World Families Forums

General Forums - Note: You must Be Logged In to post. Anyone can browse. => R1b General => Topic started by: Maliclavelli on July 31, 2012, 01:32:10 PM



Title: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 01:32:10 PM
Another interesting contribute by Dienekes. After having calculated, from the 1KGP, the ages of the most important nodes of the haplogroups, he considers specifically R-M343 and subclades.

“Most times are around 6-7 thousand years ago, but there is an outlier bump at around 15 thousand years ago. To further investigate this bump, I carried out multidimensional scaling of the collection of Y-chromosomes […]It is clear that the group of high pairwise TMRCAs correspond to the individual on the left of the figure that emerges as a clear outlier vis a vis the rest. The ID of that individual is HG00640 (from PUR population). One possibility is that this individual is M343+ due to sequencing error and belongs to a different lineage altogether. However, HG00640 is also R1-S1+ and R1b1-L278+ but R1b1a-P297-.

It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!

The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years”.

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.   


Title: Re: The age of R-M343 calculated by Dienekes
Post by: ironroad41 on July 31, 2012, 02:03:23 PM
Enjoy the new data Maliclavelli, you earned it.  It would be great if he could get some of the more "interesting" R1b subclades identified on his pictogram.  Based on what we know of the availability of haplotypes, I think the major bumps are the major subclades: P312, U106 and possibly RL21 and U152?

I would guess all the subclades above L11 are the small bumps between 343 and the major subclades?  This would support M Heinilas work.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 03:13:58 PM
Sometime they come back:

Vincent said... FWIW, most of the Puerto Ricans in the R1b1(xP297) project at FTDNA have Jewish ancestry.


I repeat:

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.   


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on July 31, 2012, 03:30:26 PM
Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 03:47:53 PM
Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

You know that Dienekes is a lover betrayed by STRs, not one who didn’t believe in them from the beginning. But say it to your friend Vincent, who, if the Puerto Rican is a Jew, that’s all right. Unfortunately I have demonstrated to him and to all the others that it isn’t so.



Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 04:04:28 PM
HG00640 is the father of HG00642, then we should detect two signals superimposed.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 04:08:04 PM
In fact they are two superimposed.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on July 31, 2012, 04:17:51 PM
These are the R1b1 of the FTDNA Project. Amongst them the Puerto Ricans. Where are the 10,000 years of difference in their STRs as to my R-23/L150+ or that of the Tuscan in 1KGP?

R1b1* (L389+) Cluster A2
67723 Humphries Samuel Humphries (b. about 1760, location unknown) Unknown Origin R1b1
11 24 15 11 13-14 12 13 12 13 13 30 14 9-9 11 11 26 15 18 30 14-14-14-16 10 11 18-23 14 16 19 16 34-34 15 11 11 8 15-16 8 10 10 8 11 9 12 19-21 17 10 12 12 13 8 12 25 21 13 11 11 13 12 11 12 12 34 15 9 15 11 28 27 19 13 10 12 12 11 9 12 11 10 11 11 32 12 12 24 13 11 10 17 15 17 13 21 16 11 15 25 12 24 17 10 14 18 9 11 11
161210 Torrescartagena   Unknown Origin R1b1
13 23 16 11 12-14 12 14 11 14 13 30 14 9-9 11 11 26 14 18 27 13-14-14-16 11 11 18-23 15 17 18 16 34-35 11 11                                                                                   48742 Quinones Andres Martin[ez] de Quinones, b.1595, Puerto Rico Unknown Origin R1b1
13 23 16 11 12-14 12 14 11 14 13 30 14 9-9 11 11 26 15 18 27 13-14-14-16 11 11 18-23 15 17 18 16 35-35 11 11 11 8 15-16 8 10 10 8 11 10 12 20-21 16 10 13 12 15 8 12 24 20 14 11 11 13 12 11 12 12                                                                                        
N26020 Segarra Octavio Segarrra, b.c. 1893, Puerto Rico Unknown Origin R1b1
13 23 16 11 12-14 12 14 11 14 13 30 14 9-9 11 11 26 15 18 27 13-14-14-16 11 11 18-23 15 17 18 16 35-35 12 11 11 8 15-16 8 10 10 8 11 10 12 19-21 16 10 13 12 15 8 12 24 20 14 11 11 13 12 11 12 12                                                                                        
56529 Marcial Rufino Marcial, c. 1840, Camuy, Puerto Rico Unknown Origin R1b1
13 23 16 11 12-14 12 14 11 14 13 30 14 9-9 11 11 26 15 18 27 13-14-14-16 11 11 18-23 15 17 19 16 35-35 11 11                                                                                   N83832 Demao DeMao Italy R1b1
13 24 16 11 12-14 12 13 12 13 13 29 14 9-9 11 11 25 15 18 28 14-14-14-14 11 11 18-22 15 16 17 16 36-36 14 8 11 8 15-16 8 10 10 8 11 10 12 19-21 15 10 12 12 14 8 12 24 21 14 11 11 13 12 11 12 13                                

And this is the Italian Mangino, R-M269 but the closest to the R1b1-s:
46835   Italy R1b1a2
13 24 16 11 11-13 12 13 12 13 13 29 15 9-9 11 11 25 15 18 30 13-14-14-16 11 11 18-23 15 17 19 16 33-38 12 12 11 8 15-16 8 10 10 8 11 10 0 20-21 16 10 12 12 13 8 12 23 20 15 11 11 13 11 11 12 13          


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Arch Y. on July 31, 2012, 04:29:18 PM
Another interesting contribute by Dienekes. After having calculated, from the 1KGP, the ages of the most important nodes of the haplogroups, he considers specifically R-M343 and subclades.

“Most times are around 6-7 thousand years ago, but there is an outlier bump at around 15 thousand years ago. To further investigate this bump, I carried out multidimensional scaling of the collection of Y-chromosomes […]It is clear that the group of high pairwise TMRCAs correspond to the individual on the left of the figure that emerges as a clear outlier vis a vis the rest. The ID of that individual is HG00640 (from PUR population). One possibility is that this individual is M343+ due to sequencing error and belongs to a different lineage altogether. However, HG00640 is also R1-S1+ and R1b1-L278+ but R1b1a-P297-.

It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!

The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years”.

Now we know very well these Puerto Ricans, from when we discussed with Sam Vass about his haplotype and we didn’t know the SNP V88. Now we know that V88+ is diffused in Africa (many thinks arrived from West Asia, I have supposed from Italy via sea or Iberia), but only from V88-, i.e. L389+, were born the European subclades. This haplotype is diffused amongst Jews of Iberian origin (only one haplotype, then introgressed from Spaniards), amongst Puerto Ricans (only one haplotype), many different haplotypes are diffused in the Isles (but come from where?), and only Italy has this haplogroup with YCAII=18-22 and 18-23, one of which is for me the ancestor of the European sublcades. It is what I have being saying from many years. And I have always said that if someone demonstrated that the Refugium of R1b were in Iberia (the Franco-Cantabrian Refugium) or even in the Isles I wouldn’t be surprised.   


So we should go with Dienekes age estimate for R1b rather than Karafet's?

Arch


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 01, 2012, 12:39:23 AM
So we should go with Dienekes age estimate for R1b rather than Karafet's?

Karafet did not estimate the TMRCA of R1b but rather R1.

For that matter, it turns out that Dienekes is also not estimating the TMRCA of R1b but rather R-L389 which is one node downstream of R-M343.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 01, 2012, 03:04:49 AM
Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

You know that Dienekes is a lover betrayed by STRs, not one who didn’t believe in them from the beginning. But say it to your friend Vincent, who, if the Puerto Rican is a Jew, that’s all right. Unfortunately I have demonstrated to him and to all the others that it isn’t so.



It's called cherry picking.


In science


    "Choosing to make selective choices among competing evidence, so as to emphasize those results that support a given position, while ignoring or dismissing any findings that do not support it, is a practice known as "cherry picking" and is a hallmark of poor science or pseudo-science.
    — Richard Somerville, Testimony before the U.S House of Representatives Committee on Energy and Commerce Subcommittee on Energy and Power, March 8, 2011[3]"

Here is an example of cherry picking,

Cohen Modal Haplotype (CMH),J1e and J2a possible Cohen clusters, have R-M429/S2/S22.The same snps found in[IJ] I1 and I2. All Italians with R-M429/S2/S22 are related to both Cohen J1e and J2a CMH, through there paternal line of descent. 


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mkk on August 01, 2012, 04:27:11 AM
Dienekes estimates for R1b's origin are in line with e.g Klyosov for the age of R1b, but his estimate for two subclades of U106 came out to over 6000 years, 2000 years more than what most other estimates have shown...



Title: Re: The age of R-M343 calculated by Dienekes
Post by: rms2 on August 01, 2012, 06:43:48 AM
I am not a statistician or any kind of a mathematician, so I am not qualified to critique this or that approach to estimating the age of this or that haplogroup, but I can make some general observations.

First, I have little faith in these age estimates. They change too often and too radically. The layman gets the impression that none of these people knows what the heck he or she is doing.

Second, they seem to be pretty malleable: one can tailor them to fit his own personal origin theory. And, all too often, one can track or predict origin theories based on the ethnicity of the advocate.

Third, variance doesn't seem to be all that reliable, since a population moving into a new area can be drawn from numerous sources and thus have a higher variance than a population in an older, established region.

So, I'm holding out hope for ancient y-dna findings, but the possibility of contamination worries me a bit.

I am glad to see vineviz posting here again.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: gtc on August 01, 2012, 07:12:38 AM
First, I have little faith in these age estimates. They change too often and too radically. The layman gets the impression that none of these people knows what the heck he or she is doing.

Ditto.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 01, 2012, 07:57:03 AM
First, I have little faith in these age estimates. They change too often and too radically. The layman gets the impression that none of these people knows what the heck he or she is doing.

Having spent some time estimating TMRCA myself, I can sympathize with the sentiment.  But I think that most credible actors are converging on a small number of refined methods that quite often produce highly concurrent estimates.

This 15kya estimate for the TMRCA of R-L389 is within 1,000 years of two different estimates that I produced using different methods (STR-based variance and SNP counting) almost four years ago.

The academics are still behind in their methodology (mostly their mutation rate assumption), but most credible amateurs are pretty much running in a pack in terms of results even when they are only tangentially coordinating.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: rms2 on August 01, 2012, 08:15:30 AM
I have a lot of respect for you and your opinions and have always found you to be reliable and unbiased, so I'll take your word for it.

Glad to see you posting here again.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Jdean on August 01, 2012, 09:44:14 AM
I have a lot of respect for you and your opinions and have always found you to be reliable and unbiased, so I'll take your word for it.

Glad to see you posting here again.

Big fat ditto on that, nice to have somebody with a real grasp of the numbers posting here again too !!!


Title: Re: The age of R-M343 calculated by Dienekes
Post by: gtc on August 01, 2012, 10:54:46 AM
Having spent some time estimating TMRCA myself, I can sympathize with the sentiment.  But I think that most credible actors are converging on a small number of refined methods that quite often produce highly concurrent estimates.

I think it would help considerably if somebody kept a league table of SNP/clade age estimates showing author attributions (be they academic or credible amateurs) and dates of publication so we could easily see at a glance where the current thinking is.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 01, 2012, 11:27:52 AM
I have several methods of calculating the time of mutation SNPs
(already posted on the forums). Here is one.

According to my calculations (already posted on the forums),
one SNP in the approximately 400,000 nucleotides (in WTY)
was in about 628 years.
In the vertical of ISOGG tree  and of Draft Tree (by T.Krahn)
be located about 164 SNPs.
This gives the time of Adam: 103,000 years

In vertical tree R1b-M343 is average about 30 SNPs.
30 x 628 = 18,840 years.

Stan


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 01, 2012, 11:46:40 AM
I have several methods of calculating the time of mutation SNPs
(already posted on the forums). Here is one.

According to my calculations (already posted on the forums),
one SNP in the approximately 400,000 nucleotides (in WTY)
was in about 628 years.
In the vertical of ISOGG tree  and of Draft Tree (by T.Krahn)
be located about 164 SNPs.
This gives the time of Adam: 103,000 years

In vertical tree R1b-M343 is average about 30 SNPs.
30 x 628 = 18,840 years.

Stan


Then the 18 SNPs found by Richard Rocca in the 2 Mexican R-U152-s of the 1KGP would mean: 628x18=11,304 years ago.

But probably what makes a mutation to become a SNP is that it is diffused and fixed (and survived) in many close lines and not simply in one unique family.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 01, 2012, 12:09:27 PM
As with STRs, different SNPs have different mutation rates. That's why some SNPs are seen across many haplogroups and have decimal values (i.e. L69.1, L69.2...). There are lengths in the Y-chromosome that are so unstable, that whatever SNPs are found there are almost useless. That blurs the lines somewhat, as the slowest STRs might be more beneficial for genetic genealogy than the fastest SNPs.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 01, 2012, 12:23:02 PM
I have a lot of respect for you and your opinions and have always found you to be reliable and unbiased, so I'll take your word for it.

Glad to see you posting here again.

Big fat ditto on that, nice to have somebody with a real grasp of the numbers posting here again too !!!

Yes, VV, would love your perspective. I've got stashes full of long R1b haplotypes all formatted with SNP information. Let me know if there is something I can send you. To be honest, I think some of the things that were forecasted earlier, have just been reaffirmed with the greater depth of data, but you might see some new twists in the data.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: alan trowel hands. on August 01, 2012, 01:13:28 PM
got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 01, 2012, 01:34:13 PM
Quote
Then the 18 SNPs found by Richard Rocca in the 2 Mexican R-U152-s of the 1KGP would mean: 628x18=11,304 years ago.
SNPs in one sample did not give a good result!

Quote
As with STRs, different SNPs have different mutation rates. That's why some SNPs are seen across many haplogroups and have decimal values (i.e. L69.1, L69.2...)
Do we have something better for dating genealogy?
STR is useful, until it does not create a second mutation in the same markers -  to about 30 generations.
So far we do not know the SNP repeated in the same place and in the same sample.
Stan


Title: Re: The age of R-M343 calculated by Dienekes
Post by: alan trowel hands. on August 01, 2012, 01:40:12 PM
Does the incorpotation of these very upstream forms of R1b  haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.  

The age of 15500 years (give or take a millenium or so) should probably be considered in terms of the climatic changes of 14000-9000BC or so which could have had a major impact on human populations and movement.  


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 01, 2012, 01:44:16 PM
SNPs in one sample did not give a good result!
The samples are 2 and not related. When it has been seen a relation father/son it has been said, and we don't know if the samples are closely or far related.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Jean M on August 01, 2012, 01:47:27 PM
Does the incorporation of these very upstream forms of R1b  haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.  

I'm assuming that. Did you see the paper on the Cohanim? J1c3 (P58) is found in nearly half of the men who report themselves members of the hereditary Jewish priesthood (Cohanim). Other haplogroups found in the Cohanim include J2a (M410), J2b (M12), J2a3h2a1c (M318), R1b1a2 (M269) and E1b1b1b2a (M123), all found in the Near East.

 M. F. Hammer, Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood, Human Genetics, vol. 126 (2009), pp. 707–717.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 01, 2012, 01:50:08 PM
@Stan

Would you mind explaining how you arrived to the conclusion that one SNP event can be estimated as occurring every 628 years?

I gotta admit, I'm rather confused by the methodology that Dienekes is using. I know Karafet.et.al.2008 did an interpolation methodology, where  the age of CT was fixed at 70 kya, and based on how downstream each SNP was with respect to CT, the age was calculated.

What I know is that the paternal germ-line autosomal mutation rates are much faster than maternal germ-line rates. Also, the mutation rate used by Dienekes was 3*10-8 mutations/nucleotide/generation. The y-chromosome has about 56 millions nucleotides, of course, I'm not sure how big the NRY section is, in terms of nucleotides, but most of the Y-chromosome is non-recombinant. So like I said before, I would greatly appreciate it, if you could explain how you came to the 628 years/SNP conclusion.



Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 01, 2012, 01:54:18 PM
got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  

I have studied these samples from many years. It is a constant that many Jewish haplotypes or clusters have a MRCA not more than 1000 years ago. This is explained by who believes to a Jewish ancestry by a bottleneck, by who doesn’t believe in it by an introgression.
If the haplogroup were Jewish before than 2000 years ago, we don’t understand why we don’t find some Jews related to this with mutations.
On the other hand the R1b1* (note: those with YCAII=18-23: the others, Eastern, with 23-23 or 21-23 have nothing to do with the European subclades) found in Europe (Iberia, Isles, Italy) have many mutations and belong to many different haplotypes.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 01, 2012, 04:44:56 PM
Does the incorpotation of these very upstream forms of R1b  haplotype among Jews in so many locations (Azkenazi and Sephardic??) implies it was around in some pre-European dispersal location in the middle east.   

That is the most reasonable inference.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 01, 2012, 04:52:07 PM
got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.) EDIT: ... well, it could be both and I suppose I should add in Italy although I'm not sure why.

EDIT: I see VV was thinking the same (the "both" part.)


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 01, 2012, 05:01:37 PM
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 01, 2012, 05:26:09 PM
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.

I'm not presenting any of these possibilities as my favorite or one as better than another, but here are some historical considerations.

1. The Jewish faith has a long tradition of Near East origin so that alternative probably doesn't need a lot of explanation.

2. The link up of Jewish migrations to/from the Rhine Valley.
Quote from: Wikipedia
"The Jews of Ashkenaz", are the Jews descended from the medieval Jewish communities along the Rhine in Germany from Alsace in the south to the Rhineland in the north.

I'll throw in another which is interesting for people who are intrigued by a PIE homeland.

3.  The Khazars of the Pontic Steppes had some number of Jewish immigrants and there are reports that many people of Khazaria converted to Judaism.
Quote from: Wikipedia
In 529, Prince Khosrau I of the Persian Empire fought the social movement led by the Zoroastrian priest Mazdak. Numerous Jewish families who supported the movement had to flee the country north of Caucasus Mountains...

Jewish communities had existed in the Greek cities of the Black Sea coast since late classical times. Chersonesos, Sudak, Kerch and other Crimean cities sustained Jewish communities, as did Gorgippia, and Samkarsh / Tmutarakan was said to have had a Jewish majority as early as the 670s. Jews fled from Byzantium to Khazaria as a consequence of persecution under Heraclius, Justinian II, Leo III, and Romanos I. These were joined by other Jews fleeing from Sassanid Persia (particularly during the Mazdak revolts), and, later, the Islamic world. Jewish merchants such as the Radhanites regularly traded in Khazar territory, and may have wielded significant economic and political influence. Though their origins and history are somewhat unclear, the Mountain Jews also lived in or near Khazar territory and may have been allied with the Khazars, or subject to them; it is conceivable that they, too, played a role in Khazar conversion

If one or more of these alternatives can be clearly ruled out as an origin for R1b found among Jews that would be clarifying.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 01, 2012, 06:47:27 PM
I have said also recently that general theories should derive from single case studied and resolved.
The Italian-American Joe Merante have a tradition in his family of Jewish extraction:
1)   his Y is R-M269 with YCAII=17-23, diffused above all in Italy (only one case I found on SMGF and put on ySearch: the Lebanese Jlelaty)
2)   his mtDNA is J1b1b1. His FGS matches perfectly a Buryat and is close to other people of the same people. What do you think about it? That his maternal line was really Jewish one, but probably from a Khazar converted, seen that Khazars have the same origin of the Turkish Buryats. Recently a Jew, whose aunt is a Jewess coming from Turkey, asked me about her mtDNA: J1b1b1. I answered him the same. Recently a complete match in HVRI has been found in the Italian Alps, and this sincerely made me desire other investigations, but an origin from some Turk tribes during the migrations of people is likable, seen that there is in the Alps also 1 hg. M.
3)   Certainly a contribute of the Khazars to the Jewish pool is likable: someone thinks to Y G2c, R1a1a, probably some Q etc


Title: Re: The age of R-M343 calculated by Dienekes
Post by: alan trowel hands. on August 01, 2012, 06:52:16 PM
I must admitt my understanding of Jewish history is practically zero but how far back was the time when the Ashkenazi and Sepharidic Jews parted ways and where was it?  Did they part company in the near east or do they have a more recent common ancestor?  I just ask because I (possibly in my ignornance) assume that the FTDNA list Dienekes linked to included both Ashkenazi and Sephardic sounding people.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Humanist on August 01, 2012, 06:54:34 PM
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.)
Or both.

Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora.

I'd put most R-M343(xL11) in the former and most R-L11 in the latter.

I'm not presenting any of these possibilities as my favorite or one as better than another, but here are some historical considerations.

1. The Jewish faith has a long tradition of Near East origin...

2. The link up of Jewish migrations to/from the Rhine Valley...

I'll throw in another which is interesting for people who are intrigued by a PIE homeland.

3.  The Khazars of the Pontic Steppes...

If one or more of these alternatives can be clearly ruled out as an origin for R1b found among Jews that would be clarifying.

Alternatives #2 and #3 can likely be ruled out for the Jewish R-L584 men.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Humanist on August 01, 2012, 07:01:30 PM
For one of the Cohanim R-L584 lines.  

Marko Heinila's tree data:

Quote
Assyrian #1, kit # 205749: TMRCA of 1848 years with Askhenazi Cohanim and Syrian Jewish men.

Assyrian #2, kit # 213562: TMRCA of 2239 years with Assyrian #1 and Askhenazi Cohanim and Syrian Jewish men. Another 1011 years (3250 years), connects him to four men.  One of the men lists France as an origin.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 01, 2012, 07:51:14 PM
got to say the project Dienekes links through to

http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp

for very upstream R1b does look dominated y Jewish names.  I am not sure what that means in terms of very deep roots of R1b as the Jewish history is one of constant upheaval and movement.  Is there evidence for where and when the Jewish people picked up these upstream forms of R1b? I have never really looked much at these forms of R1b.  
There are also some rarer forms of U152 and U106 that seem to have a little more correlation with the Jewish projects.

I speculated about this some time ago but I suspect that we'll have to come to grips with where R1b became a part of this group. Was it in the Near East or in the Rhine Valley? (which either could align with some accounts.) EDIT: ... well, it could be both and I suppose I should add in Italy although I'm not sure why.

EDIT: I see VV was thinking the same (the "both" part.)

Both Ashkenazi U152 clusters have pretty logical European NPE origins:

U152+L2+L408+ "Epstein Cluster": This group traces its own history back to the middle Rhine area (Eppstein, Germany)

U152+Z56+L4 Cluster: There are 7 in this cluster, 6 are Ashkenazim and 1 is Catholic-Mexican with 0% Jewish ancestry as per Family Finder. I ran the TMRCA using Ken's Gen7 and the age came out to the end of the Roman period at 536 AD ± 338. L4's parent (Z56), seems to be have unusually high frequency in central Italy where it could make up about a third of all U152. So to me, a NPE during the Roman period is a no-brainer.

I don't think it is a coincidence that Ashkenazim with German last names are higher in U106 and U152 and those with Slavic last names are higher in R1a. That I know of, European SNPs are not very common in Sephardi Jews.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 01, 2012, 08:01:56 PM
That I know of, European SNPs are not very common in Sephardi Jews.
But also amongst them happened many introgressions. I have studied the case of the Senior family, who has a haplotype close to mine (and my oldest ancestor was called “Signorino”). We have also paper trails that demonstrate that the Sephardic “Senyor” was a converted to Judaism who had many problems with the Community, after migrated to Holland and some of the descendants to the Isles. For what I have said before, the Sephardic R1b1* are probably introgressed from a Spaniard.



Title: Re: The age of R-M343 calculated by Dienekes
Post by: rms2 on August 01, 2012, 09:39:36 PM
Dienekes' latest  age estimates table (http://dienekes.blogspot.com/2012/08/dates-of-major-clades-of-y-chromosome.html) for the major haplogroups is not all that shocking.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 01, 2012, 10:05:14 PM
Dienekes' latest  age estimates table (http://dienekes.blogspot.com/2012/08/dates-of-major-clades-of-y-chromosome.html) for the major haplogroups is not all that shocking.

I can't resist commenting on the irony.

Hummm...for someone who swore off STR based calculations, he sure has no problem using Xue's mutation rate to calculate M343.

What a difference a year makes. Just scroll down to "UPDATE I (An epitaph for Y-STRs)." http://dienekes.blogspot.com/2011_08_01_archive.html  He summed it as
Quote from: Dienekes
The reason is simple: as clocks, they $/^#k.

Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.


Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.

EDIT: I guess he's not using STRs in his estimates so my comment on irony was off. Please ignore.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 01, 2012, 10:44:32 PM
Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.

Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.


Mike, not sure where you are getting at, but maybe you should know that Dienekes’s age estimates where done using SNPs, not STRs. He mentioned it earlier, that he is using the SNP mutation rate of 3*10-8 mutations/nucleotide/generation. Now, you are right to be skeptical of some of the haplogroups that have very small sample sizes.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 01, 2012, 10:54:17 PM
Another BIG problem with SNP based TMRCA calculations is unknown SNPs. If we look at where M153 (aka Basque marker) was a year and a half ago (one level down from P312) to where we know it exists today (10 levels down from P312), we can see very quickly the issues that can present themselves.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 02, 2012, 12:36:11 AM
Oh, well, I'm glad he decided not to throw the baby (STR diversity/generations) out with the bath water.

Am I reading the "N" column correctly? Some of the "N" values (counts) are 6, 8 and 1. If so, I wouldn't necessarily say he has a great data set to work with.


Mike, not sure where you are getting at, but maybe you should know that Dienekes’s age estimates where done using SNPs, not STRs. He mentioned it earlier, that he is using the SNP mutation rate of 3*10-8 mutations/nucleotide/generation. Now, you are right to be skeptical of some of the haplogroups that have very small sample sizes.


I didn't realize he was counting SNP mutations. That's fair if he's sticking to his guns on NOT using STRs.

I have my concerns on counting SNPs. IF I remember correctly, VV tried this and felt there were a lot of bad reads in SNP test results.  Maybe the technology is better now.

I have another concern, at least in terms of youthful haplogroups.  Are SNPs very sporadic in their occurrence? If we don't have enough territory (Y chromosome) tested and enough good reads on SNP statuses I'm not sure if this is better than using only very slow STRs. The problem being that of using a calendar to measure hours.  We would need a huge sample of lineages, right?  Wouldn't it be a problem in that most ancient lineages went extinct so that cuts down on the data as far as number of different SNP branch lengths to survey? I guess that is why Dienekes is having to use a very limited sample size (column N) in some cases.

I don't know that much about this other than Karafet used it to get the R1 TMRCA of 18.5K ybp plus or minus a huge range.

Any comments on the reliability of SNPs for measuring time?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 02, 2012, 01:45:24 AM
"Some R1b chromosomes were likely in Jewish populations per-diaspora while others were likely introduced post-diaspora."

There can only be one Cohen line with descent from Aaron if he actually existed and strict adherence to a priestly caste was maintained. Either it is R1b or IJ. It cannot be both.

"Y-chromosomal Aaron is the name given to the hypothesised ancestor of the Kohanim, a patrilineal "priestly caste " in Judaism. In Scripture, this ancestor is identified as Aaron, the brother of Moses. This has come about since the appearance in the 1990s of some relevant publications, relevant to the patrilineal ancestor of all humans, Y-chromosomal Adam."

Levant is also home to people of non Semitic descent.

As for example, Galil goyim Isaiah 9:1

The region takes its name from the Hebrew galil, "district", "circle", a noun which, in the construct state, requires a genitival noun. Hence the Biblical "Galilee of the Nations", Hebrew"galil goyim"(Isaiah 9:1). The "nations" would have been the foreigners who came to settle there, or who had been forcibly deported there. The


  Indo-European Phillistines,


In Genesis 21, Abraham agreed a covenant of kindness with the Philistine king Avimelech and his descendants.

It is not hard to entertain the idea that there was mixing between the communities, as can be seen in more recent times, and reported in the study

 Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities



"A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, ∼28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), ∼12%; J2-M172, ∼25%; T-M70, ∼16%] and in consequence Trás-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc"

    Inês Nogueiro1,
    Licínio Manco1,
    Verónica Gomes2,3,
    António Amorim2,4,
    Leonor Gusmão2,*


Title: Re: The age of R-M343 calculated by Dienekes
Post by: gtc on August 02, 2012, 02:32:15 AM
Any comments on the reliability of SNPs for measuring time?

I think Richard Rocca's post sums it up well.




Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 02, 2012, 04:14:06 AM
Another BIG problem with SNP based TMRCA calculations is unknown SNPs. If we look at where M153 (aka Basque marker) was a year and a half ago (one level down from P312) to where we know it exists today (10 levels down from P312), we can see very quickly the issues that can present themselves.
This objection is a real but does not apply to the method Dienekes is using. 

His method depends on completely re-sequencing large chunks of the Y chromosome (and, importantly, the SAME chunks for each sample).  The distance between the samples - as computed for just those chunks - is then calculated and scaled by the mutation rate.  In effect, as far as his estimates go, there are theoretically no  "unknown SNPs".

I do have a concern about the R-M269 estimates because it is quite likely that the 1000 Genomes project specifically chose to sequence regions of the Y known to be polymorphic based on prior testing and that prior testing always includes R-M269 research samples.  This is one reason I don't trust the estimate for R1b1a2a1a1a5:  it likely includes more SNPs peculiar to this clade than you would expect if you chose the sequencing region completely at random.  So the TMRCA that Dienekes estimates for R1b1a2a1a1a5 is probably too old by a significant margin.

This effect moderates pretty quickly as you move upstream, though, so ascertainment bias probably does not impact the majority of his time estimates significantly including the R-L389 estimate.

VV


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 02, 2012, 04:49:05 AM
I do have a concern about the R-M269 estimates because it is quite likely that the 1000 Genomes project specifically chose to sequence regions of the Y known to be polymorphic based on prior testing and that prior testing always includes R-M269 research samples.  This is one reason I don't trust the estimate for R1b1a2a1a1a5:  it likely includes more SNPs peculiar to this clade than you would expect if you chose the sequencing region completely at random.  So the TMRCA that Dienekes estimates for R1b1a2a1a1a5 is probably too old by a significant margin.

Then the 1KGP would be U106 biased! But then why out of 51 Tuscans we have had 15 U152 and 15 J?
And  2 R-L51, almost 4%, which is the percentage in line with Central North Italy? (I am going by heart, but these should be the percentages).


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 02, 2012, 04:53:43 AM
In case we should ask Dienekes who are these 109 people, because I ask me where are the Indian (Gujaratis) R-M207-s?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 02, 2012, 07:24:16 AM
@Stan
Would you mind explaining how you arrived to the conclusion that one SNP event can be estimated as occurring every 628 years?

I gotta admit, I'm rather confused by the methodology that Dienekes is using. I know Karafet.et.al.2008 did an interpolation methodology, where  the age of CT was fixed at 70 kya, and based on how downstream each SNP was with respect to CT, the age was calculated.

What I know is that the paternal germ-line autosomal mutation rates are much faster than maternal germ-line rates. Also, the mutation rate used by Dienekes was 3*10-8 mutations/nucleotide/generation. The y-chromosome has about 56 millions nucleotides, of course, I'm not sure how big the NRY section is, in terms of nucleotides, but most of the Y-chromosome is non-recombinant. So like I said before, I would greatly appreciate it, if you could explain how you came to the 628 years/SNP conclusion.

The SNP mutation rate in the human genome, according to textbooks of genetics, amounts to 3x10^-8 SNP per 1 base pair per the generation (30 years), that is 1x10^-9 SNP/ 1 bp/ 1 year, that is 0.000,000,001 SNP/1 bp/1 year.

