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Author Topic: R1b-P312/S116*, DF19, L238, etc. - keeping the phylogenetic tree updated  (Read 1241 times)
Mike Walsh
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« on: July 31, 2012, 04:14:02 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 P312.
http://ytree.ftdna.com/index.php?name=Draft&parent=65388520

Below is a representation of what I use in the P312xL21 Haplotype spreadsheet for P312* and DF19. Do I have it right?  Am I missing SNPs? I am representing all of L21, DF27 and U152 elsewhere. 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.

P312+  >>> R-P312; * = U152- L21- DF27-  ** = U152- L21- DF27- DF19- L617- L238-

M65+  >>> R-M65; Terminal

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

L21+  >>> R-L21; * = DF13-  ** = DF13- DF63-

DF27+  >>> R-DF27; * = Z196-  ** = Z196- L617- L86.2-

DF19+  >>> R-DF19; * = L644-  ** = L644- Z302-
L644+  >>> R-DF19/L644; Terminal
Z302+  >>> R-DF19/Z302; Terminal

L238+  >>> R-L238; Terminal

L459+  >>> R-L459; * = L21-
Z245+ >>> Unpositioned under P312

L1063+ >>> Unpositioned under P312
L1099+ >>> Unpositioned under P312
L1200+ >>> Unpositioned under P312
L147.3+ >>> Unpositioned under P312
L194+ >>> Unpositioned under P312
L253+ >>> Unpositioned under P312
Z268+ >>> Unpositioned under P312
Z274+ >>> Unpositioned under P312
L289+ >>> Unpositioned under P312
Z294+ >>> Unpositioned under P312
L484+ >>> Unpositioned under P312
L719+ >>> Unpositioned under P312
L881+ >>> Unpositioned under P312


In my opinion, you are not P312* unless you've tested U152-, L21- and DF27-, at a minimum.
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razyn
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« Reply #1 on: July 31, 2012, 08:33:42 PM »


Z245+ >>> Unpositioned under P312

L1063+ >>> Unpositioned under P312
L1099+ >>> Unpositioned under P312
L1200+ >>> Unpositioned under P312
L147.3+ >>> Unpositioned under P312
L194+ >>> Unpositioned under P312
L253+ >>> Unpositioned under P312
Z268+ >>> Unpositioned under P312
Z274+ >>> Unpositioned under P312
L289+ >>> Unpositioned under P312
Z294+ >>> Unpositioned under P312
L484+ >>> Unpositioned under P312
L719+ >>> Unpositioned under P312
L881+ >>> Unpositioned under P312 [/font]

I disagree with this call for L484.  David Reynolds disagrees with me; and obviously he has more street cred here than I do -- but on the other hand I have L484+, so I care more.

Anyway, look at the R-P312 and Subclades project results, p. 2, group Pabd, and tell me what you think.  That represents only four distinct families, maybe ten surnames; but it's not a "family SNP;" we have respectable variance, perhaps more than M153 does; and we're all elsewhere under Z220 (about six levels down from P312, to wit: DF27, Z196, Z274, Z209, Z220, L484.x).  IMO that's on the same level as Z216.  And since we haven't yet found anybody with terminal Z216+, the subclade or node to compare our L484 with is Z278.

If I'm correct, this belongs in your similar DF27 thread, not here.  (And btw there's at least one other stable version of L484, in Hg I-M223, P78.)  I don't know if Moscia's version of L484 is stable; so far it's "neither of the above," but it is in fact in the P312 family.
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Mike Walsh
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« Reply #2 on: July 31, 2012, 11:22:15 PM »

...
L484+ >>> Unpositioned under P312
 [/font]

I disagree with this call for L484.  David Reynolds disagrees with me; and obviously he has more street cred here than I do -- but on the other hand I have L484+, so I care more.

Anyway, look at the R-P312 and Subclades project results, p. 2, group Pabd, and tell me what you think.  That represents only four distinct families, maybe ten surnames; but it's not a "family SNP;" we have respectable variance, perhaps more than M153 does; and we're all elsewhere under Z220 (about six levels down from P312, to wit: DF27, Z196, Z274, Z209, Z220, L484.x).  IMO that's on the same level as Z216.  And since we haven't yet found anybody with terminal Z216+, the subclade or node to compare our L484 with is Z278.

