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

  1. #21
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    from the very beginning of comparing there had been the average difference betbeen modern humans of 8 mutation on HVR1 level and that of neanderthals to humans was 27 mutations in average. So, like Gail already said, on a CR-level we encounter hundreds of differences and noone will reach to push any neanderthal under the node of L In contrary, we probably will find more AMHs with ancient mtdna like Lake Mungo3, who precede the origin of L.
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    @german dziebel

    IIRC my studies, it is stated that , humans can impregnate a neanderthal, but a neanderthal cannot impregnate a human. Where does your theory stand in regards to this?

  3. #23
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    Quote Originally Posted by vettor View Post
    @german dziebel

    IIRC my studies, it is stated that , humans can impregnate a neanderthal, but a neanderthal cannot impregnate a human. Where does your theory stand in regards to this?
    I don't understand this stuff fully, but as far I could understand, both ways works. In fact for Densiovans who (apparently - as there is some controversy) diverged even prior to Neanderthals, the introgression is theorized to be from Denisovan males to modern human females, based on the lower Denisovan seen on the X.

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    Quote Originally Posted by German Dziebel View Post
    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.
    I mean that you cannot construct a tree using 2 mutations that fit your model while ignoring hundreds of mutations that contradict your model. You must consider the entire set of mutations found in each sample, and if you to do this, you'll see that your version of the tree is very obviously contradicted by the data.

    Quote Originally Posted by German Dziebel View Post
    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?
    Behar et al. did notice the sharing of these mutations. If you look at Figure 1 in the Behar et al. paper, you will notice that both of these mutations are underlined, as are several other mutations that are found in multiple branches of there tree. So they developed the most parsimonius tree that accounted for the fact that some mutations occurred independently in multiple branches.


    Quote Originally Posted by German Dziebel View Post
    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.
    I'm not using the word "likely" idly. There are many cases in which the same mutation occurs independently in different branches of the tree, so this explanation is reasonable and possible, while invoking a new mechanism of hydbridization of mtDNA sounds very much like special pleading. In any case, regardless of the source of these two mutations, it does not affect the mtDNA tree, as is readily apparent in Figure 1 of Behar et al. So even if hybridization did occur and two mutations were transferred, the most parsimonius tree does not change because it is based on an analysis of hundreds of mutations, not just two.

    Quote Originally Posted by German Dziebel View Post
    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.
    That "explanation" is obviously flawed. L0 and L1 did not introgress into modern humans; they are modern humans L0 and L1 have age estimates of around 130,000 years, long after the evolution of modern humans. Modern humans do not carry Neandertal mtDNA, and there is very little evidence of Neandertal autosomal DNA in modern Africans. Autosomal DNA from Neandertals is found at very low percentages in people outside of Africa, indicating admixture after modern humans left Africa. Eurasian specific mtDNA haplogroups are less than 70,000 years old. The specific mtDNA haplogroups that did migrate back to Africa are much younger than date, around 30,000 years, You keep making these claims, but where is your evidence? What phylotrees have you constructed that are consistent with the mtDNA data and that support your theory? I think if you actually try to build a mtDNA Phylotree, you will see that it is inconsistent with your theory.

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  6. #25
    Quote Originally Posted by GailT View Post
    I mean that you cannot construct a tree using 2 mutations that fit your model while ignoring hundreds of mutations that contradict your model. You must consider the entire set of mutations found in each sample, and if you to do this, you'll see that your version of the tree is very obviously contradicted by the data.
    There are dozens of sites at which individual human mtDNA sequences match Denisovans and/or Neandertals to the exclusion of other human sequences. How is this data reflected in the current tree?

    Quote Originally Posted by GailT View Post
    Behar et al. did notice the sharing of these mutations. If you look at Figure 1 in the Behar et al. paper, you will notice that both of these mutations are underlined, as are several other mutations that are found in multiple branches of there tree. So they developed the most parsimonius tree that accounted for the fact that some mutations occurred independently in multiple branches.
    Yes, he did. My bad. But his "most parsimonious tree" ignores available ancient DNA data. He retrofitted the human mtDNA tree constructed prior to the appearance of ancient DNA evidence instead of building it using ancestral states now known from Neandertal and/or Denisovan mtDNAs. Of course, some mutations occur independently in multiple branches but not those that are clearly identical with Denisovan/or Nenadertal alleles. Those are related to the human ones by descent. They are not homoplastic.

    Quote Originally Posted by GailT View Post
    I'm not using the word "likely" idly. There are many cases in which the same mutation occurs independently in different branches of the tree, so this explanation is reasonable and possible, while invoking a new mechanism of hydbridization of mtDNA sounds very much like special pleading. In any case, regardless of the source of these two mutations, it does not affect the mtDNA tree, as is readily apparent in Figure 1 of Behar et al. So even if hybridization did occur and two mutations were transferred, the most parsimonius tree does not change because it is based on an analysis of hundreds of mutations, not just two.
    See above. There are many more cases like the one highlighted by Malyarchuk.

    Quote Originally Posted by GailT View Post
    L0 and L1 did not introgress into modern humans; they are modern humans L0 and L1 have age estimates of around 130,000 years, long after the evolution of modern humans.
    We don't know that. All those "anatomically modern human" remains in Africa haven't yielded any DNA, and all the skulls of presumably behaviorally modern humans in Africa (Hofmeyr), Asia (Zhoukoudian), America (Lagoa Santa) or Europe cluster together and the African ones are not closer to the AMH skulls in Africa.

    Quote Originally Posted by GailT View Post
    Modern humans do not carry Neandertal mtDNA, and there is very little evidence of Neandertal autosomal DNA in modern Africans.
    If it's "little" by autosomal standards, it can be significant at a certain single locus such as mtDNA.

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    Quote Originally Posted by German Dziebel View Post
    Yes, he did. My bad. But his "most parsimonious tree" ignores available ancient DNA data. He retrofitted the human mtDNA tree constructed prior to the appearance of ancient DNA evidence instead of building it using ancestral states now known from Neandertal and/or Denisovan mtDNAs.
    Behar et al 2012 used several Neandertal mtDNA samples. They are included in the most parsimonious tree. There are no data that show mtDNA descent of modern humans from Neandertals or Denisovans. If you actually had such data, you would overturn the scientific consensus of the last 25 years and you could publish your findings in your journal of choice, Science, Nature, where ever you like. Claiming on a hobbyist discussion forum that the entire scientific community is wrong, without providing any data to support the claim, is not very productive.

  8. #27
    Quote Originally Posted by GailT View Post
    Behar et al 2012 used several Neandertal mtDNA samples. They are included in the most parsimonious tree. There are no data that show mtDNA descent of modern humans from Neandertals or Denisovans. If you actually had such data, you would overturn the scientific consensus of the last 25 years and you could publish your findings in your journal of choice, Science, Nature, where ever you like. Claiming on a hobbyist discussion forum that the entire scientific community is wrong, without providing any data to support the claim, is not very productive.
    Agree. We got too far here. But the hobbyist community should know that the science is not a bulletproof monolith handed down from an enlightened minority. And out-of-Africa (with all its assets such as mtDNA phylogeny or AMH remains in Africa) is a model that needs to be tested and debated, not a fact to be assumed.

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