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Author Topic: R1b-U152/S28 - keeping the phylogenetic tree updated  (Read 1286 times)
Mike Walsh
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« on: July 31, 2012, 04:03:18 PM »

I'm just looking for help keeping track of the positioning of new SNPs.

ISOGG is way ahead of FTDNA, which is expected to some extent, on recognizing SNPs that can be placed on the Y DNA phylogenetic tree.
http://isogg.org/tree/ISOGG_HapgrpR.html

Here is Thomas Krahn's draft version of the tree for U152.
http://ytree.ftdna.com/index.php?name=Draft&parent=94964529

Below is a representation of what I use in the P312xL21 Haplotype spreadsheet for U152. Do I have it right?  Am I missing SNPs? The below is actually represented in formulas in a spreadsheet so it is important that I get it right to display haplogroup labels correctly. I also try to use the asterisk and double asterisk to help denote immediate downstream SNP results.

U152+  >>> R-U152; * = M126- M160- L2-  ** = M126- M160- L2- Z36- Z56-

M126+  >>> R-U152/M126; Terminal

M160+  >>> R-U152/M160; Terminal

L2+  >>> R-U152/L2; * = L20- L196- Z49- L408-  ** = L20- L196- Z49-
L20+  >>> R-U152/L2/L20; * = M228.2-
M228.2+  >>> R-U152/L2/L20/M228; Terminal
L196+  >>> R-U152/L2/L196; Terminal
Z49+  >>> R-U152/L2/Z49; * = Z142-
Z142+  >>> R-U152/L2/Z49/Z142; * = L562-
L562+  >>> R-U152/L2/Z49/Z142/L562; Terminal
L408+  >>> R-U152/L2/L408; Terminal
Z36+  >>> R-U152/Z36; Terminal
Z56+  >>> R-U152/Z56; * = L4- S47-  ** = L4- S47- Z145-
L4+  >>> R-U152/Z56/L4; Terminal
S47+  >>> R-U152/Z56/S47; Terminal
Z145+  >>> R-U152/Z56/Z145; Terminal

Z192+ >>> Unpositioned under U152
L409+ >>> Unpositioned under U152
L443+ >>> Unpositioned under L2
L552+ >>> Unpositioned under L2
L553+ >>> Unpositioned under L2
Z367+ >>> Unpositioned under L2
Z384+ >>> Unpositioned under L2
L654+ >>> Unpositioned under L2

« Last Edit: July 31, 2012, 04:04:19 PM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Richard Rocca
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« Reply #1 on: July 31, 2012, 07:53:50 PM »

Z192 is not yet available for testing

Z367, Z258 and Z367 forms one branch below L2 and then splits off into Z34 and L20

Z291 is below L20

L409 and L443 are equal to L408

The rest for the time being seem to be family markers.
 
Thanks for maintaining the spreadsheet.
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Paternal: R1b-U152+L2*
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Maliclavelli
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« Reply #2 on: July 31, 2012, 09:21:28 PM »

Z192 is not yet available for testing

Z192 (the 2 Mexicans of 1KGP with 18 private mutations at least) and Z194 (2 Tuscans) are very important, because they could be the proof of the migrations from Italy to Iberia 7500 years ago and Tuscans have Z192 whereas the 2 Mexicans haven’t Z194, then this is the direction of the migration.
Then this is the 4th branch of U152 about which Sardinians could say something.
« Last Edit: July 31, 2012, 09:23:46 PM by Maliclavelli » Logged

Maliclavelli


YDNA: R-S12460


MtDNA: K1a1b1e

Mike Walsh
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« Reply #3 on: August 11, 2012, 05:06:24 PM »

Z192 is not yet available for testing

Z192 (the 2 Mexicans of 1KGP with 18 private mutations at least) and Z194 (2 Tuscans) are very important, because they could be the proof of the migrations from Italy to Iberia 7500 years ago and Tuscans have Z192 whereas the 2 Mexicans haven’t Z194, then this is the direction of the migration.
Then this is the 4th branch of U152 about which Sardinians could say something.

