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Thread: Some provisional calculations for haplogroup R1a based on the first FGC result

  1. #31
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    Quote Originally Posted by lgmayka View Post
    That depends on the set of figures you choose. At the moment, I prefer the rightmost column of the provisional SNP-based TMRCA calculations that Michał posted recently. (They best match the TMRCA calculations from STRs.)

    R1 : 21560
    R1a-M417 : 6048
    R1a-Z645 : 5544
    R1a-Z282 : 5376
    R1a-M458 : 4704
    R1a-L1029 : 2744

    TMRCAs will continue to improve relative to each other as we get additional full-Y examples and average their SNP counts; but the scaling of the entire TMRCA set still requires correlation with an archaeologically datable event, and/or a reliable stable SNP mutation rate.
    That is true. I was going by the Mal'ta boy's 24000 years age. He was a pre-R derivative - 5 mutations ancestral and with 35 private mutations ((1.5X on 5.8 million bases).
    I have made an assumption that his age is the approximate age of R1 for ballpark dates.

  2. #32
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    Quote Originally Posted by parasar View Post
    That is true. I was going by the Mal'ta boy's 24000 years age. He was a pre-R derivative - 5 mutations ancestral and with 35 private mutations ((1.5X on 5.8 million bases).
    Actually, these new data provide some important information regarding the age of R1. If the Mal'ta boy was indeed positive for as many as 35 private mutations, this suggests that the separation between R1a and R1b took place significantly earlier than 24 kya, most likely about 27-28 kya. Frankly speaking, I was extremely surprised that these data fit nearly exactly my previous calculations regarding the age of R and R1 (though I am perfectly aware that this is mostly coincidental):
    http://www.anthrogenica.com/showthre...5936#post15936

    When taking the distance between the TMRCAs for P and R1 from the above link (40.2-27.6=12.6) and dividing this by the number of SNPs separating these two levels in the Mal'ta study (42), we get 300 years per each mutation. Most importantly, the Mal'ta boy shows 54 mutations downstream of hg P, which places him 16.2 ky (54 x 0.3) downstream of 40.2 kya, which is 24 kya, exactly as suggested by the calibrated radiocarbon dating. Here is a tree based on the above calculations:
    MA-1 tree.jpg

    Of course, all above would be not true if a substantial number of the private mutations found in the Mal'ta boy were false positives (which cannot be easily verified).

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  4. #33
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    Quote Originally Posted by Michał View Post
    If the Mal'ta boy was indeed positive for as many as 35 private mutations, this suggests that the separation between R1a and R1b took place significantly earlier than 24 kya, most likely about 27-28 kya.
    You are apparently assuming that the very specific, unusual sequencing of the Mal'ta boy's ancient DNA is directly comparable to modern high-quality DNA scans (in terms of the number of genuine mutations vs. false positives vs. false negatives). That is not a reasonable assumption.
    Quote Originally Posted by Michał View Post
    Frankly speaking, I was extremely surprised that these data fit nearly exactly my previous calculations regarding the age of R and R1 (though I am perfectly aware that this is mostly coincidental):
    http://www.anthrogenica.com/showthre...5936#post15936
    That link does not work.
    Last edited by lgmayka; 11-26-2013 at 12:47 AM.

  5. #34
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    Quote Originally Posted by Michał View Post
    Actually, these new data provide some important information regarding the age of R1. If the Mal'ta boy was indeed positive for as many as 35 private mutations, this suggests that the separation between R1a and R1b took place significantly earlier than 24 kya, most likely about 27-28 kya. Frankly speaking, I was extremely surprised that these data fit nearly exactly my previous calculations regarding the age of R and R1 (though I am perfectly aware that this is mostly coincidental):
    http://www.anthrogenica.com/showthre...5936#post15936

    When taking the distance between the TMRCAs for P and R1 from the above link (40.2-27.6=12.6) and dividing this by the number of SNPs separating these two levels in the Mal'ta study (42), we get 300 years per each mutation. Most importantly, the Mal'ta boy shows 54 mutations downstream of hg P, which places him 16.2 ky (54 x 0.3) downstream of 40.2 kya, which is 24 kya, exactly as suggested by the calibrated radiocarbon dating. Here is a tree based on the above calculations:
    MA-1 tree.jpg

    Of course, all above would be not true if a substantial number of the private mutations found in the Mal'ta boy were false positives (which cannot be easily verified).
    The paper notes that some may be.

