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Thread: FTDNA Y Haplotree

  1. #21
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    Quote Originally Posted by Osiris View Post
    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.
    What you are seeing is an important point about the nature of FTDNA's haplotree. It is NOT purposed to be an academic or ancient population study tree. It is purposed for genetic genealogy.*

    As such, although they will add SNPs to their test packages from academic studies, they won't add branching. They have to see derived results in their database. This makes the FTDNA haplotree more oriented towards the living, or the recently living, rather than a full scale ancient tree.

    I haven't checked recently but I think that FTDNA does not have anywhere close to the full phylogenetic block of SNPs for R1b-M269. It's not too relevant to genetic genealogy so I don't think they care unless a project admin cares.

    * Note: there are some who are concerned about a strict rules-driven approach that would be consistent across all trees, be they academic in nature like an ISOGG, or whatever. However, it is apparent that FTDNA will not follow broad rules aimed at population genetics that might get in the way of consumers' genetic genealogy.
    Last edited by Mikewww; 11-15-2017 at 07:23 PM.

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  3. #22
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    Quote Originally Posted by Mikewww View Post
    The did add the number of kits per subclade in the Terminal SNP Guide but only youthful matches and any matches from SNP Packs and the like.
    Where is the Terminal SNP Guide?

  4. #23
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    Quote Originally Posted by ArmandoR1b View Post
    Where is the Terminal SNP Guide?
    You can see a screenshot or two of it under the Big Y Matches blue twistie on this web page.

    https://www.familytreedna.com/learn/...g/big-y/big-y/

    It a small section of the haplotree at the most youthful branching levels for a Big Y tester. It does list # of kits per branch but this is only for other Big Y testers. SNP Pack or Adanced Tests single SNP results are not included. Also, this is only for the youthful branching where you and the others represented have 40 or less variant differences.

    It's actually pretty neat. They just need to open to more matches.

  5. #24
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    What Armando means is that they show the number for all in that branch. What you refer to in the Big Y match list is just of matches not of all in those subclades.

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  7. #25
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    Quote Originally Posted by Contemplator View Post
    What Armando means is that they show the number for all in that branch. What you refer to in the Big Y match list is just of matches not of all in those subclades.
    I get it, Cotemplator, and I agree. This was the actual request I made several months ago. My origional request had nothing to do with Big Y matches but was just a general haplotree capability request.

    I asked more additional collapsible columns on the haplotree including a column for number of kits derived and to have that filterable so that you could say >=2 and make sure you had no personal branches or whatever kind of filtering you would like.

    I also asked for optional (user selected hide/show) columns for long haplogroup labels and for all phylogenetic equivalents (vs. lead with only SNPs). I didn't ask for synonyms, which Doug M wants but it's something for the list.

    I did not ask for this but I would like to refine my thinking and ask for an optional column for country of origin and TMRCA age estimate. They plan to do the TMRCA estimates so if that could filterable that would be cool - to look only at young branches or old branches or whatever you want.

    I think the country origin colum would almost have to be a single pie chart per branch with %s of each country.

    BTW, they are actually working on some haplotree enhancement but I have no idea what they are other the age estimates. I just give my feedback and it goes into the black box and sometime later, quite a bit later usually, something happens. If enough people ask for the same thing, something along those lines usually happens.
    Last edited by Mikewww; 11-21-2017 at 03:22 AM.

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  9. #26
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    Quote Originally Posted by Mikewww View Post
    Also, this is only for the youthful branching where you and the others represented have 40 or less variant differences.
    The variant limit FTDNA is using is 30, not 40. This is obviious in my case because my Big Y Matches page shows exactly 3 "matches"--even though, in reality, they are no more and no less related to me than anyone else in the entire I2a-Dinaric clade. Why do only these three show up? Because--perhaps due to a lower-quality run of the Big Y--they have "only" 29 or 30 mismatched variants with me.

  10. #27
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    Quote Originally Posted by Mikewww View Post
    You can see a screenshot or two of it under the Big Y Matches blue twistie on this web page.

    https://www.familytreedna.com/learn/...g/big-y/big-y/

    It a small section of the haplotree at the most youthful branching levels for a Big Y tester. It does list # of kits per branch but this is only for other Big Y testers. SNP Pack or Adanced Tests single SNP results are not included. Also, this is only for the youthful branching where you and the others represented have 40 or less variant differences.

    It's actually pretty neat. They just need to open to more matches.
    I was already familiar with that I just didn't know the name of it. There was already something extremely similar to it prior to the hg38 upgrade where a list of BigY matches could be selected based upon the SNP chosen in the dropdown box with kit's "terminal" SNP listed at the bottom with YOU next to. As Contemplator pointed it's not anything like I am looking for since what I am looking for is something that encompasses the all haplogroups so that I can extract which populations have certain haplogroups and subclades and at what percent compared to all of the other haplogroups. It would also help show how many kits total each population group has. That way we can see how big the population imbalance is and how much more testing in certain populations is needed even if there is going to be a small percentage of incorrect ancestral information due to lack of documentation or a misguided belief system. Obvious patterns have already emerged that match previous academic studies but a much larger database with NGS testing is what is needed to show which SNPs are practically non-existent in some populations. I'm not just interested in my own personal direct paternal lineage but also that of the my other lineages, the populations that they come from, and the world populations even if I don't share ancestry with them. I had been doing what I mentioned with European countries and Latin American countries and most of the haplogroups found in them with YFull. Now that I pulled total kits for you the other day from YFull I also now know the percentage of the 9036 private kits at YFull that belong to certain haplogroups. Below is a list of them above 1% in order by frequency. Later I'll figure out which macro-populations have the least percentage of participation.

