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Thread: Late European Neanderthal's mt-DNA might have been L2'3'4'5'6 derived

  1. #11
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    Quote Originally Posted by lgmayka View Post
    [URL="http://en.wikipedia.org/wiki/Introgression"]...
    But note that introgression does not imply any kind of "abnormal" inheritance or "grafting." Introgression is the statistical result of normal genetic inheritance, modified by either natural or sentient selection.
    I agree.

    The Malyarchuk et. al. scenario would be specific case of an out of norm example.

  2. #12
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    Quote Originally Posted by German Dziebel View Post
    ...
    Neandertals being a Eurasian species, this would place the root of this tree outside of Africa ...
    But I'm not 100% sure that hg R is part of that introgressed clade... Technically it is, but if we put Y-DNA and mtDNA side by side, we'll see that mtDNA R distributionally corresponds to Y-DNA CF and its typological position is different from the position of R - it's not a subset of a subset of Eurasian lineages.
    Since Malyarchuk et. al. propose an introgression from a modern human male mtDNA to a European Neanderthal female, wouldn't only the introgression event have to be outside Africa?

  3. #13
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    Quote Originally Posted by German Dziebel View Post
    ... if we put Y-DNA and mtDNA side by side, we'll see that mtDNA R distributionally corresponds to Y-DNA CF....
    I am not following you here... Most Asian mtDNA haplogroups are not R.

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    Quote Originally Posted by German Dziebel View Post
    According to Malyarchuk, these two mutations are present on all sequences classified as L2'3'4'5'6. So, yes, we can put the sequences of European Neandertals carrying these 2 mutations on the left and all human L2'3'4'5'6 sequences on the right. Neandertals being a Eurasian species, this would place the root of this tree outside of Africa and will make most of M and N as well as L6a the remnants of that Eurasian population that stayed behind and didn't colonize Africa. Hgs M1, L2, L3, L4, L5, L6b will be the lineages that migrated to Africa.
    There are several reasons why this doesn't work. First, you can't build a phylogenetic tree from two mutations in isolation. You also have to look at the hundreds of mutations that distinguish the European branch of Neandertals from L2'3'4'5'6, This is shown very clearly in Behar et al 2012, in Figure 1 on page 2 (link).

    The most likely way these two specific mutations could be shared is that they have been selected or they occurred as random mutations independently in each clade. If they are silent mutations, random mutations is more likely.

    Introgression is not very plausible, as you would have to imagine a biological process in which only those two base pairs transferred from paternal mtDNA, replacing the two base pairs in the maternal mtDNA, but none of the intervening mutations between 2758 and 7146 were transferred. In other words, a recombination of paternal and maternal mtDNA in which only two among several hundred mutations were transferred from the paternal to maternal mtDNA.

    Even if this had occurred, it would be evidence of admixture of Neandertals and modern humans. But the Neandertal maternal line became extinct, so there is still no evidence of Neandertal migration from Europe to Africa. But more importantly, the Neandertal mtDNA is very clearly not ancestral to L2'3'4'5'6, as shown in Figure 1 in Behar. Finally, if there were a scenario in which L2'3'4'5'6 originated in Eurasia, this still leaves the deepest mtDNA ancestry (L0 and L1) in Africa, and you have to explain why all other L haplogroups are found primarily in Africa today, not Eurasia.

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  6. #15
    Quote Originally Posted by Gisele H View Post
    I am not following you here... Most Asian mtDNA haplogroups are not R.
    Regional frequencies can fluctuate (e.g., hg B in America was likely more frequent in North America in the past than now), but both Y-DNA CF and mtDNA R have the widest geographic distribution worldwide and are well attested in West Eurasia, Australia and South America.

  7. #16
    Quote Originally Posted by GailT View Post
    First, you can't build a phylogenetic tree from two mutations in isolation..
    What do you mean in "isolation"? And why cannot you build a tree with 2 root mutations? I gave you examples of 1-2 mutation-based clades on human mtDNA. Currently, L2'3'4'5'6 is separated from L1 by 5 mutations, while L0 has 10 defining mutations to it. By your logic, we shouldn't have the L1 node because it's only 5 mutations and not 10.

    Quote Originally Posted by GailT View Post
    You also have to look at the hundreds of mutations that distinguish the European branch of Neandertals from L2'3'4'5'6, This is shown very clearly in Behar et al 2012, in Figure 1 on page 2 (link).
    Behar didn't notice the sharing between European Neandertals and human lineages outside of L0 and L1. So at the moment I would hold off on using him as a gold standard?

