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Maliclavelli
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« on: July 30, 2012, 04:05:30 AM »

Dienekes’
Estimating the age of Y-chromosome Adam (again)

P (Q-M242 vs. R-P224): 33,043 years

R1 (R1a-M420 vs. R1b-M343): 23,657 years (**)

R1b1a2a1a1a5 (R1b1a2a1a1a5a-Z156 vs. R1b1a2a1a1a5b-Z301): 6,476 years




Vincent said...
I suspect the 6.5 kya peak is an estimate for TMRCA of R-M269.

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Maliclavelli


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Maliclavelli
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« Reply #1 on: July 30, 2012, 06:14:46 AM »

I have chosen the first two haplotypes of the U106 FTDNA Project for R-Z301* and for R-Z156*. They are:

401 : U106 > Z381 > Z301* (Z301+, U198-, L48-, L259-, Z153- thru Z155-)
42776 Jacob Glass b. 1741 Baden?, Germany; d. 1821, PA Germany R1b1a2a1a1a
13 23 14 11 10-14 12 12 12 13 13 29 17 9-10 11 11 25 15 19 28 15-15-16-17 11 11 19-23 16 14 17 17 35-39 12 12 11 9 16-16 8 10 10 8 11 10 12 23-23 16 10 12 12 14 8 12 22 21 12 12 11 13 12 11 13 12 37 15 9 16 12 24 26 19 12 11 13 12 10 9 13 12 10 11 11 30 12 12 24 14 10 10 20 15 21 13 23 16 11 15 24 12 24 18 10 14 17 9 12 11
106361 John Cannon, 1774 POB(unk) - 1830 TN Unknown Origin R1b1a2a1a1a
13 25 14 11 11-14 12 12 12 13 13 29 17 9-10 11 11 23 15 19 29 15-16-17-17 11 10 19-23 16 15 17 18 36-38 11 12 11 9 15-16 8 10 10 8 10 10 12 23-23 17 10 12 12 14 8 12 23 21 13 12 11 14 11 11 13 12 36 15 9 17 12 24 26 19 12 11 13 12 10 9 11 12 10 11 11 29 12 13 24 13 10 10 20 15 19 12 23 18 12 17 24 12 23 18 10 14 17 9 13 11

310 : U106 > Z381 > Z156+ (check your Z305/Z306/Z307 status)
N10310 William Bess, b. 1776, Botetourt County, VA, USA Unknown Origin R1b1a2a1a1a
13 23 14 10 11-14 12 12 13 13 13 29 18 9-10 11 11 25 15 19 28 15-15-16-17 11 11 19-23 16 14 17 18 38-38 11 12 11 9 16-16 8 10 10 8 10 12 12 23-23 15 10 12 12 15 8 12 22 20 13 12 11 13 11 11 13 12 33 15 9 16 12 27 26 19 12 11 13 12 10 9 11 12 10 11 11 29 12 13 24 13 10 10 20 15 19 13 24 17 12 15 25 12 23 18 10 14 17 9 13 11
N10078 Balthazar Goll b c 1726 Southern Germany d 1799 MD Germany R1b1a2a1a1a
13 24 14 10 11-14 12 12 12 13 13 29 17 9-10 11 11 25 15 19 32 15-15-15-17 10 11 19-23 17 15 19 17 38-41 13 11 11 9 15-15 8 10 10 8 10 10 12 25-26 16 10 12 12 15 8 12 22 20 13 12 11 13 10 11 13 12 37 15 9 16 12 26 27 19 12 11 12 12 10 9 12 12 10 11 11 30 12 13 24 13 10 10 22 15 18 13 22 18 12 15 24 12 23 18 10 14 17 9 12 11


R-Z301* 42776   (A)
R-Z301* 106361 (B)

R-Z156* N10310 (a)
R-Z156* N10078 (b)

The mutation out of 111 markers are:
A vs B =38
a vs b =50
A vs a =40
B vs b =52
A vs b =52
B vs a =50

Any calculations with the Mutation Rate of 0,0022 gets a result of 2000/2500 years.
The interclade of Dienekes gives an age of 6,476 YBP, and someone would want an age at least 20% higher.

