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  • Ancient Lineage?

    This may be a stupid question but how do we know what sequence is the oldest even if we know the mutation rate? If we examine for example two mDNA samples using 3,000 base pairs and they show a difference how do we know that one is from an older vs a newer lineage? I mean they still both have the same number of base pairs. Furthermore, how do we know what the oldest lineage is from which to compare the differences and construct the tree?

    Does this makes sense?

  • #2
    Originally posted by JTR View Post
    This may be a stupid question but how do we know what sequence is the oldest even if we know the mutation rate? If we examine for example two mDNA samples using 3,000 base pairs and they show a difference how do we know that one is from an older vs a newer lineage? I mean they still both have the same number of base pairs. Furthermore, how do we know what the oldest lineage is from which to compare the differences and construct the tree?

    Does this makes sense?
    The short answer is EXTREME mathematics:

    http://en.wikipedia.org/wiki/Computa..._phylogenetics

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    • #3
      Originally posted by aeduna View Post
      The short answer is EXTREME mathematics:

      http://en.wikipedia.org/wiki/Computa..._phylogenetics


      Cliff Notes Please! No I am gonna read it - hopefully I did not bite off more than I can chew.

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      • #4
        A study was published earlier this year - see http://ac.els-cdn.com/S0002929712001...b0cdbd6e271ccf - which compared full mitochondrial sequences of almost 19,000 humans across all known haplogroups/subclades (many of them FTDNA customers) to the full mitochondrial sequences of Neanderthals. Since Neanderthals are the closest hominid species to humans, this allowed the scientists to see which mtDNA haplogroup is the closest to Neanderthal, meaning having the least differences. The haplogroup with the least differences would be the oldest human mtDNA haplogroup.

        This also allowed the study to scientically determine the tree for human mitochondrial haplogroups, based on differences from the root of the tree, haplogroup L0. This was no surprise to anyone, since this is a sub-Saharan African haplogroup and coheres with the out-of-Africa theory for modern humans, which was already widely accepted.

        By the way, the lead scientist on this study is Dr. Doron Behar, a leading expert on mtDNA and a member of FTDNA's Scientific Advisory Board - http://www.familytreedna.com/about.aspx
        Last edited by MMaddi; 23 October 2012, 12:26 AM.

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        • #5
          Originally posted by MMaddi View Post
          A study was published earlier this year - see http://ac.els-cdn.com/S0002929712001...b0cdbd6e271ccf - which compared full mitochondrial sequences of almost 19,000 humans across all known haplogroups/subclades (many of them FTDNA customers) to the full mitochondrial sequences of Neanderthals. Since Neanderthals are the closest hominid species to humans, this allowed the scientists to see which mtDNA haplogroup is the closest to Neanderthal, meaning having the least differences. The haplogroup with the least differences would be the oldest human mtDNA haplogroup.

          This also allowed the study to scientically determine the tree for human mitochondrial haplogroups, based on differences from the root of the tree, haplogroup L0. This was no surprise to anyone, since this is a sub-Saharan African haplogroup and coheres with the out-of-Africa theory for modern humans, which was already widely accepted.

          By the way, the lead scientist on this study is Dr. Doron Behar, a leading expert on mtDNA and a member of FTDNA's Scientific Advisory Board - http://www.familytreedna.com/about.aspx
          Nice! I will definately read that. But how did they do it before this study? And how is it helpful within a single haplogroup? How do you know that one sub-clade is not ancestral to the one before it? In reading Sykes he says things like - he knows Ursula is the oldest because the average mutations of Ursulians is 2.5 compared to Ursula. Thus 2.5 x the mutation rate (20,000 yrs) = 45,000 yrs. But who is Ursula, since she does not really exist, and how did they come to this as the standard by which to measure the number of changes to conclude that a certain number of mutations are subsequent to this?

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          • #6
            Originally posted by JTR View Post
            Nice! I will definately read that. But how did they do it before this study? And how is it helpful within a single haplogroup? How do you know that one sub-clade is not ancestral to the one before it? In reading Sykes he says things like - he knows Ursula is the oldest because the average mutations of Ursulians is 2.5 compared to Ursula. Thus 2.5 x the mutation rate (20,000 yrs) = 45,000 yrs. But who is Ursula, since she does not really exist, and how did they come to this as the standard by which to measure the number of changes to conclude that a certain number of mutations are subsequent to this?
            It's not that difficult. Once you've established what's the haplogroup of "mitochrondrial Eve" (L0), then you compare the full sequences of every other haplogroup/subclade to the full sequence of L0. You note a chain of mutations from the bases of the L0 full sequence. That allows you to construct a tree, using various mutations from one level to another as a diagram of the development of haplogroups/subclades.

