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Thread: STR Wars, GDs, TMRCA estimates, Variance, Mutation Rates & SNP counting

  1. #71
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    Quote Originally Posted by Mikewww View Post
    Mark, I'm updating the U106 file but it'll probably take a day or two yet. There must be something interesting about Scotland's haplotypes. I don't get the higher variance but I think you are getting higher TMRCAs. It must be related to specific slower markers that are more varied there. Anyway, let me collect the data first before we attempt any further analysis.
    I pulled your latest U106 data and posted a R1b dataset in my TRMCA Estimator sheet link posted here:
    http://www.anthrogenica.com/showthre...ll=1#post13898

    Lets do some deeper variance analysis with it when you have some time.

    MJost

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  2. #72
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    Quote Originally Posted by Mikewww View Post
    A picture is sometimes easier to understand than words so here is an illustration of how people from different haplogroups only related thousands of years ago can end up with the same STR value even though their haplogroups may have started out differently for that STR.
    Visuals sure make it easier to get the convergence (overlapping) concepts.
    This shows why it is important to have more STRs. The more off-modal or unusual STR values you have in common with a particular variety/group the more likely you really are in that group.
    In my own Variety 1130-A1's that generally have around 16 Off-modal markers from the L21 founder .
    If I ever get out of DF13* status all of my 40 plus haplotypes might just follow along with me depending on the age of the new SNP(s) found.

    Mutation Rates are sorted slower to faster left to right

    DYS: 531 / 497 / 511 / 441 / 19 / 385a / 513 / 447 / 552 / 446 / 557 / 533 / 464d / 534 / 449 / 576
    M-L21: 11 / 14 / 10 / 13 / 14 / 11 / 12 / 25 / 24 / 13 / 16 / 13 / 17 / 15 / 30 / 18
    1130A1: 12 / 15 / 11 / 14 / 15 / 12 / 11 / 24 / 25 / 14 / 15 / 12 / 18 / 16 / 31 / 17

    Off-Modal ranges:
    531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36, 712=>21 (533=<13)

    Mike, maybe a new variety designation is due.


    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  3. #73
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    Quote Originally Posted by MJost View Post
    In my own Variety 1130-A1's that generally have around 16 Off-modal markers from the L21 founder.
    MJost
    I have yet to be persuaded that modals tell us the marker values of the founder. They tell us about his most numerous survivors -- in the case of L21, several thousand years later. On the other hand, shared off-modals are really good pointers to subclades, I wouldn't argue with that.

  4. #74
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    Quote Originally Posted by razyn View Post
    I have yet to be persuaded that modals tell us the marker values of the founder. They tell us about his most numerous survivors ...
    I agree 100%, however, at least they give us a starting point for determining the ancestral values.

    ... and you can do more work with them. For instance, you can look at the modals for the peer and paragroup subclades. If they all match up with the modal for the subclade in question, your triangulation is about as good as we can get for an ancestral value.

    Such would be the case for most of the Super WAMH modal markers. You can look at L11*, U106, Z18, Z381, P312, DF27, U152, L21 and with a little bit of triangulation you can get a pretty good fix on the ancestral values for some of these.

  5. #75
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    Mikwww do u have any idea what the STR of the 4,600 year old Bell Beaker R1b is. Do u have any info to show evidence that it is R1b L11. Because I know one was positive as M269 I think it would make total sense the Bell Beaker R1b is connected with 50% R1b L11 in modern western Europe and would be under R1b L11 or at least R1b L51. Also I emailed u access to my raw data with SNP's from geno 2.0 hopefully it can help figure out if I am for sure P312 or Df27.

  6. #76
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    Quote Originally Posted by razyn View Post
    I have yet to be persuaded that modals tell us the marker values of the founder. They tell us about his most numerous survivors -- in the case of L21, several thousand years later. On the other hand, shared off-modals are really good pointers to subclades, I wouldn't argue with that.
    The modal haplotype does not necessarily correspond with the ancestral haplotype but the "modal haplotype" is simply the occurring haplotype in the set of haplotypes under study. If possible, it requires an enforcement of the SNP tree containment to eliminate convergence, along with consideration of any sub-clade structure(s) all affect the statistical confidence such as the effect of M222 subclade on the entire L21 clade. The larger the set of haplotypes the more accurate the Modal will be. Ken N is the champion of the modal method.