But this rate of the mutation were calibrated for the time of 5,000,000 years from the moment of the divergence of the man and the chimpanzee. Now it is known, that it is necessary to calibrate this rate for 6,000,000 years; so is necessary to multiply it through 5/6. The rezult: 0.000,000,00083333 SNP

Moreover it is known, that SNP mutations in Y-chromosome are occurring 4.8 times more quickly than in the entire human genome (geneticists are trying to somehow explain this phenomenon with environmental conditions of meiosis: http://en.wikipedia.org/wiki/Y_chromosome). The above rate it is necessary so to multiply through 4.8.
In the result we receive 0.000,000,004 SNP/1 base pair/1 year in NRY
................................
In most precisely tested haplogroup (e.g. R1b) we are finding
average about 164 SNPs per about 400,000 base pair in WTY (in ISOGG and TreeDraft by T. Krahn).
It is equaling 0.00041 SNPs per 1 base pair

Dividing this result by 0.000,000,004 SNP per year (in NRY) ,
we receive the result 102,500 ybp, i.e. about 103,000 ybp.
It means 1 SNP per 628 years.
Stan

Supplement
In C-T: average 115 SNPs; x 628 = 72,000 years
In R1b: average 30 SNPs, x 628 = 18,800 years
In R1a: average 25 SNPs, x 628 = 15,700 years


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 02, 2012, 08:12:02 AM
Dividing this result by 0.000,000,004 SNP per year (in NRY) ,
we receive the result 102,500 ybp, i.e. about 103,000 ybp.
It means 1 SNP per 628 years.
Stan

Supplement
In C-T: average 115 SNPs; x 628 = 72,000 years
In R1b: average 30 SNPs, x 628 = 18,800 years
In R1a: average 25 SNPs, x 628 = 15,700 years


There are a couple places where this estimation process goes wrong, but one critical one is in the final step where the number of SNPs is counted.  I'm pretty sure I know how you've performed this step, but before I criticize it let's be sure.  What are the 30 SNPs you count in R1b, and which sample(s) are they present it?

VV


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 02, 2012, 08:59:07 AM
Of the WTY results, there must be some SNPs that are found that belong to the same subclade of a the tree. We have no way of knowing how many of these occurred within the same generation. As we have seen recently with L21 getting bumped down one level from L459 and Z245, SNP estimates may have the same problems as STRs. I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 02, 2012, 09:11:57 AM
Quote
There are a couple places where this estimation process goes wrong, but one critical one is in the final step where the number of SNPs is counted.  I'm pretty sure I know how you've performed this step, but before I criticize it let's be sure.  What are the 30 SNPs you count in R1b, and which sample(s) are they present it? VV


From average is about 30 SNPs in the R1b and subclades?

Below R1 -
to: L257=29 SNPs, L1=28, L45=35, L148=35, Z343=34, M167=28, M228=30, Z35=30, L562=30, Z144=30, L705=29, L554=28, L362=29 and L658=31 SNPs.

So below R1, in R1b and subclades  is average 30.4 SNPs.
Stan


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 02, 2012, 09:33:20 AM
@R-M343(xL11)


Multiple conversions,multiple peoples multiple times in history.

Constantine the Great brought in Christianity to the Roman Empire. Is it so hard to believe that this did not happen in other areas?

It is not uncommon for rulers and or groups of people to change religion. This can be seen in the former territories of [Celtic] Galations and Median Emipire to the East; areas that also have  elevated R1b when compared to other ydna groups[Grugni et al. 2012,Roewer et al.] especially  associated  the Lurs and Talysh possible ancient[ Medes][Scythian] connection .

http://www.iranicaonline.org/articles/asagarta-sagartia-asagartiya-sagartian-old-persian-elamite-as-s-kar-ti-ia-babylonian-kursa-ga-ar-ta-a-a-greek-s

The Median empire once incorporated the ancient city of Arbil. Who's rulers had Hellenistic names [Phillistine connection?] and resided in Jerusalem.

Arbela connected to Medes;

"this man boasted of Median origin, claiming to be “of the line of Cyaxares” (Uvaxštra[hyā] taumāyā, DB 2.81). It would therefore seem that the Sagartians were neighbors of the Parthians in northeast Iran and extended westward as far as Arbela. Ptolemy (6.2.6) locates them in Media, in the region of the Zagros Gates (Ḥolvān)."

Royal house conversion;

 "Helena of Adiabene (Hebrew: הלני המלכה‎) was queen of Adiabene and wife of Monobaz I. With her husband she was the mother of Izates II and Monobaz II. She died about 56 CE. Her name and the fact that she was her husband's sister [1] indicate a Hellenistic origin. Helena became a convert to Judaism about the year 30 CE."

Royal family moving to Jerusalem;

"Adiabene (from the Ancient Greek Ἀδιαβηνή, Adiabene, itself derived from Classical Syriac: ܚܕܝܐܒ‎, Ḥaḏy’aḇ or Ḥḏay’aḇ, Old Persian/Armenian: Nodshirakan was an ancient kingdom in Assyria, with its capital at Arbela (modern-day Arbil, Iraq). Its rulers converted to Judaism from Ashurism in the 1st century.[6] Queen Helena of Adiabene (known in Jewish sources as Heleni HaMalka) moved to Jerusalem where she built palaces for herself and her sons, Izates bar Monobaz and Monobaz II at the northern part of the city of David, south of the Temple Mount. According to the Talmud, both Helena and Monbaz donated large funds for the Temple of Jerusalem."


Again, is it so hard to believe that her subjects did not also convert 2000 years ago, in an area that was known to have ancient Iranian tribes like the Medes and  R1b?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 02, 2012, 09:41:27 AM
@acekon

Maybe I missed it, but did anyone say it was hard to believe that groups of people can convert from one religion to another?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 02, 2012, 10:05:03 AM
@acekon

Maybe I missed it, but did anyone say it was hard to believe that groups of people can convert from one religion to another?




You did not miss out. I'm trying to make a point in the context of "alleged" ancestry and use a paternal caste as a proxy for a much lager group in general.   Consider that there can only be one actual paternal line of  Cohen, either it is R1b or IJ. You cannot have for example, someone who has "proof of family history"with the "Cohen" last name in and be in distinct family[4] groupings L584+ and L584- or 426-11 and 426 -10, in a strict paternal caste,it does not work that way. Therefore by process of elimination, we must conclude that people of different origins have entered the ydna gene pool just as the studies I have quoted. The correct term would be "alleged".

It should be noted that the term "Ashkenazi" is associated with Medes/Scythians.It is of different lineage from "Cohen"[Aaron] associated with Semitic peoples, it is like mixing apples and oranges.

"In the rabbinic literature, the kingdom of Ashkenaz was first associated with the Scythian region, then later with the Slavic territories"

By replacing the term "alleged" with "Ashkenaz"=[Scythian] to denote a Semitic peoples in origin, you are confusing ancestry of people who have converted, but have a completely different[Non-Semitic]  lineage.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Richard Rocca on August 02, 2012, 10:15:08 AM
Quote
You did not miss out. I'm trying to make a point in the context of "alleged" ancestry.   Consider that there can only be one actual paternal line of  Cohen, either it is R1b or IJ. You cannot have for example, someone who has "proof of family history"with the "Cohen" last name in and be in distinct family[4] groupings L584+ and L584- or 426-11 and 426 -10, in a strict paternal caste,it does not work that way. Therefore by process of elimination, we must conclude that people of different origins have entered the ydna gene pool just as the studies I have quoted. The correct term would be "alleged".

No arguments here. Nothing will ever be proven and we can only make arguments in  "likelihoods".

Quote
It should be noted that the term "Ashkenazi" is associated with Medes/Scythians.It is of different lineage from "Cohen"[Aaron] associated with Semitic peoples, it is like mixing apples and oranges.

"In the rabbinic literature, the kingdom of Ashkenaz was first associated with the Scythian region, then later with the Slavic territories"

By replacing the term "alleged" with "Ashkenaz"=[Scythian] to denote a Semitic peoples in origin, you are confusing ancestry.

Again, I seem to be missing something. Has anyone here confused Ashkenzi with Sephardi?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 02, 2012, 10:26:58 AM
@Ashkenazi-Sephardi


No, good point, in terms of continuity.

A diaspora (from Greek διασπορά, "scattering, dispersion")

 For example str matches in J1's or J2's[IJ] or even R1b's R1a if they exist, and can be found in  both groups[Ashkenazi-Sephardi]. That would be a very reasonable and logical assumption, of proving ancestry. Now put a "Cohen" [strict paternal caste]in the mix with proven ancestry, that meets the above criteria, and you have some real solid evidence{587 BCE/70 CE}[IMO].



Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 02, 2012, 11:21:32 AM
That would mean that Z156 is around 5,600 ybp.



Quote
There are a couple places where this estimation process goes wrong, but one critical one is in the final step where the number of SNPs is counted.  I'm pretty sure I know how you've performed this step, but before I criticize it let's be sure.  What are the 30 SNPs you count in R1b, and which sample(s) are they present it? VV


From average is about 30 SNPs in the R1b and subclades?

Below R1 -
to: L257=29 SNPs, L1=28, L45=35, L148=35, Z343=34, M167=28, M228=30, Z35=30, L562=30, Z144=30, L705=29, L554=28, L362=29 and L658=31 SNPs.

So below R1, in R1b and subclades  is average 30.4 SNPs.
Stan


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 02, 2012, 11:26:09 AM
Of the WTY results, there must be some SNPs that are found that belong to the same subclade of a the tree. We have no way of knowing how many of these occurred within the same generation. As we have seen recently with L21 getting bumped down one level from L459 and Z245, SNP estimates may have the same problems as STRs. I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.
I agree with you on this. I'm all for understanding SNP mutations and using them as a kind of molecular clock. However, we know less about this than STRs so its kind of like looking for the greener grass on the other side of the hill.

It makes sense to use multiple SNP counting and STR diversity methods and allow them to cross-check each other until science can refine them into a best (or at least better) method.

Am I wrong on this point about SNP counting? One other concern I have is it is like a single clock. We are using the whole regions of the Y chromosome as a single clock in SNP counting methods.

This is in contrast to STRs. Each STR, since it has a range of values, not just ancestral or derived, is its own clock. The great value of a large number of STRs is they can be averaged together per Ken Nordtvedt's description, as a composite clock. Ken says this is exactly what happens with Carbon-14 dating. Yes, some of the component clocks (single STRs) need to be deselected or better understood, but the more experiments (the more clocks) you have, the better your composite clock can be.

The STRs provide a better composite clock is the point.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 02, 2012, 12:14:29 PM
Now what would be so interesting about conversions in and around Erbil and downstream[R-M343] R1b?

As you go in a North[+/-200km] and North West direction you start to hit elevated pockets of R1b[[Grugni et al. 2012,Roewer et al.].and the ancient kingdom of Arran.

 Not to be confused with the ancient Isle Aran.

https://en.wikipedia.org/wiki/File:Eileanarainn.ogg



According to C.E. Bosworth:
“    The Georgians knew them [the Caucasian Albanians] as Rani, a form taken over in an Arabized form for the early Islamic geographical term al-Rān (pronounced ar-Rān)


Could the region of Arran or modern day Azerbaijan[perhaps a Perisan name?],
have been populated by Scythians and Medes, before they were run over by the Turks,[compare R1b in Turkic area in Grugni study with Lurs] ?




Title: Re: The age of R-M343 calculated by Dienekes
Post by: Heber on August 02, 2012, 01:43:54 PM
Dienekes has an updated post on the Dates of major clades of the Y-chromosome phylogeny.
There is a very nice table of Dates of the major clades. Of interest to me are R1 (M343), R1b1 (L278+),  R1B1a2a1A1a5 (Z301).

"Overall, it seems to me that with more samples, deep sequencing of the Y (as opposed to the low coverage of the 1000G Project), sequencing of larger regions of the Y, as well as a better estimate of the mutation rate (which can be achieved when many father-son full genomes become available), we are going to have a pretty crisp estimate of the ages of all the branching points of the tree."

http://dienekes.blogspot.ie/2012/08/dates-of-major-clades-of-y-chromosome.html

There seems to be a plethora of important lineages that coalesce around the Last Glacial Maximum (I, J, O, R1). Perhaps this too was a stressful period for humans resulting in a loss of diversity and the survival of a few lineages from the early arrivals. In the case of haplogroup I which is truly European in distribution it is tempting to imagine that it represents the emergence of the Gravettians, while its sibling J stayed in the Near East, where IJ* chromosomes have recently been found.

http://dienekes.blogspot.ie/2012/08/dates-of-major-clades-of-y-chromosome.html






Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 02, 2012, 03:28:31 PM
That would mean that Z156 is around 5,600 ybp.

Z156 is only three SNP down.
So only about 1,900 YBP.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a   L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128
•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5b   Z301


Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 02, 2012, 03:41:33 PM
Z156 is only two SNPs down from U106.L148 is eleven SNPS down from U106.




That would mean that Z156 is around 5,600 ybp.

Z156 is only three SNP down.
So only about 1,900 YBP.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a   L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128
•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5b   Z301



Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 02, 2012, 03:43:01 PM
That would mean that Z156 is around 5,600 ybp.

Z156 is only three SNP down.
So only about 1,900 YBP.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a   L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128
•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5b   Z301


It is likable. This I have written in another thread:
1
You belong to a cluster, for the values I indicated within the 67 markers (at least those already received), but of course you have also other mutations within your family line. One is DYS393=12 (I have this mutation too, but I am R.L23/L150, and this mutation is modal in my haplotype), a mutation very rare, but also rare mutations do happen. Probably your descendants will have this value for thousands of years. But you have also DYS390=25, also rare, DYS385a=12, etc. This demonstrates probably that much time has passed from the ancestor of your cluster and, like my theory says, many other mutations have happened around the modal in fast mutating markers.
But these many mutations beyond your cluster could be due also to the age of some of your ancestors: the higher the age, the higher the mutation rate.
2
Also here I am basing upon single cases examined: many people with many mutations father-son had a father aged. If this happens, this is a single case, which hasn't anythng to do with "an average per time". That individual will have those mutations and will pass them on his descendants: a clade was born.
History (and Genetics) is a science based upon the particular and not the general.

and this would be the case in which SNPs are more reliable than STRs.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 02, 2012, 04:05:51 PM
I believe that I will have to find at least nine downstream SNPs until I get to a private one. L148 is eleven SNPs downstream of U106. 628 x 11 = 6908 for U106. L148 is a private SNP .


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 02, 2012, 04:06:58 PM
The SNP mutation rate in the human genome, according to textbooks of genetics, amounts to 3x10^-8 SNP per 1 base pair per the generation (30 years), that is 1x10^-9 SNP/ 1 bp/ 1 year, that is 0.000,000,001 SNP/1 bp/1 year.

You shouldn’t express the SNP mutation rate as a function of years, because for once the generation time isn’t a fixed number, or we don’t even know if it averages out to 30 or 25, this is even more complicated when we are talking about time frames of over 50,000. Expressing the SNP mutation rate as a function of years makes it seem as if the SNPs depended on how many years have passed by, but in reality, they depend on the number of meioses, however because we cannot measure the SNP mutation as a function of meioses of the Y-chromosome, we have to get a estimate of it as a function of generations, hence expressing it in years, makes me a bit uncomfortable.

But this rate of the mutation were calibrated for the time of 5,000,000 years from the moment of the divergence of the man and the chimpanzee. Now it is known, that it is necessary to calibrate this rate for 6,000,000 years; so is necessary to multiply it through 5/6. The rezult: 0.000,000,00083333 SNP

The Pan-Homo divergences time is still a matter of great debate, and it could very well be anywhere from 5 million to 9 million years old, so that would make the constant change quite a bit. Something else to the effect of what I was saying above, is that modern day Chimpanzees reproduce when they are ~16 years old, so the generational time of 30 years old wouldn't hold any water as we move back to the time prior to the evolution of modern humans.

