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  • rainbow
    replied
    dna studies on why mutations happen

    Thanks Nathan M

    I think it would be a good idea to compare the dna of various generations or siblings, some who stayed put, and some who have wanderlust/moved a lot/travelled a lot to see how many markers (and which ones, and how, and when) have mutated. And to test the dna of people exposed to radiation and dangerous chemicals, and people who had blood transfusions and transplants.

    And for mtdna too. I wouldn't be surprised if the reason I have no FGS matches is because of a recent mutation that occurred with my grandmother, or my mom, or me.
    Last edited by rainbow; 21 February 2011, 02:58 PM.

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  • nathanm
    replied
    Originally posted by rainbow View Post
    There is someone on the forum whose brother is a 65/67 match to their paternal uncle. Two markers are different.

    A question I'd like an answer to (and fits in with the topic of thread) is.... Do mutations occur as a result of moving to another place? Do people who move away develop new mutations (or in their offspring born at the new location)? Or, do some people develop mutations during their lifetime and they feel compelled to move away when that is happening or has happened?

    I think it is odd that those who stayed stuck, living wheverer they are, didn't mutate further. Why haven't all men mutated to a new modern R1b subclade? Are men in Africa stuck in the old subclade because they stagnated and didn't move away?

    If moving doesn't cause mutations, then what does? I don't believe it is time alone.

    I hope someone is doing a study on that.
    I don't understand it completely myself, but I believe mutations are for the most part, completely random. They can be caused by external factors, however. So moving to another location won't cause mutations by itself, but something in the environment there might. For instance, different kinds of radiation can cause mutations, certain chemicals are known mutagens, viruses alter their hosts DNA, and I'd guess bacteria or other biological factors can also cause mutations. This shouldn't be a cause for alarm, though. Each one of the three trillion or so cells in our body has a copy of our DNA in its nucleus, and many hundreds or even thousands of our mtDNA. Any of these DNA copies can and do mutate, but a mutation can only be passed if it's in a sperm or egg cell.

    Most mutations, like known STRs and SNPs used in genetic genealogy, are harmless. Detrimental mutations aren't always passed on, because the cells themselves cease to function, or the embryo won't survive gestation.

    And yes, there's tons of research being done in practically every aspect of this field.

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  • rainbow
    replied
    There is someone on the forum whose brother is a 65/67 match to their paternal uncle. Two markers are different.


    A question I'd like an answer to (and fits in with the topic of thread) is.... Do mutations occur as a result of moving to another place? Do people who move away develop new mutations (or in their offspring born at the new location)? Or, do some people develop mutations during their lifetime and they feel compelled to move away when that is happening or has happened?


    I think it is odd that those who stayed stuck, living wheverer they are, didn't mutate further. Why haven't all men mutated to a new modern R1b subclade? Are men in Africa stuck in the old subclade because they stagnated and didn't move away?

    If moving doesn't cause mutations, then what does? I don't believe it is time alone.

    I hope someone is doing a study on that.
    Last edited by rainbow; 21 February 2011, 01:04 PM.

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  • Brunetmj
    replied
    HTML Code:
     I love your last sentence; that's a great character trait
    Well not according to my gf.
    If I use the G (genectics)word again
    I may be injured.

    Leave a comment:


  • nathanm
    replied
    Originally posted by Brunetmj View Post
    Again another good answer and one I can grasp. My issue at the beginning of the thread was how (to use your nice example) population 1(not shown in your chart) , can be shown to predate Smith1 and how population 1 predates all others. I think what I understand is that population 1 has more mutations than more recent groups. So it has to be more ancient
    It's not a matter of which population has more or less mutations. All we can see today are the differences. There's no way to immediately tell what the original haplotype was, or what are the mutations. But if you use the process in my example on a huge, macro level, you can theoretically build a tree for the entire world population. Of course, there are more difficulties with such a huge data-set. First, you'd need a sufficiently large, random sample, distributed relatively uniformly across the planet. Second, constructing such a tree manually would be virtually impossible. Fortunately, there's software that can do much of the heavy lifting. There's even a free (as in beer) software application, called Network, to build cladograms (unfortunately Windows only). Finally, there are the problems of back-mutation and the same mutation emerging in different populations independently. That's where interpretation of the data comes in, and requires a human in the loop. Like I said before, this whole field is bleeding edge, so lots of research is being conducted, and published continually. Like any scientific field, new research either supports or undermines previous interpretations, and the predominant theories have changed over time.

    Originally posted by Brunetmj View Post
    Secondly how did this smith group eventually emerge from population 1 through intermediate populations which is at the heart of the national geographic theory.I do see how population 1 would lose any trace of it's presence by the time it reaches Smith.
    Migration, that's where geography plays a big role. For one, really obvious example, look at the migration into North America several thousand years ago. As I understand it, the first humans into the continent crossed the Bering Strait by land or maybe ice. But once that "bridge" was gone, whether due to climate, tectonic shift, or whatever, they were separated from their parent population in Asia.