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  7. #77
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    I'm not objecting to the foundation stones of the STR variance method, only to the imprecise language use. In this case, "16 off-modal markers from the L21 founder." It's really just 16 off-modals from the L21 modal, and we don't know the L21 founder's STR marker values -- though the modal surely points in their direction, and is probably (i.e. statistically) right for quite a few of them. In older and/or more highly fragmented haplogroups (like L21) there have probably been enough back mutations (now invisible), lineage extinctions, migrations to the country doing most of the testing, and other genetic issues to skew the modal somewhat in favor of the descendants time has proven to be the most successful breeders within the sampled population. And we should not assume that their averaged haplotype (aka modal) is that of the founder. It's meaningful, but that's not what it means.

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    Quote Originally Posted by Fire Haired View Post
    Mikwww do u have any idea what the STR of the 4,600 year old Bell Beaker R1b is. Do u have any info to show evidence that it is R1b L11. Because I know one was positive as M269 I think it would make total sense the Bell Beaker R1b is connected with 50% R1b L11 in modern western Europe and would be under R1b L11 or at least R1b L51. Also I emailed u access to my raw data with SNP's from geno 2.0 hopefully it can help figure out if I am for sure P312 or Df27.
    Are you talking specifically of the R1b Bell Beaker skeleton found in Kromsdorf, Germany? I think there is limited STR information available, but I think you can find it through internet searches for the related research paper(s). It may take a couple of variations in search words but I have in my notes the name of the paper is "Emerging Genetic Patterns of the European Neolithic: Perspectives From a Late Neolithic Bell Beaker Burial Site in Germany" by Lee, published in 2012.

    If instead, you are wanting a guess at the ancestral STR values for the R1b-L11 most recent common ancestor, I think they can best be estimated by following the method I outlined in an earlier post on this thread.
    Quote Originally Posted by Mikewww View Post
    I agree 100%, however, at least they give us a starting point for determining the ancestral values.

    ... and you can do more work with them. For instance, you can look at the modals for the peer and paragroup subclades. If they all match up with the modal for the subclade in question, your triangulation is about as good as we can get for an ancestral value.

    Such would be the case for most of the Super WAMH modal markers. You can look at L11*, U106, Z18, Z381, P312, DF27, U152, L21 and with a little bit of triangulation you can get a pretty good fix on the ancestral values for some of these.

  9. #79
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    Mike, I know exactly where you are coming from.

    Mike:
    You are exactly on track. I've followed your work for 5 years and in fact used your work to understand the South Irish base haplotype. You encouraged someone to take on the South Irish project and I was the first to answer up. Alex Williamson has provided me much insight to questions regarding SNPs. Of course I primarily use Anatole's (Dr. Klyosov) work in my research. I also just confirmed Dr. Nordvedtís base haplotype of the South Irish with his primary and secondary marker sets. Understanding comparative TMRCA formulas (Anatole's and Dr. Nordvedtís in particular) is very interesting to me since both scientists take different paths to confirm areas that I incorporate in my research.

    SNPs have been overvalued because hobbyists can see them without reading or understanding anything else or simply repeat what others say without confirming the knowledge. That said, I am really starting to understand how building the STR signatures of base haplotypes and comparing them to SNPs really means while trying to clearly identify the South Irish base haplotype and the 4466 SNP and sub SNPs. SNPs occur randomly but are not inherited by the brothers, first cousins, uncles etc. so that a base haplotype can include those with and without the SNP. The base haplotype is higher in the tree. Pin pointing where this location is will naturally be a moving target because it is based on SNP testing and projected base haplotype STR signatures. I base the 4466 and South Irish haplotypes on member results who have tested + or - for SNPs so there is certainty and not speculation. There should be a continual feedback loop based on reassessment when new evidence is identified (every new 4466 + or - provides new evidence) and incorporated into the study. Every new +/- relevant SNP changes the base haplotype STR signature.