    Quote Originally Posted by GailT View Post
    The most likely way these two specific mutations could be shared is that they have been selected or they occurred as random mutations independently in each clade. If they are silent mutations, random mutations is more likely.
    You are using the word "likely" idly. I don't know what's more likely. It's of course possible that what Malyarchuk found is convergence, and he admits this, but let's not jump the gun and try to kill what may be evidence of something more important. An admixture scenario makes sense in light of the whole-genome data. All non-Africans and some Sub-Saharan Africans were showed to carry Neandertal-derived alleles. This is the bigger picture. Plus archaic admixture would explain all the phylogeographic problems with the current tree.

    Quote Originally Posted by GailT View Post
    Even if this had occurred, it would be evidence of admixture of Neandertals and modern humans. But the Neandertal maternal line became extinct, so there is still no evidence of Neandertal migration from Europe to Africa. But more importantly, the Neandertal mtDNA is very clearly not ancestral to L2'3'4'5'6, as shown in Figure 1 in Behar. Finally, if there were a scenario in which L2'3'4'5'6 originated in Eurasia, this still leaves the deepest mtDNA ancestry (L0 and L1) in Africa, and you have to explain why all other L haplogroups are found primarily in Africa today, not Eurasia.
    I've already explained it multiple times: L0 and L1 introgressed into modern Africans (who had previously absorbed Neandertal DNA in Eurasia) from archaic Africans. That's why L0 and L1 are so divergent, low-frequency and African-specific. While Neandertals didn't migrate to Africa, modern humans who carried their genes did.

  8. #17
    Quote Originally Posted by parasar View Post
    Since Malyarchuk et. al. propose an introgression from a modern human male mtDNA to a European Neanderthal female, wouldn't only the introgression event have to be outside Africa?
    As Gisele pointed out in an e-mail to me, it doesn't look like Malyarchuk has made up his mind. He writes, "Thus, if one adheres to the hybrid theory, the appearance of this combination of SNP variants in European Neanderthals could be due to the hybridization between female individuals of Neanderthals and male sapiens, which occurred after the appearance of CroMagnons in Europe (40000–50000 years ago). The results of recent genome research showed that one of the last episodes of interspecific hybridization could occur in
    Europe, most probably, in the range from 47000–65000 years ago."

    We can always imagine a scenario whereby L0 and L1 people migrated out of Africa to Europe, admixed with Neandertal women there, got their L0 and L1 haplotypes replaced by a new clade dominant and then migrated back to Africa as L2'3'4'5'6. It's a possibility, true.

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  10. #18
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    Quote Originally Posted by German Dziebel View Post
    We can always imagine a scenario whereby L0 and L1 people migrated out of Africa to Europe, admixed with Neandertal women there, got their L0 and L1 haplotypes replaced by a new clade dominant and then migrated back to Africa as L2'3'4'5'6.
    You might be able to imagine this scenario. Those of us burdened by evidence and tiresomely wedded to logical deduction have a little more difficulty. There is no trail of AMH into Europe and back to Africa at the time proposed for L0. On the evidence before us, AMH first entered Europe c. 46,000 years ago, and were carrying mtDNA U.
    Last edited by Jean M; 11-14-2013 at 03:13 PM.

  11. #19
    Quote Originally Posted by Jean M View Post
    You might be able to imagine this scenario. Those of us burdened by evidence and tiresomely wedded to logical deduction have a little more difficulty. There is no trail of AMH into Europe and back to Africa at the time proposed for L0. On the evidence before us, AMH first entered Europe c. 46,000 years ago, and were carrying mtDNA U.
    I was just trying to give out-of-Africa a chance. In my opinion, it has no chances in light of the growing ancient DNA data and all other cross-interdisciplinary evidence that we have. I still have to see evidence of your mastery of facts and logic related to modern human origins.

  12. #20
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    Quote Originally Posted by German Dziebel View Post
    I was just trying to give out-of-Africa a chance. In my opinion, it has no chances in light of the growing ancient DNA data and all other cross-interdisciplinary evidence that we have. I still have to see evidence of your mastery of facts and logic related to modern human origins.
    ????

    Do you even know what DNA and fossil data there is and what it suggests? Or will you simply restate what to my eyes seems only to be overweening pride in the extreme minority position you hold for an Out-of-Americas origin, regardless of all available DNA and fossil evidence?
     

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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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