    Originally posted by Brunetmj View Post
    I would not describe myself as a complete layman. I did take a lot of hard science at the university level including genetics. However it was a long time ago and I think we looked at fruit flys and I cut that class besides.
    I will continue to read more and learn,eventually it will come to me. What I lack in brilliance I make up with tenacity.
    Then you've got a leg up on me, I took the one, required biology class with a lab in college. I love your last sentence; that's a great character trait!

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  • Brunetmj
    replied
    Again another good answer and one I can grasp. My issue at the beginning of the thread was how (to use your nice example) population 1(not shown in your chart) , can be shown to predate Smith1 and how population 1 predates all others. I think what I understand is that population 1 has more mutations than more recent groups. So it has to be more ancient
    Secondly how did this smith group eventually emerge from population 1 through intermediate populations which is at the heart of the national geographic theory.I do see how population 1 would lose any trace of it's presence by the time it reaches Smith.
    I would not describe myself as a complete layman. I did take a lot of hard science at the university level including genetics. However it was a long time ago and I think we looked at fruit flys and I cut that class besides.
    I will continue to read more and learn,eventually it will come to me. What I lack in brilliance I make up with tenacity.

    Leave a comment:


  • nathanm
    replied
    Originally posted by Brunetmj View Post
    Rainbow- interesting thoughts. When I first asked my question at the beginning of this thread I thought that my y DNA would show African decent followed by central Asian followed by European in a kind of sequence.
    By peoples answers it appears that who came first is determined, according to this particular viewpoint,by the number of mutations on a particular and unique sequence of DNA (at least as I understand the answers). This disturbs me also but haven't had enough time yet to know why. It does have parsimony ( simplest explanation) but raises a hundred questions.
    There's lots of good information on this thread, but I'm not sure anyone directly answered your original question, so I'll give it a try. As an example, let's imagine a Smith DNA project with several men who've had a Y-DNA test. They're trying to determine if they're related, specifically if they descend from a common paternal ancestor. The following table shows their haplotypes (only 5 markers for simplicity):
    Smith A: 13-24-14-11-11
    Smith B: 13-24-14-10-11
    Smith C: 14-24-14-10-11
    Smith D: 13-24-14-11-11
    Smith E: 14-23-15-12-10
    Right away, it should be obvious Smith A & D are more closely related than any of the others. They match at all 5 markers, so probably descend from a common ancestor, we'll call him Smith X.

    A second easy observation is Smith E is not closely related to the others. Out of 5 markers, the most he matches is 1, with C. So he's either the result of an NPE, or more likely with a common surname like Smith, just a different line which independently took that surname.

    Next, Smith B matches A & D on 4 markers, and also C, but on different markers. The mutation in B is also shared by C, so they both probably descend from a common ancestor, we'll call him Smith Y. But sometime in the succeeding generations, one of C's ancestors passed on an additional mutation.

    We can also conclude A & D's ancestor X, and B & C's ancestor Y, share a common ancestor even further back, we'll call him Smith Z. We can't guess his haplotype from so few samples, but the branch from any future Smiths who test can be determined by which haplotype they match better. Any further mutations could show additional branching in the tree. Here's the tree for this example (I made the line from Y-->C longer to represent the extra mutation.):
    Code:
         Z
        / \
       /   \
      X     Y
     / \   / \
    A   D B   \
               C
    That's how they constructed the Y-DNA tree, on a micro scale. A simple example like this one can be deciphered pretty quickly, but many more samples might require a cladogram as an intermediate step. In a cladogram for this example, A & D would share a node. B would be one step removed from that node, with C one further node along the same line. You can even show E on the same cladogram, on a separate line off C, with some indication of how many steps it is removed. I attached a simplified cladogram.

    Originally posted by Brunetmj View Post
    I just need to read more and process it.
    You and me both. Genetic genealogy is on the bleeding edge of science and technology. With a few exceptions, there just isn't very much material for the layman. I highly suggest the book "Trace Your Roots with DNA" by Megan Smolenyak and (forum member) Ann Turner. It's a good overview of the whole field. Then, dive into the academic papers written on the subject; many are linked from the FTDNA website.
    Attached Files

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  • Brunetmj
    replied
    Thank you everyone. I can follow each post individually as they are clear to me.
    However I am having trouble synthesizing them
    into a whole in relationship to the theory proposed by national geographic. There are a number of good links and with some reading and time to process it will come to me. I always was the slow one in my class

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  • MMaddi
    replied
    Originally posted by jloe View Post
    Greater time-> greater opportunity for mutations to occur.

    The parent haplogroup, in this analogy Smith, has fewer mutations than the descendants. The passage of time confers the opportunity for more mutations to occur.
    And when a mutation occurs, then it defines a new haplogroup or subclade of a haplogroup. So, for instance, when a man in haplogroup A had the M60 mutation, he was no longer in haplogroup A, but was the founder of haplogroup B. Or, when a man in haplogroup J had the M267 mutation, he was no longer in haplogroup J, but was the founder of the J1 subclade - see http://www.isogg.org/tree/ISOGG_HapgrpJ.html

    So, as jloe wrote, the younger haplogroups or subclades have at least one more mutation than the previous level. It was the new mutation the founder had that distinguished the new haplogroup or subclade from the haplogroup or subclade ancestral to it.