            It's useful to look at the mtDNA tree and see how that works - http://www.phylotree.org/tree/main.htm Take, for example, the subtree for L - http://www.phylotree.org/tree/subtree_L.htm

            At the top of that subtree, you see L0. The next level shows you the mutations from L0 that define L0a'b'f'k. If you go further down the tree to L1, you'll see the specific mutations from L0 that occurred to enable us to define L1.

            Making a tree is really just an exercise in determining the order of mutations from one level to the next, which allows you to see which haplogroup or subclade descends from an earlier one. It's really not much different from making a family tree, using birth records which give you the name of the baby and its parents. The mutations are the birth records of haplogroups/subclades, both for the yDNA and mtDNA trees.

            As far as Sykes' claim in the "Seven Daughters of Eve" that U is the oldest haplogroup, he's obviously wrong. I'm not surprised by that. Sykes is more of a "pop scientist"; he's not a serious scientist like the authors of the study who actually did the analytical work to methodically establish a true mtDNA tree. By the way, if you look at the basic mtDNA tree I linked to above - http://www.phylotree.org/tree/main.htm - notice where haplogroup U sits on the tree. It's descended from R, which is descended N, which is descended from L3. That hardly looks like the oldest haplogroup. U is mainly a West Eurasian haplogroup, more European than anything. Given that modern humans came out of Africa, it's hard to believe that a West Eurasian, mainly European, haplogroup would be the oldest haplogroup!

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            • #7
              Originally posted by MMaddi View Post
              It's not that difficult. Once you've established what's the haplogroup of "mitochrondrial Eve" (L0), then you compare the full sequences of every other haplogroup/subclade to the full sequence of L0. You note a chain of mutations from the bases of the L0 full sequence. That allows you to construct a tree, using various mutations from one level to another as a diagram of the development of haplogroups/subclades.
              But that's just it how did they establish L0? L0 was around before the study you posted earlier. I understand that once you have a baseline it is easy to construct a tree - my point is apart from assuming or guessing - how do they establish this baseline since they do not actually have 'Mitochrondrial Eve.'

              Making a tree is really just an exercise in determining the order of mutations from one level to the next, which allows you to see which haplogroup or subclade descends from an earlier one. It's really not much different from making a family tree, using birth records which give you the name of the baby and its parents. The mutations are the birth records of haplogroups/subclades, both for the yDNA and mtDNA trees.
              That only works if you have the standard from which to measure these changes. Genealogical records have 'time indicators' on them. Where are the these on any mtDNA? Every one of them has the same number of bases. Just because the bases are arranged differently does not tell you the order in which those changes took place - that is that 'mtDNA A' is older than 'mtDNA B' because it has more mutations or a certain type of mutation - you need the baseline mtDNA for that.

              As far as Sykes' claim in the "Seven Daughters of Eve" that U is the oldest haplogroup, he's obviously wrong. I'm not surprised by that. Sykes is more of a "pop scientist"; he's not a serious scientist like the authors of the study who actually did the analytical work to methodically establish a true mtDNA tree. By the way, if you look at the basic mtDNA tree I linked to above - http://www.phylotree.org/tree/main.htm - notice where haplogroup U sits on the tree. It's descended from R, which is descended N, which is descended from L3. That hardly looks like the oldest haplogroup. U is mainly a West Eurasian haplogroup, more European than anything. Given that modern humans came out of Africa, it's hard to believe that a West Eurasian, mainly European, haplogroup would be the oldest haplogroup!
              I should have made it clear that Sykes was talking about U being the oldest among the Seven Daughters - not the oldest per-se. I do not know why you think he is a pop-scientist?

              Look I do not doubt that they have good reasons for their tree - I am wanting to understand why and how they arrived at it without just assuming they found the Baseline from which to measure.
              Last edited by JTR; 23 October 2012, 01:12 PM.

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              • #8
                Originally posted by JTR View Post
                But that's just it how did they establish L0? L0 was around before the study you posted earlier. I understand that once you have a baseline it is easy to contruct a tree - my point is apart from assuming or guessing - how do they establish this baseline since they do not actually have 'Mitochrondrial Eve.'
                My first post in this thread discussed the methodology of the study, which compared human full sequences to Neaderthal full sequences. That's what scientifically established L0 as the haplogroup of "mitochdondrial Eve." It's true that it would be better to have ancient DNA from 100,000+ years ago to establish this, but the study is a pretty robust proof.

                Previous to this study, it had been fairly well established through archaeology and anthropology that modern humans originated in Africa. So, yes, before this study, it had merely been an assumption (a better term is inference) that L0 is the root of the mtDNA tree. And that was based on the fact that other African haplogroups could be clearly seen to be descended from L0 based on the various mutations from the L0 bases these other haplogroups have. With this study that compared human and Neanderthal full sequences, that nails down that L0 is the oldest mtDNA haplogroup of modern humans.

