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Thread: Structure of Ydna December 2014

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    Structure of Ydna December 2014

    new paper

    http://mbe.oxfordjournals.org/conten....full.pdf+html

    As for my T-Ydna ..the oldest basal for T found is in Bhutan



    see page 26 for ages of Y
    có che un pòpoło no 'l defende pi ła só łéngua el xe prónto par èser s'ciavo

    when a people no longer dares to defend its language it is ripe for slavery.

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    Some conclusions from the paper:

    *They give a TMRCA for the whole tree of 129 KYA , and a 46 KYA date for the DR Colonization of Eurasia node.

    *"Hg E1b1a (here given a TMRCA of 6.9 KYA) has previously been associated with the expansion of Bantu languages, which spread widely from Central Africa ~3KYA together with farming and iron-working."

    *"Haplogroups I and J divide at 31 KYA, and each then divides in two at similar times of 2123 KYA. Within hg I1 is a striking star-like genealogy dating to 3.5 KYA."

    *As to y Dna "Q":
    "Here as well as an example of the common native American Q,
    native American Q-M3 lineage,we included rare examples of European Q chromosomes. One of the English chromosomes belongs to the deepest rooting
    lineage within Q (Q M-378) and may reflect the Jewish diaspora (Hammer et al 2009); the other is distantly related, shares a deep node with the Mexican 0M3 chromosome and has an STR haplotype closely related to those of scarce Scandinavian hg Q chromosomes (unpublished data)."

    *The TMRCA of hg R is19KYA, and within it bothhgs R1a and R1b compriseyoung, star-like expansionsdiscussed extensively elsewhere(Batini et al. submitted)"

    *
    "The addition of Central Asian chromosomes here contributes a sequence to the deepest subclade of R1b-M269, while another, in a Bhutanese individual, forms an outgroup almost as old as the R1a/R1b split."


    *
    "generally, the STRs perform poorly, giving a wide variety of TMRCAs for nodes with similar SNP-based dates, and correlation coefficient sconsistently below 0.6.

    The evolutionary STR mutation rate consistently overestimates, and the pedigree rate underestimates, the TMRCAs of nodes (Figure 4a).

    As expected, the pedigree mutation rate performs better for young nodes (<10 KYA; Table S6.while the evolutionary rate performs better for older nodes."

    Also,

    "This probably reflects the increasing importance of back-mutation in older clades.Despite the diminishingcost of NGS, it seems likely that researchers will wish to continue
    to use STRs in dating; in order to provide a rational framework, careful
    analysis of large datasets comprising multiple STRs and MSY sequenceswill be needed. The citizen-scientist’ community, which now generates 111-locus STR haplotypes combined with ~10-Mb MSY NGS data, may be best placed to do this."

    *"these findings support the idea that purifying selection is acting on single-copy MSY genes....
    purifying selection is ongoing, and that past claims of terminal degeneration of the Y chromosome are exaggerated...while evidence is mounting that purifying selection is acting on MSY protein-coding genes, more work is required to understand their functional roles. Candidate genes are currently lacking for some established MSY-linked phenotypessuch as HIV-AIDS progression (Sezgin et al. 2009) and coronary artery disease susceptibility(Charchar et al. 2012), and there is a clear need to
    understand the roles of non
    -coding RNA genes on the MSY, as well as the suite of protein-coding genes."

    Ed. My OCD was acting up, so I cleaned up the format a bit.


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    1 members found this post helpful.
    I haven't gone through the supplement, and probably won't have time today, but a few thoughts...

    I'm sure all the gentlemen will be relieved to hear that the past claims of terminal degeneration of the Y chromosome are exaggerated... I am glad that there is continuing research into the relationship between the different y lineages and various disease susceptibilities. I have wondered more than once whether this might have something to do with the frequency of certain lineages in certain locales. While coronary artery disease has such a late onset that its effect on procreation would be negligible, susceptibility to certain infections might not. In a town near me, church records indicate that 90% of the population died at the height of the Black Death. Might there have been a difference in survival rates based on uniparental markers? I'd also be interested to know if they are looking into the possibility that certain male lineages might have a slightly higher rate of producing males instead of females.

