R1b-L21/S145 - keeping the phylogenetic tree updated

[df.reynolds]

@ Mike, a bunch of S numbered SNPs (I guess from Wilson's lab in Scotland) have lately posted to the ISOGG R tree that are under L21, and are not on your descendancy chart.

See the last Note in the Notes section (way below the tree itself):

http://www.isogg.org/tree/ISOGG_HapgrpR.html

Thanks.
Does anyone have FTDNA kit #s or Ysearch IDs for S424+ S190- guys?

The only S424+ S190- I'm aware of in our db is kit 133832, Reddin.

-david

[Mikewww]

@ Mike, a bunch of S numbered SNPs (I guess from Wilson's lab in Scotland) have lately posted to the ISOGG R tree that are under L21, and are not on your descendancy chart.

See the last Note in the Notes section (way below the tree itself):

http://www.isogg.org/tree/ISOGG_HapgrpR.html

Thanks.
Does anyone have FTDNA kit #s or Ysearch IDs for S424+ S190- guys?

The only S424+ S190- I'm aware of in our db is kit 133832, Reddin.

-david

Thanks. It's looking like S190 is forming a nice alignment with 21-5909-LS Little Scots. S424 is TBD but 590=9 might fit.

[Mikewww]

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip
I've updated the R1b-L21 Descendancy Tree chart to include Z253 SNPs for Z2183-5. They appear to be right below L1066 or somewhere above it and below Z253.

L1066 includes 253-1066-T4 (Irish IV) haplotypes. In other words T4 is a subset of L1066 but exclusive to L226 (Irish III).

> >> > Haplogroup Tree Descendancy Chart: Graphic tree chart of the SNP
levels/positioning in the Clades table:
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg

I've updated the spreadsheet too. Tried to find as many 67 STR matches from the Cumberland Gap project. Curiously I found a guy in the Anglo-Saxon project who looks to be "pre" L226 or pre-Irish III.

> >> > Haplogroup Tree Descendancy Chart: Graphic tree chart of the SNP
levels/positioning in the Clades table:
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg

[Newragh]

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

Is there a FAQ on the L21 group site that explains this spreadsheet?

[Mikewww]

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

Is there a FAQ on the L21 group site that explains this spreadsheet?

This is it. What questions do you have?

[Newragh]

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

Is there a FAQ on the L21 group site that explains this spreadsheet?

This is it. What questions do you have?

Too many questions to waste bandwidth on this otherwise sophisticated forum. I'll just keep hitting buttons, thanks.

One thing that has always bothered me though is the placing of Louth in Leinster in the "Most Distant Known Ancestor & Origin" column, since it has only been considered to be there for 400 years. In times of interest to DNA studies, Louth was in Ulster, indeed much of the Táin Bó Cúailnge takes place in Louth. I used to live in north Louth and had a nice view of the Cooley Mountains, and Cú Chulainn's stone was just down the road.

It seems to me that this placement in Leinster, tends to make people think of the Laigin or even the Dál Cuinn, instead of the Uliad, when considering the connections of SNPs to peoples.

[Mikewww]

I've updated the L21 file again. I went through every 67 STR length R1b1a2 predicted (except 492=13) haplotype in both the French Heritage and German Language projects and compared them GD-wise and STR off-modals-wise to the L21 file, one by one. I saved the ones I thought were good "suspects" to be L21 file. The saved suspects were ones that matched on two or more slower off-modal STRs and had reasonable GDs.

It was interesting in that I check see closest GD in the L21 file and furthest GD. The furthest R1b1a2 predicted GDs to the L21's in generally from the German file. I guess that should be expected as France is closer to the Isles, but I think some of these were L11* or L23* or whatever to be so far away genetically. I wonder if there is more hidden in Germany than we know?

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

[Mikewww]

This file has been updated with a lot of suspected M222 and DF23* (and a few other suspected types).

