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Author Topic: Busby 15 Marker Data Table - Dating the results  (Read 1473 times)
Mark Jost
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« on: September 17, 2012, 02:06:17 PM »

After reading Heber's posting on Busby's Data at this link,

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

I pulled the haplotypes from TableS3-15strs and cleaned fractional allele value and removed the dups and ran 14 STRs x389i and produced reduced age results with interclade

Founder's Age for all haplotypes

Generations   StdDevInGen   YBP  +-YBP   Max    VAR    SD
165.8   70.0    4,974.6   2,100.7    7,075.4   5.6   2.4


I have a results PDF  stored in my Google Documents here:

https://docs.google.com/open?id=0By9Y3jb2fORNVXNCR2J0VGw0cUk

If you wish to use a smaller number of years per generation then recalcuated using Generations   StdDevInGen values.

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 #1 on: September 17, 2012, 02:19:22 PM »

After reading Heber's posting on Busby's Data at this link,

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

I pulled the haplotypes from TableS3-15strs and cleaned fractional allele value and removed the dups and ran 14 STRs x389i and produced reduced age results with interclade

Founder's Age for all haplotypes

Generations   StdDevInGen   YBP  +-YBP   Max    VAR    SD
165.8   70.0    4,974.6   2,100.7    7,075.4   5.6   2.4


I have a results PDF  stored in my Google Documents here:

https://docs.google.com/open?id=0By9Y3jb2fORNVXNCR2J0VGw0cUk

If you wish to use a smaller number of years per generation then recalcuated using Generations   StdDevInGen values.

MJost

Just to be clear, is  this is an interclace of L21 clades?
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Mkk
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« Reply #2 on: September 17, 2012, 02:23:01 PM »

After reading Heber's posting on Busby's Data at this link,

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

I pulled the haplotypes from TableS3-15strs and cleaned fractional allele value and removed the dups and ran 14 STRs x389i and produced reduced age results with interclade

Founder's Age for all haplotypes

Generations   StdDevInGen   YBP  +-YBP   Max    VAR    SD
165.8   70.0    4,974.6   2,100.7    7,075.4   5.6   2.4


I have a results PDF  stored in my Google Documents here:

https://docs.google.com/open?id=0By9Y3jb2fORNVXNCR2J0VGw0cUk

If you wish to use a smaller number of years per generation then recalcuated using Generations   StdDevInGen values.

MJost

Just to be clear, is  this is an interclace of L21 clades?
The data is for P312. (S116)
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Mark Jost
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« Reply #3 on: September 17, 2012, 02:24:46 PM »

After reading Heber's posting on Busby's Data at this link,

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

I pulled the haplotypes from TableS3-15strs and cleaned fractional allele value and removed the dups and ran 14 STRs x389i and produced reduced age results with interclade

Founder's Age for all haplotypes

Generations   StdDevInGen   YBP  +-YBP   Max    VAR    SD
165.8   70.0    4,974.6   2,100.7    7,075.4   5.6   2.4


I have a results PDF  stored in my Google Documents here:

https://docs.google.com/open?id=0By9Y3jb2fORNVXNCR2J0VGw0cUk

If you wish to use a smaller number of years per generation then recalcuated using Generations   StdDevInGen values.

MJost

Just to be clear, is  this is an interclace of L21 clades?

I highlighted the Founder's Age and the sigma range in the post.

In the PDF I show the IntraClade Coalescence Ages for and the
Interclade between Busby HTs and L21 and also DF13 for reference.

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 #4 on: September 17, 2012, 02:27:49 PM »

The Founder's Age is the True Sample (n-1) Age. IntraClade Coalescence Age is treated as the whole (n) population.

The Interclade is from the Founder's Pooled Standard Deviation of both clades.

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 #5 on: September 18, 2012, 03:36:54 AM »

Is the age calculated for Busby's 15 STRs making the cut?