    I think we knew most of this with regard to yDNA STRs. I wonder if Gioiello is still interested in this topic? He was talking about back mutations in older clades years ago.

    The very old R1b in Bhutan is certainly interesting, as is the data for "Q". Attaching "race" or even "ethnicity" to y Dna lineages should be one of those ideas that go straight to the trash.

    The extreme "youth" of modern y Dna subclades world-wide, and the fact that it is tied to the massive expansions after the adoption of agriculture continues to astound.

    As to the TMRCAs, I'm not sure. Maybe I'll have a clearer idea after I read the supplement.

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    If the TMRCA for Y haplotype R is less than 20,000 years, does this mean the dating of Mal'ta Boy is off? As for those young star-like clusters of R1a and R1b expansions, how young are we talking about? We do have examples from Europe that are nearly 5000 years old and appear to be a long way from where R1a and R1b are assumed to have evolved. I don't really understand the science of estimating DNA dates but I think we should be concerned when estimates appear to conflict with known dates.

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    Quote Originally Posted by Aberdeen View Post
    If the TMRCA for Y haplotype R is less than 20,000 years, does this mean the dating of Mal'ta Boy is off? As for those young star-like clusters of R1a and R1b expansions, how young are we talking about? We do have examples from Europe that are nearly 5000 years old and appear to be a long way from where R1a and R1b are assumed to have evolved. I don't really understand the science of estimating DNA dates but I think we should be concerned when estimates appear to conflict with known dates.
    Mal'ta boy is only R from a branch that split once R split from Q..........as I said before, he is not R1 or R2.
    because he has no living "relative" he was ignored in this paper, but they knew about him.
    They took the oldest living R which is R-M207.
    So, the conclusion is that mal'ta split the same time as P1-M45 emerged which is ~24,300 years ago

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    Quote Originally Posted by Sile View Post
    Mal'ta boy is only R from a branch that split once R split from Q..........as I said before, he is not R1 or R2.
    because he has no living "relative" he was ignored in this paper, but they knew about him.
    They took the oldest living R which is R-M207.
    So, the conclusion is that mal'ta split the same time as P1-M45 emerged which is ~24,300 years ago
    You may get away with that, but what about M/LT/NO/QR-M9 TRMCA 32.6 KYA?
    Ust'-Ishim is 45 KYA and was K-M9

    I estimate you should add some 50 % to the figures in the list. It would make much more sense.

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    Quote Originally Posted by Sile View Post
    Mal'ta boy is only R from a branch that split once R split from Q..........as I said before, he is not R1 or R2.
    because he has no living "relative" he was ignored in this paper, but they knew about him.
    They took the oldest living R which is R-M207.
    So, the conclusion is that mal'ta split the same time as P1-M45 emerged which is ~24,300 years ago
    No. The most common estimate for P1-M45 seems to be 35,000 years ago and for R-M207 24,000 - 35,000 years ago. Mal'ta Boy was R*. And of course he didn't have any living descendants - he died before reaching adolescence. But his first R-M207 ancestor did. Otherwise there would not have been any R1 or R2 people. But none of the oldest R-M207 people are still alive. If they were, they would be very old and would need mammoth ivory walkers in order to get around.