A few more varieties fell into the DF13* category, DF13+ and negative for each of the Big Six.

I've updated the L21 file again. I went through every 67 STR length R1b1a2 predicted (except 492=13) haplotype in both the French Heritage and German Language projects and compared them GD-wise and STR off-modals-wise to the L21 file, one by one. I saved the ones I thought were good "suspects" to be L21 file. The saved suspects were ones that matched on two or more slower off-modal STRs and had reasonable GDs.

It was interesting in that I check see closest GD in the L21 file and furthest GD. The furthest R1b1a2 predicted GDs to the L21's in generally from the German file. I guess that should be expected as France is closer to the Isles, but I think some of these were L11* or L23* or whatever to be so far away genetically. I wonder if there is more hidden in Germany than we know?

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

[Jdean]

This file has been updated with a lot of suspected M222 and DF23* (and a few other suspected types).

A few more varieties fell into the DF13* category, DF13+ and negative for each of the Big Six.

I've updated the L21 file again. I went through every 67 STR length R1b1a2 predicted (except 492=13) haplotype in both the French Heritage and German Language projects and compared them GD-wise and STR off-modals-wise to the L21 file, one by one. I saved the ones I thought were good "suspects" to be L21 file. The saved suspects were ones that matched on two or more slower off-modal STRs and had reasonable GDs.

It was interesting in that I check see closest GD in the L21 file and furthest GD. The furthest R1b1a2 predicted GDs to the L21's in generally from the German file. I guess that should be expected as France is closer to the Isles, but I think some of these were L11* or L23* or whatever to be so far away genetically. I wonder if there is more hidden in Germany than we know?

> >> > All L21 confirmed and suspected haplotypes. The 111 STR haplotypes are
also included.
https://dl.dropbox.com/u/17907527/R1b-L21_Haplotypes.zip

Cheers Mike, once I have my charger back for the new laptop I'll download it, your spreadsheet turns this one into jelly !!

[Mikewww]

I'm also one of the R1b and Subclade project co-administrators.

We'd like to help sort out the large group of R1b1a2 predicted people and
encouragement them to deep clade test. The recommendation is the hard part. If
we don't have any idea, I think the Geno 2.0 package will be the best idea.

For some circumstances, stand alone SNP testing may be the best way to proceed.
There is a middle ground where people may likely be positive for a particular,
let's say L21, but there would be still be a number of stand alone SNP
tests required to get down to the terminal SNP.

First, however, I'm thinking about trying to bite off an easier group that I
think will grow over time as SNP discovery continues. The easier group to make a
recommendation to would be those with strong matches with terminal SNPs. A
terminal SNP is just the lowest level of the Y DNA tree that one is tested
positive for. Some groups are fortunate enough that "permanent" terminal SNP may
have been discovered for them.

I'm asking for a list of "permanent" terminal SNPs for U106, P312, L21, etc.? By
"permanent", I just mean they are young enough that they won't soon get bumped
from terminal SNP status as younger SNPs below the respective SNP are
discovered. There is a youthful limit to consider. SNPs that are private, have
less than 15 diversity, won't make any official Y DNA trees. I'm calling an SNP
with just more than 15% diversity as permanent since it is likely to retain that
status for sometime as the lowest level on the tree. Ideally, we'd know the SNP
was capped at this 15-20% diversity level because an immediately upstream SNP
with low diversity pretty much assures the permanent terminal SNP really is
young.

Well, did I confuse everyone?

What are the young SNPs of L21 on the ISOGG tree?

I think L744/L745, L705.2/L706.2, L226, L193, L554, S190, L371 and maybe M222 might be good candidates. What do you think?

Some day, we might have a hundred or so of these young terminal SNPs, maybe
more.

