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    Ok here is Table-1 from the Francalacci.et.al.2013 study:

    Francalacci.et.al.2013-Table1.jpg

    There are two key components I want to add, these Table likely represent the age of certain haplogroup in Sardinians, and to a lesser extent some individuals added for some haplogroups. Nonetheless it can be very informative.

    If we use the mutation rate calibrated in this paper of 0.53*10-9mut/bp/year we arrive to an average of 205+-50 years per SNP mutation. If instead we use the mutation rate of the Poznik.et.al.2013 of 0.82*10-9mut/bp/year we arrive to an average of 133+-32 years per SNP mutations.

    Using Table-1 these are the ages of certain haplogroups using the different rates:

    Haplogroup-------------Francalacci.et.al_rate_Age------------------------Poznik.et.al_rate_Age

    Root__A---------------------------205533 ybp +- 50130 ybp---------------------------133346 ybp+-32083 ybp

    A(all)------------------------------180379.5 ybp +- 43995 ybp-------------------------- 117027 ybp +- 28157 ybp

    E+(all)-----------------------------111069 ybp +- 27090ybp----------------------------72059.4 ybp +- 17338 ybp

    F+(all)-----------------------------109634 ybp +- 26740 ybp----------------------------71128 ybp +- 17114 ybp

    IJ(all)-------------------------------79335 ybp +- 19350 ybp----------------------------51471 ybp +-12384 ybp

    K(all)--------------------------------76937 ybp +- 18765 ybp---------------------------49915 ybp +- 12010 ybp


    G(all)--------------------------------76629 ybp +- 18690 ybp----------------------------49715 ybp +- 11962 ybp

    P (all)--------------------------------73616 ybp +- 17955 ybp -------------------------47760 ybp +- 11491 ybp

    I(all)---------------------------------72468 ybp +- 17675 ybp ----------------------------47016 ybp +- 11312 ybp

    J (all)--------------------------------70377 ybp +- 17165 ybp-----------------------------45659 ybp +- 10986 ybp

    R (all)--------------------------------49446 ybp +- 12060 ybp-----------------------------32080 ybp +- 7718 ybp


    More to come.....
    Last edited by jeanL; 08-03-2013 at 08:13 PM.

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  3. #42
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    Quote Originally Posted by jeanL View Post
    Using Table-1 these are the ages of certain haplogroups using the different rates:
    [...]
    I(all)---------------------------------72468 ybp +- 17675 ybp ----------------------------47016 ybp +- 11312 ybp
    [...]
    R (all)--------------------------------49446 ybp +- 12060 ybp-----------------------------32080 ybp +- 7718 ybp[/b]
    These are actually the estimations calculated using all SNP mutations that are specific for a given haplogroup, which in case of haplogroups I and R means the time since a given lineage has been separated from J or Q, respectively. When estimating the age of expansion for haplogroups I and R, you need to deduct 124 SNPs (25.4 or 16.5 ky) and 40 SNPs (5.7 or 8.8 ky), respectively.

    Also, there seems to be an apparent correlation (at least for haplogroup I) between the sample size for a given sublineage (clade) and the number of SNPs downstream of a common ancestor. For example, the only member of I2a1b shows only 103 mutations downstream of MRCA for haplogroup I, while all three major Sardinian sublineages show much more than 200 SNPs (exceeding 260 in some cases). It seems likely that when a very small number of people representing a given haplogroup/lineage is tested, many SNPs are simply omitted because of some quality problems (so there is a huge risk of obtaining false negative results that cannot be "verified" by testing more people from the same haplogroup/lineage). In this particular case of haplogroup I, using the well represented Sardinian clade I2a1a1 seems to be more appropriate for estimating the age of this haplogroup than taking an average number of SNPs from all sublineages of haplogroup I (including those not well represented that are likely to show many false negatives), especially when it was one of the Sardinian sublineages of I2a1a1 that was used to calibrate the mutation rate.

    In other words, the MRCA of haplogroup I is dated to about 50.3 kya when using the Francalacci's rate and 32.6 kya when using the Poznik's rate, while MRCA of haplogroup IJ is dated to 75.7 kya and 49.1 kya, respectively.

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    That is an archaeological calibration based on the oldest definate modern human settlement in Europe-the proto-Aurignacian of east-central Europe.Well the first calculation for I is impossible for a totally European haplogroup. Even the second one would only work at the lower end of the range.

    If we applied the same to R and picked the more recent end of the range of the 2nd calculation then that would come in about 25000 years which is not hugely older than the normal dating for R.