                Originally posted by JTR View Post
                That only works if you have the standard from which to measure these changes. Genealogical records have 'time indicators' on them. Where are the these on any mtDNA? Every one of them has the same number of bases. Just because the bases are arranged differently does not tell you the order in which those changes took place - that is that 'mtDNA A' is older than 'mtDNA B' because it has more mutations or a certain type of mutation - you need the baseline mtDNA for that.
                Population geneticists don't look at yDNA or mtDNA SNP mutations in isolation. That's why full genome sequences of mtDNA are so important. You can see all the mutations that are there.

                Phylogenetics allows scientists to look at what are essentially "packets" of mutations that are like a trail leading up the tree. (It's the same thing that zoologists do to infer the descent of species in the animal world. They may use different measures, say physiology, but it's the same process of drawing a tree.) No, there's no time stamp on the mutation, but the presence of one mutation in relation to mutations that have been observed in an upstream haplogroup/subclade allows scientists to infer with a great deal of precision what the order is in the mutations and how some define a younger, downstream subclade.

                This is relatively easy to do with mtDNA, which only has 16,000+ bases and makes full genome sequencing possible. It's a little more difficult with yDNA, with millions of bases that can be sequenced. It's only in the last several years that even a relatively small number of men have had full yDNA sequences. So, making a haplogroup tree for yDNA is a bit more complicated. Every time a new ySNP is discovered through the Walk through the Y at FTDNA or some new full yDNA sequences, there is usually a need to redraw parts of the yDNA haplotree, based on the new SNP discoveries. But there's enough knowledge already gained in the last 20 years, especially the last 5, that the yDNA tree is accurate enough that the tweaking based on new SNPs will decline as more knowledge is gained.

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                • #9
                  Thanks for your responses MMaddi. I will certainly get to reading the material you posted.

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                  • #10
                    To add to what others have said, saying that L0 is the oldest group doesn't mean that currently living L0 closer to Mitochondrial eve. A current L0 person has on average the same number of mutations from mitochondrial Eve than an H person.

                    As is clear from the messy nomenclature of the mtdna, it took some time and a lot of data to make sense of the tree. At the beginning, scientists defined certain haplogroups based on the studies they were doing, without understanding the exact relation to each other. Only later did they understand these relations. But the names stuck.

                    cacio

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                    • #11
                      Originally posted by MMaddi View Post
                      It's not that difficult. Once you've established what's the haplogroup of "mitochrondrial Eve" (L0), then you compare the full sequences of every other haplogroup/subclade to the full sequence of L0. You note a chain of mutations from the bases of the L0 full sequence. That allows you to construct a tree, using various mutations from one level to another as a diagram of the development of haplogroups/subclades.

                      It's useful to look at the mtDNA tree and see how that works - http://www.phylotree.org/tree/main.htm Take, for example, the subtree for L - http://www.phylotree.org/tree/subtree_L.htm

                      At the top of that subtree, you see L0. The next level shows you the mutations from L0 that define L0a'b'f'k. If you go further down the tree to L1, you'll see the specific mutations from L0 that occurred to enable us to define L1.

                      Making a tree is really just an exercise in determining the order of mutations from one level to the next, which allows you to see which haplogroup or subclade descends from an earlier one. It's really not much different from making a family tree, using birth records which give you the name of the baby and its parents. The mutations are the birth records of haplogroups/subclades, both for the yDNA and mtDNA trees.

                      As far as Sykes' claim in the "Seven Daughters of Eve" that U is the oldest haplogroup, he's obviously wrong. I'm not surprised by that. Sykes is more of a "pop scientist"; he's not a serious scientist like the authors of the study who actually did the analytical work to methodically establish a true mtDNA tree. By the way, if you look at the basic mtDNA tree I linked to above - http://www.phylotree.org/tree/main.htm - notice where haplogroup U sits on the tree. It's descended from R, which is descended N, which is descended from L3. That hardly looks like the oldest haplogroup. U is mainly a West Eurasian haplogroup, more European than anything. Given that modern humans came out of Africa, it's hard to believe that a West Eurasian, mainly European, haplogroup would be the oldest haplogroup!
                      Maddi writes ,"Sykes is more of a "pop scientist"; he's not a serious scientist like the authors of the study who actually did the analytical work to methodically establish a true mtDNA tree. "
                      But, a truly serious scientist is Sykes, one of the trailblazers, to be forgiven for the poetic but "Pop" public conclusions which had the effect of making that early solid painstaking work digestible by the public. And we all benefited from the financial support of
                      Genomology that they invited!

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                      • #12
                        A related note -

                        Researchers had been using the chimpanzee genome as a reference to set the clock rate for mitochondrial mutation as chimps are the primate closest to humans.

                        Obviously, no one knows with dead certainty all that occurred in the past but one has to put-up some reasonable assumptions to even get a handle on the puzzle ... and then one corrects as new data or more reasonable assumptions become available.

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