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Maliclavelli
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« on: August 25, 2012, 08:47:25 AM »

After having thanked who banned me from Rootsweb (that he rests in peace!), this is the last posting of Prof. Anatole Klyosov:

>> From: argiedude:
>> Years ago split between R1b-P312 and R1b-U106 =
>> = 6474 years / 45% = 14400 years
> From: Vincent Vizachero:
> Despite the inferred precision in your calculations, the reality here is
> that the 1000 Genomes Y-SNP data is such an utter mess that any TMRCA
> estimate based on that data amounts to a wild guess.
>Assuming the autosomal mutation rate applies to the Y-chromosome is a wild
>assumption, and unfounded.
>Picking an "correction factor"... is a wild assumption and unfounded.
>...the clearly unsupportable conclusion your mathematical gymnastics led
>you to should serve as a caution.
>> The TMRCA of R-P312 and R-U106 as being Paleolithic is simply not
>> defensible.
My comment:
First, Vincent is right on all the five counts above.
Second, besides the above, the real problem which makes all those exercises
utterly un-scientific, is that in science you suppose to compare your
obtained data with other data available in the field, and either conclude
that they are the same, or similar, or similar in kind, or different (or
totally different). In the last case you suppose to explain why they are
different, and either explain that the "other" methodology is incorrect and
show why, or reconsider your methodology.
There are at least three sets of data available in the literature regarding
"age" of R1b-P312 and R1b-U106 (along with other "European" subclades of
R1b). One, exemplified by Myres et al (2010), Balaresque et al (2010),
Morelli et al (2010) which "showed" R1b in Europe as being Paleolithic, all
employed infamous "population mutation rates", that is "Zhivotovsky mutation
rates", and it was explained not once that the data were artificially and
wrongly "made older" by 2-3 times. Another set of data was that by Busby et
al (2011) in his "cautionary tale of Y chromosome lineage R-M269" in which
they considered "diversity" in a large R1b1a2-M269 dataset but failed to
realize that they picked an assorted and incompatible with each other
"mutation rates", in which "slow" mutations turned out to be faster then
"fast" mutations. In short, it was a mess. Hence, a "cautionary tale".
The third set of data was published in Advances in Anthropology
http://www.scirp.org/journal/aa/ in May 2012, but it was discussed at this
Forum not once. Here is what it says regarding P312 and U106. Their
respective base haplotypes are as follows:
13 24 14 11 11 14 12 12 12 13 13 29 - 17 9 10 11 11 25 15 19 29 15 15 17
17 - 11 11 19 23 15 15 18 17 36 38 12 12 - 11 9 15 16 8 10 10 8 10 10 12 23
23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12 ************ (P312)

13 23 14 11 11 14 12 12 12 13 13 29 - 17 9 10 11 11 25 15 19 29 15 15 17
17 - 11 11 19 23 16 15 17 17 37 39 12 12 - 11 9 15 16 8 10 10 8 10 10 12 23
23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 13 12 ************ (U106)
There are only 5.5 mutations between them (it looks like 6, but some
differences are fractional ones). Everyone skilled in 67 marker haplotypes
knows that 6 mutations between two 67 marker haplotypes are not many, and
cannot possibly account for 14400 years. Why I wonder such a simple thought
did not occur during that acrobatics with SNP data? Actually, 5.5 mutations
results - on average - during 5.5/0.12 = 46 "conditional" generations, which
is 48 generations corrected for reverse mutations, of about 1200 years
between them. Since both P312 and U106 have an "age" of about 4200 years,
their common ancestor lived (4200+4200+1200)/2 = 4800 years ago.
Incidentally, 4800 years is the "age" of R1b-L11, calculated independently.
More detailed calculations along with margins or error are given in the
above reference.
Please notice, 4800 ybp, not 14400 ybp. Check your methodology.
Regards,
Anatole Klyosov




Once Vincent Vizachero said to me that in this way you calculated the age between two “modal” reconstructed and not from to-day. I.e. 4800 years (given that the calculations of Klyosov are right, and it would be too long to demonstrate that they aren’t) is the age of the separation of R-P312 from R-U106. After then they have had a long life, probably not far from what Argiedude says.

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Maliclavelli


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MtDNA: K1a1b1e

ironroad41
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« Reply #1 on: August 25, 2012, 09:50:51 AM »

Anyone that believes the number of mutations is only six between the two modals is not being very "scientific" in my judgment.  In the Ian Cam of clan gregor we have a wide range of numbers of mutations at different haplotypes for a known period of time.  CDYa,b mutate at a rate of more than 1 mutation each 200 years or so,  there are many other fast mutators which have lesser rates but still may have 2 in 600 years.  Klyosov says he has a way of factoring in "hidden mutations", but it looks to me like it way undercounts.

I don't know the time difference between P 313 and U106, but I wouldn't use this analysis as a good guide?
« Last Edit: August 25, 2012, 03:42:17 PM by ironroad41 » Logged
Maliclavelli
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« Reply #2 on: August 25, 2012, 10:25:05 AM »

What you say is true, and I wonder how Klyosov may ignore it. Once I expressed my theory by three principles:
1)   mutations happen around the modal
2)   there is a convergence to the modal as time passes
3)   sometime a mutation goes to the tangent and we have the outliers.