If I'm correct, this belongs in your similar DF27 thread, not here.  (And btw there's at least one other stable version of L484, in Hg I-M223, P78.)  I don't know if Moscia's version of L484 is stable; so far it's "neither of the above," but it is in fact in the P312 family.

I'm not really making a call on L484. That's what I meant by "unpositioned." I don't know where it fits. It sounds there is some disagreement. How many versions of L484 are there? More than one under P312?

The "under P312" just means somewhere under P312 which includes DF27. As far as the spreadsheet goes, that means if a guy is P312 of any variety, including DF27, his L484- or L484+ result will be in the relevant Downstream SNPs column.
« Last Edit: July 31, 2012, 11:24:18 PM by Mikewww » Logged

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razyn
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« Reply #3 on: August 01, 2012, 01:17:32 AM »

I'm not really making a call on L484. That's what I meant by "unpositioned."

What did you mean by "Do I have it right?"  I'm just saying, we have this "pseudo N/S cluster" identified from STRs about 16 months ago by Larry Mayka; thoroughly tested (as soon as FTDNA made the tests available); and all tested examples so far found to be positive for DF27, Z196, Z209, Z220, and L484 -- and negative for Z216.  How could that be any more positioned

There are those who consider the variable nature of L484 unstable; but our cluster has a TMRCA of about 1500 years, so it (the one in Z220) isn't all that unstable.  You might think it's younger than that, and Zhivotovsky might think it's older, but it clearly doesn't shed its L484 skin every generation or two.  We shared this SNP before our diverging lines settled in Prussia, England and France... unless we migrated from one of those to the other two.

Quote
I don't know where it fits. It sounds there is some disagreement. How many versions of L484 are there? More than one under P312?

Two under R-P312, one under I-M223, and two others in E and T, I think.  The fact that it doesn't have decimal points assigned to the two tested, and thus demonstrably stable, examples is a matter of bookkeeping, not testing.  Also, there may be a better name for L484 than "SNP."  Hans van Vliet has a bunch of those under his hat, but I don't.  Binary event on the Y chromosome that makes visible, heritable branches on the phylogenetic tree, or whatever.
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Mike Walsh
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« Reply #4 on: August 01, 2012, 12:56:06 PM »

I'm not really making a call on L484. That's what I meant by "unpositioned."

What did you mean by "Do I have it right?"  I'm just saying, we have this "pseudo N/S cluster" identified from STRs about 16 months ago by Larry Mayka; thoroughly tested (as soon as FTDNA made the tests available); and all tested examples so far found to be positive for DF27, Z196, Z209, Z220, and L484 -- and negative for Z216.  How could that be any more positioned?  

There are those who consider the variable nature of L484 unstable; but our cluster has a TMRCA of about 1500 years, so it (the one in Z220) isn't all that unstable.  You might think it's younger than that, and Zhivotovsky might think it's older, but it clearly doesn't shed its L484 skin every generation or two.  We shared this SNP before our diverging lines settled in Prussia, England and France... unless we migrated from one of those to the other two.

Quote
I don't know where it fits. It sounds there is some disagreement. How many versions of L484 are there? More than one under P312?

Two under R-P312, one under I-M223, and two others in E and T, I think.  The fact that it doesn't have decimal points assigned to the two tested, and thus demonstrably stable, examples is a matter of bookkeeping, not testing.  Also, there may be a better name for L484 than "SNP."  Hans van Vliet has a bunch of those under his hat, but I don't.  Binary event on the Y chromosome that makes visible, heritable branches on the phylogenetic tree, or whatever.

Rayzn, I have no bone to pick one way or another on this. I just want to treat L484 consistently with other SNPs. I'm not trying to supplant ISOGG and generally just follow what they do. I do make exceptions when it is clear that an SNP fits somewhere prior to all of the FTDNA lab validation. That's basically saying I trust Richard Rocca, Greg Magoon, etc. if they feel certain of where an SNP fits.

By "have it right?" in this case what I'm asking is L484 properly classified as an unpositioned SNP?  I see your case is that this instance of L484 is well positioned downstream of the Z196/Z209/Z220 branch of DF27 and parallel to Z216.

I'm fine with that, so the only remaining question is this a very stable Unique Event Polymorphism (UEP)? I think the concept of a UEP is somewhat false, from a technical standpoint, but it is important to know if something is very stable.