I can filter the I for instant aging now. Any requests?

popCode   HG      sampleID
SPA-V   S116      VAL108
ENG-SW   S116      COR700
ITA-C   S116      NOR35
GER-F   S21      GER030
ENG-NW   S116      CUM230
BAS   S116      HGDP00512
SPA-V   M269      VAL199
ALPS   M269      CAD17
Logged

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 #6 on: September 18, 2012, 10:34:22 AM »

Ok, I had to revise the previous Busby 15 STR (14 used) age estimate I posted due to the DYS635's being posted incorrectly under DYS636 which after the correction reduced the founders age from 165.8 to 152.4 generations.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/edit

I apologize for any mistakes.

MJost
Logged

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)
Jarman
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« Reply #7 on: September 18, 2012, 04:34:35 PM »

Ok, I had to revise the previous Busby 15 STR (14 used) age estimate I posted due to the DYS635's being posted incorrectly under DYS636 which after the correction reduced the founders age from 165.8 to 152.4 generations.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/edit

I apologize for any mistakes.

MJost


39 lashes with a wet noodle.  No wait - make that an unwound DNA ribbon.
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Mark Jost
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« Reply #8 on: September 18, 2012, 07:44:40 PM »

Ok, I had to revise the previous Busby 15 STR (14 used) age estimate I posted due to the DYS635's being posted incorrectly under DYS636 which after the correction reduced the founders age from 165.8 to 152.4 generations.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/edit

I apologize for any mistakes.

MJost


39 lashes with a wet noodle.  No wait - make that an unwound DNA ribbon.
[/quote
Thanks for the reduction in punishment. I tend to hurry... thats why I am not a Programmer....

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 #9 on: September 18, 2012, 07:48:47 PM »

I added a Variance breakdown Page to the PDF with M269 by Population Codes.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/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)
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« Reply #10 on: September 18, 2012, 11:24:31 PM »

Added S116/P312 Variance breakdowns per popluation locations and added combo areas.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/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 #11 on: September 19, 2012, 10:30:31 AM »

Ok, I don't know why I didn't show the extend the decimal precision on the variances so I re-posted the change as a newest version. I also added a combined M269 and S116(P312) chart then sorted all by variance on the last page.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/edit

MJost
Logged

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 #12 on: September 19, 2012, 10:57:36 PM »

I just ran the S21/U106's from Busby's data and also I now combined them with M269 and S116/P312 breakdowns by population codes and combo codes.

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/edit

MJost
Logged

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 #13 on: September 20, 2012, 11:43:35 AM »

The Founders age in Generations for just the M269 Haplotypes is 144.4. The S116(P312) only is calculates out to 141.1 generations. That is three generations and the generation Sigma show each to be 62.8 and 61.9 respectively.

On the plus sides, that is 4,331 to 6,090 years old for M269, and nearly the same range for S116(P312)  4,232 to 6,090 ybp.  M269 has strong variance in ALB and ALPS excluding first three low sample number locations.

S116(P312) appears to have a few standouts in the largest variances. Throw out WAL(es)-S, BAS and GRE due to small samples; ENG(land)-SW and POR-C & SPA-C, and then SPA-all has the top spots.

S21(U106) has about the same generation age as S116 but checking out the population Variance (throw out BAS), has Norway in the lead as the most variance.

Interesting.

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)
Richard Rocca
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« Reply #14 on: September 20, 2012, 12:00:06 PM »

The Founders age in Generations for just the M269 Haplotypes is 144.4. The S116(P312) only is calculates out to 141.1 generations. That is three generations and the generation Sigma show each to be 62.8 and 61.9 respectively.

On the plus sides, that is 4,331 to 6,090 years old for M269, and nearly the same range for S116(P312)  4,232 to 6,090 ybp.  M269 has strong variance in ALB and ALPS excluding first three low sample number locations.

S116(P312) appears to have a few standouts in the largest variances. Throw out WAL(es)-S, BAS and GRE due to small samples; ENG(land)-SW and POR-C & SPA-C, and then SPA-all has the top spots.

S21(U106) has about the same generation age as S116 but checking out the population Variance (throw out BAS), has Norway in the lead as the most variance.

Interesting.