    Haplogroup Percent
    R1b 28.23%
    I1 14.82%
    R1a 11.58%
    J1 8.26%
    I2 7.56%
    E 6.60%
    N 5.72%
    J2 4.99%
    T 2.62%
    G 2.58%
    Q 2.32%

  11. #28
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    Quote Originally Posted by lgmayka View Post
    The variant limit FTDNA is using is 30, not 40. This is obviious in my case because my Big Y Matches page shows exactly 3 "matches"--even though, in reality, they are no more and no less related to me than anyone else in the entire I2a-Dinaric clade. Why do only these three show up? Because--perhaps due to a lower-quality run of the Big Y--they have "only" 29 or 30 mismatched variants with me.

    They say it’s 40 but if you’re right, that would explain why my initial 5 Hg 38 matches disappeared. They were all in the 31 to 38 range.

    Big Y - Results – Matching
    The Matching tab displays your terminal SNP matches. Your terminal SNP determines the terminal (final) subbranch (on the Y-DNA haplotree) to which you belong.

    A person is considered a match if they have 40 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

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  13. #29
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    I am posting this here to show what FTDNA should be showing us with the FTDNA Y Haplotree data. As BigY customers we are paying a lot of money and data like this could be provided by adding a simple algorithm. By using the kits at YFull I got country information, region, number of kits (count), % of kit out of the total kits, Male population for the country, % of the world male pop for the country, and the kit imbalance is the % of kits divided by % of world male pop. Due to how the data is extracted I had to include about 662 academic kits but 1000 Genomes was not included. The kits that show unknown are kits that put that they do not know where their paternal line is from. I have the data for almost 130 countries but I only posted the first 35 plus the unknown.

    Population Region Count %Kits Male Pop %World Male Pop Kit Imbalance
    Sweden Europe: Western 606 7.54% 4,766,410 0.13204% 57.12
    Saudi Arabia Asia: Western 565 7.03% 16,576,600 0.45922% 15.31
    Finland Europe: Western 494 6.15% 2,664,325 0.07381% 83.30
    United Kingdom Europe: Western: British Isles 435 5.41% 31,126,179 0.86229% 6.28
    England Europe: Western: British Isles 414 5.15% 26,505,000 0.73427% 7.02
    United States of America America: Northern 375 4.67% 157,464,952 4.36226% 1.07
    Ireland Europe: Western: British Isles 355 4.42% 2,295,078 0.06358% 69.49
    Italy Europe: Southern 336 4.18% 29,641,275 0.82115% 5.09
    Russia* Europe: Eastern 327 4.07% 65,846,331 1.82415% 2.23
    Scotland Europe: Western: British Isles 308 3.83% 2,647,500 0.07334% 52.26
    Germany Europe: Western 247 3.07% 40,618,773 1.12526% 2.73
    Poland Europe: Eastern 227 2.83% 18,458,635 0.51136% 5.52
    Norway Europe: Western 201 2.50% 2,526,378 0.06999% 35.74
    Kuwait Asia: Western 148 1.84% 2,014,406 0.05581% 33.01
    Qatar Asia: Western 104 1.29% 1,659,035 0.04596% 28.16
    Portugal Europe: Southern 97 1.21% 5,134,348 0.14224% 8.49
    Ukraine Europe: Eastern 89 1.11% 20,855,089 0.57775% 1.92
    China Asia: Eastern 82 1.02% 717,723,466 19.88314% 0.05
    France Europe: Western 76 0.95% 31,116,980 0.86204% 1.10
    Netherlands Europe: Western 58 0.72% 8,312,578 0.23028% 3.13
    Spain Europe: Southern 56 0.70% 23,181,920 0.64221% 1.09
    Lebanon Asia: Western 56 0.70% 2,449,561 0.06786% 10.27
    United Arab Emirates Asia: Western 55 0.68% 6,551,636 0.18150% 3.77
    Armenia Asia: Western 53 0.66% 1,529,955 0.04238% 15.56
    Unknown 51 0.63%
    Belarus Europe: Eastern 48 0.60% 4,341,499 0.12027% 4.97
    Turkey Asia: Western 46 0.57% 36,791,927 1.01925% 0.56
    Iraq Asia: Western 45 0.56% 17,085,207 0.47331% 1.18
    Lithuania Europe: Western 43 0.54% 1,387,789 0.03845% 13.92
    Bulgaria Europe: Eastern 42 0.52% 3,510,350 0.09725% 5.38
    Bahrain Asia: Western 41 0.51% 828,610 0.02296% 22.23
    Czech Republic Europe: Eastern 38 0.47% 5,265,481 0.14587% 3.24
    India Asia: Southern 34 0.42% 647,356,171 17.93375% 0.02
    Switzerland Europe: Western 34 0.42% 3,982,372 0.11032% 3.84
    Denmark Europe: Western 33 0.41% 2,787,072 0.07721% 5.32
    Mexico America: Northern 30 0.37% 59,208,881 1.64027% 0.23

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  15. #30
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    Those aren't all kits from FTDNA though.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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