Moreover it is known, that SNP mutations in Y-chromosome are occurring 4.8 times more quickly than in the entire human genome (geneticists are trying to somehow explain this phenomenon with environmental conditions of meiosis: http://en.wikipedia.org/wiki/Y_chromosome). The above rate it is necessary so to multiply through 4.8.
In the result we receive 0.000,000,004 SNP/1 base pair/1 year in NRY

That is not known to me, I know that the paternal germ-line mutates faster than the maternal one does, but I didn’t know what the fudge factor was, I thought that number was still being worked on.

In most precisely tested haplogroup (e.g. R1b) we are finding
average about 164 SNPs per about 400,000 base pair in WTY (in ISOGG and TreeDraft by T. Krahn).
It is equaling 0.00041 SNPs per 1 base pair

Dividing this result by 0.000,000,004 SNP per year (in NRY) ,
we receive the result 102,500 ybp, i.e. about 103,000 ybp.
It means 1 SNP per 628 years.
Stan

Supplement
In C-T: average 115 SNPs; x 628 = 72,000 years
In R1b: average 30 SNPs, x 628 = 18,800 years
In R1a: average 25 SNPs, x 628 = 15,700 years


Thanks, I appreciate the calculations, would you be willing to estimate it the age for R1b-M269, and R1b-P312 using that methodology?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 02, 2012, 05:57:40 PM
Of the WTY results, there must be some SNPs that are found that belong to the same subclade of a the tree. We have no way of knowing how many of these occurred within the same generation. As we have seen recently with L21 getting bumped down one level from L459 and Z245, SNP estimates may have the same problems as STRs. I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.

I think Dienekes is wrong to totally dismiss STR-based TMRCA estimation.  On the other hand, we do have a pretty good idea of SNP mutation rates so I see no barrier to using SNPs as an accurate clock IF the method is well-designed.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 02, 2012, 06:00:05 PM
So below R1, in R1b and subclades  is average 30.4 SNPs.

It looks to me as if you are counting SNPs in the ISOGG tree.  If that's what you are doing, the method is fatally flawed.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 02, 2012, 06:04:07 PM
One other concern I have is it is like a single clock. We are using the whole regions of the Y chromosome as a single clock in SNP counting methods.
No, I'd say you should think of each nucleotide as an individual clock.  A very slow-ticking clock, but a clock nonetheless.

So that sequencing 400kbp of Y-DNA is like a composit clock of 400,000 individual slow-moving clocks.  Like having a haplotype of 400,000 VERY slow STRs, in effect.

Going from memory, I recall once estimating that the composite Y-SNP clock is potentially as accurate as a composite Y-STR clock of 100ish STRs.

VV


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Jarman on August 02, 2012, 06:31:07 PM
Z156 is only three SNP down.
So only about 1,900 YBP.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a   L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128
•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5b   Z301


I think you forgot L132.1 beneath L1, or L127.2 beneath L128. That would make Z156 about 2500 ybp counting from the bottom. (Interestingly, using Klyosov's STR formula I calculated the age of Z156 was about 2750 ybp.)  But I know the proponants of SNP counting want us to count from the top of the tree and assume no SNPs are missing between Z381 and Z156 and that Z156 should be the same age as Z301. I don't understand that reasoning.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 02, 2012, 06:54:10 PM
One other concern I have is it is like a single clock. We are using the whole regions of the Y chromosome as a single clock in SNP counting methods.
No, I'd say you should think of each nucleotide as an individual clock.  A very slow-ticking clock, but a clock nonetheless.

So that sequencing 400kbp of Y-DNA is like a composit clock of 400,000 individual slow-moving clocks.  Like having a haplotype of 400,000 VERY slow STRs, in effect.

Going from memory, I recall once estimating that the composite Y-SNP clock is potentially as accurate as a composite Y-STR clock of 100ish STRs.

VV
Okay, so it is like many, many clocks with only one tick in them.... at least we think except for rare cases.

Yes, I can see there is a trade-off between many more clocks that are like calendars (SNPs) and versus watches (STRs) with second hands... sounds like a statistical evaluation for Nordtvedt.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 03, 2012, 03:10:37 AM

Quote from: Richard
I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.
......It makes sense to use multiple SNP counting and STR
......Each STR, since it has a range of values, not just ancestral or derived, is its own clock. The great value of a large number of STRs is they can be averaged
......The STRs provide a better composite clock is the point.

Experiment
Is Table 22 slow markers STR  (by Aklyosov) useful to calculate the TMRC human and chimpanzee?
My experiment.
Flipping a coin for man and chimpanzee; eagle (allel +1), tails (allel -1).
Here the results:

DYS472,  number of mutations 5     observed mutations / GD = 1
DYS425, number of mutations 25   observed mutations / GD = 3
DYS436, number of mutations 30   observed mutations / GD = 10
DYS426, number of mutations 45   observed mutations / GD = 13
DYS490,  number of mutations 65   observed mutations / GD = 3
DYS454,  number of mutations 80   observed mutations / GD = 2
DYS455,  number of mutations 80   observed mutations / GD = 4
DYS578,  number of mutations 85   observed mutations / GD = 5
DYS641,  number of mutations 85.  observed mutations / GD = 7
DYS590,  number of mutations 85   observed mutations / GD = 1
............., ....................................,    ............................................,
The experiment showed there is no connection between the number of actual mutations and the number of observed mutations.
This table is also unsuitable for calculating the times of Adam.
Repeated and back mutations are basically uncountable.
In 67 marker haplotype mutations multiple (in the same marker) may be formed at the beginning. And they are uncountable!!!  Therefore doubted their usefulness, especially for time over a thousand or several thousand years.
Stan


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 03, 2012, 03:27:18 AM
Repeated and back mutations are basically uncountable.

I am saying this from many years, but they don't understand this. Mike has asked infinite times that I explain him my principles:

1) mutations around the modal
2) convergence to the modal as time passes
3) sometime a mutation goes for the tangent and we have the outliers

All the aDNA, which we have had some STRs, was under of at least a factor of 2.5 as to their calculations, but nothing to do. Not only Nordtvedt, but also Klyosov (I have exchanged many letters with him on the Dienekes' Anthropology Blog) didn't understand this. After he began to use these 22 slowest mutators with better results.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 03, 2012, 07:18:43 AM
There are only 100 Z156 tests out of the 7000 U106 men tested. When we get to 1000 tests then we will have a better understanding of this group and a lot more SNPs. Do you think that L132.1 and L127.2 are private SNPs?
L48 are the most tested group. Do you know which country has  the highest divesity?


Z156 is only three SNP down.
So only about 1,900 YBP.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a   L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128
•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5b   Z301


I think you forgot L132.1 beneath L1, or L127.2 beneath L128. That would make Z156 about 2500 ybp counting from the bottom. (Interestingly, using Klyosov's STR formula I calculated the age of Z156 was about 2750 ybp.)  But I know the proponants of SNP counting want us to count from the top of the tree and assume no SNPs are missing between Z381 and Z156 and that Z156 should be the same age as Z301. I don't understand that reasoning.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 03, 2012, 07:49:23 AM
Z156 is three six SNP down.
So only about 1900 3800 ybp.

•   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a   S264/Z156
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a*   -
•   •    •   •    •   •    •   •    •   •    •   •    •    R1b1a2a1a1a5a1   S376/Z305,  Z306, Z307
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1*   -
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1a  L1/S26
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1b   P89.2
•   •    •   •    •   •    •   •    •   •    •   •    •   •    R1b1a2a1a1a5a1c   L128 L127.2 (priv.)

I think you forgot L132.1 beneath L1, or L127.2 beneath L128. That would make Z156 about 2500 ybp counting from the bottom. (Interestingly, using Klyosov's STR formula I calculated the age of Z156 was about 2750 ybp.)  But I know the proponants of SNP counting want us to count from the top of the tree and assume no SNPs are missing between Z381 and Z156 and that Z156 should be the same age as Z301. I don't understand that reasoning.
Improved (with the help of Tree Draft)


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Jarman on August 03, 2012, 08:09:09 AM
There are only 100 Z156 tests out of the 7000 U106 men tested. When we get to 1000 tests then we will have a better understanding of this group and a lot more SNPs. Do you think that L132.1 and L127.2 are private SNPs?
L48 are the most tested group. Do you know which country has  the highest divesity?

ISOGG lists those two SNPs as "under investigation".  I doubt there are enough Continental results to calculate Z156 diversity.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 08:21:57 AM

Quote from: Richard
I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.
......It makes sense to use multiple SNP counting and STR
......Each STR, since it has a range of values, not just ancestral or derived, is its own clock. The great value of a large number of STRs is they can be averaged
......The STRs provide a better composite clock is the point.
....
Is Table 22 slow markers STR  (by Aklyosov) useful to calculate the TMRC human and chimpanzee?....
The experiment showed there is no connection between the number of actual mutations and the number of observed mutations.
This table is also unsuitable for calculating the times of Adam.
Repeated and back mutations are basically uncountable.
In 67 marker haplotype mutations multiple (in the same marker) may be formed at the beginning. And they are uncountable!!!  Therefore doubted their usefulness, especially for time over a thousand or several thousand years.
Stan

Stan and Maliclavelli, my understanding from Bob Chandler and Ken Nordtvedt is that back mutations are accounted for. in the mutation rates (EDIT) . I guess Maliclavelli is suggesting they don't understand this. I guess I don't either because to me it is logical to see how non-observed mutations force a mutation rate calibration adjustment, but they don't stop the generally observable expansion of diversity altogether.

Ultimately, there is greater STR diversity, on average, with a greater number of generations, which correlates, although not perfectly, with time.

There probably are ranges of time that different characteristics are useful for. This would be similar to the law of diminishing returns in economics. An example would be that STRs with high numbers of repeats may appear to saturate.

Any method is probably only relevant for a given time frame or situation. We need to understand what time frame. There may be some situations where one method is better than another. What works for a chimpanzee branch of the ape family may not work for a branch of Levantine farmers or the branch my 2nd cousin and I are on.

EDIT: This has been corrected. Back mutations are accounted for, but not in mutation rates.  See post by VV above.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 08:48:08 AM
So below R1, in R1b and subclades  is average 30.4 SNPs.

It looks to me as if you are counting SNPs in the ISOGG tree.  If that's what you are doing, the method is fatally flawed.

On the Hg I forum Ken Nordtvedt responded to an inquiry I made on this topic.
Quote from: Ken Nordtvedt
Using snp counts as clock across the board for different parts of the tree requires absence of bias in the construction of the source of the snps to be counted --- even before one brings in some calibration argument
and
Quote from: Ken Nordvedt
It is important to realize that the snp counts in each tree branch segment are the statistically independent observables, and the node times the items to be estimated from those branch segment snp counts.
http://archiver.rootsweb.ancestry.com/th/index/Y-DNA-HAPLOGROUP-I/2012-08

I would think that Dienekes would understand this. Is the data set he is using unbiased?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 09:18:10 AM
Stan and Maliclavelli, my understanding from Bob Chandler and Ken Nordtvedt is that back mutations are accounted for in the mutation rates. I guess Maliclavelli is suggesting they don't understand this. I guess I don't either because to me it is logical to see how non-observed mutations force a mutation rate calibration adjustment, but they don't stop the generally observable expansion of diversity altogether.

Mike, what is the usual timeframe where mutation rates are calibrated? For the most part germ-line mutations are computed from father-son pairs, which is essentially a single generation. On the other hand people like Klyosov calibrate mutation rates using family trees with known paper trail and also have their y-DNA STRs available. Now, setting aside the problem with the calibration method of Klyosov, do you think the behavior of the back mutations, and of the STRs overall is completely captured in a time frame of one generation(Observed father-son pairs), or even 1300-1500 years, as to be able to extrapolate that to time frames that are from 3-5 times longer(i.e. 5000+ybp).


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 09:35:20 AM
Stan and Maliclavelli, my understanding from Bob Chandler and Ken Nordtvedt is that back mutations are accounted for in the mutation rates. I guess Maliclavelli is suggesting they don't understand this. I guess I don't either because to me it is logical to see how non-observed mutations force a mutation rate calibration adjustment, but they don't stop the generally observable expansion of diversity altogether.

Mike, what is the usual timeframe where mutation rates are calibrated? For the most part germ-line mutations are computed from father-son pairs, which is essentially a single generation. On the other hand people like Klyosov calibrate mutation rates using family trees with known paper trail and have their y-DNA STR tested. Now, setting aside the problem with the calibration method of Klyosov,

I've never calculated mutation rates. It is obvious they are highly controversial although many of the leading hobbyists are used similar rates. I noticed that Ken Nordtvedt is using some of the rates calculated by Marko Heinila so there is some good collaboration. I know Ken also uses rates that Bob Chandler derived. They may be using rates from Leo Little as well (I'm not sure.)

I clearly do not defend Klyosov on anything he does as I don't understand some of the statements he makes.

I would never say STR variance is perfectly aligned with time in a linear fashion. However, most generally seem to accumulate added diversity with time. Do you disagree? This is not to say a timeframe of relevancy, or what some call linear duration doesn't apply.

do you think the behavior of the back mutations, and of the STRs overall is completely captured in a time frame of one generation(Observed father-son pairs), or even 1300-1500 years, as to be able to extrapolate that to time frames that are from 3-5 times longer(i.e. 5000+ybp).

I understand what Bob Chandler and Ken Nordtvedt are saying when they say back-mutations are accounted for in the mutation rates, but I would never use a qualifier such as they are "completely" 100% accounted for perfectly.

The questions you are asking about the timeframes are the same ones I am asking. I don't know what methods are best for what timeframes. That is what I was trying to say in this post.
... Any method is probably only relevant for a given time frame or situation. We need to understand what time frame....




Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 10:18:58 AM
I would never say STR variance is perfectly aligned with time in a linear fashion. However, most generally seem to accumulate added diversity with time. Do you disagree? This is not to say a timeframe of relevancy, or what some call linear duration doesn't apply.

Well I don’t disagree with the statement that STR variance accumulates with time; I however do not think currently we are measuring variance correctly. I think that effects such as back mutations, changes in modal value due to TMRCA being longer than mutational time are being ignored thus leading to an erroneous estimate of diversity, that’s all. Also, I know this question has been asked a bunch of times, but I would say that STR mutation rates do indeed depend on haplogroups, however not in the way most people think. Take for example, let’s say we measured the mutation rate of DYS492 in a sample of mostly J2 man who have a modal value of say 17, this mutation rate is gonna be faster than the actual mutation rate of say R1a man who have a modal value of 13 in that same locus. So in a sense, they do differ from haplogroup to haplogroup, only, when the modal values of the haplogroups for a given locus are different. 


I understand what Bob Chandler and Ken Nordtvedt are saying when they say back-mutations are accounted for in the mutation rates, but I would never use a qualifier such as they are "completely" 100% accounted for perfectly.

The questions you are asking about the timeframes are the same ones I am asking. I don't know what methods are best for what timeframes. That is what I was trying to say in this post.

Think about this, what are the chances of actually seeing a back-mutation in a time frame of 1500 years, what STRs have a higher likelihood of actually having a back-mutation in such timeframe. Now what are the chances of a back-mutation occurring in a timeframe that is 5 times that? Do you think slow STRs (i.e.μ~=10-4) would experience a back-mutation in timeframes of 1500 years, so what would that mean in terms of their calibrated mutation rates?





Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 11:16:51 AM
I would never say STR variance is perfectly aligned with time in a linear fashion. However, most generally seem to accumulate added diversity with time. Do you disagree? This is not to say a timeframe of relevancy, or what some call linear duration doesn't apply.