MJost


Important for all to note that Norway has the highest U106 variance in the Busby study and that the data is new to that study and was not part of the Myres 2011 dataset.
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Mark Jost
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« Reply #15 on: September 20, 2012, 12:25:07 PM »

RichardR,

Hey is there anything else out there that would dispute this Kingship of M269 and S21 in Norway? The S116(P312) was so strong in the southern Isle, I see a dominate footprint in the North Sea area of the origin of the two subclades of M269 that hugged the coast line from Norway to the south western part Wales, which assumes a strong North Sea coastal Continental presence as well.


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 #16 on: September 20, 2012, 01:06:56 PM »

... Hey is there anything else out there that would dispute this Kingship of M269 and S21 in Norway? The S116(P312) was so strong in the southern Isle, I see a dominate footprint in the North Sea area of the origin of the two subclades of M269 that hugged the coast line from Norway to the south western part Wales, which assumes a strong North Sea coastal Continental presence as well.

Mark, U106 is being discussed in the "early U106" thread. Please join and comment on the data you see of U106's origin and ancient migration paths.  This is critical. If U106 was along the North Sea early in its ancestry then the probability gravity pulling L11's origin toward the Atlantic facade increases greatly even though many only associate it with the Anglo-Saxon Invasion era as far the Isles go, and Germanic languages and peoples in general.
« Last Edit: September 20, 2012, 01:08:34 PM by Mikewww » Logged

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Mark Jost
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« Reply #17 on: September 20, 2012, 03:09:58 PM »

Added STRs used and the Modal and Mean STR values for each Clade along with the mutation rates used to the previous PDF

https://docs.google.com/file/d/0By9Y3jb2fORNVXNCR2J0VGw0cUk/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)
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« Reply #18 on: September 21, 2012, 12:27:49 PM »

MikeW and other in the past have questioned several issues such as selection of STRs to be used, the number of those, and others. Linear stabilization of various STRs into a deeper ancestry was  discussed.

In looking at the Busby 15 STRs, I used the L21 database as another clade as reference. I noticed that the L21 age calculated using the same STRs (14) vs 111(100) was virtually the same....

L21 Founder's Age using 111 marker less (11 STRs not used: 385,389i,459,464,CDY)
Generations StdDevInGen YBP +-YBP Max VAR SD
118.9  22.5  3,567.9  674.7  4,242.6  28.0  5.3

Using Busby's 15 STR's x389i

30 N=750 Clade L21 ALL
114.4  55.8  3,433.5  1,672.9  4.2  2.1

4.5 generations difference between using 14 vs 100 STRs.

I though that this was an interesting correlation that helps confirm that sheer volume of STRs per haplotype levels the playing field of linearity.

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: September 21, 2012, 01:36:39 PM »

MikeW and other in the past have questioned several issues such as selection of STRs to be used, the number of those, and others. Linear stabilization of various STRs into a deeper ancestry was  discussed.

In looking at the Busby 15 STRs...

Mark, this is what I was talking about over in the STR Wars thread.


Quote from: Busby
Fifteen Y-STRs with mutation rates, range of alleles and estimate of duration of linearity. All STRs investigated in this study are shown with their mutation rates (μ), estimated from Ballantyne et al. [33], and range of observed alleles, R, with 95% CI is taken from the YHRD [34]. θ(R)/2μ is an estimate of the duration of linearity of an STR."

In this an excerpt of that table with the duration of linearity column. I added the "S127"s and "xxx"s to show what markers he used in his S127(L11) STR variance calculations and which ones appeared to be too short in duration according to his own method to go back over 5000 years.
Quote from: Busby

Y-STR _____ θ(R)/2μ   
DYS448 ___ 25,381   
DYS392 ___ 19,244   S127
DYS438 ___ 12,465   S127
DYS390 ___ 9,211  S127
DYS393 ___ 5,648  S127
DYS439 ___ 4,861   S127 xxx
DYS437 ___ 4,357   S127 xxx
DYS635 ___ 4,221   
DYS456 ___ 3,289   
DYS389II __ 3,111   S127 xxx
DYS391 ___ 2,554   S127 xxx
DYS458 ___ 1,944   
DYS19 ____ 1,888  S127 xxx
Y-GATA-H4 _ 1,630   
DYS389I ___ 953  S127 xxx

Maybe you can figure this out.  This is where Busby lost me. Six of the ten STRs he used weren't fit close to for the purpose unless you assume R-L11 is even younger yet.
http://www.worldfamilies.net/forum/index.php?topic=10513.msg130016#msg130016

The problem that Busby has brought forward is the saturation or slow down in observable mutations for certain STRs the further back in time you go. The linear durations above don't agree with Heinilla's but I actually trust Heinilla's more. 

