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Author Topic: Interclades for the DF13 Big Six  (Read 1389 times)
Mike Walsh
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« on: October 16, 2012, 12:11:07 PM »

R1b-L21>DF13>DF41* guys with 111 markers
f47694   MacMillan
f176148   Duffy
f35212   McCrere
f240201   Walker
f29705   McCown

111(94) Markers   Sheet  Mutation Rate:

 STRs not used: 385,389i,459,464,CDY,YCAII,395S1 & 413

L21 ALL (111Markers) 
YrsPerGen*  Count
30   N=1048

Founder'sAge  Generations  StdDevInGen  YBP  +-YBP   Max  VAR   

SD
114.6   32.1  3,438.8  963.5  4,402.3  12.738  3.569


R1b-L21>DF13>DF41*
YrsPerGen*  Count
30   N=5

Founder'sAge  Generations  StdDevInGen  YBP  +-YBP  Max  VAR   

SD

105.3  21.4  3,158.1  643.3  3,801.4  24.100  4.909            

TRUE MRCA  InterClade AB Founder      
Pooled SD Clades  A & B  Interclade

YrsPerGen*
30

Interclade GAB: L21* for L21 ALL (111Markers) & R1b-L21>DF13>DF41*

Founder'sAge  Generations  StdDevInGen  YBP  +-YBP  PooledVar   

PooledSD
   
113.4  22.3  3,402.3  667.7  25.964  5.095

Mark, have you tried to do interclade ages for the whole subclades of the Big Six against each other?  For instance DF41 and DF21, DF41 and DF49, DF41 and L513, DF41 and Z253, DF41 and Z255, DF21 and DF49, DF21 and L513, etc.

I think we are putting a tidy floor underneath DF13's age.  We already pretty good ceilings for P312 (P312 and U106's TMRCA), and L21 (L21 and U152's TMRCA, L21 and DF27's TMRCA) so we'll have L21 and DF13 pretty well cornered in, despite concerns about intraclade bias, because you'll have done it through interclade calculations.
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razyn
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« Reply #1 on: October 16, 2012, 12:38:22 PM »

I now see this kind of thing on nearly every thread, and I still don't see what's so exciting about it, when the margin of error is plus or minus a millennium.  Weren't the previous calculations significantly tighter?  I suppose it's highly ingenious to do it Mark's way, with the selective deletions of problematic STR markers and all that; but what is actually helpful about having increased confidence in a result -- plus or minus 32 generations?  That kind of span isn't going to correlate with linguistics or pottery, let alone with carbon 14 or dendrochronology.  Anything you try to associate with it goes out of focus in step 2.

I was more interested in Hans van Vliet's approach, especially the pairwise mismatch stuff, but he posted about twice and nobody followed up.  (I did tell him he'd get more traffic if he were talking about L21 clades.)  Anyway, I believe with his approaches the more downstream SNPs were trending on the young side, compared to these.  That's just an impression, there weren't very many points of comparison.
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Mark Jost
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« Reply #2 on: October 16, 2012, 02:11:30 PM »


Mark, have you tried to do interclade ages for the whole subclades of the Big Six against each other?  For instance DF41 and DF21, DF41 and DF49, DF41 and L513, DF41 and Z253, DF41 and Z255, DF21 and DF49, DF21 and L513, etc.

I think we are putting a tidy floor underneath DF13's age.  We already pretty good ceilings for P312 (P312 and U106's TMRCA), and L21 (L21 and U152's TMRCA, L21 and DF27's TMRCA) so we'll have L21 and DF13 pretty well cornered in, despite concerns about intraclade bias, because you'll have done it through interclade calculations.

DF13's Big Six Interclade GAB.

https://docs.google.com/file/d/0By9Y3jb2fORNMUVUTF83LW9HN28/edit

MJost

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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #3 on: October 16, 2012, 02:23:26 PM »

Quote
That kind of span isn't going to correlate with linguistics or pottery, let alone with carbon 14 or dendrochronology.  Anything you try to associate with it goes out of focus in step 2.