Not only CDY but I wonder also about DYS464, given modal at 15-15-17-17 both for P312 and U106. The modal is an abstraction, only the most diffused values, but we know that only a few lines survive, and I think that only the outliers may give us the number of the hidden mutations. Klyosov never replied to this post of mine, in spite I have invited him many times:

This posting of mine, posted here and published also by Dienekes, is waiting some response, above all from Anatole Klyosov:


An interesting haplotype of R1a1a (M17) has been found in the paper of Gunjan Sharma et al., Genetic Affinities of the Central Indian Tribal Population, PLoS one,  February 2012:
DYS19=18
DYS385=14-17
DYS389=15-30
DYS390=28
DYS391=12
DYS392=14
DYS393=13
DYS437=17
DYS439=13
DYS448=22
DYS456=17
DYS458=17

At first sight it could seem we have found the R-M420 not found so far in India with its DYS492=14, which presupposes a 13, whereas all the other R1a1a haplotypes have 11 or 10 and 12 from 11, but this haplotype has been tested for M17, then it isn’t an R-M420. Also the extremely large variance of the other markers makes us think that this value 14 derives from a modal 11 (or what was the modal at the origin of this subclade). Then again all the discourses about “modal” and “variance”, as I have supported many times, are worth nothing.
But I think it would be something to say about the TMRCA of 10.97+/-1.86 kya (25 y for generation) even though calculated by the Zhivotovsky rate. It is clear that these R1a1a-s belong to different clades and the massive presence of the clade most usually found falsifies the calculation. It is clear that this haplotype is an outlier, but for this more interesting, because testifies all the mutation gone mostly for the tangent and not around the modal. If we calculate the intraclade between two of these haplotypes, for instance with this closer to the modal: 15, 11-14, 14-32, 24,10, 11, 12,14,10, 20, 15,16 we have 32 mutations. Also using the usual mutation rate of 0,0022, we have:
(454x32)/28=518
518x25=12,950
and I have used a generation of 25 years and not 32 as I use usually, and I haven’t considered  other mutations around the modal.

Conclusions? The ancientness of the haplogroups is much much more than it is usually thought.

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Maliclavelli


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MtDNA: K1a1b1e

ironroad41
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« Reply #3 on: August 25, 2012, 11:55:12 AM »

What you say is true, and I wonder how Klyosov may ignore it. Once I expressed my theory by three principles:
1)   mutations happen around the modal
2)   there is a convergence to the modal as time passes
3)   sometime a mutation goes to the tangent and we have the outliers.


I will reexpress your comments into my understanding.  1. this is clear 2. I'm not sure what the convergence is to as time passes since multisteps can mess things up for a slow mutator for a long time, but one still prevails.  3.  In general we observe mutations about the modal for the slower mutators, with faster mutators we observe a range of +/- 2 to 3 steps emerging, but again after a while no additional variance is generated.  So we have your 3 rules plus two additional observations. a. multistep mutations occur about 5% of the time with deltas of up to 5 or 6 steps very rarely.  Multiple mutations can occur at meiosis, up to three have been observed.

Relative to your R1a example, My haplotype is similar in that I have had 22 slow mutations over 111 dys loci.  This is in addition to an uncountable number of mutations at the faster mutators.  My analysis indicates a TMRCA for R Z 253 similar to your example c.  11K BP +/_ 1.5Kyears.  My understanding is that M. Jost is running my haplotype through the most recent Nordtvedt variance model to see what he gets.

One thing all of this discussion is demonstrating is that use of either SNP's or STR's to estimate time are fraught with difficulties.
« Last Edit: August 25, 2012, 01:10:52 PM by ironroad41 » Logged
Maliclavelli
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« Reply #4 on: August 25, 2012, 12:13:26 PM »

Yes, multistep mutations do occur and are very important. A friend of mine had a son with DYS456=11 as to his 14! And many mutations are due to the age of the father: I spoke about this some months ago, and now has been published a peer review paper about this.  It is clear that they will have an its own evolution. My theory took in consideration the most diffused mutations, i.e. 1 step forwards or downwards.
« Last Edit: August 25, 2012, 12:16:36 PM by Maliclavelli » Logged

Maliclavelli


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MtDNA: K1a1b1e

ironroad41
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« Reply #5 on: August 25, 2012, 03:47:17 PM »

Anyone that believes the number of mutations is only six between the two modals is not being very "scientific" in my judgment.  In the Ian Cam of clan gregor we have a wide range of numbers of mutations at different haplotypes for a known period of time.  CDYa,b mutate at a rate of more than 1 mutation each 200 years or so,  there are many other fast mutators which have lesser rates but still may have 2 in 600 years.  Klyosov says he has a way of factoring in "hidden mutations", but it looks to me like it way undercounts.

I don't know the time difference between P 313 and U106, but I wouldn't use this analysis as a good guide?

On another board I was made aware that L48 is a large subclade of U 106 and has a different "modal" at 390, 23 vs 24.  Since the number of entries for the subclade is larger that its ancestral sub clade, it changed the "most common"/modal value.

This is another example where mixing subclades gives bad results, majority vote wins.  I have also argued this shouldn't be done for TMRCA estimates as, I believe, it will shorten the estimate for the older subclade.
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