I.e. the germ line mutation rate has definitely lost against the evolutionary one.
« Last Edit: July 30, 2012, 06:54:00 AM by Maliclavelli » Logged

Maliclavelli


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ironroad41
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« Reply #2 on: July 30, 2012, 09:19:17 AM »

I also note that Terry Robb on rootsweb has used the same approach and confirmed (agreed with) some of Dienekes data.

I don't agree that germline rates are so bad, however they are very inaccurate for slow mutators.  The basic problem is the mutational process and the number of mutations which occur over time.  Some of the faster mutators have a high probability of l or more mutations within 500 to 600 years.  Then how many mutations can you expect in 5000 to 6000 years.  What is really false is the concept of GD, which assumes that one mutation away from the modal is really one whereas in fact it could be much higher.  Further since many of the "medum fast" mutators have a limited range, modal +/-1, there are many hidden mutations.

I think we now have a tool to dewarp the "hobbyists" time.
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Mark Jost
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« Reply #3 on: July 30, 2012, 09:56:09 AM »

Just for fun I ran the Gen111T using the builtin Marko's MutRate of 0.243231 on your two clades using the four HTs and the True (Ken's Words) TMRCA founders age of both was
 
Age at 30yrGen: 4,294.5, SD years: 253.8, Generations= 143.1 and GenSD=8.5


YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z301* GA coal=   46.3   13.8   1,387.6   413.7
YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z156+ GB coal=   88.4   19.1   2,651.8   571.9
      Diff =   42.1      1,264.2   
100/111 Markers      SheetMutRate:   0.243231         
   TRUE   TMRCA Founder   Generations   StdDev   YBP   + - YBP
30      GAB=   143.1   8.5   4,294.5   253.8

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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: July 30, 2012, 12:07:28 PM »

Just for fun I ran the Gen111T ...

There are some U106 guys who are interested in understanding the TMRCA for Z156. Would you consider analyzing interclade ages right above and below Z156 ?

1. Breaking down the interclades below Z156 may require using 67 markers. There are 71 Z156+ L1+ folks at 67 markers with 39 that are Z156+ L1- so I think a valid interclade TMRCA could be done for Z156+ L+ versus L1-. Can you run an interclade for Z156+ L1+ and Z156+ L-?

2. We have 31 Z156+ folks at 111 STRs. Can you run a straight intraclade TMRCA on this ?

3. We have 218 Z301+ folks at 111 STRs. Z301 is a peer for Z156, Z301 includes L48 and U198 so it is big.  Can you run an interclade for Z301 and Z156 at 111 ?

4. Another good interclade that would also help understand U106 better is Z381 and Z18. Z381 is above Z301 and we have 249 111 STR Z381 folks. We have 44 111 STR Z18 folks and since Z18 is a direct peer to Z381 this would be a good comparison.
« Last Edit: July 30, 2012, 12:12:30 PM by Mikewww » Logged

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« Reply #5 on: July 30, 2012, 01:22:54 PM »

Just for fun I ran the Gen111T using the builtin Marko's MutRate of 0.243231 on your two clades using the four HTs and the True (Ken's Words) TMRCA founders age of both was
 
Age at 30yrGen: 4,294.5, SD years: 253.8, Generations= 143.1 and GenSD=8.5


YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z301* GA coal=   46.3   13.8   1,387.6   413.7
YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z156+ GB coal=   88.4   19.1   2,651.8   571.9
      Diff =   42.1      1,264.2   
100/111 Markers      SheetMutRate:   0.243231         
   TRUE   TMRCA Founder   Generations   StdDev   YBP   + - YBP
30      GAB=   143.1   8.5   4,294.5   253.8


I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.

All these factors have been presented for consideration, but there are a core group of people who won't listen.

I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.
« Last Edit: July 30, 2012, 01:23:56 PM by ironroad41 » Logged
Maliclavelli
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« Reply #6 on: July 30, 2012, 01:30:43 PM »

Of course I did a rough calculation, but if R-Z156 and R-Z301 are 6476 years old (and even not more like I think), then R-L51 could be amongst the agriculturalists who from Italy landed to Valencia and Central Portugal 7500 years ago and with them some R-P312 and perhaps also R-U152 like those found in Mexico and the most ancient of this haplogroup like those found in Tuscany in the 1KGP.