Well I don’t disagree with the statement that STR variance accumulates with time; I however do not think currently we are measuring variance correctly. I think that effects such as back mutations, changes in modal value due to TMRCA being longer than mutational time are being ignored thus leading to an erroneous estimate of diversity, that’s all. Also, I know this question has been asked a bunch of times, but I would say that STR mutation rates do indeed depend on haplogroups, however not in the way most people think. Take for example, let’s say we measured the mutation rate of DYS492 in a sample of mostly J2 man who have a modal value of say 17, this mutation rate is gonna be faster than the actual mutation rate of say R1a man who have a modal value of 13 in that same locus. So in a sense, they do differ from haplogroup to haplogroup, only, when the modal values of the haplogroups for a given locus are different. 

Are you saying that mutation rates are different at higher STR number of repeats? We know there is a study that shows the observable mutation rate on certain high repeat STRs slows down a the high numbers.  Is that what you are referring to?

Are you referring to the fact that different lineages would have different historical mutation rates if we were to calculate each lineages' independently?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 11:22:14 AM

I understand what Bob Chandler and Ken Nordtvedt are saying when they say back-mutations are accounted for in the mutation rates, but I would never use a qualifier such as they are "completely" 100% accounted for perfectly.

The questions you are asking about the timeframes are the same ones I am asking. I don't know what methods are best for what timeframes. That is what I was trying to say in this post.

Think about this, what are the chances of actually seeing a back-mutation in a time frame of 1500 years, what STRs have a higher likelihood of actually having a back-mutation in such timeframe. Now what are the chances of a back-mutation occurring in a timeframe that is 5 times that? Do you think slow STRs (i.e.μ~=10-4) would experience a back-mutation in timeframes of 1500 years, so what would that mean in terms of their calibrated mutation rates?

What are you saying? What timeframes do you think we should use 1) SNP counting for?  2) slow only STRs?  3) mix of slow, medium and fast STRs? and why?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 03, 2012, 12:37:22 PM
Rhetorical question about mutation rates[R-M343] out of Africa and back to Africa and out of Africa part 2.

Why do we have 7 billion people on the planet with 4 blood groupings, and yet so many other mutations, str's and snp's, when the following happened?

1]  Humans have 46 chromosomes. Gorillas, Chimpanzees, and Orangutans have 48. The explanation is:

a. that humans lost two chromosomes?

b. that Gorillas, Chimpanzees, and Orangutans gained two chromosomes?

c. that there was a splitting of two humans chromosomes in the Gorillas, Chimpanzees, and Orangutans?

d. that there was fusion of two chromosomes in humans?

2]  23andme posts humans with Neanderthal score?

 Neandertal is an extinct species (Homo neanderthalensis) of the Homo genus that inhabited Europe and parts of western Asia from about 250,000 years ago until as recent as 30,000 years ago.  

Are we a result of various mutation rates between Gorillas, Chimpanzees, and Orangutans and Neandertals?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 12:59:01 PM
...
1]  Humans have 46 chromosomes. Gorillas, Chimpanzees, and Orangutans have 48. ...

This may be why we want to segregate data about other species versus homo sapiens sapiens. Their physical properties may be quite different, to the say the least. In other words, findings may not necessarily be generalized between species.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 02:41:43 PM
Are you saying that mutation rates are different at higher STR number of repeats? We know there is a study that shows the observable mutation rate on certain high repeat STRs slows down a the high numbers.  Is that what you are referring to?

Nope, I’m talking about that for any given STR the mutation rate is a function of the repeat number, higher repeat values have higher mutation rates. Marko H noticed this too when working on his data, but yeah essentially the “saturation” effect is because when an STR reaches certain number of repeats it becomes too unstable and it basically mutates back and forth in between two values. For example dinucleotides can have a mutation rate variation from ~10-5.5 mutations/generation when the repeat number is 5, to  ~10-4 when the repeat number is 10. So if you have a dinucleotide STR in a population where the modal is 10, it is 31.63 times more likely to mutate at any given generation than the same dinucleotide STR on a population where the modal was 5. So yes essentially mutation rates are a function of repeat number. If you think about it, the more repeat values a DNA segment has, the more prone it is to slippage, and hence the more likely it is to add or lose a base pair, thus making it less stable.

Are you referring to the fact that different lineages would have different historical mutation rates if we were to calculate each lineages' independently?

Basically, if the modal (There is yet another issue with the assumption that modal==ancestral value, but that’s a different story) values are different for two populations, using the mean mutation rate obtained from one, might not be accurate to apply on a different one.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 02:46:12 PM
What are you saying? What timeframes do you think we should use 1) SNP counting for?  2) slow only STRs?  3) mix of slow, medium and fast STRs? and why?


That’s not an easy question to answer, and honestly, I couldn’t answer it before running multiple computer simulations first(Which I plan to do in the future). As for the SNPs I don’t know, but I would say that SNPs are good as long as the sections of the DNA analyzed are unbiased(That is the contain mostly neutral genes, and little linkage disequilibrium*(For autosomal SNPs, NRY doesn't have LD)), there is also the effects of an expanding population. (i.e. The expected number of offspring in a coalescence model is >1)


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 04:56:52 PM
I would think that Dienekes would understand this. Is the data set he is using unbiased?
That's a question that can only be answered by investigating HOW the 1000G project chose the regions of the Y that they did.  I haven't done that in a while, and I haven't kept up to date on new releases very well so I can't say for sure.

That said I'm sure there is some ascertainment bias at play, but how much?

Anyway,  the impact of the ascertainment bias diminishes greatly as one move up the tree.  Within R-M269, the bias -if there is any - would have a strong impact on TRMCA estimates.  By the time you reach node estimates for R-P297 and upstream, the impact moderates quickly.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 05:09:59 PM
I understand what Bob Chandler and Ken Nordtvedt are saying when they say back-mutations are accounted for in the mutation rates, but I would never use a qualifier such as they are "completely" 100% accounted for perfectly.

There seems to be some confounding of two different problems in this thread.

One is back mutations.  In other words, in a particular lineage a STR mutates from 12 to 13 and then back to 12.  If you are using a variance-based approach, such mutations ARE accounted for.  Not in the mutation rate, but in the method of calculating genetic distance.  I can explain HOW later if someone wants.

A completely different problems is one of STR saturation.  When people talk about linearity, this is what they are referring to.  STRs tend to have definite ranges of alleles, and no matter how much time passes the value for a particular STR is unlikely to exceed this range.

Imagine a marker that has a starting value of 12, which happens to be (though we have no prior knowledge of this) its midpoint value.  This marker has a 4% total mutation rate, but this really means there are two mutation rates p(up) and p(down).  For this marker, imagine a 2% probability of mutating up and a 2% probability of mutation down.  Now say it happens to mutate up, to 13.  The total mutation rate might be 4% still, but p(up) is now only 1% and p(down) is 3%.  It might hit a value (e.g. 15) at which p(up) is 0% and p(down) is 4%.  After a couple generations, this marker has reached its maximum variance value and is considered "saturated".  It's relationship between mutations and  time is not linear.

Now most commonly used STRs seem to be essentially linear over very short periods of time.  But all markers can become non-linear over a long enough period of time.

A full suite of STRs can provide relatively linear TMRCA estimates for a haplogroup that is 5,000 years old.  But one that is 50,000 years old cannot be accurately estimated with fast-moving STRs.

In short, back mutations themselves are not a concern for variance-based TMRCA estimates.  Non-linearity is a concern, and the concern is best addressed by marker selection.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 05:48:13 PM
If a marker has a 4% total mutation rate, all this means is that it either has a 4% mutation rate up or down, or that when adding (That is say backwards is 2% and forward is 6%, this would produce a mutational bias of 4% forward) the two mutation rates up or down, it produces a 4% mutation rate in one direction (forward or backwards), however the simple addition doesn’t work because the forward and backward mutations are independent events in a sense. So what happens when a marker mutates from 12 to 13, is that now the mutability of the marker increases, so the marker is more likely to mutate from 13 to 14, or from 13 back to 12 than it was prior to the occurrence of the mutation from 12 to 13. Markers only saturate when the mutation rate as a function of repeat value doesn’t change much, and the mutation rate has reached a value high enough where it becomes unstable. That is the region of the DNA becomes prone to slippage or deletions far too often, so it causes the STR to toggle between two values. Now the observable range of allele values doesn’t completely describe the saturation effect, it is possible with time for one marker that saturates at say 24-25 repeats to actually produce a value of 27, however such events would be extremely rare, but they are observable, and they do happen every now and then. As for a time frame of 5000 years, which is roughly 200 generations (assuming 25 years per generation), any marker with a mutation rate higher than 0.005 mut/generations would in fact yield an erroneous modal value, and thus undermine the real TMRCA of the population being analyzed. 


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 06:11:19 PM
...   As for a time frame of 5000 years, which is roughly 200 generations (assuming 25 years per generation), any marker with a mutation rate higher than 0.005 mut/generations would in fact yield an erroneous modal value, and thus undermine the real TMRCA of the population being analyzed. 

Thanks.

I count 54 of 67 STRs, according to Chandler/Little, would qualify to be useful for 5000 years. This is using your .005 mut/gen guideline.  54 is still a pretty decent number of available STRs. The 13 "too fast" markers include DYS464 (4 of them) and CDY (2 of them) so we've been whittling down to this anyway.

It appears the 36 markers that I've worked with in the past from Heinila's linear duration analysis is even slightly more conservative than your guideline.  Your guideline actually fits some what nicely with the 50 marker set of mixed speed markers... and it makes some sense that the relative variances between haplogroups (in R1b-L11) seems most steady with the 50 marker set.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 03, 2012, 06:24:05 PM
Of the WTY results, there must be some SNPs that are found that belong to the same subclade of a the tree. We have no way of knowing how many of these occurred within the same generation. As we have seen recently with L21 getting bumped down one level from L459 and Z245, SNP estimates may have the same problems as STRs. I'm not saying one is better than the other, but certainly we have more data about STR mutation rates than SNP mutation rates, so to swear off one and then use the other does not make sense to me.

I think Dienekes is wrong to totally dismiss STR-based TMRCA estimation.  On the other hand, we do have a pretty good idea of SNP mutation rates so I see no barrier to using SNPs as an accurate clock IF the method is well-designed.

I don't if the content in the quote below is accurate, but I think it would be important if my interpretation of what he is saying is on target.
There has been a intensive discussion about the quality of TMRCA estimates. It has been looked into through theoretical considerations and reflected against historical informations more or less backed up by empirical research. Carbon and isotopic dating artefacts associated with past populations gave us time lines to hold against these TMRCA calculations.

In genetic genealogy we use the SNPs indicators for speciation events while the diversity of the STR based haplotypes is seen as anagenetic developments within monophylitic clusters.

By excluding the multi and fast markers in the STR based haplotypes an effort is made to replace the SNP based synapomorphic characters with sets of STR markers and in doing so we come to a TMRCA estimate.

The mechanism of the variation in the VNTR is (mostly) DNA replication slippage while SNP is the consequence of a fixed mutation caused by external influences such as metabolic stress and/or ionising radiation. STR events are more or less internal; SNP novelties have external causes.
...
Hans
http://www.worldfamilies.net/forum/index.php?topic=10752.msg133690#msg133690

Hans/Spanjol, can you add to this.?

If SNPs are externally caused, does it follow that traumatic environmental events could cause an increase in SNPs. That would mean that SNP mutation rates are subject to geography, climate and who knows what.... at least more so than STR mutation rates.

I hope SNPs are reliable clocks so I'm not looking for ways to shoot the concept for fun. I just would like to confirm this is a logical way to go.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 06:32:55 PM
If a marker has a 4% total mutation rate, all this means is that it either has a 4% mutation rate up or down, or that when adding (That is say backwards is 2% and forward is 6%, this would produce a mutational bias of 4% forward) the two mutation rates up or down, it produces a 4% mutation rate in one direction (forward or backwards), however the simple addition doesn’t work because the forward and backward mutations are independent events in a sense. So what happens when a marker mutates from 12 to 13, is that now the mutability of the marker increases, so the marker is more likely to mutate from 13 to 14, or from 13 back to 12 than it was prior to the occurrence of the mutation from 12 to 13.

STR mutation behavior is complex, so any simple model is bound to have limitations. But the best way to think about it is probably to model three different variables:  a probability of mutation along with two dependent variables:  the likelihood of that mutation being up, and the likelihood of that mutation being down.  I simplified the math for an example, but as long as your model incorporates this differential p(up) vs p(down) relationship of a function of allele value for a given marker, you are probably on sound footing.

Markers only saturate when the mutation rate as a function of repeat value doesn’t change much, and the mutation rate has reached a value high enough where it becomes unstable. That is the region of the DNA becomes prone to slippage or deletions far too often, so it causes the STR to toggle between two values.
When we talk about "saturation" in this context, it means saturation of variance.  Maybe you are repeating this but inarticulately?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 06:34:53 PM

The mechanism of the variation in the VNTR is (mostly) DNA replication slippage while SNP is the consequence of a fixed mutation caused by external influences such as metabolic stress and/or ionising radiation. STR events are more or less internal; SNP novelties have external causes.
All mutations have external causes:  external slippage is external to the DNA being replicated.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 06:37:22 PM
As for a time frame of 5000 years, which is roughly 200 generations (assuming 25 years per generation), any marker with a mutation rate higher than 0.005 mut/generations would in fact yield an erroneous modal value, and thus undermine the real TMRCA of the population being analyzed. 
And for the record, there is no such thing as an "erroneous modal value" unless you are simply bad at arithmetic.

The modal value is simply a calculated central value for a series of observed numbers.  You take the values you can observe, and call the middle one the "modal".  It can never be wrong unless you the observer can't count.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 06:55:43 PM
And for the record, there is no such thing as an "erroneous modal value" unless you are simply bad at arithmetic.

The modal value is simply a calculated central value for a series of observed numbers.  You take the values you can observe, and call the middle one the "modal".  It can never be wrong unless you the observer can't count.

Erroneous modal value as in the modal value=/=ancestral value of the MRCA. One assumption when calculating TMRCA is that the modal value is such that it minimizes mutations in a set, when the TMRCA is older than 1/mu then the modal value could in fact no longer represent the ancestral value, so measuring diversity from the modal value would lead to underestimating the TMRCA.  That is if an individual has an ancestral value of 8 in a locus that has a mutation rate of 0.005 mut/gen, after 200 generations most of its progeny its either going to have a value of 7 or 9, so when randomly analyzing a subset of the descendants of that man, the modal value could appear to be either a 7 or a 9, thus leading to a lower calculation of diversity, because the modal value =/= ancestral value anymore.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 07:29:16 PM
Erroneous modal value as in the modal value=/=ancestral value of the MRCA.

This might matter if you are positing a systemic bias is mutational direction.  What's the evidence for that?  It would be strongly non-normal distributions of alleles, but that's not what we observe.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 08:15:21 PM
This might matter if you are positing a systemic bias is mutational direction.  What's the evidence for that?  It would be strongly non-normal distributions of alleles, but that's not what we observe.

There is a systematic bias of mutation with time, and the modal does change with time, you want proof for that:

Modal values for haplogroup G2a

Ancient DNA: http://www.worldfamilies.net/forum/index.php?topic=10646.0 (http://www.worldfamilies.net/forum/index.php?topic=10646.0)

Avellanar Cave, Catalonia 5000 BC

DYS456:15
DYS389II:29
DYS385:14/14
DYS393:13
GATAH4: 12
DYS448:22

Treilles Cave, SW France 3000 BC

DYS456:14 *There is actually 1 sample that has the ancestral value of 15
DYS389II:30
DYS385:13/15
DYS393:14
GATAH4: 11
DYS448:20

So there you have it, just in 2000 years the modal values of those STR positions changed for the same haplogroup G2a. Also, the distribution of alleles for some haplogroups do look strongly non-normal for some STRs.

For example haplogroup I (n=5700) has the following allele distributions:

DYS393: 12 (3%), 13 (68%), 14 (17%), 15 (11%)
DYS390: 21 (1%), 22 (39%), 23 (45%), 24 (11%), 25 (3%), 26 (1%)
 DYS19: 13 (1%), 14 (51%), 15 (33%), 16 (11%), 17 (4%)
DYS390: 21 (1%), 22 (39%), 23 (45%), 24 (11%), 25 (3%), 26 (1%)
DYS391: 9 (1%), 10 (84%), 11 (14%), 12 (1%)

So yes, we know two things:

Mutation rate is a function of repeat number, so a mutation from 12==>13 is more likely to occur than one from 11==>12. In the same matter a mutation from 13==>14 is more likely to occur than a mutation from 12==>13.