Doesnt Carbon14 dating have some variance? 'Over the historical period from 0 to 10,000 years BP, the average width of the uncertainty of calibrated dates was found to be 335 years'

Quote

I was more interested in Hans van Vliet's approach, especially the pairwise mismatch stuff, but he posted about twice and nobody followed up.  (I did tell him he'd get more traffic if he were talking about L21 clades.)  Anyway, I believe with his approaches the more downstream SNPs were trending on the young side, compared to these.  That's just an impression, there weren't very many points of comparison.

SNPs?

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mike Walsh
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« Reply #4 on: October 16, 2012, 05:08:49 PM »

I now see this kind of thing on nearly every thread, and I still don't see what's so exciting about it, when the margin of error is plus or minus a millennium.  Weren't the previous calculations significantly tighter?  I suppose it's highly ingenious to do it Mark's way, with the selective deletions of problematic STR markers and all that; but what is actually helpful about having increased confidence in a result -- plus or minus 32 generations?  That kind of span isn't going to correlate with linguistics or pottery, let alone with carbon 14 or dendrochronology.  Anything you try to associate with it goes out of focus in step 2.

I was more interested in Hans van Vliet's approach, especially the pairwise mismatch stuff, but he posted about twice and nobody followed up.  (I did tell him he'd get more traffic if he were talking about L21 clades.)  Anyway, I believe with his approaches the more downstream SNPs were trending on the young side, compared to these.  That's just an impression, there weren't very many points of comparison.

I don't think we will eve get to the point where STR variance analysis will get us to a generation or two of something 4000 years ago, but if we have a more confident range of a couple of hundreds years either way, is that much better than a range of a thousand or two either way?

The part that I'm excited about is that interclade analysis overcomes concerns of intraclade biases. A large subclade sample, say of M222 for L21 or of L21 for P312, does sway the variance.
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alan trowel hands.
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« Reply #5 on: October 16, 2012, 05:20:06 PM »

what I am not getting is the significantly younger ages that Mark is getting.  They are so young (well post-beaker) that it seems very hard to correlate.  These dates do not work with a beaker model at all. 
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razyn
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« Reply #6 on: October 16, 2012, 05:44:47 PM »

SNPs?

MJost

Yes.  TMRCA approach to the dating of mutations -- you may prefer to call it something else, like the ages of haplogroups or subclades, but we are both talking about SNPs: when some given mutation must have happened (insofar as that may be reconstructed from the haplotypes of its known survivors -- while knowingly oversampling the Isles and Iberia, and skimping on both France and anyplace east of the Rhine).

To me it just seems kind of quixotic to go to such lengths to achieve a feeling of precision (to six or eight decimal places) about a couple of the data points -- when the sample is still rather poor, many SNPs must still be unknown, and the length of a generation is speculative.  In general I applaud any desire for better precision; I just don't see how these numbers could be perceived as anything like it.
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Mike Walsh
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« Reply #7 on: October 16, 2012, 05:44:57 PM »

what I am not getting is the significantly younger ages that Mark is getting.  They are so young (well post-beaker) that it seems very hard to correlate.  These dates do not work with a beaker model at all.  

I forgot what Mark got for an interclade age between P312 and U106? Was it much younger than 4500-4200 years before present?

I think we all have some skepticism of the mutation rates. The 1-67 database and analysis have been around for a long time so I don't think the way germ-line mutation rates are caculated will change much.  As far as 68-111, I'm still a little leery. We don't have the tens of thousand of haplotypes for that yet.
« Last Edit: October 16, 2012, 08:27:57 PM by Mikewww » Logged

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« Reply #8 on: October 16, 2012, 06:21:20 PM »

I just reran this at 67 markers

Interclade GAB: L11/S127* for U106 ALL (67Markers) & R-P312 ALL
Count N=1237
Count N=1638

Generations  StdDevInGen  YBP  +-YBP  PooledVar   PooledSD
121.2   33.0   3,637.2   990.9   13.473   3.671



I forgot what Mark got for an interclade age between P312 and U106? Was it much younger than 4500-4200 years before present?



Quote

I think we all have some skepticism of the mutation rates. The 1-67 database and analysis have been around for a long time so I don't the way germ-line mutation rates are caculated will change much.  As far as 68-111, I'm still a little leery. We don't have the tens of thousand of haplotypes for that yet.

But is the best we have for now.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #9 on: October 16, 2012, 06:35:02 PM »

what I am not getting is the significantly younger ages that Mark is getting.  They are so young (well post-beaker) that it seems very hard to correlate.  These dates do not work with a beaker model at all. 