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« Reply #7 on: July 30, 2012, 01:35:37 PM »

Just for fun I ran the Gen111T using the builtin Marko's MutRate of 0.243231 on your two clades using the four HTs and the True (Ken's Words) TMRCA founders age of both was
 
Age at 30yrGen: 4,294.5, SD years: 253.8, Generations= 143.1 and GenSD=8.5


YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z301* GA coal=   46.3   13.8   1,387.6   413.7
YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z156+ GB coal=   88.4   19.1   2,651.8   571.9
      Diff =   42.1      1,264.2   
100/111 Markers      SheetMutRate:   0.243231         
   TRUE   TMRCA Founder   Generations   StdDev   YBP   + - YBP
30      GAB=   143.1   8.5   4,294.5   253.8


I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.

All these factors have been presented for consideration, but there are a core group of people who won't listen.

I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.

Did you ever got round to expressing your concerns to Ken, if it's online somewhere I would be very interested in reading the discussion.
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Maliclavelli
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« Reply #8 on: July 30, 2012, 01:37:18 PM »

I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.
ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.
All these factors have been presented for consideration, but there are a core group of people who won't listen.
I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.
I have expressed these principles from many years:
1) mutations around the modal
2) convergence to the modal as time passes
3) sometime a mutation go for the tangent and we have the outliers, which should be the most interesting for calculating the TMRCA.
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Maliclavelli


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« Reply #9 on: July 30, 2012, 01:49:08 PM »

Of course I did a rough calculation, but if R-Z156 and R-Z301 are 6476 years old (and even not more like I think), then R-L51 could be amongst the agriculturalists who from Italy landed to Valencia and Central Portugal 7500 years ago and with them some R-P312 and perhaps also R-U152 like those found in Mexico and the most ancient of this haplogroup like those found in Tuscany in the 1KGP.

Gioiello, archaeologically, who were these agriculturalists that you always mention?

The major group of agriculturalists that went from Italy to Iberia circa 7500 YBP would be the Cardium Pottery Culture (aka Impressed Ware Culture). Before they were in Italy, they seem to have come from the Levant by way of the Balkans. Ancient DNA from Cardium samples from Spain have turned up mostly G2a. Both Cardial and G2a have an opposite distribution in Italy to that of R1b, with Cardial and G2a being more common in the south-center and R1b being more common in the north-center.
« Last Edit: July 30, 2012, 01:55:27 PM by Richard Rocca » Logged

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Maliclavelli
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« Reply #10 on: July 30, 2012, 02:14:20 PM »

Gioiello, archaeologically, who were these agriculturalists that you always mention?
The major group of agriculturalists that went from Italy to Iberia circa 7500 YBP would be the Cardium Pottery Culture (aka Impressed Ware Culture). Before they were in Italy, they seem to have come from the Levant by way of the Balkans. Ancient DNA from Cardium samples from Spain have turned up mostly G2a. Both Cardial and G2a have an opposite distribution in Italy to that of R1b, with Cardial and G2a being more common in the south-center and R1b being more common in the north-center.
Rich, I have always asked if the agriculturalists from Italy were autochthonous or migrants from East. The paper of Battaglia, I have read again yesterday, points she too to a first demic diffusion from Anatolia to South Balkans and after for a cultural diffusion. I think that the same happened in Italy, above all Central-Northern one.
I have said that Italy had many cultures and many haplogroups:
1)   Sardinia probably with a Caucasian language and hg. I-M26, G, and of course some ancient R (R-M18 etc. ) if hg. R was nearby
2)   An Etruscan-Rhaetian-Camun language intermediate between Caucasian and IE
3)   An Indo-European language above all in the Ligurian zone (and you know that Tuscany is genetically similar to Liguria for its percentage of R-U152)

All depends from where these agriculturalists started. We know, after Zilhao and others, that they started from Sardinia, from Tuscany, from Liguria.
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Maliclavelli


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« Reply #11 on: July 30, 2012, 02:30:14 PM »

Just for fun I ran the Gen111T using the builtin Marko's MutRate of 0.243231 on your two clades using the four HTs and the True (Ken's Words) TMRCA founders age of both was
 
Age at 30yrGen: 4,294.5, SD years: 253.8, Generations= 143.1 and GenSD=8.5


YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z301* GA coal=   46.3   13.8   1,387.6   413.7
YrsPerGen*   Count   Coalescence Age   Generations   StdDev   YBP   + - YBP
30   N=2   U106 > Z381 > Z156+ GB coal=   88.4   19.1   2,651.8   571.9
      Diff =   42.1      1,264.2   
100/111 Markers      SheetMutRate:   0.243231         
   TRUE   TMRCA Founder   Generations   StdDev   YBP   + - YBP
30      GAB=   143.1   8.5   4,294.5   253.8


I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.