The expected time for at least one mutation to occur in all descendants of individual X for any given STR is 1/mu, where mu is the mutation rate of the STR.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 08:25:12 PM
There is a systematic bias of mutation with time, and the modal does change with time, you want proof for that:
Not sufficient proof, sorry.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 03, 2012, 08:27:34 PM
Also, the distribution of alleles for some haplogroups do look strongly non-normal for some STRs.

For example haplogroup I (n=5700) has the following allele distributions:

Again, this is incorrect reasoning.  That sample has a great deal of substructure, with differential reproductive success and uneven sampling.

We used to think that DYS393 was abnormally distributed in R-M269 until we discovered the substructure that explained it.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 08:31:59 PM
Not sufficient proof, sorry.

How so? The modal values for G2a changed in at least 7 STRs in a time frame of 2000 years, if that isn't proof, then I don't know what it is.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 03, 2012, 08:43:01 PM
Again, this is incorrect reasoning.  That sample has a great deal of substructure, with differential reproductive success and uneven sampling.

We used to think that DYS393 was abnormally distributed in R-M269 until we discovered the substructure that explained it.

No the reasoning isn’t incorrect, there is definitely I1 and I2 subclades mixed in there, however that doesn’t stop some STRs from showing normal distributions, whereas other do not show anywhere near a normal distribution. Now, the main point on a more observable scale, is that when estimating the TMRCA of I1 and I2 one might choose a modal value of 23 for DYS390, however for all we know the allele value of their true ancestor could have been something else, for example 22 or 24. So in a sense what I am saying is that on a macro-scale this is more observable, but it does happen too on a micro-scale. The modal values of U106 and P312 differ by very little, however, that doesn’t mean that the ancestral value for those positions (STRs) that differ was either one of the modal values of either P312 or U106.  In fact it is possible for STRs that have the same modal allele values for both U106 and P312 to have a different ancestral allele value from the modal value. 


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 06:13:21 AM
No the reasoning isn’t incorrect, there is definitely I1 and I2 subclades mixed in there, however that doesn’t stop some STRs from showing normal distributions, whereas other do not show anywhere near a normal distribution.

It does stop you from being able to use that "mixed in there" data to infer whether or not the behavior of STRs is symmetrical or not.  Polluted pools of haplotype data like that are simply not useful for some purposes, like this one.

Now, the main point on a more observable scale, is that when estimating the TMRCA of I1 and I2 one might choose a modal value of 23 for DYS390, however for all we know the allele value of their true ancestor could have been something else, for example 22 or 24.

As a matter of procedure, when you use self-variance to estimate TMRCA you don't actually ever "choose a  modal value".


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 09:31:35 AM
Not sufficient proof, sorry.

How so? The modal values for G2a changed in at least 7 STRs in a time frame of 2000 years, if that isn't proof, then I don't know what it is.
I wasn't asking for evidence that STRs mutate.  I was asking for evidence that they systematically mutate in one direction, evidence which is still lacking.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 09:51:16 AM
I wasn't asking for evidence that STRs mutate.  I was asking for evidence that they systematically mutate in one direction, evidence which is still lacking.

That’s not what I said originally, I said that any given STR would likely attain one mutation in all its descendants in a mutational timeframe of 1/mu. I never said that it was one-directional, and I showed how in a time-frame of 2000 years the modal values of G2a changed by one mutation (either up or down) in at least 7 STR markers. So the evidence is there, and what is more, what I’m talking about, is actually a biological concept, which is called expected time for mutation. The only thing that would prevent it for happening would be total symmetry on mutation rates, however we know mutation rates are asymmetrical, because they are strongly dependant on the number of repeats, so there will always be a bias either forward or backward depending on the number of repeats of the STR. This bias is what makes the modal values change in a timeframe of 1/mu. This is what makes the STRs change, i.e.:

Avellanar Cave, Catalonia 5000 BC ==> Treilles Cave, SW France 3000 BC

DYS456:15==>14
DYS389II:29==>30
DYS385:14/14==>13/15
DYS393:13==>14
GATAH4: 12==>11
DYS448:22==>20

PS: Yeah one doesn’t choose the modal value, the modal value is the most frequent value on a distribution, hence the 50th percentile of the distribution of allele.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 10:12:24 AM
I showed how in a time-frame of 2000 years the modal values of G2a changed by one mutation (either up or down) in at least 7 STR markers.

Actually, you showed that some G2a samples have different haploytpes than others.  Unless all modern G2a men are descended from the men buried in those caves, comparing the modal values for one ancient family to the modal values for all modern ones has no relevance to this discussion.

Anyway, even if the modal values for a population shift over time it doesn't complicate the TMRCA estimation process.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 11:50:02 AM
Actually, you showed that some G2a samples have different haploytpes than others.  Unless all modern G2a men are descended from the men buried in those caves, comparing the modal values for one ancient family to the modal values for all modern ones has no relevance to this discussion.

What the two burials showed is not that some G2a samples have different haplotypes, but that the modal of G2a in Europe or at least SW Europe circa 5000 BC was different from the modal of G2a in SW Europe circa 3000 BC. We are taking about relatively close regions(i.e. Avellanar vs. Treilles) in space, yet their modal values changed at least in 7 STRs.  So the point wasn’t to compare those values to the values of modern day people, but to show how modals change with time. Moreover, even if modern day people aren’t descendants of those men buried on those caves, they would still share a common ancestor by the virtue of both being G2a, so here is a little experiment:
Modern modal values for European G2a+ derived clades from Rootsi.et.al.2012:

DYS456:15
GATAH4:12
DYS385:14/14
DYS393: 14
DYS448:21
DYS389II: 29

So the modal value of DYS456 went from being 15 as measured in the sample from 5000 BC, to 14 as measured in the sample from 3000 BC to 15 again in modern day European samples. Same thing happened to GATAH4, DYS385, DYS389. However it is not impossible to imagine that in between 3000 BC and present day the modal values of some of those STRs changed a couple of times. Which leads to the conclusion that modal values aren’t static with time, and that they might change due to different reasons, and bottlenecks aren’t the one reason that would change them, the expectation value is independent of demography. That is a locus with a mutation rate of mu, will attain a mutation in all its descendants in a timeframe of 1/mu regardless if the population was bottlenecking 50% of the time, or 80% of the time. So the mutational bias would manifest itself in the changes of modal throughout time. That is, if a bottleneck were to occur, the chances that the mutant would survive are small relative to the nonmutant under a model of nonmutational bias. This is mostly because the vast majority of the population at any given point in time would have the modal value whereas the offmodal values would be a minority, however the fact that the modal changes with time, which is evident in the case of G2a+ derived clades in Europe, means that the modal value is gradually shifting with time, so bottlenecks probably catalyze the shift, but unless there was a mutational bias, a bottleneck shouldn’t change the modal value of an STR, yet we see changes in modal values with time, so even if we were to attribute these changes to bottlenecks, it wouldn’t disprove that there is a directional bias in mutations which shifts the modal with time.

Anyway, even if the modal values for a population shift over time it doesn't complicate the TMRCA estimation process.


Well, it does complicate things, because for once the assumption that the modal value represents the ancestral value is one that is made. Hence why diversity is measured as a function of mutations from the so called modal value, if the modal value no longer represent the ancestral value, then the diversity measurements would lead to erroneous estimates for TMRCA. Of course, like I said before, this only happens when the MRCA of a haplogroup lived longer than the timeframe of 1/mu for any given STR. So hence why I mentioned earlier that for timeframes of 200 generations, STRs with mutation rates faster than 0.005 mut/gen could in fact have a modal value that is not the ancestral value any longer.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 12:03:16 PM
What the two burials showed is not that some G2a samples have different haplotypes, but that the modal of G2a in Europe or at least SW Europe circa 5000 BC was different from the modal of G2a in SW Europe circa 3000 BC.
It doesn't show this, no matter how often you repeat it.

That is a locus with a mutation rate of mu, will attain a mutation in all its descendants in a timeframe of 1/mu regardless if the population was bottlenecking 50% of the time, or 80% of the time.

No, after 1/mu only some descendants will exhibit a mutation.  On AVERAGE each will have 1 mutation:  some will have zero.  Some will have 1. Some will have 2.  And so on.
Actually, this is not quite the right way to express this.  After 1/mu about half of descendents will still have the ancestral value, either because their lineage never had a mutation or because they had multiple mutations that caused a reversion.

Well, it does complicate things, because for once the assumption that the modal value represents the ancestral value is one that is made. Hence why diversity is measured as a function of mutations from the so called modal value, if the modal value no longer represent the ancestral value, then the diversity measurements would lead to erroneous estimates for TMRCA.
This just isn't true:  it's not the way the math works.  

For one thing, there is no " assumption that the modal value represents the ancestral value." In fact, the fact that  such an assumption is NOT needed is one benefit of using variance to estimate TMRCA.

For another, directional drift in allele values (even if this happens, for which we have no evidence) would not have any impact on expressed variance.  In theory, a STR could have allele drift so strong that NO descendants have the ancestral value and STILL the TMRCA estimate would be accurate.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 04, 2012, 12:06:17 PM
So the modal value of DYS456 went from being 15 as measured in the sample from 5000 BC, to 14 as measured in the sample from 3000 BC to 15 again in modern day European samples.

Many thanks, JeanL. Hope that Mikewww has understood what I did mean with "mutations around the modal" and "convergence to the modal as time passes".


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 04, 2012, 12:12:13 PM
@^^JeanL


Ditto, quite brilliant!


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 04, 2012, 12:18:55 PM
So the modal value of DYS456 went from being 15 as measured in the sample from 5000 BC, to 14 as measured in the sample from 3000 BC to 15 again in modern day European samples.

Many thanks, JeanL. Hope that Mikewww has understood what I did mean with "mutations around the modal" and "convergence to the modal as time passes".

But there is a 3rd possibility, that a mutation goes for the tangent. The actual differences amongst the haplogroups are due to this: sometimes a value is almost the same, sometimes is very different.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 04, 2012, 12:39:03 PM
So the modal value of DYS456 went from being 15 as measured in the sample from 5000 BC, to 14 as measured in the sample from 3000 BC to 15 again in modern day European samples.

Many thanks, JeanL. Hope that Mikewww has understood what I did mean with "mutations around the modal" and "convergence to the modal as time passes".

I think we are getting the terminology for modal and ancestral values convoluted. We should keep in mind that modal values are related to a specific population measured. Naturally, the modal values may be different for different populations. Also, naturally, the TMRCAs for different populations will be different as their MRCAs were likely different people.

An SNP is just a signpost on a branch. We don't know how high or low on the branch unless we consider it context of other SNPs in the vicinity (on the tree.) The MRCA for a population with an SNP may not be the MRCA for everyone who ever had that SNP. The neat thing is all the new SNP discoveries which can help fence in how the tree grew through interclade analysis.

LOL, I've been criticized on this, but maybe there wasn't a lot of utility in what I just wrote. It's just definition based.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 04, 2012, 12:47:04 PM
So the modal value of DYS456 went from being 15 as measured in the sample from 5000 BC, to 14 as measured in the sample from 3000 BC to 15 again in modern day European samples.

Many thanks, JeanL. Hope that Mikewww has understood what I did mean with "mutations around the modal" and "convergence to the modal as time passes".

But there is a 3rd possibility, that a mutation goes for the tangent. The actual differences amongst the haplogroups are due to this: sometimes a value is almost the same, sometimes is very different.

Maliclavelli, I welcome you to my place where utility is sometimes marginal. Please consider we have to laugh a bit from time to time.

@^^JeanL
Ditto, quite brilliant!

Acekon, I also welcome you to my place of marginal utility. Cheerleaders are important, too. LOL.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 04, 2012, 01:13:16 PM
Maliclavelli, I welcome you to my place where utility is sometimes marginal. Please consider we have to laugh a bit from time to time.

I think that nobody may reproach me laugh, irony and even sarcasm, for what my knowledge of English permits me. “Marginal utility” is an economic theory. As to Genetics we could call “saturation”, but I prefer satisfaction.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 01:14:03 PM
It doesn't show this, no matter how often you repeat it.

Whatever, it does show it, but if you choose to ignore it, and go for the highly improbable alternative hypothesis, be my guest.

Actually, this is not quite the right way to express this.  After 1/mu about half of descendents will still have the ancestral value, either because their lineage never had a mutation or because they had multiple mutations that caused a reversion.

In theory that doesn’t happen, nor in practice, let me put it this way, assuming the most probable scenario, after a time of 1/mu the vast majority of the descendants would not have the ancestral value, and this is coming from actually doing computer simulations, not just talking about it. For example if a locus has a mutation of 1/10 or 0.01 mutations per generation, and an individual has 10 offsprings, then the expectation is that then at least one of them will have a mutation. Then on the next generation each one of the 10 offsprings have 10 offsprings, for the 9 nonmutant offsprings, there is an expectation that each would produce 1 mutant offsprings, so we will have 9 mutant offsprings in the second generation, now for the mutant offspring there is an expectation that he will produce 9 offspring which carry his mutation, and 1 which will carry a new mutation, which could be either back to the ancestral value or forward to a new value. So in the second generation instead of having 10 mutants offspring as would be expected for a population size of 100, we will have 18 offsprings which would carry at least one mutation. Now you carry this for 10 generations and one would see how the majority of the population after the 10 generations would no longer carry the ancestral value.

This just isn't true:  it's not the way the math works. 

Really!!! I would politely differ.


For one thing, there is no " assumption that the modal value represents the ancestral value." In fact, the fact that  such an assumption is NOT needed is one benefit of using variance to estimate TMRCA.

Then we must be talking about different methodologies, because for once, one of the things assumed when calculating TMRCA is that the modal value represents the ancestral value, so a measure of how many haplotypes are different from the modal on average times the mutation rate of the haplotypes would give us the TRMCA. Now if the reference frame is wrong, then the measurements are wrong, because what would count as 1 mutation could in fact be 2, and more over the vast majority of people that have the modal value would in fact count as 1 mutation or more, so there is a large amount of variance that is being ignored.

For another, directional drift in allele values (even if this happens, for which we have no evidence) would not have any impact on expressed variance.  In theory, a STR could have allele drift so strong that NO descendants have the ancestral value and STILL the TMRCA estimate would be accurate.

Well, let me put it this way, in your theory that could happen, in the theories I have studied that doesn’t happen, and expected mutation time is a very real concept, and in computer simulations (Using an expanding population under a Wright-Fisher model) that TMRCA does get undermined, so it is not drift, is about probabilities, and I feel we are going into a dead end, because you seem to be unfamiliar with the concepts I am talking about, so we are just going in circles. So it is not about drift, drift occurs mostly on autosomal DNA, on the SNPs, SRTs on Y-chromosomes behave like haploids, well they are haploids. So it’s not so much that they undergo drift, but that under a Gaussian probability model, each lineage under a tree is expected to attain a mutation in a time frame of 1/mu under a mutational bias model.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 02:07:21 PM
In theory that doesn’t happen, nor in practice, let me put it this way, assuming the most probable scenario, after a time of 1/mu the vast majority of the descendants would not have the ancestral value, and this is coming from actually doing computer simulations, not just talking about it.

Instead of playing word games, why don't you just make the computations instead?  You'd see where you are making your mistakes, I think, instead of relying on me to point them out.

In this case, the number of expected mutations per lineage in a pool of descendants  after time 1/mu is indeed 1.

It is also the case that roughly half of the descendants will still have the ancestral value. How can this be, you ask?  Why let me tell you: back mutations.