I agree. The scenario is very unlikely that R1b Bell Beakers spread all across the Isles only to die off and be re-populated by a later P312+ people. There is no doubt in my mind that L21, at least in its earliest incarnation, was present with Isles Bell Beakers 4500 years ago.
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Mark Jost
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« Reply #10 on: October 16, 2012, 06:37:38 PM »

The MarkoH rates summary with out the multi-copy markers included are
111(94) Markers   67(50)Markers   37(24) Markers
0.228937   0.111128   0.075157

The sum of mutations just the last 44 totals

0.057716

Much slower. As you see the first 37 without MCM's is 0.075

Here is Marko's detail on how he computed the 111 marker STRs rates.

"A set of mutation rate estimates based on about 4,000 haplotypes at 111 STR level. Estimation method considers haplotype pairs as random draws from a model distribution of observed STR matches. Overall scaling is according to YHRD data. Ballantyne et al. data and results from a large 1-67 dataset was used for cross-validation. Error in overall scale is about 5%, and in relative rates from about 20% to 100% from fast to slow loci. Rate sums are 0.13, 0.17, 0.29 for 1-37, 1-67, 1-111, respectively, with about 7% error. (Mutation rates have strong dependence on the repeat number, and accurate general results do not exists. Errors are then considered relative to FTDNA public dataset allele distribution average. )

Marko Heinila"

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mike Walsh
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« Reply #11 on: October 17, 2012, 08:38:55 AM »

...  when some given mutation must have happened (insofar as that may be reconstructed from the haplotypes of its known survivors -- while knowingly oversampling the Isles and Iberia, and skimping on both France and anyplace east of the Rhine)...

Rayzn, do you see what I'm saying about interclades calculations overcoming biases?

For example, let's say we are looking at U106 and P312 as brothers and will check for their interclade ancestor. Let's and we feel that U106 is undersampled in certain territories. That could be throwing things off. Although I don't think it is necessarily the case but if all the U106 in the oversampled region, let's say England, were of a young variety, that wouldn't throw bias P312 in the same manner. The interclade age between two has reduced bias because it is separated two known related groups into separate groups for calculations. For biases to come through and impacted the interclade age, you'd need something like 492=13 to have occurred in P312 for the oversampled regions as well as for U106.
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Mark Jost
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« Reply #12 on: October 17, 2012, 11:30:30 PM »

I calculated M269, L23, L11 and P312 Interclades and add them to the Big Six list.

https://docs.google.com/file/d/0By9Y3jb2fORNMUVUTF83LW9HN28/edit

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
razyn
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« Reply #13 on: October 18, 2012, 12:44:09 AM »

Rayzn, do you see what I'm saying about interclades calculations overcoming biases?

Yes, I've seen that for most of a year, or however long you've been saying it.  That's why I wanted tests for Z209, Z220, and Z216 -- and took them (once offered), until I hit a negative.  That's also why I think L484x needs to get a decimal, and a following digit, and be hung on the ISOGG tree (under Z220).  So you'd have something (besides some lame Z220*) to compare with Z216, interclade.

I don't think we have an actual argument, here.
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Mark Jost
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« Reply #14 on: November 28, 2012, 04:03:35 PM »

I just recently ran a new TMRCA Estimator for Sample IntraClade Coalescence (n-1) Age  (Mean Allele values of a sample that represents the entire unknown population).

and A Founder's Modal (Ken's method).

https://docs.google.com/open?id=0By9Y3jb2fORNeHcxYzFpMUVXYTg

Ken Original  IntraClade Coalescence (n) treated the set of data a the whole known population, which is great for close related families. Think mutation count fractions using Coalescence to create an generation age. Where both Clades have very close means or modals, calculation age results are also close.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #15 on: November 28, 2012, 04:20:23 PM »

I just recently ran a new TMRCA Estimator for Sample IntraClade Coalescence (n-1) Age  (Mean Allele values of a sample that represents the entire unknown population).

and A Founder's Modal (Ken's method).

https://docs.google.com/open?id=0By9Y3jb2fORNeHcxYzFpMUVXYTg

Ken Original  IntraClade Coalescence (n) treated the set of data a the whole known population, which is great for close related families. Think mutation count fractions using Coalescence to create an generation age. Where both Clades have very close means or modals, calculation age results are also close.