    Quote Originally Posted by jeanL View Post
    Ok here is Table-1 from the Francalacci.et.al.2013 study:

    Francalacci.et.al.2013-Table1.jpg

    There are two key components I want to add, these Table likely represent the age of certain haplogroup in Sardinians, and to a lesser extent some individuals added for some haplogroups. Nonetheless it can be very informative.

    If we use the mutation rate calibrated in this paper of 0.53*10-9mut/bp/year we arrive to an average of 205+-50 years per SNP mutation. If instead we use the mutation rate of the Poznik.et.al.2013 of 0.82*10-9mut/bp/year we arrive to an average of 133+-32 years per SNP mutations.

    Using Table-1 these are the ages of certain haplogroups using the different rates:

    Haplogroup-------------Francalacci.et.al_rate_Age------------------------Poznik.et.al_rate_Age

    Root__A---------------------------205533 ybp +- 50130 ybp---------------------------133346 ybp+-32083 ybp

    A(all)------------------------------180379.5 ybp +- 43995 ybp-------------------------- 117027 ybp +- 28157 ybp

    E+(all)-----------------------------111069 ybp +- 27090ybp----------------------------72059.4 ybp +- 17338 ybp

    F+(all)-----------------------------109634 ybp +- 26740 ybp----------------------------71128 ybp +- 17114 ybp

    IJ(all)-------------------------------79335 ybp +- 19350 ybp----------------------------51471 ybp +-12384 ybp

    K(all)--------------------------------76937 ybp +- 18765 ybp---------------------------49915 ybp +- 12010 ybp


    G(all)--------------------------------76629 ybp +- 18690 ybp----------------------------49715 ybp +- 11962 ybp

    P (all)--------------------------------73616 ybp +- 17955 ybp -------------------------47760 ybp +- 11491 ybp

    I(all)---------------------------------72468 ybp +- 17675 ybp ----------------------------47016 ybp +- 11312 ybp

    J (all)--------------------------------70377 ybp +- 17165 ybp-----------------------------45659 ybp +- 10986 ybp

    R (all)--------------------------------49446 ybp +- 12060 ybp-----------------------------32080 ybp +- 7718 ybp


    More to come.....

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    Quote Originally Posted by Michał View Post
    These are actually the estimations calculated using all SNP mutations that are specific for a given haplogroup, which in case of haplogroups I and R means the time since a given lineage has been separated from J or Q, respectively. When estimating the age of expansion for haplogroups I and R, you need to deduct 124 SNPs (25.4 or 16.5 ky) and 40 SNPs (5.7 or 8.8 ky), respectively.
    You are right about that, I should have noticed that. In any case R is actually 43 SNPs downstream, so correcting for that put their age as:

    Haplogroup-------------Francalacci.et.al_rate_Age------------------------Poznik.et.al_rate_Age

    R(all)-------------------40631 ybp +- 9910 ybp --------------------------26361 ybp +-6342 ybp

    I(all)-------------------47048 ybp +- 11475 ybp --------------------------30524 ybp +- 7344 ybp

    R1(R1a/R1b)------------32841 ybp +- 8010 ybp ---------------------------21307 ybp +- 5126 ybp

    R1b(V88/P297)----------26691 ybp +-6510 ybp ----------------------------17317 ybp +- 4166 ybp

  6. The Following User Says Thank You to jeanL For This Useful Post:

     Michał (08-03-2013)

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    Quote Originally Posted by Michał View Post
    These are actually the estimations calculated using all SNP mutations that are specific for a given haplogroup, which in case of haplogroups I and R means the time since a given lineage has been separated from J or Q, respectively. When estimating the age of expansion for haplogroups I and R, you need to deduct 124 SNPs (25.4 or 16.5 ky) and 40 SNPs (5.7 or 8.8 ky), respectively.

    Also, there seems to be an apparent correlation (at least for haplogroup I) between the sample size for a given sublineage (clade) and the number of SNPs downstream of a common ancestor. For example, the only member of I2a1b shows only 103 mutations downstream of MRCA for haplogroup I, while all three major Sardinian sublineages show much more than 200 SNPs (exceeding 260 in some cases). It seems likely that when a very small number of people representing a given haplogroup/lineage is tested, many SNPs are simply omitted because of some quality problems (so there is a huge risk of obtaining false negative results that cannot be "verified" by testing more people from the same haplogroup/lineage). In this particular case of haplogroup I, using the well represented Sardinian clade I2a1a1 seems to be more appropriate for estimating the age of this haplogroup than taking an average number of SNPs from all sublineages of haplogroup I (including those not well represented that are likely to show many false negatives), especially when it was one of the Sardinian sublineages of I2a1a1 that was used to calibrate the mutation rate.