All these factors have been presented for consideration, but there are a core group of people who won't listen.

I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.

Did you ever got round to expressing your concerns to Ken, if it's online somewhere I would be very interested in reading the discussion.
The most extensive set of discussions between VV, Nordtvedt and myself were on DNA Forums, my handle there was mcg11, unfortunately those discussions are gone.

There are a couple of existing threads where I and to some degree Jean L. have presented data ( Leo LIttle charts) which demonstrated that diversity was questionable because mutational rate appears to vary with allele value, these are fairly recent comments.

I have disputed GD, as a measure of time, for as long as I can remember.  A haplotype is a snapshot in time not a history.

I am not trashing anyone here, not Nordtvedt, nor Mike.  All I can honestly say is that I have questioned the variance model from day one and I still do.  That said, lets get on with understanding the real time frame of events.

I have my "blind spots", based on the climactic data I believe we will find that the redistribution of the Major sub clades of R1b occurred from the aftermath of the inundation of doggerland, which was from 9000 to c. 6000 BC the site of the best climate in Europe.

In summary, all my technical career I was a systems analyst who specialized in modelling complex processes, that was my forte'.  I am familiar with math of course but I would agree with comments I've read previously that Ken N is outstanding.
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Mark Jost
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« Reply #12 on: July 30, 2012, 04:41:22 PM »

I will have a look, since I worked with the Isle U106 guys before.

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 #13 on: July 30, 2012, 04:45:03 PM »


 The most extensive set of discussions between VV, Nordtvedt and myself were on DNA Forums, my handle there was mcg11, unfortunately those discussions are gone.

There are a couple of existing threads where I and to some degree Jean L. have presented data ( Leo LIttle charts) which demonstrated that diversity was questionable because mutational rate appears to vary with allele value, these are fairly recent comments.

I have disputed GD, as a measure of time, for as long as I can remember.  A haplotype is a snapshot in time not a history.

I am not trashing anyone here, not Nordtvedt, nor Mike.  All I can honestly say is that I have questioned the variance model from day one and I still do.  That said, lets get on with understanding the real time frame of events.

I have my "blind spots", based on the climactic data I believe we will find that the redistribution of the Major sub clades of R1b occurred from the aftermath of the inundation of doggerland, which was from 9000 to c. 6000 BC the site of the best climate in Europe.

In summary, all my technical career I was a systems analyst who specialized in modelling complex processes, that was my forte'.  I am familiar with math of course but I would agree with comments I've read previously that Ken N is outstanding.


Yes I remember you from DNA-Forums, we discussed probability a few times.

Ken left that place over 2 yrs ago (due to a tiff concerning the Corner Pub, which I thought slightly bizarre and a real shame) so you presumably haven’t conversed with him anytime recently. He has also produced several updates to his spreadsheet since then so either your concerns are covered in it or he doesn’t agree it's much of an issue.

Mike has asked  about back mutations and the answer (can't remember if it was Ken or John  Chandler) that came back is they are covered in the mutation rate.

In the most resent version of Ken's spreadsheet he uses Jean L.'s mutation rates so I’m guessing he and Jean discussed this, perhaps Jean could comment ?
« Last Edit: July 30, 2012, 05:22:29 PM by Jdean » Logged

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« Reply #14 on: July 31, 2012, 06:41:05 AM »


 The most extensive set of discussions between VV, Nordtvedt and myself were on DNA Forums, my handle there was mcg11, unfortunately those discussions are gone.

There are a couple of existing threads where I and to some degree Jean L. have presented data ( Leo LIttle charts) which demonstrated that diversity was questionable because mutational rate appears to vary with allele value, these are fairly recent comments.

I have disputed GD, as a measure of time, for as long as I can remember.  A haplotype is a snapshot in time not a history.

I am not trashing anyone here, not Nordtvedt, nor Mike.  All I can honestly say is that I have questioned the variance model from day one and I still do.  That said, lets get on with understanding the real time frame of events.

