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Ghost Populations in Our Genetic Closet
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As some of you know the supplement on the Cardial ancient genome presents some really strange results. Look at the gene flow edges around the Mbuti. I have used TreeMix a fair amount, and I’ve seen some weird things of which I have not spoken. I’m sure others have as well. My assumption when I see something this peculiar is that it is an artifact of ascertainment bias or TreeMix just being TreeMix.

After the welter of novel analytic methods and ancient DNA I think perhaps we need to reconsider dismissals. Usually when you’re using TreeMix you’re looking for only a constrained set of the hypotheses. You pretty much ignore or shove aside “results” which bubble out of the woodwork. But sometimes this marginalia can take center sage. When the original TreeMix paper came out it had a figure which indicated gene flow from the base of the Amerindian lineage to Russians. This was very peculiar. We now know what was happening. It was the signal of the admixture of the Ancient North Eurasians, represented by the Mal’ta boy. Similarly, the evidence of Austro-Melanesian admixture in some Amazonian peoples has been there in the SNP-chip data for years. It was just overlooked. Why? Because it didn’t make sense.

The examples are pretty numerous now. What is going on in my opinion is that the method of TreeMix is searching for the nearest proxy for donor populations when those populations are no longer present. That produces bizarre results in some cases, as the topologies confound our expectations. But the problem isn’t in the topologies, it’s in our interpretative framework. A reticulated genetic graph filled with implicit positions which are representative of extinct lineages which nevertheless contributed genes to extant lineages is going to be harder to unpack than our previous understanding. But what needs to happen is we need to update our understanding….

 
• Category: Science • Tags: Genomics 
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  1. Anonymous says:     Show CommentNext New Comment

    Maybe the link between Mbuti and Early farmers at TreeMix is due to some backflow from Eurasians into Africa associated to a farming expansion south into this continent? That would explain this results.

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    • Replies: @Razib Khan
    that seems quite possible. people have been hinting at deep-time back migration too, earlier than farmers.
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  2. @Anonymous
    Maybe the link between Mbuti and Early farmers at TreeMix is due to some backflow from Eurasians into Africa associated to a farming expansion south into this continent? That would explain this results.

    that seems quite possible. people have been hinting at deep-time back migration too, earlier than farmers.

    Read More
    • Replies: @Josh Lipson
    Connection to the ostensibly Mesolithic Balkan/Aegean/Anatolian E1b1b lineages?
  3. @Razib Khan
    that seems quite possible. people have been hinting at deep-time back migration too, earlier than farmers.

    Connection to the ostensibly Mesolithic Balkan/Aegean/Anatolian E1b1b lineages?

    Read More
    • Replies: @Josh Lipson
    Never mind; didn't notice the direction of the flow.
  4. @Josh Lipson
    Connection to the ostensibly Mesolithic Balkan/Aegean/Anatolian E1b1b lineages?

    Never mind; didn’t notice the direction of the flow.

    Read More
    • Replies: @Shaikorth
    The direction of the flow can also be from Mbuti branch to Stuttgart and other farmers, Treemix is not consistent with this. Lazaridis et al. supplements have such results for instance. They interpreted the edge as basal admix into EEF, but time will tell if that was the right call.
  5. and I’ve seen some weird things of which I have not spoken.

    Care to share? I think it would be really interesting to see. As you pointed out, many of these be real signals rather than just noise.

    Also – re: La-Brana – I thought I’d just point out this paper that had a weird Hadza/Lithuanian admixture signal. http://www.sciencemag.org/content/343/6172/747.abstract?sid=736c3d26-56ca-4f23-930f-1fdf773fd92d

    Read More
    • Replies: @Razib Khan
    lots of times weird edges will move from the basal around around mbuti/khoisan to non-african groups, like papuans, or vice versa. the interesting thing is that often it's not west africans, but these ancient HG groups. i pretty much dismissed them out of hand, since i mentally assume that west africans would be more likely to have non-african affinities. what i'm getting at in this post is that some of these gene flows might just be because there is a "population X" in the graph that's missing, and the likelihood is trying to get maximized by finding proxies....
    , @notanon

    Also – re: La-Brana – I thought I’d just point out this paper that had a weird Hadza/Lithuanian admixture signal.
     
