. That could be reflective of a wave of ancestry related to East Africa and not to West Africa and West Eurasia, that survived in East Asia, or to gene flow between West Eurasia, India and West Africa that didn't include East Asia.

    Lieberman didn’t just make the case for Southeast Asia and West Europe as ‘protected zones’; Japan was included as well, and the parallels between historical processes in Japan and Western Europe are too many to count. Other than the belt of ‘protected zones’, Lieberman also makes the case that the ‘exposed zones’, where agricultural peoples come to the edge of the steppes, are another group united via parallels, with China, N India, Russia, and the Middle East under e.g. the Ottomans. Comparing adjacent exposed and protected societies brings us another level pregnant with parallels, such as Japan vs China, NW Europe vs Russia, and so on.

    I really recommend the book by the way. It has shaped my view of state-society interaction greatly, and, while it talks about ‘parallels’, it makes you realise just how deep and how different are the institutional histories in different places.

    Read More
  14. notanon says:

    My guess, mostly based on geography and iodine, is tidal.

    OoA clockwise and counter-clockwise around the coasts but then the people who ended up north of the Himalayas developed some traits which led to the tide reversing – clockwise and counter-clockwise around the Himalayas – all the way back to Africa again, with some refuge populations along the way surviving the flood.

    Read More
  15. Nicky says:

    Desperately waiting for decent(full genome with good coverage) aDNA from Asia(with the exception of Siberia and Anatolia, since we have some samples from there), since we still don’t have any. I hope that at least this year we will see some.

    Read More
    • Replies: @Shaikorth
    Full genomes with good coverage (30x or more) might even show something from modern populations we don't so easily see with commonly used datasets (HGDP, Human Origins, even 1000Genomes which has about 4x coverage)

    http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=2835e138-64aa-430e-93c7-e26fae8d6d1a&cKey=81377fa1-c158-4e63-a740-674921aa23b2&mKey=724c3001-0be7-4c9f-b314-ddac3db6fc2a
    https://twitter.com/tysonaclark/status/733946309728710656

  16. A genetic link between Africans (east and west) and east Asians or Oceanians is not a figment of anyone’s imagination, it can be seen in HLA haplotypes also. Plus a similar link between west Africa and western Europe may also be observed.

    Read More
  17. Shaikorth says:
    @Nicky
    Desperately waiting for decent(full genome with good coverage) aDNA from Asia(with the exception of Siberia and Anatolia, since we have some samples from there), since we still don't have any. I hope that at least this year we will see some.

    Full genomes with good coverage (30x or more) might even show something from modern populations we don’t so easily see with commonly used datasets (HGDP, Human Origins, even 1000Genomes which has about 4x coverage)

    http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=2835e138-64aa-430e-93c7-e26fae8d6d1a&cKey=81377fa1-c158-4e63-a740-674921aa23b2&mKey=724c3001-0be7-4c9f-b314-ddac3db6fc2a

    Read More
  18. backup says:
    @Razib Khan
    will check tonight.

    Could it be that archaics skew the results because Mbuti shares a lot of ancestral with them?

    Read More

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