Some lineages will have experienced no mutations at all ( a little less than 40% fall in this category)

Some lineages will have experienced precisely one mutation (a little less than 40% fall in this category)

Some lineages will have experienced two or more mutations (about 25%, or so).  Among these, some lineages will have experienced reversing ("back" mutations).

The end result is that after time 1/mu the average number of mutations per descendant is 1, the percentage of descendants with the ancestral allele is a little less than 50%, and the percentage of lineages with at least one mutation is about 65%.

Then we must be talking about different methodologies, because for once, one of the things assumed when calculating TMRCA is that the modal value represents the ancestral value, so a measure of how many haplotypes are different from the modal on average times the mutation rate of the haplotypes would give us the TRMCA.

That's simply not an accurate description of how variance-based methods are performed. 

You take the variance of the alleles observed in the present, divide by mu, and get the TMRCA estimate.  That's it.  Done.  The mean allele is implicitly used in the variance calculation, but not because it is presumed to be the ancestral value, and the mode is never used implicitly or explicitly.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 04, 2012, 02:41:49 PM
@Mikewww

LOL, for sure I'm not the sharpest tool in the shed.LOL.

Get out of JeanL's way- Timberrrrr, LOL

http://www.crowntreesurgeons.co.uk/enlarged/image1257264023.jpg

http://www.youtube.com/watch?v=WCgkEGeBNz0

All the calculations are in flux, including the anchors. Wrong 5000 year old anchor[or cherry picked to format preconceived ideas or bias] in str's, wrong conclusion[wrong input, wrong output].

You know I married an Irish girl. For example [membrane transport protein of uncertain specificity (CO2 or NH3) and unknown physiological role] the deletion or mutation p36.13-p34.3 [20k-30k?] would also change infant mortality rates, and by extension models of mutation. Fortunately I also carry the mutation and she did not have to take any mercury base shots.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 02:46:17 PM

Instead of playing word games, why don't you just make the computations instead?  You'd see where you are making your mistakes, I think, instead of relying on me to point them out.

I have done computer simulations, and plenty of them, and I’m not relying on you to point anything out, it’s become clear that you are ignorant of certain biological concepts, and like I said before we will just be going in circles.

In this case, the number of expected mutations per lineage in a pool of descendants  after time 1/mu is indeed 1.
It is also the case that roughly half of the descendants will still have the ancestral value. How can this be, you ask?  Why let me tell you: back mutations.

Not really, like I said before under a mutational bias model that would not hold true, however under a neutral model the modal value wouldn’t change with time, but that is not what is observed in aDNA, and that is not what is observed in computer simulations.

Some lineages will have experienced no mutations at all ( a little less than 40% fall in this category)

Some lineages will have experienced precisely one mutation (a little less than 40% fall in this category)

Some lineages will have experienced two or more mutations (about 25%, or so).  Among these, some lineages will have experienced reversing ("back" mutations).

Where are you pulling those numbers from? Did you miss the explanation I gave you, here let me reiterate it, one individual has 10 offsprings, and one of the locus has a mutation rate of 0.5 that is ½ chances of mutating per generations per offspring. So after one generation 5 offsprings are mutant, 5 are non mutant, then on the second generation the 5 offsprings that are mutant each have 5 offsprings that are mutant, and 5 offsprings that are nonmutant, the same thing happens to the offsprings that are nonmutant. Even if we assume that all mutations that happened to the offsprings of the mutant people are back mutations, then it would still give 50/100 mutants offsprings after two generations, hence why the vast majority of offsprings would not have the ancestral value. Of course that is under the unlikely scenario that all mutations on the mutant offsprings back mutate, when in reality some of them could back mutate while others would mutate forward.

The end result is that after time 1/mu the average number of mutations per descendant is 1, the percentage of descendants with the ancestral allele is a little less than 50%, and the percentage of lineages with at least one mutation is about 65%.

(http://i1133.photobucket.com/albums/m582/jeanlohizun/Simulation-Fig1.jpg)
http://i1133.photobucket.com/albums/m582/jeanlohizun/Simulation-Fig1.jpg (http://i1133.photobucket.com/albums/m582/jeanlohizun/Simulation-Fig1.jpg)

What you are seeing is the allele distribution of a computer simulation. The demography is as follows, the  ancestral value is 8, the forward mutation rate is 0.5, that is 1 in 2 chances of mutating per generation per offsprings, the backward mutation rate is 0.4, thus producing a mutational bias of ~0.1 foward. The population expands for 10 generations, the expansion takes places for the first two generations (that is expected number of offsprings>1 for the first two generations), and then for the other 8 the population stabilizes to a constant population size (that is expected number of offsprings=1), all expectations are modeled as Poisson distributions. At the end of the experiment 200 individuals are randomly collected, and their allele values are analyzed in the histogram shown above. What it is observed is that the most frequent value, that is a 9, is actually 1 mutation away from the ancestral value, which was 8, only 40 individuals out of 200 individuals retained the ancestral value, so 20% of the population, that is nowhere near half.

That's simply not an accurate description of how variance-based methods are performed. 

You take the variance of the alleles observed in the present, divide by mu, and get the TMRCA estimate.  That's it.  Done.  The mean allele is implicitly used in the variance calculation, but not because it is presumed to be the ancestral value, and the mode is never used implicitly or explicitly.

Ok here is the problem, if you refer to most studies out there, you will see that when they say variance they refer to average number of mutations per marker or per haplotype, measured from the most frequent haplotype. So mutation rates are calibrated based upon that assumption, that the modal haplotype represents the ancestral haplotype, hence mutations away from the modal can be used as a measurement of time. Now if you mean variance as in the standard deviation of a set squared, again, the mean value is still being used to calculate the standard deviation, and you are assuming that the normal distribution describes the model, when in fact, if the modal value=/= ancestral value, then mutations do not occur as measured from the center value, so your mean (That is the ancestral value from which you would measure the number of mutations) would be different, and hence your standard deviation would be greater, and hence the variance would be greater. So in a nutshell what I am saying is that in order to use the calibrated mutation rates, the number of mutations that have occured with time should be measured from the ancestral value, if the values that are the 50th percentile aren't the ancestral, then the real mean value would be different, thus causing the distribution to be skewed relative to the ancestral value.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 04, 2012, 02:52:29 PM
@Mikewww
LOL, for sure I'm not the sharpest tool in the shed.LOL.
Get out of JeanL's way- Timberrrrr, LOL
http://www.youtube.com/watch?v=WCgkEGeBNz0

I tried your youtube link and got a blank screen with static. It said "An error occurred. Please try again later."  It is probably more appropriate than you imagined, but since our utility (as cited per B.S for me)  is limited, I agree, let's get out of the way. No need for cheerleading.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 03:34:10 PM
Not really, like I said before under a mutational bias model that would not hold true, however under a neutral model the modal value wouldn’t change with time, but that is not what is observed in aDNA, and that is not what is observed in computer simulations.

Maybe if you program the simulations with a directional bias, as you described.

Where are you pulling those numbers from?

They are the only possible outcome of a normal (or Poisson) distribution for a single marker after time 1/mu.

If your simulations are giving you different outputs, they are either wrong or designed to produce a non-normal distribution.


What it is observed is that the most frequent value, that is a 9, is actually 1 mutation away from the ancestral value, which was 8, only 40 individuals out of 200 individuals retained the ancestral value, so 20% of the population, that is nowhere near half.
Because you rigged your simulations with a directional bias, of course.

And given the logical errors in your examples, I'm not willing to trust that you wrote the simulation correctly in other ways either.

Ok here is the problem, if you refer to most studies out there, you will see that when they say variance they refer to average number of mutations per marker or per haplotype, measured from the most frequent haplotype.

Strawman.  WHICH studies say that?  If you quote and cite one that does, I'll show you how it is wrong.

I'll give you a counter pre-emptively:  

Quote
Expansion times and their standard deviations (SDs) were calculated using 11 STRs (DYS19, DYS389I, DYS389II DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS460), whose mutation rates have been individually es- timated (Gusmao et al. 2005). The allelic variance of each STR was divided by the estimated mutation rate, and the mean of the variances was multiplied by 25 (intergeneration time in years).

Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages
Berniell-Lee et al.
http://mbe.oxfordjournals.org/content/26/7/1581.full.pdf+html

You'll find no shortage of authors who do it the same way.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 04:28:27 PM

Ok here is the problem, if you refer to most studies out there, you will see that when they say variance they refer to average number of mutations per marker or per haplotype, measured from the most frequent haplotype.

Strawman.  WHICH studies say that?  If you quote and cite one that does, I'll show you how it is wrong.

You may be thinking of the description sometimes provided by authors who cite Goldstein et al.

These folks are using ASD, which is a similar calculation but not necessarily the same as using self-variance (which has the advantage I mentioned earlier of not requiring an assumption about ancestral values).


Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 04, 2012, 05:46:07 PM
Uncalled for on my part!


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 06:23:33 PM
Maybe if you program the simulations with a directional bias, as you described.

But there is a directional bias, have you missed the discussion where I mentioned that under a neutral model, the modal values of a haplogroup wouldn’t change with time, yet they do. Also, the fact that mutation rates depend on repeat number, the higher the repeat number the higher the mutation rate for the most part, so yes, in essence there is a directional bias.

They are the only possible outcome of a normal (or Poisson) distribution for a single marker after time 1/mu.

If your simulations are giving you different outputs, they are either wrong or designed to produce a non-normal distribution.

Well for once a Normal or Gaussian distribution isn’t the same as a Poisson distribution for small values, but setting that aside, if we take into account a directional bias, which I have shown that exists, then there is an expectation for a mutation to occur in a timeframe of 1/mu, where this mu is the resulting directional bias, that is, mu=~0.1 for a set that has a forward mutation of 0.5 and a backwards mutation of 0.4. So my simulations are designed to produce realistic results based upon the known concepts of directional bias.  BTW the allele distribution produced at the end, was very clearly a normal distribution, centered around 9, in case you missed it.

Because you rigged your simulations with a directional bias, of course.

And given the logical errors in your examples, I'm not willing to trust that you wrote the simulation correctly in other ways either.

I couldn’t care less what you are willing to trust or not, I never hid that there was a directional bias, and when I said a 1/mu timeframe, I meant the resulting mutational bias.

Strawman.  WHICH studies say that?  If you quote and cite one that does, I'll show you how it is wrong.

I'll give you a counter pre-emptively: 

Quote
Expansion times and their standard deviations (SDs) were calculated using 11 STRs (DYS19, DYS389I, DYS389II DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS460), whose mutation rates have been individually es- timated (Gusmao et al. 2005). The allelic variance of each STR was divided by the estimated mutation rate, and the mean of the variances was multiplied by 25 (intergeneration time in years).

Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages
Berniell-Lee et al.
http://mbe.oxfordjournals.org/content/26/7/1581.full.pdf+html

You'll find no shortage of authors who do it the same way.

Myres.et.al.2010 study supplementary Table-2 , column F says “Avg Var”, yet if you calculate it, you see, average variance is calculated from the median haplotypes of each populations, hence the average variance is calculated as the average value mut/marker or mut/haplotype. Also, yes I am aware that the method is called the ASD(Average-Squared-Distance), here is what Busby.et.al.2011 says about ASD:

Quote from: Busby.et.al.2011
While acknowledging uncertainty, researchers usually report the age of Y chromosome lineages based on differences between individuals across multiple STRs, often using average squared distance (ASD) or related summary statistics [25,26] as unbiased estimators of coalescence time, T.

So there you have it, the ASD methodology, which does make use of the modal values is the most commonly used method. In fact when mutation rates are calibrated using pedigrees the ASD method is used, so those mutation rates couldn’t be used in a different method. Now measured mutations rates from father-son pairs have the issue that mutation rates depend on repeat number, and also that you are measuring a mutation across a generation, so once more, if the mean, median, modal, or whatever you want to call it, isn’t the ancestral value, then the variance would be undermined. Yes the median value is a mathematical concept, yes in this case under the assumption of a normal distribution that would be the correct value to use, but the point is, that when the modal changes with time the true distribution of mutations isn’t normal, because what you are counting as 0 mutations could in fact be -1 or 1, so it wouldn’t be a normal distribution centered around 0 mutations, but a normal distribution centered around -1 or 1 mutations.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 09:34:50 PM
But there is a directional bias, have you missed the discussion where I mentioned that under a neutral model, the modal values of a haplogroup wouldn’t change with time, yet they do. Also, the fact that mutation rates depend on repeat number, the higher the repeat number the higher the mutation rate for the most part, so yes, in essence there is a directional bias.

You've mentioned a lot of things that aren't true, and this is one.  Modal values of populations change for a host of reason, including genetic drift.


Myres.et.al.2010 study supplementary Table-2 , column F says “Avg Var”, yet if you calculate it, you see, average variance is calculated from the median haplotypes of each populations, hence the average variance is calculated as the average value mut/marker or mut/haplotype.
No, variance is not the same as counting mutations.  It is counting squared differences.  The distinction matters mathematically a great deal.

So there you have it, the ASD methodology, which does make use of the modal values is the most commonly used method.

You quoted one study which says it does NOT use the mode, then claim it uses the MEDIAN, all in support of a conclusion that MODE is the most commonly used method. You aren't making sense.

Besides, as I said before, it doesn't matter.  If Busby is calculating TMRCA wrong, then so what?  I'm not using his conclusions and neither are you.  My point originally was that TMRCA estimates using strict self-variance calculations are not influenced by any of this.  The variance provides a TMRCA estimate that is not affected in the least by any sort of directional bias, even if such a bias even existed.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 10:08:31 PM
You've mentioned a lot of things that aren't true, and this is one.  Modal values of populations change for a host of reason, including genetic drift.

Just because you don’t understand them doesn’t mean they aren’t true. Also like I said before genetic drift doesn’t happen on STRs, well it does happen, but it takes a timeframe way longer than 1/mu, certainly drift wouldn't manisfest itself in 7 STRs in a timeframe of 2000 years, for more info refer to the post below:

 http://www.worldfamilies.net/forum/index.php?topic=10906.msg136139#msg136139 (http://www.worldfamilies.net/forum/index.php?topic=10906.msg136139#msg136139)

For the explanation of why under a directional neutral model the modal shouldn’t change with time even if bottlenecks occurred, and why under a directional biased model it does change with time regardless of the demography.

No, variance is not the same as counting mutations.  It is counting squared differences.  The distinction matters mathematically a great deal.

Yeah I know variance is the standard deviation squared, thanks though for refreshing the concept. Nonetheless, my point was that a lot of people call "the average number of mutations per marker" variance, of course that isn’t statistical variance, but a measurement of variance nonetheless.

You quoted one study which says it does NOT use the mode, then claim it uses the MEDIAN, all in support of a conclusion that MODE is the most commonly used method. You aren't making sense.

Myres.et.al.2010 picked the median haplotype per population, and then they counted mutations relative to that haplotype, so their avg var is not in fact variance (As in squared difference from the mean value) but simply the average number of mutations from the so called median, so yes, they did count mutations. In fact I replicated the same average variance when using a model that picks modal values for each STR independently, and then counting mutations from that modal value.


Besides, as I said before, it doesn't matter.  If Busby is calculating TMRCA wrong, then so what?  I'm not using his conclusions and neither are you.  My point originally was that TMRCA estimates using strict self-variance calculations are not influenced by any of this.  The variance provides a TMRCA estimate that is not affected in the least by any sort of directional bias, even if such a bias even existed.

Who is talking about Busby.et.al calculating TMRCA or not, I cited him to show that most scientists used the ASD methodology when estimating TMRCA. Well ok using self-variance calculations aren’t influenced by any of this, then what mutation rates do you use? The ones calculated from pedigrees assuming that the modal value is the ancestral value, or the ones measured from father-son pairs, which actually are basically an average of different mutation rates, as mutation rates for a given STR depends on the repeat value. Therefore the so called self-variance methodology, which is the interclade methodology fails to account for variation in the mutation rate as a function of repeat value. So yes, in a sense the self-variance or interclade isn’t subject to the modal variation with time, however, it fails due to other things, such as mutation rate being a function of repeat value.