Where are these two SNPs described?  I can't find them on Richard R's  "U152 Proposed Phylogeny" at http://u152.org/.
http://u152.org/
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Maliclavelli
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« Reply #4 on: August 11, 2012, 05:37:07 PM »

Look at the paper of Rocca et al., Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach, PLoS One 2012, p. 4.
« Last Edit: August 11, 2012, 05:41:09 PM by Maliclavelli » Logged

Maliclavelli


YDNA: R-S12460


MtDNA: K1a1b1e

Richard Rocca
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« Reply #5 on: August 11, 2012, 05:41:05 PM »

Look at the paper of Rocca et al., PLoS ONE 2012. p. 4.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041634

The primers for Z194 were recently validated, so hopefully we can have folks start testing for it soon.
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Mike Walsh
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« Reply #6 on: August 13, 2012, 06:06:15 PM »

The P312xL21 haplotypes file now has the latest U152 info that I have found.
https://dl.dropbox.com/u/17907527/R1b-P312xL21_Haplotypes.zip

Below is the Clades table portion of the spreadsheet that controls labeling of haplogroups. Hopefully, it is now correct. I added Z192 and Z194 just so we are ready for them.


U152+  >>> R-U152;  * = M126- M160- L2-  ** = M126- M160- L2- Z36- Z56-,  Equivalents: S28

M126+  >>> R-U152/M126; Terminal

M160+  >>> R-U152/M160; Terminal

L2+  >>> R-U152/L2;  * = Z367- L196- Z49-  ** = Z367- L196- Z49- L408-,  Equivalents: S139
Z367+  >>> R-U152/L2/Z367;  * = L20-  ** = L20- Z34-,  Equivalents: Z258,Z384,Z1905
L20+  >>> R-U152/L2/Z367/L20;  * = M228.2-  ** = M228.2- Z291-,  Equivalents: S144,Z383,Z1908,Z1910
M228.2+  >>> R-U152/Z367/L2/Z367/L20/M228; Terminal
Z291+  >>> R-U152/Z367/L2/Z367/L20/Z291; Terminal
Z34+  >>> R-U152/L2/Z367/Z34; Terminal,  Equivalents: S368,Z33,Z151,Z259,Z276
Z35+  >>> R-U152/L2/Z367/Z34/Z35; Terminal
L196+  >>> R-U152/L2/L196; Terminal
Z49+  >>> R-U152/L2/Z49;  * = Z142-  ** = n/a,  Equivalents: Z68
Z142+  >>> R-U152/L2/Z49/Z142;  * = L562-  ** = n/a
L562+  >>> R-U152/L2/Z49/Z142/L562; Terminal,  Equivalents: S211,Z51,Z55
L408+  >>> R-U152/L2/L408; Terminal,  Equivalents: L409,L443

Z36+  >>> R-U152/Z36; Terminal

Z56+  >>> R-U152/Z56;  * = L4- S47-  ** = n/a,  Equivalents: Z42,Z43,Z47
L4+  >>> R-U152/Z56/L4; Terminal,  Equivalents: S178
S47+  >>> R-U152/Z56/S47; Terminal,  Equivalents: Z45,Z48
Z144+  >>> R-U152/Z56/Z144; Terminal,  Equivalents: Z145,Z146,Z147

Z192+  >>> R-U152/L192;  * = Z194-  ** = n/a
Z194+  >>> R-U152/L192/L194; Terminal

Z258+ >>> Unpositioned under L2
L409+ >>> Unpositioned under L2
L443+ >>> Unpositioned under L2
L552+ >>> Unpositioned under L2
L553+ >>> Unpositioned under L2
Z384+ >>> Unpositioned under L2
Z145+ >>> Unpositioned under Z56
Z146+ >>> Unpositioned under Z56

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