I guess you think it is. That's reasonable.  Do we have an opposing argument to this? I do have a concern if L484 is found in two other instances within P312. That forces me to have manual adjustments to the haplogroup labeling, although it clearly makes sense to create a new "variety" under Z220 that has L484+.  What are the biological characteristics of L484? Is it known to be unstable or should it be considered stable?  Is it a UEP marker in the Hg I-M223 Y DNA tree?
« Last Edit: August 01, 2012, 05:35:27 PM by Mikewww » Logged

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razyn
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« Reply #5 on: August 01, 2012, 01:47:53 PM »

I do have a concern if L484 is found in two other instances within P312.

I think it's been found three times elsewhere in P312 (probably, elsewhere in DF27, though that test will only be batched tonight) -- and all three of them may be Ben Moscia.  Once in his WTY, once at 23andMe as parsed by Adriano Squecco, and finally by an L484 SNP test at FTDNA.  Then he tested Z220 and it wasn't derived, so he's not in the pseudo N/S cluster with me, Hall and Reno (and the Richerts, who haven't tested L484 yet).

I'm not positive that the L484 "discovery" was Ben's WTY, but he did have that test, and I believe the L prefix means it was discovered in the FTDNA lab.  (And in several haplogroups, but your question is about R-P312.)

With regard to SNPs, UEPs, and I believe there are some binary events that are neither (insertions and deletions), a rose by any other name, etc.  I'm idly interested in seeing the name of my SNP/UEP in lights (on the ISOGG tree), but more actively interested in its being part of TMRCA variance-based calculations, yours and other people's.  I think you could compare one example from each of those four families, and get a pretty good L484.x node to compare (interclade) with Z278.  And that could be useful e.g. for refining the dates, geography, and directionality of several "Iberian" genetic events.
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Mike Walsh
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« Reply #6 on: August 04, 2012, 11:50:17 AM »

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

L881+ >>> Unpositioned under P312

We've had some L881+ results come in. Although its not quite there, I think odds are high this will break through the private status barrier.

f26020    Howland    P312+ L881+ L875+ M65- U152- L21-
f37812    De Halsal  P312+ L881+ M65- U152- L21-
f221355   Jester     P312+ L881+
fH1295    Sutton     P312+ L881+

What do we know about position L881 and L875?  Have there been control sample or other WTY or HG1000 project results that help us position this?

f27045    White    L644+ L1200- L881-
f93184    Ranney    DF19+ L1063+ Z302- L881-
f51865    McFarlane P312+ M65- U152- L21- DF27- DF19- L238- L459- Z245- L881- Z229-
f90959    Bowker    DF27+ Z196- L617- Z225- L147.3- L719- L881- L1231- Z229-


From the above it is still possible that L881 is descendant of DF27, correct? since we don't know of a L881+ DF27- person.  Does anyone have a status for DF27 in L881+ people or L881 in L238+ people?

« Last Edit: August 04, 2012, 11:52:34 AM by Mikewww » Logged

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« Reply #7 on: August 04, 2012, 12:00:33 PM »

I do have a concern if L484 is found in two other instances within P312.

I think it's been found three times elsewhere in P312 (probably, elsewhere in DF27, though that test will only be batched tonight) -- and all three of them may be Ben Moscia.  Once in his WTY, once at 23andMe as parsed by Adriano Squecco, and finally by an L484 SNP test at FTDNA.  Then he tested Z220 and it wasn't derived, so he's not in the pseudo N/S cluster with me, Hall and Reno (and the Richerts, who haven't tested L484 yet).

I'm not positive that the L484 "discovery" was Ben's WTY, but he did have that test, and I believe the L prefix means it was discovered in the FTDNA lab.  (And in several haplogroups, but your question is about R-P312.)

With regard to SNPs, UEPs, and I believe there are some binary events that are neither (insertions and deletions), a rose by any other name, etc.  I'm idly interested in seeing the name of my SNP/UEP in lights (on the ISOGG tree), but more actively interested in its being part of TMRCA variance-based calculations, yours and other people's.  I think you could compare one example from each of those four families, and get a pretty good L484.x node to compare (interclade) with Z278.  And that could be useful e.g. for refining the dates, geography, and directionality of several "Iberian" genetic events.