    The Geno 2.0 results (once the troubleshooting is complete) will provide invaluable evidence of the SNP hierarchy and the specific base haplotype analyses. Much work needs to be done for this to occur.

    The hobbyists have provided a wealth of SNP testing that has given more clarity to the phylogenetic trees for SNPs and base haplotype analysis.

    That said, much work needs to be done to answer these questions about SNPs and base haplotypes. This is the basis of my current research.

    What is it really all about? I believe it comes down to understanding a member's sub branch so they can see the best possible picture of their actual sub branch. Where did they come from? What group did they belong in? What is the migration pattern of their ancestors? Can they pinpoint a location so they can visit and say to themselves "my ancestors could very well have walked this path, lived in this town, or shared this common history"? This is the reason I overlap the research with family histories that can be compared and reviewed in the sub branch grouping. Curiously this is also the way scientists test their TMRCA theories.

    Sidebar:
    I first started my efforts trying to find clan or surname signatures. This turned not to be the rule of thumb. However, the very rare clan or surname signatures still may be possible to identify. In particular the Eoganacht Aine - O'Kirby surname, Eoganacht Locha Lein - Moriarty surname, Eoganacht Chaisil - Sullivan Mor. As with any science it's the bottleneck, the exception or error that proves a point. In this case it may be groups with fewer members. In identifying the 4466 and/or South Irish STR signature (they are not the same and where they are in relation to each other is still a moving target), I noticed that using primary and secondary marker sets that I have found possible uniqueness in the STR marker signatures of those with the Kirby, Moriarty or Sullivan Mor ancestry.

    These groups are not extinct but small in numbers which may hold the key to possible sub group STR signatures. I've also seen groupings of surnames in sub branches, however since I'm not absolutely convinced of the sub branches yet this remains to be seen. My current delay in building sub branches is that the Geno 2.0 SNP results need troubleshooting from the programming and system testing level and cannot yet be relied upon. Once the Geno 2.0 SNP results are stable, I'll first build the 4466 SNP hierarchy and then separate out those with the 4466 STR signature and sub SNP signatures before building sub branches. I have already seen excellent results that may prove that there is a strong relationship between STR signatures and the 4466 sub SNPs. This identified sub branch will likely have a TMRCA calculation that is in the reasonable range and may confirm that this sub branch is relevant within 300 years.

    I very likely will not be adding much input into this forum in the present since I have a mountain of work in front of me, however this sub forum is the basis of my research and I will be contributing in the future.

    Kathleen


    Quote Originally Posted by Mikewww View Post
    This may seem a little off track, but bear with me. This is about understanding MRCAs....

    What's the value of a haplogroup?

    What's the value of an SNP?

    You might be surprised to hear me say this but I think there is very little value in haplogroups and SNPs
    ... at least in and of themselves.

    A haplogroup is just a group of people with a common ancestor.

    An SNP is just a single nucleotide polymorphism, a mutation, that marks the group of people with a common ancestor. It is just a signpost on a branch of the human family tree. The true nature of the haplogroup of people, any commonality in culture, location, etc., many not align with the SNPs have marked the lineages. The SNP could mark either a subset or superset of the true group of people we care about.

    This gets into some notions about value and philosopical concerns, but these are the points I'm getting at.

    1) I do not care too much about all of the extinct lineages of mankind. There are many, many extinct lineages. On the Y chromosome/paternal side probably there are many, many more lineages that have gone extinct than those who survive.

    2) I do care about how we got here and how, where, when and why they did what they did to get us to where we are today.

    I think these notions are just conveying that what many hobbyists may care about most is the connection to genealogy and deeper ancestry.... and specifically our ancestry.

    The net is that the most recent common ancestors (MRCAs) of the various branches remaining today (and in recent history) are critical people to try understand. The more MRCAs we can understand better at more layers and branches in the tree, then the more we have a chance to understand our ancestry.

