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TigerMW
04-10-2015, 02:53 PM
It's been over a year since I tried to maintain this, given all of the Next Gen Sequencing results that are discovering branching, but I've taken another cut at this.

http://tinyurl.com/R1b-Tree-Chart

You should be able to open this with any .pdf viewer. You probably will want to use the zoom and pan features.

This is not intended to be a full tree. that would be impossible without a wall board or mural. To give you an idea here is a draft L21 tree. There are about 500 branches on it now and this is just one small piece of R1b.
http://tinyurl.com/R1b-L21-Tree-Chart

I expect that there will be feedback on which branches are important or large enough to be included on this kind of simplified and high level tree chart. Please post feedback or corrections here. If there aren't any errors I'd be dog goned surprised.

The bulk of the people that are testing are downstream of P311 so that is where I'm showing a little more of the edges of the tree. In effect this "big picture" look is the early branching plus the most numbers branches.

This is all in support of the R1b Gateway project. We have almost 7000 members now.

https://www.familytreedna.com/public/R1b

David Mc
04-10-2015, 07:12 PM
Wonderful work, Mike. Thank you very much! I am assuming your "Western Atlantic" designation refers to present locations more than assumed origins?

TigerMW
04-10-2015, 10:18 PM
Wonderful work, Mike. Thank you very much! I am assuming your "Western Atlantic" designation refers to present locations more than assumed origins?
Hi, David. Thanks.

I used some legacy terminology on the chart because sometimes that comes up. In this case, we know that FTDNA uses "WAMH" or the Western Atlantic Modal Haplotype. My intent was to indicate that STR set generally overlaps people downstream of P311.

This draft tree chart is created for the R1b project. In that project I try to explain a few things like what WAMH is. See:
https://www.familytreedna.com/groups/r-1b/about/background
https://www.familytreedna.com/groups/r-1b/about/results

I try to list the R1b specific scientific papers on the about-results page.

R.Rocca
04-13-2015, 01:14 PM
It's been over a year since I tried to maintain this, given all of the Next Gen Sequencing results that are discovering branching, but I've taken another cut at this.

http://tinyurl.com/R1b-Tree-Chart

You should be able to open this with any .pdf viewer. You probably will want to use the zoom and pan features.

This is not intended to be a full tree. that would be impossible without a wall board or mural. To give you an idea here is a draft L21 tree. There are about 500 branches on it now and this is just one small piece of R1b.
http://tinyurl.com/R1b-L21-Tree-Chart

I expect that there will be feedback on which branches are important or large enough to be included on this kind of simplified and high level tree chart. Please post feedback or corrections here. If there aren't any errors I'd be dog goned surprised.

The bulk of the people that are testing are downstream of P311 so that is where I'm showing a little more of the edges of the tree. In effect this "big picture" look is the early branching plus the most numbers branches.

This is all in support of the R1b Gateway project. We have almost 7000 members now.

https://www.familytreedna.com/public/R1b

@mike, as always, you can find the latest U152 tree in the project results page: https://www.familytreedna.com/groups/r-1b-u152/about/results

The surname clusters are documented all the way on the right-most colum and can be ignored.

TigerMW
04-13-2015, 02:05 PM
@mike, as always, you can find the latest U152 tree in the project results page: https://www.familytreedna.com/groups/r-1b-u152/about/results

The surname clusters are documented all the way on the right-most colum and can be ignored.

Thanks, yes, that is what I looked at, primarily your "U152 and Subclades Phylogenetic Tree". What does "Floating SNP" mean?

What's the status for SNP names on some of those? For instance, "6628883(T/C)" and the block associated with it? I could not find anything in YBrowse. This is a little different than what I'm use to. In the world of L21 I'm use to having FGC, YSEQ and Yfull almost simultaneously naming these things and sometimes FTDNA too. It's craziness in synonyms.

I'm trying to show major and famous subclades even if they are downstream a couple of steps, in some cases. For instance, I've added M222 and SRY2627 and added a crooked connector line to indicate there were multiple steps. Am I missing something in U152 that everyone will ask "where is it?"

http://tinyurl.com/R1b-M343-Tree-Chart

R.Rocca
04-13-2015, 03:12 PM
Thanks, yes, that is what I looked at, primarily your "U152 and Subclades Phylogenetic Tree". What does "Floating SNP" mean?

