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

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

    This is big!!! Like really big!!!!

    Mitochondrial DNA Polymorphisms Shared between Modern Humans and Neanderthals: Adaptive Convergence or Evidence for Interspecific Hybridization?

    Quote Originally Posted by Malyarchuk.et.al.2013

    Abstract—An analysis of the variability of the nucleotide sequences in the mitochondrial genome of modern humans, neanderthals, Denisovans, and other primates has shown that there are shared polymorphisms at positions 2758 and 7146 between modern Homo sapiens (in phylogenetic cluster L2'3'4'5'6) and Homo neanderthalensis (in the group of European neanderthals younger than 48 000 years).It is suggested that the convergence may be due to adaptive changes in the mitochondrial genomes of modern humans and neanderthals or interspecific hybridization associated with mtDNA recombination.
    Malyarchuk.et.al.2013-Figure-1.jpg
    Last edited by jeanL; 11-13-2013 at 04:57 PM.

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    It would be very big if it really provided evidence of interbreeding. But the proposed basis of that would be a blow to those who wish to see Neanderthals as the same species as Homo sapiens.

    during interspecific hybridization, the leakage of the paternal mtDNA is possible due to the fact that the system of eliminating the paternal mtDNA (along with the sperm cytoplasm) is strictly speciesspecific and may fail at interspecific hybridization. Although cases of interspecific hybridization are rare, they are described in the literature for different groups of animals, including mammals
    They conclude that convergent adaptation is more likely:

    Therefore, it is likely that the convergence of the A415T amino acid variant of cytochromeсoxidase 1 in the mtDNA phylogenetic groups of modern humans and Neanderthals may have arisen as a result of adaptation to the changing conditions of the environment. In summary, it should be noted that the question of whether the convergence of polymorphism variants in the coding region of mtDNA of modern humans and Neanderthals is a consequence of adaptive changes in their mitochondrial genomes or interspecific hybridization associated with mtDNA recombination remains open.

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    Quote Originally Posted by Jean M View Post
    It would be very big if it really provided evidence of interbreeding. But the proposed basis of that would be a blow to those who wish to see Neanderthals as the same species as Homo sapiens.
    They conclude that convergent adaptation is more likely:
    Well the amino acid change of A415T would make sense, but we are talking about two distant SNPs in here, one in position 2758, one in 7146, so you can explain one as convergent evolution, but what about the other?? How about a third explanation that European Neanderthal's might have carried L2'3'4'5'6, and West Asian Neanderthal didn't carry them, and that L2'3'4'5'6 split from L1 and L0 a long time ago, and L2'3'4'5'6+ and that L2'3'4'5'6 are actually Neanderthal derived clades. How does this fit with the Out of Africa scenario?? Mind you, this isn't just one Neanderthal carry it, but all European Neanderthal carrying it, from Croatia to Germany to Spain.

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    Quote Originally Posted by jeanL View Post
    How about a third explanation that European Neanderthal's might have carried L2'3'4'5'6, and West Asian Neanderthal didn't carry them, and that L2'3'4'5'6 split from L1 and L0 a long time ago, and L2'3'4'5'6+ and that L2'3'4'5'6 are actually Neanderthal derived clades.
    Doesn't work at all. The Neanderthals do not carry L2'3'4'5'6. They simply have two substitutions in common with L2'3'4'5'6. We cannot have a scenario in which L2'3'4'5'6 in toto passed from Neanderthal to Homo sapiens. As the paper says, it has long been understood that Neanderthals and Homo sapiens are on different branchlines from a common ancestor. As the paper says, the only form of hybridization which could be postulated to create this effect of two substitutions in common is the (highly unlikely) leakage of the paternal mtDNA from some Neanderthal (who managed get far enough south to interbreed with L2'3'4'5'6).
    Last edited by Jean M; 11-13-2013 at 05:58 PM.

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    Quote Originally Posted by Jean M View Post
    Doesn't work at all. The Neanderthals do not carry L2'3'4'5'6. They simply have two substitutions in common with L2'3'4'5'6
    .

    No need to be so categorical. Under the hypothesis that L2'3'4'5'6 introgressed from Neandertals, the absence of all other mutations that define the L2'3'4'5'6 clade in modern humans on European Neandertal sequences only means that on modern humans they arose after the introgression. Whatever modern humans had before got replaced by this Neandertal-derived clade. And this clade migrated to Africa as the presence of a basal M1 lineage in Africa and a basal L6 lineage outside of Africa suggest. L1 and L0 are out of the picture and may have also introgressed into modern Afrcian populations from archaic Africans.

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    Quote Originally Posted by German Dziebel View Post
    .No need to be so categorical. Under the hypothesis that L2'3'4'5'6 introgressed from Neandertals, the absence of all other mutations that define the L2'3'4'5'6 clade in modern humans on European Neandertal sequences only means that on modern humans they arose after the introgression. Whatever modern humans had before got replaced by this Neandertal-derived clade. And this clade migrated to Africa as the presence of a basal M1 lineage in Africa and a basal L6 lineage outside of Africa suggest. L1 and L0 are out of the picture and may have also introgressed into modern Afrcian populations from archaic Africans.
    Can you tell us what your definition of genetic introgression is?

    Also, are you saying that events at 2758 and 7146 for the base of one of your trees?
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    Introgression, I believe, is the transfer of genetic material outside the normal mtDNA and nuclear DNA inheritance process whereby in a introgressive hybridization event a sequence is grafted onto another.

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    Quote Originally Posted by Richard A. Rocca View Post
    Can you tell us what your definition of genetic introgression is?
    I keep the exact content of the term "introgression" open. It depends on how we end up treating Neandertals or other archaic populations - as extinct populations within our own species or as different species. In the former case, introgression would mean simply admixture between two previously isolated populations (recall Polynesians some of whom are almost fixed at Y-DNA C2 but it's an ancient lineage they picked up from a replaced population in Near Oceania and not an authentic Asian lineage); in the latter a more complex process of hybridization with backcrossing.

    Quote Originally Posted by Richard A. Rocca View Post
    Also, are you saying that events at 2758 and 7146 for the base of one of your trees?
    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.

    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.

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    Quote Originally Posted by parasar View Post
    Introgression, I believe, is the transfer of genetic material outside the normal mtDNA and nuclear DNA inheritance process whereby in a introgressive hybridization event a sequence is grafted onto another.
    Introgression initially meant a specific kind of selective breeding across species, particularly plants:
    ---
    Introgression, also known as introgressive hybridization, in genetics (particularly plant genetics) is the movement of a gene (gene flow) from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species.
    ---

    If we extrapolate the definition to humans, and to natural selection rather than guided breeding, we end up with the notion of a specific highly advantageous mutation that jumps from one population group to another, in a 2-step process of hybridization followed by natural selection. An example is described in this paper: "Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage".

    Population geneticists extend the defintion even further to refer to a specific genetic pattern which has jumped from one population group to another by any means--i.e., with or without the operation of natural selection. So for example, a population geneticist might claim that R1a-CTS6 (the so-called Ashkenazi Levite clade) introgressed into the ancient or medieval Jewish community from another group.

    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.
    Last edited by lgmayka; 11-14-2013 at 12:17 AM.

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    Quote Originally Posted by lgmayka View Post
    An example is described in this paper: "Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage".
    Certainly wasn't from Neanderthals. They didn't carry the variant D.

    As I recall that paper was one several guessing what wonderful things we might have inherited from Neanderthals which turned out incorrect on the publication of the Neanderthal genomes.
    Last edited by Jean M; 11-14-2013 at 12:46 AM.

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