Rayzn, can you get an instance number from Thomas Krahn on your version of L484? In other words, your version is the nth discovered occurrence. If you get me that, even if it will never hit official Y DNA trees, I'll manually insert it on the spreadsheet for the Z220+ guys who are L484+ so that we can keep track of it separately.
« Last Edit: August 04, 2012, 12:01:09 PM by Mikewww » Logged

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df.reynolds
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« Reply #8 on: August 04, 2012, 01:41:56 PM »


Z245+ >>> Unpositioned under P312

L1063+ >>> Unpositioned under P312
L1099+ >>> Unpositioned under P312
L1200+ >>> Unpositioned under P312
L147.3+ >>> Unpositioned under P312
L194+ >>> Unpositioned under P312
L253+ >>> Unpositioned under P312
Z268+ >>> Unpositioned under P312
Z274+ >>> Unpositioned under P312
L289+ >>> Unpositioned under P312
Z294+ >>> Unpositioned under P312
L484+ >>> Unpositioned under P312
L719+ >>> Unpositioned under P312
L881+ >>> Unpositioned under P312 [/font]

I disagree with this call for L484.  David Reynolds disagrees with me; and obviously he has more street cred here than I do -- but on the other hand I have L484+, so I care more.

Anyway, look at the R-P312 and Subclades project results, p. 2, group Pabd, and tell me what you think.  That represents only four distinct families, maybe ten surnames; but it's not a "family SNP;" we have respectable variance, perhaps more than M153 does; and we're all elsewhere under Z220 (about six levels down from P312, to wit: DF27, Z196, Z274, Z209, Z220, L484.x).  IMO that's on the same level as Z216.  And since we haven't yet found anybody with terminal Z216+, the subclade or node to compare our L484 with is Z278.

If I'm correct, this belongs in your similar DF27 thread, not here.  (And btw there's at least one other stable version of L484, in Hg I-M223, P78.)  I don't know if Moscia's version of L484 is stable; so far it's "neither of the above," but it is in fact in the P312 family.

Dick,

I wouldn't go so far as to say we disagree, rather that I encourage caution when it comes to any "flippy" SNP (as Thomas refers to them), and believe that they require more investigation than a "normal" SNP does.

In the case of L484, Thomas' db reports 16 derived out of 28 tests. Taking a very quick look, I can see 4 of the 16 in R-P312 and 8 of the 16 in Hg I. Of the 12 ancestral, I see 5 in R-P312. Personally, as a disinterested outsider, I would want to see more testing done before forming an opinion as to the stability of this particular state change for L484.

But if you are wanting to get L484 onto the ISOGG Hg-R tree, it isn't my opinion that matters, anyway. You should be talking to Vince Tilroe, who is the current coordinator for R-P312. :)

Regards,
david
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razyn
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« Reply #9 on: August 04, 2012, 02:20:47 PM »

Rayzn, can you get an instance number from Thomas Krahn on your version of L484?

I have just written to ask him for that.  And I see that while I was doing so, Dave Reynolds has chimed in.  Things seem to be moving along, although I'm not sure who does and doesn't work on a weekend.  Meanwhile, we have a couple of grandsons descending on us Monday, and I'll be doing my thing as patriarch of a Y-DNA lineage for a short while.  Dave thinks I may need to contact Vince Tilroe; and I suspect Ken Nordtvedt has some interest also (because he's been the propagandist for the largely successful testing of I-M223 project members for L484).

Btw of the sixteen derived results for L484 tests in Gbrowse, twelve are visible in the SNP Results display of the I-M223 project.  The other four are R-P312: three under Z220+ (Hulan, Hall, and Reno/Raynaud); and the fourth is Moscia, who has just tested Z220-, and has a DF27 test in progress.  Five other Z209/Z220 guys tested L484- (on the basis of some enthusiasm expressed on forums, mainly by Hans van Vliet and me, that turned out to be a little optimistic but not wholly misplaced).  Their results at least give us some pretty clear boundary markers for off-modals that line up with L484+ in this haplogroup (the North/South Cluster of yore -- this being a field in which year before last can be perceived as "yore").