I have my "blind spots", based on the climactic data I believe we will find that the redistribution of the Major sub clades of R1b occurred from the aftermath of the inundation of doggerland, which was from 9000 to c. 6000 BC the site of the best climate in Europe.

In summary, all my technical career I was a systems analyst who specialized in modelling complex processes, that was my forte'.  I am familiar with math of course but I would agree with comments I've read previously that Ken N is outstanding.




Mike has asked  about back mutations and the answer (can't remember if it was Ken or John  Chandler) that came back is they are covered in the mutation rate.

In the most resent version of Ken's spreadsheet he uses Jean L.'s mutation rates so I’m guessing he and Jean discussed this, perhaps Jean could comment ?

I have two comments.  1.  It was thought it covered back mutations, but it doesn't.  Yes, if we had a true drunkards walk process it would but we don't.  You can't account for back mutations in a modal +/-1 scenario.  It doesn't work!

I believe that ken's most recent versions use M. Heinila's mutation rates not Jean L.?
« Last Edit: July 31, 2012, 10:30:05 AM by ironroad41 » Logged
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« Reply #15 on: July 31, 2012, 11:39:11 AM »


 The most extensive set of discussions between VV, Nordtvedt and myself were on DNA Forums, my handle there was mcg11, unfortunately those discussions are gone.

There are a couple of existing threads where I and to some degree Jean L. have presented data ( Leo LIttle charts) which demonstrated that diversity was questionable because mutational rate appears to vary with allele value, these are fairly recent comments.

I have disputed GD, as a measure of time, for as long as I can remember.  A haplotype is a snapshot in time not a history.

I am not trashing anyone here, not Nordtvedt, nor Mike.  All I can honestly say is that I have questioned the variance model from day one and I still do.  That said, lets get on with understanding the real time frame of events.

I have my "blind spots", based on the climactic data I believe we will find that the redistribution of the Major sub clades of R1b occurred from the aftermath of the inundation of doggerland, which was from 9000 to c. 6000 BC the site of the best climate in Europe.

In summary, all my technical career I was a systems analyst who specialized in modelling complex processes, that was my forte'.  I am familiar with math of course but I would agree with comments I've read previously that Ken N is outstanding.




Mike has asked  about back mutations and the answer (can't remember if it was Ken or John  Chandler) that came back is they are covered in the mutation rate.

In the most resent version of Ken's spreadsheet he uses Jean L.'s mutation rates so I’m guessing he and Jean discussed this, perhaps Jean could comment ?

I have two comments.  1.  It was thought it covered back mutations, but it doesn't.  Yes, if we had a true drunkards walk process it would but we don't.  You can't account for back mutations in a modal +/-1 scenario.  It doesn't work!

I believe that ken's most recent versions use M. Heinila's mutation rates not Jean L.?

Yes stupid me, of course it wasn't Jean L. but Marko Heinila, he posts here occasionally I wonder what his view is ?.

BTW you talk about all of this as it were the consensus which I'm pretty sure it isn’t. Perhaps you could qualify your statements with something like 'it's my opinion' rather than 'it was thought'.
« Last Edit: July 31, 2012, 11:41:36 AM by Jdean » Logged

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« Reply #16 on: July 31, 2012, 02:06:02 PM »

As long as I have Maliclavelli, Jean L. supporting this new work, I'm not worried.
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« Reply #17 on: July 31, 2012, 07:04:19 PM »

As long as I have Maliclavelli, Jean L. supporting this new work, I'm not worried.

A minority view which ever way you look at it
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« Reply #18 on: July 31, 2012, 07:18:32 PM »

I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong? Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

Why do you say that?

You may think I'm needling you, but all I'm needling is things that you say that don't make sense, at least to me. Maybe I'm wrong, by why are you throwing in some remark about sparse data when Nordtvedt got started. He hasn't retired his mind on this stuff and maintains a huge database of Hg I haplotypes. Everything I've seen is that he evolves his mathematical models to whatever works. He is is a true scientist, at least that I can see, and has been acknowledged as such. In other words, he seeks the truth. I don't think he has a Doggerland theory or Cro-Magnon theory or Bronze Age theory that he has much passion about. He just wants to figure it out.

... I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.

