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Thread: ISOGG 2016 Y-DNA haplogroup R1b tree

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    ISOGG 2016 Y-DNA haplogroup R1b tree

    Does someone understands something about this new 2016 ISOGG R1b YDNA haplogroup tree, more precisely the following extracted R1b1c and R1b1a2 branches?
    Is there now no link between V88 and R1b1c?
    Is there no contradiction between the presentation of R1b1a2 branch and the following statement of ISOGG?
    “Paragroup R1b1* and R1b1c-V88 are found most frequently in SW Asia and Africa. The African examples are almost entirely within R1b1c and are associated with the spread of Chadic languages”.


    • • R1b M343/PF6242
    • • • R1b1 L278, CTS46, CTS910/FGC66/PF6244, CTS2134/FGC47/PF6253, CTS2229/FGC31/PF6254,
    • • • • R1b1a L754/PF6269/YSC0000022, A702/Z8137, CTS3063/V2515, CTS3794/PF6256/S4229, CTS4244/PF6257/V2997/YSC0001279, CTS4764/FGC59/PF6041, CTS5454/M6955, CTS7585, CTS8436/PF6259, CTS8612/PF6260, CTS9972/PF6261/V3867, FGC35/PF6150, FGC36/Y409, FGC41/M12190/SK2062/V1501/Y108/Z8135, L761/PF6258/YSC0000266, L820/PF6262/V4199/YSC0000211, L1068/PF6264/YSC0000223, L1345/PF6266/YSC0000224, PF6249, PF6263, PF6271
    • • • • • R1b1a1 L388/PF6468, L389/PF6531
    • • • • • • R1b1a1a P297/PF6398, CTS3876/PF6458, CTS5082, CTS5577/FGC38/PF6464, CTS7904/FGC32/PF6471, CTS7941/FGC51/PF6472, CTS9018/FGC188/PF6484, CTS11985/PF6523, FGC57/L1067/M12189/PF6424/SK2079/Z8148, FGC69/L320/PF6092/Z8143, L502/PF6487, L585/PF6499, L752/PF6483, PF6418/YSC0000061, PF6451/YSC0000166, PF6459/S3848, PF6463, PF6475/S17/YSC0000269, PF6498, PF6501, PF6506, PF6524
    • • • • • • • R1b1a1a1 M73, M478
    • • • • • • • R1b1a1a2 M269, CTS623, CTS2664/PF6454, CTS3575/PF6457, CTS8591, CTS8665/FGC464/PF6479, CTS8728/L1063/PF6480/S13, CTS10834, CTS11468/FGC49, CTS12478/PF6529, F1794/PF6455, L265/PF6431, L407/PF6252, L478/PF6403, L482/PF6427, L483, L500/PF6481, L773/PF6421/YSC0000276, L1353/PF6489/YSC0000294, M520/PF6410, PF6399/S10, PF6404, PF6505/YSC0000225, PF6409, PF6411, PF6425, PF6430, PF6432, PF6434, PF6438, PF6443, PF6482/YSC0000203, PF6485/S3, PF6494, PF6495, PF6497/YSC0000219, PF6500, PF6507, PF6509, L150.1/PF6274.1/S351.1
    • • • • • • • • R1b1a1a2a L23/PF6534/S141, L49.1/S349.1
    .
    .
    • • • • • R1b1a2 PF6279/V88
    • • • • • • R1b1a2a M18
    • • • • • • R1b1a2b V35
    • • • • • • R1b1a2c V69
    • • • • •R1b1b~M335
    • • • • •R1b1c PH155, F2482, PH200, PH491, PH861, PH885, PH1030, PH1165, PH1187, PH1417, PH1554, PH1769, PH1840, PH2150, PH2274, PH2588, PH2675, PH2768, PH2778, PH2813, PH3272, PH3508, PH3516, PH3826, PH3939, PH4174, PH4622, PH4673, PH4796, PH5173, SK2056, SK2058, SK2060, SK2061

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    Quote Originally Posted by grouza31 View Post
    Does someone understands something about this new 2016 ISOGG R1b YDNA haplogroup tree, more precisely the following extracted R1b1c and R1b1a2 branches?
    Is there now no link between V88 and R1b1c?
    Is there no contradiction between the presentation of R1b1a2 branch and the following statement of ISOGG?
    “Paragroup R1b1* and R1b1c-V88 are found most frequently in SW Asia and Africa. The African examples are almost entirely within R1b1c and are associated with the spread of Chadic languages”.
    It is just a change in terminology, which is based on the number and relationship of the known branches of R1b, not in the facts of distribution. This happens all the time with Y haplogroups, the terminology is always changing (for instance last year's O2a1 is now O1b1a1a, and O3 is now O2!). The names like "R1b1bc" are just a convenience (and often confusing), what matters is the *defining mutation* - V88. So it doesn't matter if they call it R1b1c, or R1b1a2, or R1b1b, it is the same thing. Yes, to be consistent they should have changed the name on that page, but it will still be different everywhere else anyway, and it makes no difference what you call it: it's still the same thing, V88.