Onward and upward, trail blazers.
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Mike Walsh
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« Reply #10 on: August 06, 2012, 09:17:09 AM »

Rayzn, can you get an instance number from Thomas Krahn on your version of L484?

I have just written to ask him for that.  And I see that while I was doing so, Dave Reynolds has chimed in.  Things seem to be moving along, although I'm not sure who does and doesn't work on a weekend.  Meanwhile, we have a couple of grandsons descending on us Monday, and I'll be doing my thing as patriarch of a Y-DNA lineage for a short while.  Dave thinks I may need to contact Vince Tilroe; and I suspect Ken Nordtvedt has some interest also (because he's been the propagandist for the largely successful testing of I-M223 project members for L484).

Btw of the sixteen derived results for L484 tests in Gbrowse, twelve are visible in the SNP Results display of the I-M223 project.  The other four are R-P312: three under Z220+ (Hulan, Hall, and Reno/Raynaud); and the fourth is Moscia, who has just tested Z220-, and has a DF27 test in progress.  Five other Z209/Z220 guys tested L484- (on the basis of some enthusiasm expressed on forums, mainly by Hans van Vliet and me, that turned out to be a little optimistic but not wholly misplaced).  Their results at least give us some pretty clear boundary markers for off-modals that line up with L484+ in this haplogroup (the North/South Cluster of yore -- this being a field in which year before last can be perceived as "yore").

Onward and upward, trail blazers.
My use of L484 in the spreadsheet has nothing to do with ISOGG or FTDNA's uses... and doesn't need to although I want don't want to show something totally in conflict. If you can give me an instance for L484+ under Z220+, as long as it is consistent there I'll use it to mark people in the spreadsheet.  I have to do this manually though, since it can be counted on (in and of itself) for placement purposes within P312.

It looks like L484.xforNS is a brother of Z216, correct?
« Last Edit: August 06, 2012, 09:19:23 AM by Mikewww » Logged

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« Reply #11 on: August 06, 2012, 10:25:03 AM »

If you can give me an instance for L484+ under Z220+, as long as it is consistent there I'll use it to mark people in the spreadsheet.  I have to do this manually though, since it can be counted on (in and of itself) for placement purposes within P312.

It looks like L484.xforNS is a brother of Z216, correct?

I'll give you the instance number for it if Thomas answers my email.  I expect he gets a lot of analogous requests.

If anybody has tested Z216+ and Z278-, yes, that would be an apparent brother to our L484+ and Z216- guys.  My impression is that nobody's terminal SNP is Z216, yet.  (It's also my impression that nobody's terminal SNP is actually Z209, they just haven't all tested for Z220.)
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« Reply #12 on: August 06, 2012, 11:33:22 PM »

Here is a copy of all the R1b-P312xL21 haplotypes I have. The 111 STR haplotypes are included in the ExtHts tab.
https://dl.dropbox.com/u/17907527/R1b-P312xL21_Haplotypes.zip

The Clades tab shows the hierarchy I use for deriving an SNP path based haplogroup label. I've pasted it below.

P312+  >>> R-P312; * = U152- L21- DF27-  ** = U152- L21- DF27- DF19- L617- L238-

M65+  >>> R-M65; Terminal

DF19+  >>> R-DF19; * = L644-  ** = L644- Z302-
L644+  >>> R-DF19/L644; Terminal
Z302+  >>> R-DF19/Z302; Terminal

L238+  >>> R-L238; Terminal

L459+  >>> R-L459; * = L21-

Z245+ >>> Unpositioned under P312
L1063+ >>> Unpositioned under P312
L1099+ >>> Unpositioned under P312
L1200+ >>> Unpositioned under P312
L147.3+ >>> Unpositioned under P312
L194+ >>> Unpositioned under P312
L253+ >>> Unpositioned under P312
Z268+ >>> Unpositioned under P312
Z274+ >>> Unpositioned under P312
L289+ >>> Unpositioned under P312
Z294+ >>> Unpositioned under P312
L484+ >>> Unpositioned under P312
L719+ >>> Unpositioned under P312
L881+ >>> Unpositioned under P312
L875+ >>> Unpositioned under P312


An R1b-L21 file and R1b-U106 version will be forthcoming. There is a lot of great data here for interclade analysis, geographic analysis, etc.
« Last Edit: August 06, 2012, 11:34:09 PM by Mikewww » Logged

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