    I am not saying that all of the old extinct lineages were not important people or that SNPs are useless. I'm just trying to say they are most important in how they help us understand who we are and how we got here. They are just bread crumbs from an old trail.

    Superconducting supercolliders smash atoms and look at the residue of the accident to try to get more detail on the characteristics of the atom. In the case of genetics; the accidents, bottlenecks, growth spurts, etc. have already taken place but, likewise, we are looking at the residue to try to ascertain what happened.

    I don't care when an SNP first occurred. I care about the expansion and movements of my ancestry. The SNP marked haplotroup ages may help put a maximum age in place for my ancesty. That's good, but it's not really the haplogroup I'm after.


    P.S. Science may be interested in who the genetic Adam was or wasn't and some other things. That's fine with me but I'm really after understanding how we, the survivors, got here.

  10. #80
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    Below please find my SNP-based TMRCA estimations (in ky) for different R1b clades (and some upstream haplogroups) present in Sardinia. These estimations are based on an assumed mutation rate of 0.7 10^-9 per nucleotide per year (chosen for some reasons mentioned in another thread), while the numbers given in parentheses correspond to the TMRCA values calculated using the mutations rates 0.82 and 0.53, as proposed by Poznik and Francalacci, respectively).

    63.0 (53.7-82.8) haplogroup F
    61.9 (52.8-81.3) haplogroup IJK
    58.8 (50.1-77.3) haplogroup K
    40.2 (34.3-52.9) haplogroup P
    36.6 (31.2-48.2) haplogroup I
    33.5 (28.6-44.1) haplogroup R
    27.6 (23.5-36.3) haplogroup R1
    22.9 (19.5-30.1) R1b-P25
    14.9 (12.5-19.6) R1b-V88
    8.6 (7.3-11.3) R1b-M269
    8.3 (7.1-10.9) R1b-L23
    7.6 (6.5-10.0) R1b-L51
    7.4 (6.3-9.7) R1b-Z2105
    7.2 (6.1-9.5) R1b-M269(xL23)
    6.6 (5.6-8.6) R1b-L11
    6.2 (5.3-8.2) R1b-P312
    6.1 (5.2-8.0) R1b-U152

    Assuming that the number of downstream mutations found in members of some poorly represented subclades is not a reliable source of data (due to some technical reasons associated with using the low pass sequencing method), I have instead used the distance (i.e. the number of SNPs) between a parent clade and a common ancestor of a given subclade as a basis for calculating the age (TMRCA) of every subclade. For estimating the age of haplogroup F, I have used the average number of mutations downstream of haplogroup F in members of the well-represented (in Sardinia) clade I2a-M26, which was about 404 mutations. It is worth noting that the average number of mutations downstream of haplogroup F in clade R1b-U152 (a clade that is also frequent in Sardinia, but not as common as I2a-M26) was close to the above number but, nevertheless, evidently lower (392). Thus, when basing similar calculations on this slightly reduced number of SNPs found in members of R1b-U152, we get lower TMRCA values, as shown below.

    61.3 (52.3-80.6) haplogroup F
    60.2 (51.3-79.1) haplogroup IJK
    57.1 (48.7-75.0) haplogroup K
    38.5 (32.9-50.6) haplogroup P
    34.9 (30.0-45.9) haplogroup I
    31.8 (27.1-41.8) haplogroup R
    25.9 (22.1-34.0) haplogroup R1
    21.2 (18.1-27.9) R1b-P25
    13.3 (11.3-17.4) R1b-V88
    6.9 (5.9-9.0) R1b-M269
    6.6 (5.6-8.6) R1b-L23
    5.9 (5.1-7.8) R1b-L51
    5.6 (4.8-7.4) R1b-Z2105
    5.5 (4.7-7.2) R1b-M269(xL23)
    4.8 (4.1-6.4) R1b-L11
    4.5 (3.9-5.9) R1b-P312
    4.4 (3.7-5.7) R1b-U152

    Neither of the above sets of TMRCAs can be considered secure, but I think the first approach is slightly more likely to give correct values when using those Sardinian data alone.
    Last edited by Michał; 10-11-2013 at 06:23 PM.

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