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Thread: Cladogram from STR Values

  1. #1
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    Cladogram from STR Values

    I would appreciate your thoughts about the best method for drawing a cladogram from STR values.

    I have a group of men who share a close 37 marker match and are divided between two surnames, X and Y. I would like to try to create a cladogram to make an educated guess about whether X descended from Y, Y from X or both from another common ancestor, Z.

    I found instructions for creating cladograms using McGee's Y Utility at
    http://lawsondna.org/results/cladograminstruction.html
    Unfortunately this approach uses Fluxus which is available only for Windows, not for my Mac. I explored Phylip, which doesn't offer this function, and MacClade, which is no longer supported in Mac OS X. So I thought I would consult a bit before deciding whether to spend some $$ to partition my Mac to run Windows programs.

    A few questions:

    1. Are you aware of any other programs that will run on a Mac to create cladograms from STRs?

    2. If not, do you have any ideas for creating cladograms manually? I have made spreadsheets to compare each of the results with the modal and minimum values, and partitioned the group into clusters based on shared mutations. But I'm not sure where to go from there in plotting the differences in a cladogram.

    3. If drawing a diagram manually isn't feasible, would you draw any conclusions regarding the earlier surname on the basis of distance from the modal or minimum haplotypes? If so, which one would give the better insight?

    Thanks!

    Jim

  2. #2
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    In case others are interested I found two useful tools:

    Mesquite, a suite of programs for biologists that is Mac compatible:http://mesquiteproject.org

    A manual methodology developed by John Robb: http://www.johnbrobb.com/Content/DNA...usDiagrams.pdf

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     ChrisR (10-14-2016),  TŠltos (06-03-2015)

  4. #3
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    Isn't there a Windows on Mac software app?
    http://www.imore.com/how-install-win...-spending-dime

    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

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    Quote Originally Posted by MJost View Post
    Isn't there a Windows on Mac software app?
    http://www.imore.com/how-install-win...-spending-dime

    MJost
    Yes, however I found Mesquite quite easy to use and John Robb had some good comments about Fluxus, so in the end I found good solutions without using a Windows program.

    What I found was that the premilinary indication is that family X descended from Y, not the other way around, although we still have some test results in process that may refine that conclusion.

  6. #5
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    Quote Originally Posted by jbarry6899 View Post
    Yes, however I found Mesquite quite easy to use and John Robb had some good comments about Fluxus, so in the end I found good solutions without using a Windows program.

    What I found was that the premilinary indication is that family X descended from Y, not the other way around, although we still have some test results in process that may refine that conclusion.
    Fluxus performs better when you have clear cut branches out towards the leafs. It does infer where a missing allele value should be and gets messy if you don't put a major ancestral subclade modal into the mix in order to 'Root' the tree.

    More markers 'more better'.

    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

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  8. #6
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    Yes, in this case I was trying to infer the root, so Mesquite and the Robb manual method were useful. One of the problems is that two of the men in family X tested with Ancestry in the old days and have only 32 markers in common with the others. Recently I was able to track down another man from this line and his 37 marker test is under way. Depending on the results we may purchase an upgrade to more markers or to BigY.

    FYI, all of this is being done in preparation for testing on the remains of one of the Earls of Barrymore. (http://www.anthrogenica.com/showthre...more#post82999

    In this case family X (Barry) is generaly considered to be Anglo-Norman Irish and associated primarily with County Cork. Family Y is Christopher, a common surname in County Waterford. There is one subgroup of Barry men, probably I-L22 uN, which implies a Norse origin, and who have a number of close matches to Christopher men from County Waterford, a Viking stronghold. The phylogenetic trees generated by Mesquite and the Robb method imply that these Barrys were descended from a Christopher, not the opposite. So this tends to make the I-L22 Barry group a less likely candidate to match the Earl, whose line is traced directly to the original Anglo-Norman family.

    There are uncertainties in this analysis, but it is useful background for the project. This discussion on NPEs is also part of our background research: http://www.anthrogenica.com/showthre...mily#post84018

    I have an excruciatingly detailed background paper on DNA testing and Barry family history if anyone has the interest to read it: https://dl.dropboxusercontent.com/u/...20History.docx

  9. #7
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    You could use McGee's Utility to enter your haplotypes and produce a modal for those Hts. But small number of haplotypes may cause a skewing effect if swamped with a subgroup that is closely related from the rest. It is far better to use a major ancestral subclade modal with wider geographical distribution. Example I prefer to use L21's modal for every subclade under it.

    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

  10. #8
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    Quote Originally Posted by MJost View Post
    You could use McGee's Utility to enter your haplotypes and produce a modal for those Hts.

    MJost
    Yes, I have looked at that as well. The Christopher samples are closer to the modal haplotype, but again the small sample size and the interrelationships introduce uncertainties.

    The hope is that testing of the Earl will yield some strong evidence. Based on nearly 100 test results we have three candidate groups that may relate to him: this I-L22 group and two in R1b, Z49 (27 men) and L159.2 (9 men). The forensic examination and taking of samples is scheduled for mid August, so time will tell.

  11. #9
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    Sounds interesting. May take a long time.

    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

  12. #10
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    Quote Originally Posted by MJost View Post
    Sounds interesting. May take a long time.

    MJost
    Yes, we are hoping to get some preliminary results by the end of the year, but I've been working on this family for more than 30 years so I can wait a little longer.

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