EDIT: I changed the above text, the self-variance methodology does make the assumption that the mean value is the ancestral value. In fact Stumpf and Goldstein.et.al.2001 talk about the self-variance method (Average Squared Difference is used), and this is what they say:

Quote from: Stumpf.et.al.2001

For a single locus, the squared distance is given by
Δi=(li -la)2

where la denotes the ancestral allele length and i refers to a present chromosome.


Also more from Stumpf.et.al.2001

Quote from: Stumpf.et.al.2001

In addition to the mean square errors of the estimates for TMRCA using the real ancestral alleles in Eq. 3, we also show the errors that result if the most common allele is assumed to be ancestral.

[...]

Uncertainty concerning the mutation rate and process presents a serious limitation for model-free approaches. In the case of microsatellites, deviations from the SMM (39, 40) could result in substantial biases that are hard to detect in model-free analyses. Important possible deviations from the SMM include variable step size (σ2 > 1) that has been observed at low frequency (46), directional bias in the mutation process (47), length dependence in the mutation rate (48) and step size, and a dependence on the size of the repeated motif.

Finally, it is clear that microsatellite allele length is constrained, in part as a result of the mutation process (49, 50), and this will influence the dynamic of distance measures.


So basically back in 2001 Stempf and Goldstein were already aware of the directional bias and the mutation rate dependence in repeat value.

This is what the said relative to variations in mutation rate relative to repeat value

Quote from: Stempf.et.al.2001

Length-dependent mutation rates.

A general mutation parameter may thus be written in the form

μ= μ(l)σ2(l)              (5)

(39), where μ(l) and σ2(l) are the mutation rate and variance of step size, respectively. In the simplest instance of a length-dependent mutation process, the functional form will be linear; quite generally this form also describes more complicated functional dependencies to first order:

μ(l)= μ0 + μll         (6)

To describe length dependence, we use the results of (48) for a set of 10 microsatellite loci in a large sample of Y chromosomes. This mutation rate model was implemented in the coalescent simulations as follows. In the generation of the simulated data sets we use μ= 0.0028 but assume that this corresponds to the average allele length (i.e., l= 16.96) in (46), and we adjust the mutation rate after each mutation event according to the new repeat length. When we estimate the genealogical depth of a haplogroup from Eq. 4, we calculate a length-adjusted mutation rate for each locus from Eq. 6 by using the average repeat size at that locus in the haplogroup. This procedure yields reliable estimates for TMRCA (Fig. 2B). If, however, the mutation rate is assumed to be constant, estimates for TMRCA may significantly deviate from their true values. As expected, accuracy again increases with the number of loci.



Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 04, 2012, 11:26:00 PM
Just because you don’t understand them doesn’t mean they aren’t true. Also like I said before genetic drift doesn’t happen on STRs, well it does happen, but it takes a timeframe way longer than 1/mu, certainly drift wouldn't manisfest itself in 7 STRs in a timeframe of 2000 years, for more info refer to the post below:
I think you don't even know what genetic drift is.

http://en.wikipedia.org/wiki/Genetic_drift


Title: Re: The age of R-M343 calculated by Dienekes
Post by: JeanL on August 04, 2012, 11:34:33 PM
I think you don't even know what genetic drift is.

http://en.wikipedia.org/wiki/Genetic_drift

Here have some reading about how natural selection can simulate genetic drift:

http://www.genetics.org/content/155/2/909.full.pdf (http://www.genetics.org/content/155/2/909.full.pdf)

PS: Random drift doesn't have the power to change modal values in timeframes of 1/mu, directional bias does.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: razyn on August 05, 2012, 02:14:30 PM
In case the actual subject of this thread interests anyone who is still reading it, Dienekes posted a pertinent comment on RootsWeb today:

http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-08/1344183559

It could be perceived as impertinent.  He concluded thus:

Quote
I realize that a lot of people have invested a lot in Y-STRs, and they
served their purpose for a while, but they're now a historical relic.
Of course people might still find some use for the abundant datasets
that have accumulated, but personally I see little reason to perfect
the oil lamp after we've discovered electricity.

To me, it seems more like seeing little reason to look at a watch since the Aztecs perfected the calendar.  And that has more to do with why one wants to know the time, than what time it is.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 05, 2012, 02:44:25 PM
SNPs are the way to go.YSTRs are history.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Elkate on August 05, 2012, 02:58:55 PM
In case the actual subject of this thread interests anyone who is still reading it, Dienekes posted a pertinent comment on RootsWeb today:
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-08/1344183559
It could be perceived as impertinent.  He concluded thus:
Quote
I realize that a lot of people have invested a lot in Y-STRs, and they
served their purpose for a while, but they're now a historical relic.
Of course people might still find some use for the abundant datasets
that have accumulated, but personally I see little reason to perfect
the oil lamp after we've discovered electricity.
To me, it seems more like seeing little reason to look at a watch since the Aztecs perfected the calendar.  And that has more to do with why one wants to know the time, than what time it is.
Soon everyone will have a list of about 20,000 SNPs, eg, the road from Adam,
including a 2-3 SNP own (private)


Title: Re: The age of R-M343 calculated by Dienekes
Post by: vineviz on August 05, 2012, 03:30:00 PM
SNPs are the way to go.YSTRs are history.
Not yet, and not for every purpose.

Sequencing 10 million bp of Y-DNA yields a clock that is roughly as precise as a Y-STR haplotype of 111 markers (they have the same sum of mutation rate).

Y-SNPs have some advantages, but they also have some disadvantages.  I think the idea of replacing STRs with SNPs is somewhat romantic, but won't be the panacea that some seem to believe.

Anyway, the best results will flow from using all the available data not just one kind or another as the situation warrants.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Maliclavelli on August 05, 2012, 03:34:34 PM
Of course we all have elaborated our theories by the means we had at our disposal and we will see who has won and who has lost. These SNPs, when at our disposal, will be able to serve our purpose like aDNA: they will say which is the line of descent of the various haplogroups.
But science will lose its humanity. It will become a mere technique.




Title: Re: The age of R-M343 calculated by Dienekes
Post by: acekon on August 05, 2012, 04:20:02 PM
Having a rather unusual str sequence of my first 12 makers and getting  an exact 12/12 match, as well as belonging to the ht-35 project I was very excited[393-12/.00076][389II-31/.00242]. However the person was of no recent relation{500-900}, even though he comes from the same region.


Perhaps a combination of extended str's and snp's. in the future will be the way to go

It is not the science, but the man behind the science, it cut's both ways. IMO science  is the great equalizer, for humanity. I look forward to the day when someone who has been looked down upon by society in a caste system like an "untouchable" is proven to share the same genetics with everybody else; showing we are all related directly or indirectly!


Thanx to moderator, rms2 for allowing free speech, bad spelling,and ideas to be shared.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Jarman on August 05, 2012, 04:35:34 PM
SNPs are the way to go.YSTRs are history.

So very very wrong. The quest for ancient ancestors is of course interesting but it is secondary to genealogical DNA testing.  The original and still main use of DNA testing by genealogists is to obtain STR haplotypes for comparison with other researchers' haplotypes to find relationships and possibly get around those stone walls the paper trails run into. We need STRs for genealogy - I hope we don't lose sight of that and I hope the academics keep using STRs too.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: stoneman on August 06, 2012, 04:52:33 AM
I have a gd of 40 from an Irish U106 man and a gd of 17 from an Irish L21 man. Which man am I more closely related to? The U106 man.
How are ystrs reliable? A difference at one marker and you are in a different subclade, for example dys492 .A null at 439 is another example.




SNPs are the way to go.YSTRs are history.

So very very wrong. The quest for ancient ancestors is of course interesting but it is secondary to genealogical DNA testing.  The original and still main use of DNA testing by genealogists is to obtain STR haplotypes for comparison with other researchers' haplotypes to find relationships and possibly get around those stone walls the paper trails run into. We need STRs for genealogy - I hope we don't lose sight of that and I hope the academics keep using STRs too.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 06, 2012, 09:05:03 AM
I have a gd of 40 from an Irish U106 man and a gd of 17 from an Irish L21 man. Which man am I more closely related to? The U106 man.
How are ystrs reliable?  

STRs can vary up or down so you can get convergence. This makes them unreliable, in and of themselves, as single markers for a subclade. For instance, you can't really say YCAII=18,23 marks a single subclade. That's why many people look at STR signatures or patterns of multiple unusual STR values.

This does not mean STRs are unreliable for genealogy purposes or measuring diversity for populations.


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 09, 2012, 02:07:12 AM
The Rootsweb conversation between Anatole Klyosov, Dienekes Pontikos and Argiedude is becoming amusing. I don't like to copy posts from other forums too much but this is too good to resist.

I really don't care if what they call "R1b1a2a1a1a5" is 7K ybp or 3.5K ybp. I don't care if Anatole is right or Dienekes is right, but it will be a good thing if we can understand SNP counting methods a little better and it's definitely good fun.

LOL.

Quote from: Argiedude
I obtained identical estimates as you did in all the ages you posted, but I didn't take into account this issue (divide result by 2 to account for mutations accumulating on 2 chromosomes after splitting apart).
For example, take I2a1. Your graph gives an age estimate of 23 kya, by comparing L158 with L178. I compared ...(L158) with ...(L178) and obtained the following:
Total SNPs...18692
Valid SNPs (didn't have a no call in either chromosome)...17146
Variant SNPs...240
...(the rate used by Dienekes for his estimate)...3x10^-8
Generation used by Dienekes...25 years
Total bases in 1000Genomes data (approximately)...9,300,000

240 / {[9,300,000 x (17146 / 18692)] x 3x10^-8} x 25 = 23.4 kya

I didn't divide by 2 at any point and my result was the same.

Basically, Argiedude was asking Dienekes if he remembered to divide by 2.

Quote from: Dienekes
I remembered.

Quote from: Anatole K
MY RESPONSE:

VERY interesting. The "Argiedude" data shed light on a mystery with the SNP-based calculations conducted by Pontikos. If his response "I remembered" was truthful, then he must have obtained 46,000 ybp for I2a1, divided by 2, and finally obtained 23,000 ybp. However, for the same set of SNP Argidude obtained 23,400 ybp, which, after division by 2 should results in 11,700 ybp.

Since argiedude has clearly showed how he obtained the dta, and Pontikos did not, it is time to know  how he did it.

This can explain the error which Pontikos obtained with the "age" of R1b1a2a1a1a5 of 7,000 ybp, since he apparently did not divide it by 2, to obtain 3,500 ybp, the likely "age" for the subclade, as I have noticed earlier. He did not want to admit it, and never answered the question on the origin of that 7,000 ybp, which Didier and myself repeatedly addressed to Pontikos.

If so, most or all the figures on the Pontikos list are in error, and represent double figures (100% error). If so, I retract my statement that SNP-calculated numbers by Pontikos give the same numbers as our STR-based calculations, because his numbers are erroneous, either most of them or all of them.

There is one way only for him to explain the situation: present the calculations for both the R1b1a2a1a1a5 subclade, and for some other haplogroups and subclades on his list. I would not have pressed for the matter, however, Pontikos poured a lot of venom on my STR-based calculations, at his blog and at this Forum. Now, it turned out that HIS data are highly questionable.

Anatole Klyosov
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-08/1344477731

Does anyone know? Is Argiedude's point on target?

  

 


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Arch Y. on August 09, 2012, 03:46:28 AM
The Rootsweb conversation between Anatole Klyosov, Dienekes Pontikos and Argiedude is becoming amusing. I don't like to copy posts from other forums too much but this is too good to resist.

I really don't care if what they call "R1b1a2a1a1a5" is 7K ybp or 3.5K ybp. I don't care if Anatole is right or Dienekes is right, but it will be a good thing if we can understand SNP counting methods a little better and it's definitely good fun.

LOL.

Quote from: Argiedude
I obtained identical estimates as you did in all the ages you posted, but I didn't take into account this issue (divide result by 2 to account for mutations accumulating on 2 chromosomes after splitting apart).
For example, take I2a1. Your graph gives an age estimate of 23 kya, by comparing L158 with L178. I compared ...(L158) with ...(L178) and obtained the following:
Total SNPs...18692
Valid SNPs (didn't have a no call in either chromosome)...17146
Variant SNPs...240
...(the rate used by Dienekes for his estimate)...3x10^-8
Generation used by Dienekes...25 years
Total bases in 1000Genomes data (approximately)...9,300,000

240 / {[9,300,000 x (17146 / 18692)] x 3x10^-8} x 25 = 23.4 kya

I didn't divide by 2 at any point and my result was the same.

Basically, Argiedude was asking Dienekes if he remembered to divide by 2.

Quote from: Dienekes
I remembered.

Quote from: Anatole K
MY RESPONSE:

VERY interesting. The "Argiedude" data shed light on a mystery with the SNP-based calculations conducted by Pontikos. If his response "I remembered" was truthful, then he must have obtained 46,000 ybp for I2a1, divided by 2, and finally obtained 23,000 ybp. However, for the same set of SNP Argidude obtained 23,400 ybp, which, after division by 2 should results in 11,700 ybp.

Since argiedude has clearly showed how he obtained the dta, and Pontikos did not, it is time to know  how he did it.

This can explain the error which Pontikos obtained with the "age" of R1b1a2a1a1a5 of 7,000 ybp, since he apparently did not divide it by 2, to obtain 3,500 ybp, the likely "age" for the subclade, as I have noticed earlier. He did not want to admit it, and never answered the question on the origin of that 7,000 ybp, which Didier and myself repeatedly addressed to Pontikos.

If so, most or all the figures on the Pontikos list are in error, and represent double figures (100% error). If so, I retract my statement that SNP-calculated numbers by Pontikos give the same numbers as our STR-based calculations, because his numbers are erroneous, either most of them or all of them.

There is one way only for him to explain the situation: present the calculations for both the R1b1a2a1a1a5 subclade, and for some other haplogroups and subclades on his list. I would not have pressed for the matter, however, Pontikos poured a lot of venom on my STR-based calculations, at his blog and at this Forum. Now, it turned out that HIS data are highly questionable.

Anatole Klyosov
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-08/1344477731

Does anyone know? Is Argiedude's point on target?




Too bad Ken Nordvedt wasn't involved in this "soap opera" drama. Maybe he could be J.R. Ewing. I like nothing more than to read or hear about really brilliant men to argue their theories, point out flaws in each others maths and poke holes into the theories. I often wondered what a celebrity deathmatch would be like with Stephen Hawking, Leonard Susskind, Lisa Randall, Brian Greene, Michiu Kiko and Lawrence Krauss. I would put my bets on Leonard or Lisa.

Arch


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Arch Y. on August 09, 2012, 03:53:26 AM
SNPs are the way to go.YSTRs are history.

Did you hear about the newest trend in worm holes? Just like black holes, STRs are so passe. ;-) Who needs M-theory when you can have, Z-theory (spoken in Dr. Evil voice).

Arch


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mark Jost on August 09, 2012, 12:17:43 PM
When looking at mutations over two branches, a mutation count between two points to a mrca point requires to be divided by two to calculate an average number of mutations back to the mrca.

If a count of mutations is following only one branch, it is not divided by two.

Dienekes just replied that he was half wrong due to the data format, which I dont understand since its only one Y Chromsome strand?


Title: Re: The age of R-M343 calculated by Dienekes
Post by: Mike Walsh on August 12, 2012, 01:19:48 AM
The Rootsweb conversation between Anatole Klyosov, Dienekes Pontikos and Argiedude is becoming amusing. I don't like to copy posts from other forums too much but this is too good to resist.

Too bad Ken Nordvedt wasn't involved in this "soap opera" drama.

My opinion on this is based on direct conversations (my personal judgement of them), but has been reinforced by their formal credentials.

There is no question, in my opinion, that none of these guys hold a candle to Ken when comes to the math and understanding/applying statistics