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    Quote Originally Posted by Aberdeen View Post
    No. The most common estimate for P1-M45 seems to be 35,000 years ago and for R-M207 24,000 - 35,000 years ago. Mal'ta Boy was R*. And of course he didn't have any living descendants - he died before reaching adolescence. But his first R-M207 ancestor did. Otherwise there would not have been any R1 or R2 people. But none of the oldest R-M207 people are still alive. If they were, they would be very old and would need mammoth ivory walkers in order to get around.
    What are you talking about, mal'ta does not have M207

    https://drive.google.com/folderview?...p=sharing#list

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    Quote Originally Posted by bicicleur View Post
    You may get away with that, but what about M/LT/NO/QR-M9 TRMCA 32.6 KYA?
    Ust'-Ishim is 45 KYA and was K-M9

    I estimate you should add some 50 % to the figures in the list. It would make much more sense.
    paper states
    these are the oldest markers

    (ii) Ancient population expansion: Within clade DR of the tree lies a deep Paleolithic lineage radiation, giving rise to haplogroups G, HF5, IJ, LT, NO and P, dating to between 23 and 33 KYA (we note that a single variant identified elsewhere (Poznik et al. 2013) resolves the polytomy of haplogroups G and H, with G branching earlier).


    M ans S and R and Q come after P

    you need to check the order that haplogroups are formed

    Ust was K-M526

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    Quote Originally Posted by Sile View Post
    paper states
    these are the oldest markers

    (ii) Ancient population expansion: Within clade DR of the tree lies a deep Paleolithic lineage radiation, giving rise to haplogroups G, HF5, IJ, LT, NO and P, dating to between 23 and 33 KYA (we note that a single variant identified elsewhere (Poznik et al. 2013) resolves the polytomy of haplogroups G and H, with G branching earlier).


    M ans S and R and Q come after P

    you need to check the order that haplogroups are formed

    Ust was K-M526
    Usht'-Ishim was K-M526 + 2 out of 7 SNPs for haplo X (pre-NO)
    This was after split from MP and after split from LT
    MP is ancestral to P and hence also to Q and R

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    Quote Originally Posted by Sile View Post
    What are you talking about, mal'ta does not have M207

    https://drive.google.com/folderview?...p=sharing#list
    Mal'ta Boy had Y haplotype R - see for example Dienekes' Blog of November 20, 2013. Elsewhere it's stated to be specifically R* - not R1 or R2 but still R.

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    Quote Originally Posted by Aberdeen View Post
    Mal'ta Boy had Y haplotype R - see for example Dienekes' Blog of November 20, 2013. Elsewhere it's stated to be specifically R* - not R1 or R2 but still R.
    R* = dead line

    in genetics an asterix means no more SNP found, no more branches........dead end..............I stated this many many months ago. Dead line means no ydna relatives

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    Quote Originally Posted by Sile View Post
    R* = dead line

    in genetics an asterix means no more SNP found, no more branches........dead end..............I stated this many many months ago. Dead line means no ydna relatives
    The fact that a particular branch of R didn't produce any direct descendants doesn't make it not R. And, given how few people were around back then, the man who was the paternal ancestor of R1 and R2 was probably about a third cousin to Mal'ta Boy.
    Last edited by Aberdeen; 07-12-14 at 23:49.

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    Quote Originally Posted by bicicleur View Post
    You may get away with that, but what about M/LT/NO/QR-M9 TRMCA 32.6 KYA?
    Ust'-Ishim is 45 KYA and was K-M9

    I estimate you should add some 50 % to the figures in the list. It would make much more sense.
    Here, we favoured a
    rate (1.0 x 10-9/bp/year) estimated directly from NGS analysis of MSY sequences in a deeprooting
    pedigree (Xue et al. 2009). Though the direct nature of the analysis and the proven
    transmission of newly arising variants are positive features, the study’s major disadvantage is
    that its mutation rate rests on only four observations. These numbers will improve as other
    resequencing studies are published, but meanwhile other studies (Mendez et al. 2013;
    Scozzari et al. 2014) have taken the genome-wide de novo mutation rate (based on a larger
    number of observations) and scaled it to account for male-specific transmission, thus inferring
    slower rates of 0.62 x 10-9 (Mendez et al. 2013) or 0.64 x 10-9 (Scozzari et al. 2014). Criticism
    of this approach (Elhaik et al. 2014) has been based on its indirect nature, and the fact that the
    resulting rates are at odds with phylogenetic mutation rate estimates (1.5 – 2.1 x 10-9 /bp/year
    (Skaletsky et al. 2003; Kuroki et al. 2006)) based on human-chimpanzee MSY comparisons.
    Calibration based on archaeological dates and assumptions about colonisation history (such as
    the peopling of the Americas (Poznik et al. 2013) or of Sardinia (Francalacci et al. 2013))
    has also been applied, although it introduces other sources of uncertainty. Further analysis of
    deep-rooting pedigrees, combined with accumulating data on well-dated ancient DNA, should
    help to give more reliable mutation rate estimates in the near future.