    This may be nothing to do with it but given that OoA supposedly spread all the way to China then it seems obvious (to me at least) they'd have spread up the Atlantic coast to the Baltic also.

    And then if there was an HG back migration all the way back from SE Asia at some point then outside SSA refuge regions along the Atlantic coast - furthest point from the back migration - might actually be some of the most likely places to find a trace of that earlier layer.
  6. @Josh Lipson
    Never mind; didn't notice the direction of the flow.

    The direction of the flow can also be from Mbuti branch to Stuttgart and other farmers, Treemix is not consistent with this. Lazaridis et al. supplements have such results for instance. They interpreted the edge as basal admix into EEF, but time will tell if that was the right call.

    Read More
  7. @CupOfCanada

    and I’ve seen some weird things of which I have not spoken.
     
    Care to share? I think it would be really interesting to see. As you pointed out, many of these be real signals rather than just noise.

    Also - re: La-Brana - I thought I'd just point out this paper that had a weird Hadza/Lithuanian admixture signal. http://www.sciencemag.org/content/343/6172/747.abstract?sid=736c3d26-56ca-4f23-930f-1fdf773fd92d

    lots of times weird edges will move from the basal around around mbuti/khoisan to non-african groups, like papuans, or vice versa. the interesting thing is that often it’s not west africans, but these ancient HG groups. i pretty much dismissed them out of hand, since i mentally assume that west africans would be more likely to have non-african affinities. what i’m getting at in this post is that some of these gene flows might just be because there is a “population X” in the graph that’s missing, and the likelihood is trying to get maximized by finding proxies….

    Read More
    • Replies: @CupOfCanada
    I get that. I think it's interesting to try to infer what these ghost populations may have been as all.

    Re: ancient HG groups in Africa, presumably if we went back in time 10,000 years, there would only have been HG groups in Africa, yet this Afrasian/Khoisan (and other groups) divide would still exist. Would it be unreasonable to think that the progenitors of Bantu groups were just one group among many groups with deeply divided lineages?

    And if we're talking about the possibility of a back-migration, an Africa-Melanesia link could predate that, no? Africa may have looked very different from a genetic standpoint a various points in the past.
  8. Thanks Razib. So this paper shows a migration edge from Mbuti into Stuttgart (and also La Brana). Lazaridis and Skoglund had a migration edge from Dinka into Sardinia, Stuttgart, Otzi, Gokhem if I recall correctly. I would love to know some of the interesting Treemix results which you have generated (future blog posts?) The rare HLA haplotype A66-B41 was found to be a private haplotype in Baka or Biaka pygmies according to a paper a few years ago, however it ‘re-appears’ in the Swiss, Czechs, Poles and Russians according to the open access database. All components are at highest frequency and diversity in SSA. There are quite a few connections between Cameroon and Sudan with HLA which also encompass the pygmies. I wish I also had some data from Chad.

    Read More
  9. @Razib Khan
    lots of times weird edges will move from the basal around around mbuti/khoisan to non-african groups, like papuans, or vice versa. the interesting thing is that often it's not west africans, but these ancient HG groups. i pretty much dismissed them out of hand, since i mentally assume that west africans would be more likely to have non-african affinities. what i'm getting at in this post is that some of these gene flows might just be because there is a "population X" in the graph that's missing, and the likelihood is trying to get maximized by finding proxies....

    I get that. I think it’s interesting to try to infer what these ghost populations may have been as all.

    Re: ancient HG groups in Africa, presumably if we went back in time 10,000 years, there would only have been HG groups in Africa, yet this Afrasian/Khoisan (and other groups) divide would still exist. Would it be unreasonable to think that the progenitors of Bantu groups were just one group among many groups with deeply divided lineages?