[razyn]

I don't find your posts especially confusing, but the ISOGG criteria page leaves something to be desired.  Never have really understood what they mean by their 15% and 20% threshholds, for example:

http://www.isogg.org/tree/ISOGG_SNP_Requirements.html

Just the other day I came across a site that explains that -- assuming he's right.  Anyway it's an L21 intensive site, and I don't always read everything that's posted about your group, since it isn't mine.  Thought you might want to make a recommendation, pro or con, about what this Casey guy is doing.  It's quite elaborate; looks helpful to me, but I'm an L21 tyro.  I'll paste in a link to his L744 analysis; one may move upward in the website, and on his toolbar there is an Analysis button that lists many of these (for other SNPs):

http://www.rcasey.net/DNA/R_L21/Analysis/R_L21_Analysis_L744.html

[Mikewww]

... I'm asking for a list of "permanent" terminal SNPs for U106, P312, L21, etc.? By
"permanent", I just mean they are young enough that they won't soon get bumped
from terminal SNP status as younger SNPs below the respective SNP are
discovered. There is a youthful limit to consider. SNPs that are private, have
less than 15 diversity, won't make any official Y DNA trees. I'm calling an SNP
with just more than 15% diversity as permanent since it is likely to retain that
status for sometime as the lowest level on the tree. Ideally, we'd know the SNP
was capped at this 15-20% diversity level because an immediately upstream SNP
with low diversity pretty much assures the permanent terminal SNP really is
young.
L705.2/L706.2, L226, L193, L554, S190, L371 and maybe M222 might be good candidates. What do you think?

Some day, we might have a hundred or so of these young terminal SNPs, maybe
more.

I'm not trying to build an SNP predictor. I actually think those can be quite misleading. On the other hand, if someone has a nice match to a far downstream SNP, I'm not sure (for Y DNA purposes) if they need to buy a full Geno 2.0 package. It it's up to the individual to weight the prices and risks.

I don't think we have too many reliable "permanent" terminal SNPs but this will give you an idea of where I'm trying to go.

https://dl.dropbox.com/u/17907527/R1bTerminalSNPRecommender.xlsm

This needs lots of work and probably a couple of the SNPs in there have no right to be thought of as permanently terminal, but some do.  I need to back this off to an earlier version of Excel so it'll be more compatible but the idea is just copy your haplotype row (the whole row) in from an FTDNA project screen and Paste Special / Values into the yellow area of the spreadsheet. You can sort by GD with the "modals" in the spreadsheet. If you come up within a GD of 7/8 or less have a 100% signature match, or nearly so, you might consider the stand-alone SNP test.

I do foresee the day (maybe two years from now) where we'll have a couple of hundred of reliable terminal SNPs for R1b with more coming.

[Mikewww]

I'm finding there are still probably not more than a dozen identified "permanent" terminal SNPs across R1b. There are really hundreds that haven't been identified yet. I'm going to put this idea on hold until we see what's really NOT in Geno 2.0. SNPs that aren't in Geno 2.0 are ones we have to be sure to check for before deciding to order Geno 2.0.

... I'm asking for a list of "permanent" terminal SNPs for U106, P312, L21, etc.? By
"permanent", I just mean they are young enough that they won't soon get bumped
from terminal SNP status as younger SNPs below the respective SNP are
discovered. There is a youthful limit to consider. SNPs that are private, have
less than 15 diversity, won't make any official Y DNA trees. I'm calling an SNP
with just more than 15% diversity as permanent since it is likely to retain that
status for sometime as the lowest level on the tree. Ideally, we'd know the SNP
was capped at this 15-20% diversity level because an immediately upstream SNP
with low diversity pretty much assures the permanent terminal SNP really is
young.
L705.2/L706.2, L226, L193, L554, S190, L371 and maybe M222 might be good candidates. What do you think?

Some day, we might have a hundred or so of these young terminal SNPs, maybe
more.

I'm not trying to build an SNP predictor. I actually think those can be quite misleading. On the other hand, if someone has a nice match to a far downstream SNP, I'm not sure (for Y DNA purposes) if they need to buy a full Geno 2.0 package. It it's up to the individual to weight the prices and risks.