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  • jloe
    replied
    The molecular clock is the core concept I think for tracing the age of haplogroups: http://en.wikipedia.org/wiki/Molecular_clock

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  • jloe
    replied
    MMaddi,

    I'm fairly certain the Genographic Maps have not been updated at all in years.
    So, yes what MMaddi said about R1b means that the R1b map in the Genographic Project
    is incorrect.

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  • MMaddi
    replied
    Originally posted by rainbow View Post
    The ydna and mtdna migration maps at the Genographic Project are a must-see!

    If you see the maps it will make sense. You can hover your mouse over it or click on the ydna lines you want to see.
    I haven't checked the Genographic Project migrations map and timeline recently, but even as recently as last year their map/timeline was mistaken about the R1b haplogroup. That's the largest haplogroup among European men, through its subclade, R1b1b2.

    The old orthodoxy says that R1b was in Europe before and during the Ice Age and that R1b men were the cave painters of 30,000+ years ago. This is just plain wrong and in the last few years population geneticists have significantly lowered their estimates of the age of R1b.

    Dr. Hammer of the University of Arizona (which does DNA testing for FTDNA) and his team came out with a study in 2008 (see http://www.familytreedna.com/pdf/Kar...-all-GR508.pdf ) which estimates that R1, parent haplogroup of R1b, is only about 18,000 years old. Since most believe that R originated in Central Asia, it seems impossible in terms of time and geography that the European cave painters were R1b men.

    So, if the Genographic Project map/timeline is still portraying R1b as the haplogroup of men in Ice Age Europe, that should just be ignored.

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  • jloe
    replied
    Originally posted by Brunetmj View Post
    [HTML]
    1. Smith -> mutates> adds e
    2. Smithe -> mutates> adds e
    3. Smithee -> mutates> adds y][/1. Smith -> mutates> adds e
    Smith has fewer mutations than smithee which means he is the more ancient which confuses me given the other answers
    Greater time-> greater opportunity for mutations to occur.

    The parent haplogroup, in this analogy Smith, has fewer mutations than the descendants. The passage of time confers the opportunity for more mutations to occur.

    To use another analogy, atoms under radioactive decay at a predictable rate. If we find an isotope of Carbon in an old piece of human remains, we can date the remains by the amount of Carbon - 14 decay that has occurred. It is predictable but the rate is probabilistic. http://archaeology.about.com/od/rterms/g/radiocarbon.htm
    Last edited by jloe; 20 February 2011, 11:13 PM.

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  • Brunetmj
    replied
    [HTML]
    1. Smith -> mutates> adds e
    2. Smithe -> mutates> adds e
    3. Smithee -> mutates> adds y][/1. Smith -> mutates> adds e
    2. Smithe -> mutates> adds e
    3. Smithee -> mutates> adds ]
    I like the analogy but it means
    Smith has fewer mutations than smithee which means he is the more ancient which confuses me given the other answers

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  • MMaddi
    replied
    Originally posted by Brunetmj View Post
    [HTMLOne model consistent with the data ][/HTML]
    I guess I am not asking my question well. I am not really asking about who first populated France.
    I am asking what data is being used to support a genetic migratory theory. So let me try to rephrase my question. First , haplotypes are based on the sequence of ACTG. Then the age of a particular haplotype is based on the number of mutations within it. More mutations the more ancient the haplotype. All subject to traditional error probability and scientific debate.. Is this essentially correct?
    To help you understand the progression from the oldest haplogroup to the younger ones, which is generally a journey from Africa to Asia and then to Australia and Europe and lastly to the New World, it's useful to look at the yDNA haplogroup tree at http://www.isogg.org/tree/ISOGG_YDNATreeTrunk.html

    In this tree, the roots (origin) are at the top and the younger haplogroups are found below. (This gives you the terms "upstream" for older and "downstream" for younger.) Haplogroup A is the oldest and is found at significant levels only in Africa. It's defined by the SNPs M91 and P97, which are mutations at one specific location on the y chromosome. In turn, B, also found at significant levels only in Africa, is defined by the SNPs M60, M181, P85 and P90, which are mutations at specific locations from the original (ancestral) values found in A. You can find more information about specific SNPs at http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html - including their location on the y and the ancestral value (A, C, G or T) by clicking on the rs number.

    It's not until you get to the C haplogroup that you find significant populations in the haplogroup outside Africa. Men in this haplogroup have the M91 and P97 SNPs found in haplogroup A, but they have other SNPs (P143, M130/RPS4Y711, M216, P184, P255 and P260) not found in A. Therefore, A is the older haplogroup. Since A and B are found at significant levels only in Africa and C is found outside Africa, it strongly suggests that modern humans developed in Africa and migrated from there into Asia, where haplogroup C is found. Scroll down at http://www.isogg.org/tree/ISOGG_HapgrpC.html to read the "Notes" which discuss this.

    There's more details involved with all the other haplogroups, but that should give you an idea of how to use the haplogroup tree and SNP index to understand the migrations of humans over tens of thousands of years.

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