    I would favour the slower rates of 0.62 or 0.64

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    What's wrong with this study's pedigree-based STR estimates? It's giving age estimates pretty consistently 2x too high. And given their Table 2 estimates being pretty consistent with estimates we've seen from other studies that use pedigree-based STR estimates, that seems to mean that their pedigree-based estimates are being scaled weirdly. Their figure 4a shows pretty tight fits around lines that show estimates 2x too high. Seems that they're putting a lot of stock into the 5 or so sub-10k YBP estimates that cluster to the right of the line. Are they using a particular scale?

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    Quote Originally Posted by Aberdeen View Post
    The fact that a particular branch of R didn't produce any direct descendants doesn't make it not R. And, given how few people were around back then, the man who was the paternal ancestor of R1 and R2 was probably about a third cousin to Mal'ta Boy.
    I never said he was not R , I said he did not have R-M207 as you stated he did.

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    Quote Originally Posted by sparkey View Post
    What's wrong with this study's pedigree-based STR estimates? It's giving age estimates pretty consistently 2x too high. And given their Table 2 estimates being pretty consistent with estimates we've seen from other studies that use pedigree-based STR estimates, that seems to mean that their pedigree-based estimates are being scaled weirdly. Their figure 4a shows pretty tight fits around lines that show estimates 2x too high. Seems that they're putting a lot of stock into the 5 or so sub-10k YBP estimates that cluster to the right of the line. Are they using a particular scale?
    They are not using dead lines, only using people who are living and they are using these as finding how old these tested peoples markers are

    ages shown and compared with others in table 6

    http://mbe.oxfordjournals.org/conten...ised281014.xls

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    Quote Originally Posted by Sile View Post
    I never said he was not R , I said he did not have R-M207 as you stated he did.
    I don't know a lot about genetics so you'll have to explain that to me. Does ISOGG have it wrong?

    www.isogg.org/tree/ISOGG_HapgrpR.html

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    Quote Originally Posted by Aberdeen View Post
    I don't know a lot about genetics so you'll have to explain that to me. Does ISOGG have it wrong?

    www.isogg.org/tree/ISOGG_HapgrpR.html
    Mal'ta is R* , which means an extinct line..........he did not have M207 ..........is it hard to understand that his line is non existant

    he fits closest to current R haplogroup........most likely they did not want to asscoiate a new alpha marker to him

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    Quote Originally Posted by Sile View Post
    Mal'ta is R* , which means an extinct line..........he did not have M207 ..........is it hard to understand that his line is non existant

    he fits closest to current R haplogroup........most likely they did not want to asscoiate a new alpha marker to him
    Oh, so ISOGG isn't wrong, just really sloppy in showing R* under R-M207. But you haven't explained why you think that. And please - no more nonsense about R* not being R because R* is an extinct line, because that idea is just sile. If you think Mal'ta Boy was actually somewhere between P and R, please explain the science of it. I'd really like to understand why you think ISOGG was either mistaken or sloppy in saying R=M207 and that R* is a subset of M207. If there's a reason why you don't agree, you should be able to explain