I don't think we have too many reliable "permanent" terminal SNPs but this will give you an idea of where I'm trying to go.

https://dl.dropbox.com/u/17907527/R1bTerminalSNPRecommender.xlsm

This needs lots of work and probably a couple of the SNPs in there have no right to be thought of as permanently terminal, but some do.  I need to back this off to an earlier version of Excel so it'll be more compatible but the idea is just copy your haplotype row (the whole row) in from an FTDNA project screen and Paste Special / Values into the yellow area of the spreadsheet. You can sort by GD with the "modals" in the spreadsheet. If you come up within a GD of 7/8 or less have a 100% signature match, or nearly so, you might consider the stand-alone SNP test.

I do foresee the day (maybe two years from now) where we'll have a couple of hundred of reliable terminal SNPs for R1b with more coming.

[Mikewww]

I've updated the R1b-L21 Haplotypes spreadsheet under the Links at the Yahoo Group. It's the same link if you've bookmarked it.

I've also updated the L21 descendancy tree to reflect Z2185's insertion under Z253 but above L1066.
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg

Wow, I can see us hitting the Z with 5 digit mark. When do we hit Z10000?

[Mikewww]

I've updated the R1b-L21 Haplotypes spreadsheet under the Links at the Yahoo Group. It's the same dropbox link if you've bookmarked it. This reflects the position of L563 under DF41. However, please note that group home page is now:
http://groups.yahoo.com/group/R1b-L21-Project/

I've also updated the L21 descendancy tree
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg

Here is the Clade table that the graphic tree describes:

L21+  >>> R1b-L21;  * = DF13-  ** = DF13- DF63-,  Equivalents: S145,M529  R1b1a2a1a1b3
DF13+  >>> R1b-L21>DF13;  * = L513- DF21- DF49- Z253- Z255- DF41-  ** = L513- DF21- DF49- Z253- Z255- DF41- L144- L371- L555- L96-,  Equivalents: S521  R1b1a2a1a1b3a
L513+  >>> R1b-L21>DF13>L513;  * = L193- L706.2-  ** = L193- L706.2- L9- L10- L577- L908- L909- L69-,  Equivalents: DF1,S215,Z249,Z250  R1b1a2a1a1b3a2
DF1+  >>> R1b-L21>DF13>L513;  * = L193- L706.2-  ** = L193- L706.2- L9- L10- L577- L908- L909- L69-,  Equivalents: L513,S215,Z249,Z250  R1b1a2a1a1b3a2
L193+  >>> R1b-L21>DF13>L513>L193; Terminal,  Equivalents: S176  R1b1a2a1a1b3a2b
L706.2+  >>> R1b-L21>DF13>L513>L706.2;  * = L705.2-  ** = n/a  R1b1a2a1a1b3a2c
L705.2+  >>> R1b-L21>DF13>L513>L706.2>L705.2; Terminal  R1b1a2a1a1b3b3a
L705+  >>> R1b-L21>DF13>L513>L706.2>L705.2; Terminal  R1b1a2a1a1b3b3a
L69.5+  >>> R1b-L21>DF13>L513>L69.5;  * = P66-  ** = n/a  
P66+  >>> R1b-L21>DF13>L513>L69.5>P66; Terminal,  Equivalents: P66_1,P66_2,P66_3  R1b1a2a1a1b3a2a
DF21+  >>> R1b-L21>DF13>DF21;  * = P314.2- Z246-  ** = P314.2- Z246- L720- S424-,  Equivalents: S192  R1b1a2a1a1b3a7
P314.2+  >>> R1b-L21>DF13>DF21>P314;  * = L362-  ** = n/a,  Equivalents: S220.2  R1b1a2a1a1b3a7a
L362+  >>> R1b-L21>DF13>DF21>P314>L362; Terminal  R1b1a2a1a1b3a7a1
Z246+  >>> R1b-L21>DF13>DF21>Z246;  * = DF25-  ** = n/a,  Equivalents: S280  R1b1a2a1a1b3a7b
DF25+  >>> R1b-L21>DF13>DF21>Z246>DF25;  * = DF5-  ** = n/a,  Equivalents: S253  R1b1a2a1a1b3a7b1
DF5+  >>> R1b-L21>DF13>DF21>Z246>DF25>DF5;  * = L627- L658-  ** = n/a,  Equivalents: S191  R1b1a2a1a1b3a7b1a
L627+  >>> R1b-L21>DF13>DF21>Z246>DF25>DF5>L627;  * = L626-  ** = n/a  R1b1a2a1a1b3a7b1a1
L626+  >>> R1b-L21>DF13>DF21>Z246>DF25>DF5>L627>L626;  * = L625-  ** = n/a  
L625+  >>> R1b-L21>DF13>DF21>Z246>DF25>DF5>L627>L626>L625; Terminal  
L658+  >>> R1b-L21>DF13>DF21>Z246>DF25>DF5>L658; Terminal  R1b1a2a1a1b3a7b1a2
L720+  >>> R1b-L21>DF13>DF21>L720; Terminal,  Equivalents: S299  R1b1a2a1a1b3a7c
S424+  >>> R1b-L21>DF13>DF21>S424;  * = S190-  ** = n/a,  Equivalents: S426  R1b1a2a1a1b3a7d
S190+  >>> R1b-L21>DF13>DF21>S424>S190; Terminal,  Equivalents: S308,S309,S427  R1b1a2a1a1b3a7d1
DF49+  >>> R1b-L21>DF13>DF49;  * = DF23-  ** = n/a,  Equivalents: S523  R1b1a2a1a1b3a1
DF23+  >>> R1b-L21>DF13>DF49>DF23;  * = M222-  ** = n/a  R1b1a2a1a1b3a1a
M222+  >>> R1b-L21>DF13>DF49>DF23>M222; Terminal,  Equivalents: Page84,USP9Y+3636  R1b1a2a1a1b3a1a1
Z253+  >>> R1b-L21>DF13>Z253;  * = L226-  ** = L226- Z2185- L554-,  Equivalents: S218  R1b1a2a1a1b3a6
L226+  >>> R1b-L21>DF13>Z253>L226; Terminal,  Equivalents: S168  R1b1a2a1a1b3a6a
Z2185+  >>> R1b-L21>DF13>Z253>Z2185;  * = L1066-  ** = n/a  
L1066+  >>> R1b-L21>DF13>Z253>Z2185>L1066;  * = L895-  ** = n/a  R1b1a2a1a1b3a6c
L895+  >>> R1b-L21>DF13>Z253>Z2185>L1066>L895; Terminal,  Equivalents: L894  
L554+  >>> R1b-L21>DF13>Z253>L554; Terminal  R1b1a2a1a1b3a6b
Z255+  >>> R1b-L21>DF13>Z255;  * = L159.2-  ** = n/a,  Equivalents: S219  R1b1a2a1a1b3a5
L159.2+  >>> R1b-L21>DF13>Z255>L159; Terminal,  Equivalents: S169.2  R1b1a2a1a1b3a5a
DF41+  >>> R1b-L21>DF13>DF41;  * = L744-  ** = L744- L563-,  Equivalents: S524  R1b1a2a1a1b3a9
L744+  >>> R1b-L21>DF13>DF41>L744;  * = L745-  ** = n/a,  Equivalents: S388,L746>S310  R1b1a2a1a1b3a9a
L745+  >>> R1b-L21>DF13>DF41>L744>L745; Terminal,  Equivalents: S463  R1b1a2a1a1b3a9a1
L563+  >>> R1b-L21>DF13>DF41>L563; Terminal  
L144+  >>> R1b-L21>DF13>L144; Terminal,  Equivalents: S175,L195  R1b1a2a1a1b3a4
L371+  >>> R1b-L21>DF13>L371; Terminal,  Equivalents: S300  R1b1a2a1a1b3a8
L555+  >>> R1b-L21>DF13>L555; Terminal,  Equivalents: S393  R1b1a2a1a1b3a10
L96+  >>> R1b-L21>DF13>L96; Terminal  R1b1a2a1a1b3a3
L743+  >>> R1b-L21>DF13*>L743; Terminal  
DF63+  >>> R1b-L21>DF63; Terminal,  Equivalents: S522  R1b1a2a1a1b3b
L69+ >>> Unpositioned under L21
L159.?+ >>> Unpositioned under L21
L130+ >>> Unpositioned under DF13
L152+ >>> Unpositioned under DF13
L192.1+ >>> Unpositioned under L513
L195+ >>> Unpositioned under DF13
L319.1+ >>> Unpositioned under L21
L302+ >>> Unpositioned under DF49
L526+ >>> Unpositioned under DF13
L557+ >>> Unpositioned under DF13
L561+ >>> Unpositioned under DF13
L564+ >>> Unpositioned under DF13
L580+ >>> Unpositioned under DF13
L583+ >>> Unpositioned under DF13
L643+ >>> Unpositioned under DF13
L679+ >>> Unpositioned under DF13
L9+ >>> Unpositioned under L513
L10+ >>> Unpositioned under L513
L577+ >>> Unpositioned under L513
L908+ >>> Unpositioned under L513
L909+ >>> Unpositioned under L513
Z248+ >>> Unpositioned under DF25
L641+ >>> Unpositioned under DF21
L642+ >>> Unpositioned under DF21
S424+ >>> Unpositioned under DF21
S426+ >>> Unpositioned under DF21
L894+ >>> Unpositioned under Z253
DF73+ >>> Unpositioned under Z253
L1308+ >>> Unpositioned under Z253
Z2183+ >>> Unpositioned under Z2185
Z2184+ >>> Unpositioned under Z253
L746+ >>> Unpositioned under DF41
zzM37+ >>> Unpositioned under L21
Z245+ >>> Unpositioned under L21
L459+ >>> Unpositioned under L21