    In other words, the MRCA of haplogroup I is dated to about 50.3 kya when using the Francalacci's rate and 32.6 kya when using the Poznik's rate, while MRCA of haplogroup IJ is dated to 75.7 kya and 49.1 kya, respectively.
    Based on the fact I is the oldest pretty well purely European clade and the first certain modern humans in Europe were the proto-Aurignacians of c. 42000BC. if they correlate, it suggest the truth could lie half way between te two figures you just quoted suggesting that averaging the two methodologies might be close to the truth. There is a slightly early group called the Bohunician dating to about 3 or 4 thousand years earier but the jury is still out as not anatomical remains have been found and they may have moved back out in a cold snap and left no cultural impact after comparable to the Aurignacians who clearly did.

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    Quote Originally Posted by Mikewww View Post
    That rate of SNPs per generation is about 3 times less than what Xue came up with, right? or maybe the coverage of the Y chromosome is different.

    A calibrated human Y-chromosomal phylogeny based on resequencing

    Wei Wei et al
    "8.97 Mb... ...using the directly measured SNP mutation rate of 1.0 ◊ 10−9 mutations per nucleotide per year or 3.0 ◊ 10−8 mutations per nucleotide per generation (Xue et al. 2009). Where necessary, we converted estimates in generations to estimates in years using 30 yr per generation.
    http://genome.cshlp.org/content/23/2/388.full#


    Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree
    Xue et all

    http://www.cell.com/current-biology/...822(09)01454-7

    "... in 10.15 Mb; ... The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 x 10^8 mutations/nucleotide/generation (95% CI: 8.9 x 10^9 -7.0 x 10^8), consistent with estimates of 2.3 x 10^8 -6.3 x 10^8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed."


    So same approximate length but slightly different results between the two papers. But what about the later amount in the Human-Chimp comparisons. I am not sure what I am reading here? Anyone?


    Paper overview: http://www.sanger.ac.uk/about/press/2009/090827.html

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
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    Quote Originally Posted by MJost View Post
    So same approximate length but slightly different results between the two papers. But what about the later amount in the Human-Chimp comparisons. I am not sure what I am reading here? Anyone?
    This is how I understand the whole issue:
    Xue et al. (2009) have estimated the mutation rate (by sequencing two distant cousins) to be 3 x 10^-8 per nucleotide per generation. Since they found only four mutations in those two tested people, their calibration could not be very precise, as we need to assume a huge margin of error in such case. Nevertheless, this particular mutation rate (equivalent to 1 x 10^-9 per nucleotide per year) was used by Wei et al. (2012) to make some further estimations as to the age of some clades in their tree (but they did not make any additional calibration, they've just used the estimated mutation rate provided by Xue et al.).

    We have now received two additional Y-DNA mutation rates thanks to the calibration performed by Francallacci et al. (who used the Sardinian haplogroup I2a) and Poznik et al. (who used the American haplogroup Q). Francalacci also mentions similar estimates provided by Mendez et al. (2013) "from the genome-wide mutation rate observed from de novo mutations adjusted for Y chromosome–specific variables".

    Thus, using different calibration methods, people have come to some slightly different estimations regarding the mutation rates in chromosome Y, and these are as follows:

    1 x 10^-9 per nucleotide per year (Xue et al.)
    0.82 x 10^-9 per nucleotide per year (Poznik et al.)
    0.617 x 10^-9 per nucleotide per year (Mendez et al.)
    0.53 x 10^-9 per nucleotide per year (Francalcci et al.)

    Based on the above, I think it is secure to assume that the "true" mutation rate is close to 0.7 (0.6-0.8), although this may of course change in the future when some more reliable analyses are performed.

    EDIT: As for the human-chimpanzee study, I am not sure what generation time should we use in such case, but assuming that this is calculated for humans, their result (2.3 x 10^-8 per nucleotide per generation) is equivalent to 0.77 x 10^-9 per nucleotide per year, which is quite consistent with all above estimations.
    Last edited by Michał; 08-04-2013 at 05:11 PM.

  10. #48
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    Quote Originally Posted by MJost View Post
    A calibrated human Y-chromosomal phylogeny based on resequencing

    Wei Wei et al
    "8.97 Mb... ...using the directly measured SNP mutation rate of 1.0 ◊ 10−9 mutations per nucleotide per year or 3.0 ◊ 10−8 mutations per nucleotide per generation (Xue et al. 2009). Where necessary, we converted estimates in generations to estimates in years using 30 yr per generation.
    http://genome.cshlp.org/content/23/2/388.full#


    Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree
    Xue et all

    http://www.cell.com/current-biology/...822(09)01454-7

    "... in 10.15 Mb; ... The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 x 10^8 mutations/nucleotide/generation (95% CI: 8.9 x 10^9 -7.0 x 10^8), consistent with estimates of 2.3 x 10^8 -6.3 x 10^8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed."