What's the status for SNP names on some of those? For instance, "6628883(T/C)" and the block associated with it? I could not find anything in YBrowse. This is a little different than what I'm use to. In the world of L21 I'm use to having FGC, YSEQ and Yfull almost simultaneously naming these things and sometimes FTDNA too. It's craziness in synonyms.

I'm trying to show major and famous subclades even if they are downstream a couple of steps, in some cases. For instance, I've added M222 and SRY2627 and added a crooked connector line to indicate there were multiple steps. Am I missing something in U152 that everyone will ask "where is it?"

http://tinyurl.com/R1b-M343-Tree-Chart

As you know, 90% of novel SNPs are neither named nor available via Sanger sequencing. So, many do not yet have SNP aliases and are not on YBrowse. In the case above, this is a NGS found SNP at Y-chromosome position 6628883 that has an ancestral value of "T" and a derived state of "C".

Cofgene
04-14-2015, 01:16 AM
Since we want to emphasize the higher volume branches for U106 I would suggest
1) remove A2150, L6, and S18632 from the top level under U106. They are very small minor stublets.
2) Under the Z18 branch down several levels is the major L257 group. A good number of lineages fork around L257
3) Under Z381-> Z156 the Z304 level splits into two major branches DF98 and DF96 (need to support those royal Wettin's)
4) For Z301->S1688 lets add the important U198 region under S1688
5) Under L48 it would be good to add L47 which splits to L44 and Z159. Then also add Z9-> Z30 which splits to Z1 and Z331->Z326 (8.5% of the U106er's are under Z331. Go nulls!)

https://app.box.com/s/afqsrrnvv2d51msqcz2o

Megalophias
04-14-2015, 01:37 AM
This is cool. So M335 *is* under L389?

Not putting B1 on there yet? I'm guessing there'll end up being quite a bit in South Asia but I could be wrong.

smal
04-14-2015, 08:15 AM
This is cool. So M335 *is* under L389?

There are no proofs that M335+ is L389+ too. Based on STRs the M335+ samples are clustered with the L278* samples.

TigerMW
04-14-2015, 11:37 AM
There are no proofs that M335+ is L389+ too. Based on STRs the M335+ samples are clustered with the L278* samples.
Are Vince Vizachero's conclusions wrong? The R-M343 (M73- M269-) project clearly diagrams M335 as parallel to P297 and downstream of L389/PF6531.
https://www.familytreedna.com/public/R1b1Asterisk/

The impression I had was that Vince and Thomas Krahn thought L389 was an equivalent a good replacement for P25. Do we have to go back to using P25? The branching apparently supports that M335 is parallel to P297 and they have a common ancestor after L278.

I think we also have Peter posting here. Perhaps he knows the rationale.

I see we've had this conversation before:
http://www.worldfamilies.net/forum/index.php?action=printpage;topic=11603.0

It seems crazy we are still talking about this. I see two M335+ guys in the project.
24282 Graf
156198 Burger

L389 is available on the Orders/Advanced Tests/SNP menu as Sanger Sequenced.

smal
04-14-2015, 01:00 PM
Are Vince Vizachero's conclusions wrong? The R-M343 (M73- M269-) project clearly diagrams M335 as parallel to P297 and downstream of L389/PF6531.
https://www.familytreedna.com/public/R1b1Asterisk/

Yes, I think it was wrong. This conclusion was made a long time ago. I am planning to change this diagram.

1. M343, M415, L278 (28 SNPs)

1.1. PH1165, F3599
1.1.1. M335 (most probable position based on STRs)

1.2 L754 (29 SNPs)

1.2.1 V88

1.2.2 L389
1.2.2.1 CTS5330
1.2.2.2 P297
1.2.2.2.1 M73
1.2.2.2.2 M269
Look at more detaled tree here (http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=75080&viewfull=1#post75080).

There are 29 SNPs (at least) in the L754 block. We could select one of them instead P25.