MJost

My interclade estimates for DF49 came out older than P312 as well ?? which is why I haven’t said anything about how old it could be :)

Did you do any calcs for U152
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Mark Jost
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« Reply #16 on: November 28, 2012, 04:46:28 PM »

I just recently ran a new TMRCA Estimator for Sample IntraClade Coalescence (n-1) Age  (Mean Allele values of a sample that represents the entire unknown population).

and A Founder's Modal (Ken's method).

https://docs.google.com/open?id=0By9Y3jb2fORNeHcxYzFpMUVXYTg

Ken Original  IntraClade Coalescence (n) treated the set of data a the whole known population, which is great for close related families. Think mutation count fractions using Coalescence to create an generation age. Where both Clades have very close means or modals, calculation age results are also close.

MJost

My interclade estimates for DF49 came out older than P312 as well ?? which is why I haven’t said anything about how old it could be :)

Did you do any calcs for U152

I noticed that the mean ages are close, all with in the comfort zone for variance
Notice the two different groupings to maybe see a clear picture. The second is the DF49 and DF23's

InterClade Coalescence (n-1) Age DF49* & DF13 All
IntraClade Coalescence (n-1) Age DF49 ALL xM222   

No nothing for U152. Maybe one of their guys can run the selections and produce theirs.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Jdean
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« Reply #17 on: November 28, 2012, 04:56:39 PM »

I just recently ran a new TMRCA Estimator for Sample IntraClade Coalescence (n-1) Age  (Mean Allele values of a sample that represents the entire unknown population).

and A Founder's Modal (Ken's method).

https://docs.google.com/open?id=0By9Y3jb2fORNeHcxYzFpMUVXYTg

Ken Original  IntraClade Coalescence (n) treated the set of data a the whole known population, which is great for close related families. Think mutation count fractions using Coalescence to create an generation age. Where both Clades have very close means or modals, calculation age results are also close.

MJost

My interclade estimates for DF49 came out older than P312 as well ?? which is why I haven’t said anything about how old it could be :)

Did you do any calcs for U152

I noticed that the mean ages are close, all with in the comfort zone for variance
Notice the two different groupings to maybe see a clear picture. The second is the DF49 and DF23's

InterClade Coalescence (n-1) Age DF49* & DF13 All
IntraClade Coalescence (n-1) Age DF49 ALL xM222   

No nothing for U152. Maybe one of their guys can run the selections and produce theirs.

MJost

Yes they're all to close together really to make comfortable predictions of which is the oldest via these sorts of calcs, though of course P312 is older than L21 which is older than DF13 etc. :)

DF49 is looking to be pretty old though !!

Hopefully I'll have a few more recruits soon, I've had some quite encouraging emails plus a really nice one of an admin refusing to contact his member until the DF49 project has stumped up all costs, must be nice to have so much power :)
« Last Edit: November 28, 2012, 05:00:33 PM by Jdean » Logged

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Mark Jost
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« Reply #18 on: November 29, 2012, 05:33:53 AM »


Yes they're all to close together really to make comfortable predictions of which is the oldest via these sorts of calcs, though of course P312 is older than L21 which is older than DF13 etc. :)

DF49 is looking to be pretty old though !!

Hopefully I'll have a few more recruits soon, I've had some quite encouraging emails plus a really nice one of an admin refusing to contact his member until the DF49 project has stumped up all costs, must be nice to have so much power :)

Fee collection is, I guess, one way to pay for ones expertise.

I just looked at Alex's new Phylogram of 111 marker L21 guys without a L21*'s and guess what subcladed was at the root of the tree? DF49.

Its posted on the L21 Yahoo files section under Alex Williams Nov 28.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #19 on: November 29, 2012, 09:37:28 AM »


I just looked at Alex's new Phylogram of 111 marker L21 guys without a L21*'s and guess what subcladed was at the root of the tree? DF49.

Its posted on the L21 Yahoo files section under Alex Williams Nov 28.

MJost

Great, I've been keeping an eye out for Alex's next update. Hopefully he'll be posting one for 67 loci results soon too !!
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