    So same approximate length but slightly different results between the two papers. But what about the later amount in the Human-Chimp comparisons. I am not sure what I am reading here? Anyone?


    Paper overview: http://www.sanger.ac.uk/about/press/2009/090827.html

    MJost
    As per Xue, Y. et al. a separation from a common ancestor [born 1805AD] 13 generations back lead to a difference of 4 mutations between two 13th generation descendants.
    "The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11◊ or 20◊, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in ∼10.15 Mb; eight of these had occurred in vitro and four in vivo."

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    Quote Originally Posted by Michał View Post
    This is how I understand the whole issue:
    Xue et al. (2009) have estimated the mutation rate (by sequencing two distant cousins) to be 3 x 10^-8 per nucleotide per generation. Since they found only four mutations in those two tested people, their calibration could not be very precise, as we need to assume a huge margin of error in such case. Nevertheless, this particular mutation rate (equivalent to 1 x 10^-9 per nucleotide per year) was used by Wei et al. (2012) to make some further estimations as to the age of some clades in their tree (but they did not make any additional calibration, they've just used the estimated mutation rate provided by Xue et al.).

    We have now received two additional Y-DNA mutation rates thanks to the calibration performed by Francallacci et al. (who used the Sardinian haplogroup I2a) and Poznik et al. (who used the American haplogroup Q). Francalacci also mentions similar estimates provided by Mendez et al. (2013) "from the genome-wide mutation rate observed from de novo mutations adjusted for Y chromosome–specific variables".

    Thus, using different calibration methods, people have come to some slightly different estimations regarding the mutation rates in chromosome Y, and these are as follows:

    1 x 10^-9 per nucleotide per year (Xue et al.)
    0.82 x 10^-9 per nucleotide per year (Poznik et al.)
    0.617 x 10^-9 per nucleotide per year (Mendez et al.)
    0.53 x 10^-9 per nucleotide per year (Francalcci et al.)

    Based on the above, I think it is secure to assume that the "true" mutation rate is close to 0.7 (0.6-0.8), although this may of course change in the future when some more reliable analyses are performed.

    EDIT: As for the human-chimpanzee study, I am not sure what generation time should we use in such case, but assuming that this is calculated for humans, their result (2.3 x 10^-8 per nucleotide per generation) is equivalent to 0.77 x 10^-9 per nucleotide per year, which is quite consistent with all above estimations.
    Thanks for the information and your opinion Michał. Xue appears to now be the old Gold standard, but Posnik et al and Francalcci et all are now inline for the new standard? Why would Francalcci be that much lower and should his be a justifiable contender?

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  12. #50
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    Quote Originally Posted by MJost View Post
    Xue appears to now be the old Gold standard, but Posnik et al and Francalcci et all are now inline for the new standard? Why would Francalcci be that much lower and should his be a justifiable contender?
    The problem with the mutation rate estimated by Xue is that it cannot be considered as sufficiently reliable (or rather sufficiently precise). Even when assuming that the actual mutation rate is indeed very close to 1.0, as they have calculated, they could have easily found two or six mutations (instead of four) in those two distant cousins (just by chance), which could have led to the estimated mutation rate 0.5 or 1.5, respectively (which is of course a huge difference when applying such “calibrated” mutation rate to some further estimations).

    By contrast, Poznik and Francalacci have used much larger numbers in their calculations, which includes not only more people tested but also significantly larger distance to the common ancestor and hence much larger number of mutations in each descending lineage (so the number of mutations found in each lineage should be less prone to deviate from the average). Therefore, their calculations should provide a mutation rate that shows a much lower margin of error. The only disadvantage of their method is the much lower reliability of their initial assumptions as to the age of a given “point of reference”, i.e. the assumed age of the expansion of the American Indian population (in the case of Poznik) or the assumed age of the expansion of the Sardinian I2a population (in the case of Francallacci).

    Regardless of all above, it seems to me that the major problem with using those estimated mutation rates in practice is that the “SNP detection rate” in many such sequencing analyses is definitely insufficient. A good example is that mentioned in one of my previous posts. The apparent underestimation of the number of mutations present in two “identical” I2a1b lineages tested by Francalacci (only 103 mutations downstream of the I1/I2 branching point) could have led to the calculated age of haplogroup I that is about 2.5 times lower than the age calculated using the very large number of the Sardinian I2a1a lineages, each showing about 250 mutations downstream of the I1/I2 branching point.
    Last edited by Michał; 08-04-2013 at 11:15 PM.

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