    And if we’re talking about the possibility of a back-migration, an Africa-Melanesia link could predate that, no? Africa may have looked very different from a genetic standpoint a various points in the past.

    Read More
  10. @CupOfCanada

    and I’ve seen some weird things of which I have not spoken.
     
    Care to share? I think it would be really interesting to see. As you pointed out, many of these be real signals rather than just noise.

    Also - re: La-Brana - I thought I'd just point out this paper that had a weird Hadza/Lithuanian admixture signal. http://www.sciencemag.org/content/343/6172/747.abstract?sid=736c3d26-56ca-4f23-930f-1fdf773fd92d

    Also – re: La-Brana – I thought I’d just point out this paper that had a weird Hadza/Lithuanian admixture signal.

    This may be nothing to do with it but given that OoA supposedly spread all the way to China then it seems obvious (to me at least) they’d have spread up the Atlantic coast to the Baltic also.

    And then if there was an HG back migration all the way back from SE Asia at some point then outside SSA refuge regions along the Atlantic coast – furthest point from the back migration – might actually be some of the most likely places to find a trace of that earlier layer.

    Read More
  11. Hi Razib,

    I have always been fascinated by the possibility that we might discover ghost populations using data we have at the present moment alone.

    One of the things we could do, since I suspect that Africans are highly paraphyletic with respect to Eurasians, is to assemble a number of Africans, incl. Khoisan, Pygmy, West African and Nilotic groups, plus Stuttgart, Loschbour, and Papuan alone.

    It will be very interesting to see where the Basal Eurasian edge emerges when confronted with this profusion of basal diversity. Would you be able to carry out this analysis?

    Alternatively, Dienekes’ idea that the modern human expansion began in Arabia, and that hunter-gatherer Africans are a mix of eurasian ancestry and something that diverged much longer ago, may also explain this, though it fails to explain why the edge into mbuti shares drift with stuttgart specifically.

    Read More
  12. Anonymous says: • Website     Show CommentNext New Comment

    I suppose you all know that several types of mtDNA L lineages are found in Europe. And I’m not only talking of some L3 subclades, also some L1b and L2a ones, for instance (including in such regions as Norway or Russia (e.g. “Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs” Boris A Malyarchuk et. al >> http://www.ncbi.nlm.nih.gov/pubmed/18398433 – also one mtDNA L2 in 74 Norwegian samples: http://hpgl.stanford.edu/publications/EJHG_2002_v10_521-529.pdf)).

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  13. I am reminded of some results which Dienekes generated with TreeMix and posted on his blog in 2012:-

    “64% (French_Basque, Sardinian)-to-Yoruba, (85% Nganasan, *)-to-Mongol, 68% Nganasan-to-Selkup, 92% (Nganasan,*)-to-Tuva, 15% Oroqen-to-(Yakut,Evenk), 15% Nganasan-to-Oroqen, 82% Yakut-to-Yukagir, 90% Evenk-to-Dolgan, 43% Hezhen-to-Buryat, 14% Sardinian-to-Bulgarian
    [...]UPDATE (March 20): I have repeated the experiment with HGDP San, rather than Yoruba as the outrgroup: There is now a 63% migration edge from (Basque, Sardinian) to San.”

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  14. I wonder if there is some statistical means by which modern and ancient DNA data could be used to estimate how many “ghost populations” that really existed have been lost yet are ancestors of known populations?

    TreeMix is clearly a bad tool to do so, but Admixture seems to naturally generate such ghost populations and it seems to be somewhat possible to discern when adding additional hypothetical ancestral populations is ceasing to be meaningful.

    Read More
  15. Would it be possible to get some sort of expert take on the line prof. Sykes pushed in his latest book? The one in which he analyzes nuclear DNA taken from the purported descendants of the Caucasian version of Bigfoot and claims the discrepancies are significant?

    If you do not have access to the book, I could send you that part of the chapter.

    Is is possible that Sykes is so much of a publicity hound/bungler, that he managed to misidentify say, admixture from an African-American slave (Turk slavers brought some to the area)?

    Read More

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