Anyway, the point I would have is more STRs are better. In my experience with cross-validating subclades within R1b, where we know for certain which are older within the phlyogenetic tree, I had better consistency when using a large number of STRs, like in the 30's and above. Below that I had occurrences where a haplogroup that had to be younger (i.e. U198 versus U106) ended up being more diverse than its grandparent.  My observations where that we did NOT need that many haplotypes in the sample with a high number of STRs. Once you get up to 50, and even above 20 to some extent, the relationships between haplogroups tend to stabilize and match the phylogenetic tree.

It's probably a good thing for someone to write a paper on... the trade-off between number of haplotypes and depth of data.
« Last Edit: September 21, 2012, 01:44:05 PM by Mikewww » Logged

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« Reply #20 on: September 21, 2012, 11:03:41 PM »

I havent kept up on the lateset STRs, so if you provide a list of those out of 111 markers that should be used we can run some examples against the L21 data.

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 #21 on: September 29, 2012, 06:24:25 PM »

I plotted my Busby 15 STRs variance results to a Google map here.
M269 and S116 colored pins with the Combined variacne over several HTs with there own pin showing overall area results.

http://tinyurl.com/BusbyVarianceLocations
 
Balloons - M269 Red to Yellow to Green High to Low grouping of Variances

Pins -P312 Red to Yellow to Blue High to Low grouping of Variances

What does this clinal distribution most likely reflect?

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 #22 on: September 29, 2012, 08:57:47 PM »

I plotted my Busby 15 STRs variance results to a Google map here.
M269 and S116 colored pins with the Combined variacne over several HTs with there own pin showing overall area results.

http://tinyurl.com/BusbyVarianceLocations
 
Balloons - M269 Red to Yellow to Green High to Low grouping of Variances

Pins -P312 Red to Yellow to Blue High to Low grouping of Variances

What does this clinal distribution most likely reflect?

MJost


Except for P312 in western Iberia the high points seem rather spotty. If I had to make a conclusion about anything here it would be P312 did not originate in Italy or the Alps.
Thanks for sharing your map.
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« Reply #23 on: September 30, 2012, 01:07:09 PM »

I plotted my Busby 15 STRs variance results to a Google map here.
M269 and S116 colored pins with the Combined variacne over several HTs with there own pin showing overall area results.

http://tinyurl.com/BusbyVarianceLocations
 
Balloons - M269 Red to Yellow to Green High to Low grouping of Variances

Pins -P312 Red to Yellow to Blue High to Low grouping of Variances

What does this clinal distribution most likely reflect?

MJost


Except for P312 in western Iberia the high points seem rather spotty. If I had to make a conclusion about anything here it would be P312 did not originate in Italy or the Alps.
Thanks for sharing your map.

If you drop the first three highest variances for S116(P312) Wal,BAS & GRE, the next eight with significant HTs seem to point to the Atlantic Coast cline as shown largest to smaller variance values

N=16   S116(P312) // ENG-SW
N=17   S116(P312) // ENG-C & SW
N=127   S116(P312) // POR-C & SPA-C
N=227   S116(P312) // SPA ALL
N=112   S116(P312) // POR-N & SPA-V
N=36   S116(P312) // ITA-N
N=23   S116(P312) // POR ALL

Needed a review of P312's along the northwest and north ends of France.

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)
Jarman
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Posts: 58


« Reply #24 on: September 30, 2012, 05:19:08 PM »

I added U106 Variances to the Busby Variance Map M269_P312_U106

http://tinyurl.com/BusbyVarianceLocations


The importance is he Red locations for the three Subclades.

MJost

Why the void in northern Germany?
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