[Mikewww]

I've updated the spreadsheet and tree chart. L563 is now positioned under DF41.

We've got over 1200 111 STR confirmed and suspected haplotypes to go with all of the shorter ones.

I've updated the R1b-L21 Haplotypes spreadsheet under the Links at the Yahoo Group. It's the same dropbox link if you've bookmarked it. This reflects the position of L563 under DF41. However, please note that group home page is now:
http://groups.yahoo.com/group/R1b-L21-Project/

I've also updated the L21 descendancy tree
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg

....

[Mark Jost]

I preloaded over 6200 L21 67 markers into the TMRCA estimator for those who may not want to cut and paste the dataset from MikeW's 10312012 spreadsheet. I also have taken the 111 Marker and filled in the missing column data and stored it into the the Backup sheet which can be copied at any time back in to either CladeA and B to check out what how Extended haplotypes preform like.

Highspeed internet and a fast computer recommend for Filtering and interclade calculations.

https://docs.google.com/open?id=0By9Y3jb2fORNSU9Lbi1rYXl4NUU
 
MJost

[Mikewww]

I've update this file with large number of folks from Campbell, Wilson and Doherty projects.... also a few more Kingston people.

I've updated the R1b-L21 Haplotypes spreadsheet under the Links at the Yahoo Group. It's the same dropbox link if you've bookmarked it. This reflects the position of L563 under DF41. However, please note that group home page is now:
http://groups.yahoo.com/group/R1b-L21-Project/

I've also updated the L21 descendancy tree
https://dl.dropbox.com/u/17907527/R1b-L21_Descendancy_Tree.jpg