    It has changed because they now recognize the existence of a newly-discovered branch of R1b, R1b-PH155, which recent studies found in Tajikistan and Bhutan. The branches of V88 and L389 (from which M269 is descended) are more closely related to each other than to PH155, united by the SNP L389, so their shared lineage is now R1b1a. The position of the very rare mutation M335 is still unknown so it gets its own branch R1b1b - although in reality it may belong to one of the others - while R1b-PH155 ends up being R1b1c.

    With mitochondrial DNA haplogroups they do the opposite, leave the names the same and just add on new levels - but then it's just as confusing, because you end up with D2 being a branch of D4e1, D being a sister of M80 under M, and M being part of L3. (But mtDNA doesn't have proper defining mutations so you really don't have much choice.)
    Last edited by Megalophias; 02-16-2016 at 05:28 PM.

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    Quote Originally Posted by Megalophias View Post
    It is just a change in terminology, which is based on the number and relationship of the known branches of R1b, not in the facts of distribution. This happens all the time with Y haplogroups, the terminology is always changing (for instance last year's O2a1 is now O1b1a1a, and O3 is now O2!). The names like "R1b1bc" are just a convenience (and often confusing), what matters is the *defining mutation* - V88. So it doesn't matter if they call it R1b1c, or R1b1a2, or R1b1b, it is the same thing. Yes, to be consistent they should have changed the name on that page, but it will still be different everywhere else anyway, and it makes no difference what you call it: it's still the same thing, V88.

    It has changed because they now recognize the existence of a newly-discovered branch of R1b, R1b-PH155, which recent studies found in Tajikistan and Bhutan. The branches of V88 and L389 (from which M269 is descended) are more closely related to each other than to PH155, united by the SNP L389, so their shared lineage is now R1b1a. The position of the very rare mutation M335 is still unknown so it gets its own branch R1b1b - although in reality it may belong to one of the others - while R1b-PH155 ends up being R1b1c.

    With mitochondrial DNA haplogroups they do the opposite, leave the names the same and just add on new levels - but then it's just as confusing, because you end up with D2 being a branch of D4e1, D being a sister of M80 under M, and M being part of L3. (But mtDNA doesn't have proper defining mutations so you really don't have much choice.)
    Many thanks.

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    If I’m not mistaken, ISOGG 2016 R1b tree is partly based on the experimental tree of Ray Banks. Why ISOGG does not integrate, particularly at the V88 branch, the most detailed data of Smal R1b tree or those established by YFull?
    Are there no consensus of everyone on R1b established by Smal or that of Yfull?
    Or are there other reasons?

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    grouza 31, these new changes in the ISOGG tree have occured due to my activity. Of course, I plan to improve the V88 branch as well. However, this is time consuming process. I need to prepare an elaborate submission. And V88 is only one of many clades which have to be improved.

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    "ISOGG" is not a formal, or legal, institution. Its tree has little scientific oversight, if any. It does not receive financial support either. Katherine Borges controls all aspects of the ISOGG.org internet domain.

    Ray Banks was appointed by Katherine Borges' friend Alice Fairhurst to take over management of the ISOGG tree. Ray is an hg G specialist, but has poor knowledge of haplogroup R. Neither Katherine, Alice, or Ray are professional scientists themselves.

    Smal is the R1b-V88 expert. Currently, he is attempting to rectify his tree with with Ray's understanding of the tree. However, it will take a while before that part of the ISOGG tree is updated, due to the number of changes that are required, and the fact that all changes are still hand-coded with an HTML editor and saved as HTML documents on Katherine's website.
    Last edited by VinceT; 02-17-2016 at 12:12 PM.

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    Small and Vincent, thank you for your explanation.
    Small, I know you're a great expert and a great champion. We thank you very much for your work.

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    Quote Originally Posted by VinceT View Post
    "ISOGG" is not a formal, or legal, institution. Its tree has little scientific oversight, if any. It does not receive financial support either. Katherine Borges controls all aspects of the ISOGG.org internet domain.

    Ray Banks was appointed by Katherine Borges' friend Alice Fairhurst to take over management of the ISOGG tree. Ray is an hg G specialist, but has poor knowledge of haplogroup R. Neither Katherine, Alice, or Ray are professional scientists themselves.
    If Neither Katherine, Alice, or Ray are professional scientists themselves, on what basis and who develops the scientific and technical recommendations like the one below?
    I chose this particular recommendation because we had on other thread discussions on the relationship between SNPs, Y STR and Y haplogroup tree building.
    Some people said that Y STR is not used in the development of Y haplogroup tree and there is no connection between STR and SNP.
    How then interpret this recommendation of ISOGG even if they are not professional scientists?

    • Sanger Sequencing
    Examples of Sanger sequencing are the tests at the company ySeq and the Advanced Tests (SNP) at Family Tree DNA. STR testing is available, for instance, at Genebase and Family Tree DNA. Acceptable testing for this category consists of Sanger sequencing which targets a short segment of Y-DNA.

    The objective of the ISOGG Tree at this time is to include all SNPs that arose prior to about the year 1500 C.E. This guideline may be measured through STR diversity or alternative evidence.

    Where a new terminal subgroup is being added, STR marker results or other evidence des-cribed below for two men with the new SNP are needed.