TigerMW
04-14-2015, 01:39 PM
Yes, I think it was wrong. This conclusion was made a long time ago. I am planning to change this diagram.

1. M343, M415, L278 (28 SNPs)

1.1. PH1165, F3599
1.1.1. M335 (most probable position based on STRs)

1.2 L754 (29 SNPs)

1.2.1 V88

1.2.2 L389
1.2.2.1 CTS5330
1.2.2.2 P297
1.2.2.2.1 M73
1.2.2.2.2 M269
Look at more detaled tree here (http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=75080&viewfull=1#post75080).

There are 29 SNPs (at least) in the L754 block. We could select one of them instead P25.

Can you reach Graf or Burger? Unless you think it is a waste of money. I'll donate to buy one of them an L389 test. What would make M335's position conclusive?

Should we test an M335 person for L754 or PH1165 or PF3599 first? I don't trust STR positioning, particularly this long ago.

M335 is an important subclade so I think we want it positioned firmly and I don't know when we will see an NGS test for it.

It is confirmed that L278 is downstream of M343, right? I think so as the ISOGG tree has it as downstream and I know Ray Banks wouldn't put it up with some evidence of an M343+ L278- person.

Here's what ISOGG has:
• • R1b M343/PF6242
• • • R1b* -
• • • R1b1 P25_1, P25_2, P25_3, L278, M415/PF6251
• • • • R1b1* -
• • • • R1b1a P297/PF6398, L320
• • • • • R1b1a* -
• • • • • R1b1a1 M73, M478
• • • • • R1b1a2 M269, etc.
• • • • R1b1b M335
• • • • R1b1c V88/PF6279

smal
04-14-2015, 02:45 PM
Can you reach Graf or Burger? Unless you think it is a waste of money. I'll donate to buy one of them an L389 test. What would make M335's position conclusive?


I can try. Their last logins were more then a year ago.


Should we test an M335 person for L754 or PH1165 or PF3599 first? I don't trust STR positioning, particularly this long ago.
It could be better, but we do not have L754 or PH1165 or PF3599 for an individual ordering yet.


It is confirmed that L278 is downstream of M343, right? I think so as the ISOGG tree has it as downstream and I know Ray Banks wouldn't put it up with some evidence of an M343+ L278- person.

Here's what ISOGG has:
R1b M343/PF6242
R1b* -
R1b1 P25_1, P25_2, P25_3, L278, M415/PF6251
R1b1* -
R1b1a P297/PF6398, L320
R1b1a* -
R1b1a1 M73, M478
R1b1a2 M269, etc.
R1b1b M335
R1b1c V88/PF6279

Unfortunately, there are no M343+ L278- samples in FTDNA projects. М343 > L278 split can be known from old articles. I think we need to re-examine it also.

Megalophias
04-14-2015, 03:41 PM
What is P25 for anyway? Is anyone really R1b* P25-? On FTDNA R1b* project I see one V88 who is P25- but everyone else is P25+. A back mutation? A typo?

CTS3063 seems to unite V88 and L389 against B1, but I don't see any M335 who have been tested for CTS3063 either. Would CTS3063 be equivalent to L754?

rms2
04-14-2015, 07:04 PM
I remember reading some years ago that P25 is unstable and subject to back mutation. There are SNPs on the same level (as far as we know they are, anyway) that are apparently more stable.

smal
04-14-2015, 07:16 PM
What is P25 for anyway? Is anyone really R1b* P25-? On FTDNA R1b* project I see one V88 who is P25- but everyone else is P25+. A back mutation? A typo?
This is the false negative result or back mutation. Look at here (http://yhrd.org/pages/resources/bad_ysnps) about P25 problems. In addition, there are several false positive M269 resuls in the M343 project too.


CTS3063 seems to unite V88 and L389 against B1, but I don't see any M335 who have been tested for CTS3063 either. Would CTS3063 be equivalent to L754?
Yes, CTS3063 is equivalent to L754.

newtoboard
04-14-2015, 10:41 PM
This is cool. So M335 *is* under L389?