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    Quote Originally Posted by Aberdeen View Post
    Oh, so ISOGG isn't wrong, just really sloppy in showing R* under R-M207. But you haven't explained why you think that. And please - no more nonsense about R* not being R because R* is an extinct line, because that idea is just sile. If you think Mal'ta Boy was actually somewhere between P and R, please explain the science of it. I'd really like to understand why you think ISOGG was either mistaken or sloppy in saying R=M207 and that R* is a subset of M207. If there's a reason why you don't agree, you should be able to explain
    read maciano paper in this forum

    http://dienekes.blogspot.be/2013/11/...geny-from.html

    mal'ta is reclassified by some from R* to MA-1

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    I am sure as Genetics is at its infancy there will be modifications to classes of Haplogroups as vanished groups are hypothesized and placed in between or ahead of the "known and present Haplogroups". There are gaps in the migrations and many groups vanished when the seas rose 300 feet. Of course, it was the closing of the North and South American continents that created the Gulf Stream which is probably the main cause of ending the Ice Age. The rise of the seas was gradual taking 23,000 years as was the continental movements 2 inches a year for a continent.

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    Quote Originally Posted by Sile View Post
    read maciano paper in this forum

    http://dienekes.blogspot.be/2013/11/...geny-from.html

    mal'ta is reclassified by some from R* to MA-1
    I'd gladly read Maciamo's paper if you tell me where to find it - no doubt that would finally provide some clarity. But the article by Dienekes that you linked to says that scientists have discovered that there was a Y haplotype MP that lead to M and P (which led to Q and R) and it says that Mal'ta Boy was R. Scientists refer to him as MA-1 rather than Mal'ta Boy and MA-2 refers to the other set of remains found in the area that was less well preserved. These are not references to haplotypes. Is that what you've been on about all this time? LOL!
    Last edited by Aberdeen; 09-12-14 at 07:11.

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    Quote Originally Posted by bicicleur View Post
    Usht'-Ishim was K-M526 + 2 out of 7 SNPs for haplo X (pre-NO)
    This was after split from MP and after split from LT
    MP is ancestral to P and hence also to Q and R
    LT split off , from K , way before MPS was created........it was not the same time.

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    Quote Originally Posted by bicicleur View Post
    Here, we favoured a
    rate (1.0 x 10-9/bp/year) estimated directly from NGS analysis of MSY sequences in a deeprooting
    pedigree (Xue et al. 2009). Though the direct nature of the analysis and the proven
    transmission of newly arising variants are positive features, the study’s major disadvantage is
    that its mutation rate rests on only four observations. These numbers will improve as other
    resequencing studies are published, but meanwhile other studies (Mendez et al. 2013;
    Scozzari et al. 2014) have taken the genome-wide de novo mutation rate (based on a larger
    number of observations) and scaled it to account for male-specific transmission, thus inferring
    slower rates of 0.62 x 10-9 (Mendez et al. 2013) or 0.64 x 10-9 (Scozzari et al. 2014). Criticism
    of this approach (Elhaik et al. 2014) has been based on its indirect nature, and the fact that the
    resulting rates are at odds with phylogenetic mutation rate estimates (1.5 – 2.1 x 10-9 /bp/year
    (Skaletsky et al. 2003; Kuroki et al. 2006)) based on human-chimpanzee MSY comparisons.
    Calibration based on archaeological dates and assumptions about colonisation history (such as
    the peopling of the Americas (Poznik et al. 2013) or of Sardinia (Francalacci et al. 2013))
    has also been applied, although it introduces other sources of uncertainty. Further analysis of
    deep-rooting pedigrees, combined with accumulating data on well-dated ancient DNA, should
    help to give more reliable mutation rate estimates in the near future.

    I would favour the slower rates of 0.62 or 0.64
    when KLT split apart, LT became P326 and K became known as M526 ..................they split of the same time.

    the LT branch was reclassified as K1 and the K-M526 was reclassified as K2

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