Remember, Dienekes is the guy who says "STRs #$%*ck". Is he using them again?
« Last Edit: July 31, 2012, 07:20:56 PM by Mikewww » Logged

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« Reply #19 on: July 31, 2012, 07:23:30 PM »

I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.
ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.
All these factors have been presented for consideration, but there are a core group of people who won't listen.
I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.
I have expressed these principles from many years:
1) mutations around the modal
2) convergence to the modal as time passes
3) sometime a mutation go for the tangent and we have the outliers, which should be the most interesting for calculating the TMRCA.

Since you've expressed these principles for many years, it should be easy for you to explain them comprehensively, yet concisely.  Do you have a paragraph on each of your three points that explains them and why they have a significant impact?
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« Reply #20 on: July 31, 2012, 08:38:31 PM »

I agree with what Ironroad41 has said and he knows English long better than me:

1
I also note that Terry Robb on rootsweb has used the same approach and confirmed (agreed with) some of Dienekes data.
I don't agree that germline rates are so bad, however they are very inaccurate for slow mutators.  The basic problem is the mutational process and the number of mutations which occur over time.  Some of the faster mutators have a high probability of l or more mutations within 500 to 600 years.  Then how many mutations can you expect in 5000 to 6000 years [?].  What is really false is the concept of GD, which assumes that one mutation away from the modal is really one whereas in fact it could be much higher.  Further since many of the "medum fast" mutators have a limited range, modal +/-1, there are many hidden mutations.

If I can add something, I have done in the past the sample of DYS391, which rotates above all around the values 10/11, except when the mutations go for the tangent, in fact values like 13 or 14 for hg. R are very meaningful (Maliclavelli).
2
I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.

All these factors have been presented for consideration, but there are a core group of people who won't listen.

I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.
« Last Edit: July 31, 2012, 08:40:39 PM by Maliclavelli » Logged

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« Reply #21 on: August 01, 2012, 05:50:04 PM »

I agree with what Ironroad41 has said and he knows English long better than me:

1
I also note that Terry Robb on rootsweb has used the same approach and confirmed (agreed with) some of Dienekes data.
I don't agree that germline rates are so bad, however they are very inaccurate for slow mutators.  The basic problem is the mutational process and the number of mutations which occur over time.  Some of the faster mutators have a high probability of l or more mutations within 500 to 600 years.  Then how many mutations can you expect in 5000 to 6000 years [?].  What is really false is the concept of GD, which assumes that one mutation away from the modal is really one whereas in fact it could be much higher.  Further since many of the "medum fast" mutators have a limited range, modal +/-1, there are many hidden mutations.

If I can add something, I have done in the past the sample of DYS391, which rotates above all around the values 10/11, except when the mutations go for the tangent, in fact values like 13 or 14 for hg. R are very meaningful (Maliclavelli).
2
I admire all your work Mark and I am not critical of  you.  The variance model assumed to simulate the mutational process is wrong.  Ken Nordtvedt should be congratulated for all his work, but he started when the data was sparse.

ASD/Variance is based on the random/drunkards walk model where the drunk is 5 steps from the pole after taking 25 steps (square law).  The problem is that dys loci wander very little away from the modal and don't keep drifting away as the model predicts.  Even the fastest mutators saturate after about +/- two steps from the modal.  Two steps add complexity and can cause as much as 5 or 6 steps away, but only rarely.   The diversity of many dys loci is low and on top of that it appears from Leo Littles data that mutation rate varies with allele value.

All these factors have been presented for consideration, but there are a core group of people who won't listen.

I really believe that time has been warped and I hope that Dienekes/trobb will continue to present their estimates for the R1b clades.


Thank you. That helps me understand your principles.

I have expressed these principles from many years:
1) mutations around the modal
2) convergence to the modal as time passes
3) sometime a mutation go for the tangent and we have the outliers, which should be the most interesting for calculating the TMRCA.

What did you mean by #3 and its impact?
« Last Edit: August 01, 2012, 05:52:07 PM by Mikewww » Logged

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« Reply #22 on: August 01, 2012, 07:12:43 PM »

What did you mean by #3 and its impact?
I did mean that, for instance, DYS391 mutates above all from 10 to 11 and from 11 to 10.
If a mutation for the tangent happens, it could mutate from 11 to 12 or from 10 to 9, and so on.
We have in Middle East some hg. R with DYS391=14 or 15, practically inxistent in Europe. Evidently there happened a mutation for the tangent.
« Last Edit: August 01, 2012, 07:13:08 PM by Maliclavelli » Logged

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