    "SNPs were filtered for quality (using VQHIGH as the threshold, as defined by Complete Genomics) ... only a few (11) mutations were detected that are likely to be false positives ...it is assumed that recurrent mutation is less likely than a sequencing error ... . One position among the 35 private to MA-1 is characteristic of a distant hg – namely C3c14 ... 10 additional phylogenetically non-concordant positions in MA-1 were found ...."
    http://www.nature.com/nature/journal...re12736-s1.pdf

    The two R1a on their NJ tree happen to be GIH L657+

  6. #35
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    Quote Originally Posted by lgmayka View Post
    ...

    That link does not work.
    http://www.anthrogenica.com/showthre...5936#post15936

    40.2 (34.3-52.9) haplogroup P
    ...
    33.5 (28.6-44.1) haplogroup R
    27.6 (23.5-36.3) haplogroup R1

  7. #36
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    Quote Originally Posted by lgmayka View Post
    You are apparently assuming that the very specific, unusual sequencing of the Mal'ta boy's ancient DNA is directly comparable to modern high-quality DNA scans (in terms of the number of genuine mutations vs. false positives vs. false negatives). That is not a reasonable assumption.
    This is not exactly true. My main conclusion that R1a is older than 24 ky was actually based solely on the sequencing results received for the Mal'ta boy, though of course this required assigning all his alleles (both ancestral and derived) to some proper positions on the Y-DNA tree (and this was the only moment when the data from the modern high-quality scans was used).

    Let me explain my line of reasoning again. If the analysis of all Y-DNA sequences available for the Malta boy identified 35 loci that show the presence of some derived alleles that are not shared by any known R1 members, while the same analysis revealed 23 loci that are known to have the derived status in all known R1 members but are ancestral in the Mal'ta boy, this clearly suggests that R1 is older than 24 ky.

    The main reason of some uncertainty in this case is associated with the unknown number of false positives among those 35 private mutations found in MA-1, but we simply need to trust the authors of the paper who have tried to exclude all such non-secure "private" (i.e. false positives) mutations. When judging based on the relatively low proportion of some discordant SNPs found among all phylogenetically relevant SNPs analyzed in the Mal'ta boy, I wouldn't expect that the number of those false positives among those 35 private mutations was high enough to undermine the above conclusion.

    Quote Originally Posted by lgmayka View Post
    That link does not work.
    Sorry about that (and thank you, Parasar, for providing a correct link).

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  9. #37
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    Quote Originally Posted by parasar View Post
    "SNPs were filtered for quality (using VQHIGH as the threshold, as defined by Complete Genomics) ... only a few (11) mutations were detected that are likely to be false positives ...it is assumed that recurrent mutation is less likely than a sequencing error ... . One position among the 35 private to MA-1 is characteristic of a distant hg – namely C3c14 ... 10 additional phylogenetically non-concordant positions in MA-1 were found ...."
    This indicates that they have tried to exclude all those potential "false positives", while reporting only those 35 private SNPs that are likely to be "genuine" mutations.

  10. #38
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    Estimated dating of Y-chromosome events

    Hello. I'm a new member with a layman's interest in Y-chromosome dating (especially R1b-L11). My comment isn't directly about R1a: Is there a better thread for discussing Y-chromosome mutation rates in general?

    I think the recent analysis of the 24,000-year old Siberian boy by Raghavan-Skoglund will finally place tighter bounds on the mutation rate. I hope forum members will review my comments here.

    The chart at the top of that page has date labels based on my old guess -- a 1/140 mutation rate. Just Click here to ignore my uninteresting discussion and see the same tree with the 1/165 mutation rate implied by Raghavan-Skoglund's paper.

    (I do hope experts will review my derivation of the mutation rate, and help guess how big the "error bars" are.)

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  12. #39
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    Welcome to the forum James Allen!

  13. #40
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    Quote Originally Posted by jamesdowallen View Post
    I hope forum members will review my comments here.
    I think your approach is a correct one. There are some minor points in your description of your procedure that are not clear to me. For example, you seem to equate the R-L node in the Francalacci tree with the R-N node in the Raghavan tree (which is not the same). Also, I found some minor errors in your calculations (for example,” the distance from F-breakup to Siberian boy and to present” is 101 and 160 SNPs, respectively, and not 98 and 155 as you wrote) but this does not affect your final outcome though.

    Most importantly, your average mutation rate (when recalculated from the value of 166 years per mutation for the region covered by Francalacci) is about 0.66 x 10^-9 per nucleotide per year, which is consistent with the average value for the three previously known mutation rates, as provided by Francalacci, Poznik and Mendez, respectively. This is also very close to the 0.7 mutation rate I have used in my previous calculations cited above.

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