Not putting B1 on there yet? I'm guessing there'll end up being quite a bit in South Asia but I could be wrong.

Is this the divergent lineage also found in Tajiks?

Megalophias
04-14-2015, 11:39 PM
Yeah, the defining SNP B1 is from Karmin et al 2015, which has the Tajik. The Bhutanese R1b* from Hallast et al 2014 shares 37/59 SNPs with him.

eta: but upon rechecking, B1 itself is NOT one of those shared SNPs, so we need a different defining SNP. PH155 maybe?

I don't know if the L389- M335- V88- Indian guys from FTDNA are really in the same clade, but maybe smal does.

Megalophias
04-15-2015, 08:59 PM
Whoops, bhu-0984 doesn't actually have B1. I guess PH1165 would do. It's just annoying not having any name for the clade.

If M335 does belong under PH1165 as smal suggests, then it would be part of the same clade.

So to avoid changing all the terminology as much as possible, something like this?

R1b-M343
-------R1b1-L754
--------------R1b1a'b-L389
--------------------R1b1a-P297
----------------------------R1b1a1-M73 (widespread but by far most frequent in Turko-Mongolic people)
----------------------------R1b1a2-M269 (ubiquitous)
--------------------R1b1b-CTS5330 (mostly Latin Americans so far?)
--------------R1b1c-V88 (Lake Chad region, S Egypt, North Africa, Sardinia, S Levant, Jews, rarely Iran)
-------R1b2-PH1165 (so far containing a Tajik, a Bhutanese, a Uyghur, and an Indian)
--------------R1b2a-M335? (if position is right - containing a couple of Germans, a Turk, and a Yunnanese Hui?)

ADW_1981
04-15-2015, 09:38 PM
R1b-V88 should also include Libyans, Sudanese, Jordan, Israel/Palestine, Saudi Arabians, and Yemeni Jews. I've actually never heard of any Iranians popping up R1b-V88 despite an old map which implied R1b took a route quite literally through the Zagros or southern Iran. Neither of which is likely.

Megalophias
04-16-2015, 07:35 PM
R1b-V88 should also include Libyans, Sudanese, Jordan, Israel/Palestine, Saudi Arabians, and Yemeni Jews. I've actually never heard of any Iranians popping up R1b-V88 despite an old map which implied R1b took a route quite literally through the Zagros or southern Iran. Neither of which is likely.

Myres et al 2011 found 1/150 Iranians was V88 (they re-genotyped the samples from Regueiro et al 2006 for Iran, I think). Bekada et al 2013 reports 2/566 V88, which I guess was pooled from somewhere but I can't access the supp info right now. On the other hand Grugni et al 2012 found 7/938 Iranians were R1b*-M343(xM73, M269), but none were V88.

So there is a little V88 in Iran, but not much.

I haven't seen the map you speak of. Why is a route through Iran unlikely? It looks like we know very little about its older branches.

MichaelK
02-22-2016, 07:07 AM
Some deep discussions going on around here.

Off to continue browsing for any discussions on my newly tested, A823+

Gravetto-Danubian
02-22-2016, 07:48 AM
I can try. Their last logins were more then a year ago.


It could be better, but we do not have L754 or PH1165 or PF3599 for an individual ordering yet.



Unfortunately, there are no M343+ L278- samples in FTDNA projects. М343 > L278 split can be known from old articles. I think we need to re-examine it also.

Have you tried contacting the authors of previous studies with some of the rare samples? You might strike luck and they're willing to re-test or even donate the sample for you to test

Btw: where have CTS 5330 been found (if at all) ?

lgmayka
02-22-2016, 03:45 PM
Off to continue browsing for any discussions on my newly tested, A823+
YFull haplotree for R-A823 (http://yfull.com/tree/R-A823/).

VinceT
02-23-2016, 05:36 AM
Revisions for R-U106:


R-A1243 falls below R-FGC3861/Z8056.
R-S19589 is positioned upstream of R-S11493 according to BritainsDNA, although the R-U106 Project at FTDNA hasn't been able to locate any FTDNA customers belonging to it as yet.


R-U106 currently has nearly a half-dozen samples assigned to R-U106*.