    1 STR Diversity
    To be accepted the SNP must be observed in at least two individuals and must meet the STR diversity requirement. A SNP that does not meet this requirement will be classified as a Pri-vate SNP (see definition above).

    The STR diversity requirement is met if the following conditions are satisfied:
    a. If the SNP is a Non-Terminal Branch SNP, no further proof of diversity is required.
    b. Genetic distance is calculated using the Infinite Alleles Model (IAM). A marker for which there is a null value in one sample must be discarded from the calculations. Otherwise, most laboratories use the IAM.
    c. All markers tested by both individuals must be compared.
    d. If 74 markers (or fewer) are compared, the minimum genetic distance to meet the di-versity requirement is 5.
    e. If 75 (or more) markers are compared, the diversity requirement is a minimum of 7%, computed by dividing the genetic distance by the number of markers compared, and rounding to the nearest integer value.

    Alternative Evidence
    If the submitter can otherwise provide evidence that the common ancestor of the two samples can be reasonably expected to have lived more than 500 years ago, this will also be considered.

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    Not trying to defend the above but the point is that the structure of the tree is solely built from SNPs. The reference to STRs above is restricted to dating terminal SNPs (and workarounds like presumably paper trails are acceptable alternatives).
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    Quote Originally Posted by grouza31 View Post
    If Neither Katherine, Alice, or Ray are professional scientists themselves, on what basis and who develops the scientific and technical recommendations like the one below?
    I chose this particular recommendation because we had on other thread discussions on the relationship between SNPs, Y STR and Y haplogroup tree building.
    Some people said that Y STR is not used in the development of Y haplogroup tree and there is no connection between STR and SNP.
    How then interpret this recommendation of ISOGG even if they are not professional scientists?

    • Sanger Sequencing
    Examples of Sanger sequencing are the tests at the company ySeq and the Advanced Tests (SNP) at Family Tree DNA. STR testing is available, for instance, at Genebase and Family Tree DNA. Acceptable testing for this category consists of Sanger sequencing which targets a short segment of Y-DNA.

    The objective of the ISOGG Tree at this time is to include all SNPs that arose prior to about the year 1500 C.E. This guideline may be measured through STR diversity or alternative evidence.

    Where a new terminal subgroup is being added, STR marker results or other evidence des-cribed below for two men with the new SNP are needed.

    1 STR Diversity
    To be accepted the SNP must be observed in at least two individuals and must meet the STR diversity requirement. A SNP that does not meet this requirement will be classified as a Pri-vate SNP (see definition above).

    The STR diversity requirement is met if the following conditions are satisfied:
    a. If the SNP is a Non-Terminal Branch SNP, no further proof of diversity is required.
    b. Genetic distance is calculated using the Infinite Alleles Model (IAM). A marker for which there is a null value in one sample must be discarded from the calculations. Otherwise, most laboratories use the IAM.
    c. All markers tested by both individuals must be compared.
    d. If 74 markers (or fewer) are compared, the minimum genetic distance to meet the di-versity requirement is 5.
    e. If 75 (or more) markers are compared, the diversity requirement is a minimum of 7%, computed by dividing the genetic distance by the number of markers compared, and rounding to the nearest integer value.

    Alternative Evidence
    If the submitter can otherwise provide evidence that the common ancestor of the two samples can be reasonably expected to have lived more than 500 years ago, this will also be considered.
    Each research lab had their own sample data-set and their own Y-SNP identifiers, and their own Y-phylogenies. The ISOGG's tree began as an effort to compile those various Y-phylogenies and Y-SNP identifiers together and reconcile them with each other. However these trees and variants were generally biased towards anonymous samples from specific population groups.

    Since ISOGG has a genealogical focus, there is an ongoing debate among the haplogroup project experts to make ISOGG tree genealogically relevant, or at least able to bridge the gap between anthropological relevancy and genealogical relevancy. Unfortunately, that realm has seldom been explored by professional population geneticists, and as such has fallen into the hands of citizen scientists and amateurs.

    The current recommendation has been set after extensive discussion by the haplogroup experts appointed to maintain and review the ISOGG's tree, and is periodically reviewed and debated as new testing technologies become available. Since none of these experts have first-hand experience using these technologies themselves in a professional laboratory setting, these recommendations are often reviewed and debated - by those same citizen scientists and amateurs.

    (I absolutely do not mean to knock against those involved in citizen science, since on several occasions citizen scientists have noted patterns and inconsistencies in professionally acquired research that eventually were invalidated by subsequent research.)

    The STR diversity requirement was derived from a controversial interpretation of p>0.05 used by the [now-defunct?] Y-Chromosome Consortium, on which the ISOGG Y-tree was initially derived from. The implied interpretation was that diversity within a set of haplotypes belonging to any particular haplogroup should vary by at least 5% of the markers used by the set of haplotypes, in order to be statistically relevant in the phylogeny. As Y-STRs are so much more volatile (and prone to back-mutations) than Y-SNPs, it is hoped that this particular recommendation will eventually fall into obsolescence, if it hasn't already.
    Last edited by VinceT; 02-17-2016 at 09:38 PM.

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