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Thread: FTDNA Y Haplotree

  1. #11
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    The think that bothers me about the FTDNA haplotree is that they won't release all the synonyms
    hidden behind "more ..." as a single file, that does not require a million clicks to get.

    Many web pages for many purposes are specifically designed to be hard to use,
    this is a great example.

    This makes it near useless form many purposes.
    Last edited by dtvmcdonald; 10-26-2017 at 08:24 PM.

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  3. #12
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    Quote Originally Posted by dtvmcdonald View Post
    The think that bothers me about the FTDNA haplotree is that they won't release all the synonyms
    hidden behind "more ..." as a single file, that does not require a million clicks to get...
    You mean phylogenetic equivalents, not synonyms, right?

    I hate the "more" pop-up bubble. It's an eyesore to look at the equivalents. This is one of the things I think should be collapsible/expandable with a drop down or twistie.

    A work-around would be a CSV export of the the tree with all phylogenetic equivalents. I've asked for this.
    Last edited by Mikewww; 10-27-2017 at 11:09 PM.

  4. #13
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    I've done research on "private" branches or branches that have only a single person on them.

    I have my opinions about "private" being a temporal state and that very few valid Y SNPs are really private, but let me set that aside.

    Here is the reporting. I have found that there are only two subclades that have any private branches at all on FTDNA's tree. One is R1b and the other is not R of any type. I think I know what the other one is but I don't want to throw any one under the bus (not a bus I would drive due to my views above but some do.)

    The use of private branch actually is related to SNP Packs, supporting them so to speak. In the case I know of, L513, the private branches represented are represented by valid SNPs related to large surname groups with many close matches at 67 STRs (and probably at 111 STRs). When all this Big Y conversion stuff is done I'll go back see which are really still private.

    This part is not a report, just my estimate. I think there 5 or 6 may be up to 8 SNP Packs with these private SNPs sitting on haplotree branches. The private SNPs are well within the minority for these packs. To give you idea of the scope of this, FTDNA has about a 105 SNP Packs. I'm just saying this is the exception rather than the rule. We should not generalize L226 or L513 to the rest of the world. Of the 105 packs, about 50 are R1b packs. I've had hands-on experience on many of those.

    The FTDNA rule is there should be two people in the FTDNA database* with derived calls that are consistent before a branch can be added to the haplotree. As we know, this is not a hard and fast rule.

    * Note: this is not the same thing as being in an SNP Pack. Any SNP from any source can be made available in SNP Pack if it is feasible for Mass Spectrometry testing process.
    Last edited by Mikewww; 10-30-2017 at 11:06 PM.

  5. #14
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    Quote Originally Posted by Mikewww View Post
    What does it do and what is in it.
    The FTDNA haplotree is an active, integrated database. It is not just a superficial chart or display done in HTML or .PDF formats.

    I don't know what I/T data technologies they use but it is nevertheless a structured database that is designed to be used by multiple applications. The display of the haplotree on your myFTDNA account's "Haplotree & SNPs" gray button is just one application that uses the haplotree data structure.

    Other applications that use the haplotree data structure are the project system displays and tools such as the Y Classic Report or Y DNA SNP Reports. That's what I mean by integrated. This tree's data structure is integrated to other applications on other web pages beyond just the "Haplotree & SNPs" display itself.

    Haplogroup assignment is automated with updates driven by individual's SNP results and a comparison with the haplotree database. This is why it is possible for your haplogroup label to change even if you haven't done any new SNP testing - the tree itself changed.

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  7. #15
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    In addition, I have found when an incorrect haplogroup assignment has been made (most often with the Genographic 2.0 Next Generation results, but can be from other tests), I contact the tree manager at FTDNA (Michael Sager). He removes this spurious haplogroup assignment, and the IT system automatically assigns a new haplogroup for the individual. In every case I have worked with FTDNA thus far, this new (automatic) assignment has been correct.
    Gedmatch DNA: M032736 Gedcom: 6613110.
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    co-administrator: Y-DNA R-U106 Haplogroup Project

  8. #16
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    Quote Originally Posted by Mikewww View Post
    You mean phylogenetic equivalents, not synonyms, right?

    A work-around would be a CSV export of the the tree with all phylogenetic equivalents. I've asked for this.
    I mean both synonyms and phylogenetic equivalents.

    I don't consider the CSV export of the tree (with column 1 being the "indent level" on the tree) as a work-around ...
    I consider it to the THE primary thing for distribution. And please, one column for each phylogenetic equivalent, with synonymous names
    all in one column, separated by semicolons.

    Its exceedingly easy to generate this CSV file from a database. One, automated,
    update a week of the CSV file would do nicely. A database is not as good for distribution.
    Last edited by dtvmcdonald; 11-07-2017 at 06:06 PM.

  9. #17
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    There are more private branches than that.

    I'm a listed branch on the tree. Just me.

    Its true that when I appeared, there was another person matching through a phylogenetically
    equivalent SNP but that was bogus, in a pseudo-STR. He's actually one level up.

    But I'm happy to remain. And its in a SNP Pack, and should remain there ... we suspect
    other people who should match. After oh so long .... they have the phylogeny in that area
    RIGHT ... we don't want another screwup!

  10. #18
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    On Nov 11th, at the FTDNA conference, Jim Brewster of FTDNA spoke about the haplotree. Blogger Jennifer Zinck took notes. Here is a general status from the notes.
    http://www.ancestorcentral.com/13th-...ence-saturday/

    Quote Originally Posted by JenniferZinck
    Next Jim Brewster presented “Y-Haplotree and SNP Pack Update.” Jim showed a Y Chromosome Consortium Tree from 2002. He then shared the R Haplotree from 2010 and it fit about four screenshots. Today the tree is massive and takes up many screens of trees. The B tree at this time last year had 13 branches with less than 100 trees and no Big Y tests. Now there are 13 branches, over 2,700 SNPS, and has incorporated 82 Big Y tests.

    Jim shared the overall number of SNPs on the Halpotree as presented by Alice Fairhurst in 2013.

    2006 436 SNPs

    2008 790 SNPs

    2010 935 SNPs

    September 2013 3,610 SNPs

    Then they introduced the Big Y.

    May 2015 6,556 SNPs

    Nov 2016 23,757 SNPs

    Nov 2917 58,590 SNPs
    So there are nearly 60,000 SNPs on their tree now. We can see about 35,000 were added in just the last year so the growth has doubled for the 2017 (conf-conf) year! I attribute this to project admins and analysis but FTDNA proactively updated some branches.

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  12. #19
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    I noticed something that I think is new. Previously only the SNPs that were lit green were the ones that I was positive for on the haplogroup R page only. Now I've got green SNPs on R, P, K, F and A. I also see a few scattered around like on J which would be SNPs that happened more than once in the tree. Or were they always there and I just never noticed? But I swear I was looking at the A tree a few months ago and didn't see any SNPs lit green.

  13. #20
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    Also is there any talk about how certain nodes are missing? Take the SNP L413 which ISOGG has as the first SNP for BT. At FTDNA's tree the A tree doesn't have that branch and the B tree starts below it. Therefore the tree that we see just seems incomplete.

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