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vineviz
08-06-2012, 11:40 AM
Here is what the structure of the R1b tree should be, down to the level of R-M73 and R-M269.

http://vizachero.com/R1b1/R1btreev2.png

vineviz
08-06-2012, 02:48 PM
Another nomenclature change for R1b-L23+ upstream folks is in the works, then.

Maybe not. ISOGG currently has L278, M415, & P25 on a separate branch from M343 and I think this is wrong. If they move these SNPs up a node when they add L389, then all the R-M269 guys will have the same long-form names they currently have.


Do you anticipate any more deep restructuring in R1b-M343's phylogeny in the future? Does the current data indicate anything like that such as a group of R1b-M343 (xV88,L389) individuals?

Until FTDNA offer L389 we won't really know for sure. All the evidence I have suggests that all R-M343 men will either be R-L389 or R-V88: I don't think there are any R-M343(xV88,L389) men. If there are then they are very, very few.

parasar
08-06-2012, 03:27 PM
...

Until FTDNA offer L389 we won't really know for sure. All the evidence I have suggests that all R-M343 men will either be R-L389 or R-V88: I don't think there are any R-M343(xV88,L389) men. If there are then they are very, very few.

What would be the key STRs to look at to distinguish L389 folk in absence of a test for L389?
Thanks.

vineviz
08-06-2012, 03:54 PM
What would be the key STRs to look at to distinguish L389 folk in absence of a test for L389?
R-L389 is quite old (TMRCA of about 16kya) which makes it hard to summarize the whole clade with even a handful of key STRs.

There are a few markers that can help: DYS413=19,21 is usually R-L389 for example, at least in R-M343, but not all R-L389 have it and DYS454=11 is a pretty good signal too (but some R-V88 have it).

http://www.familytreedna.com/public/R1b1b1/default.aspx?section=yresults

ADW_1981
08-06-2012, 05:25 PM
I believe there are about 4 kits (out of 9 total) who are probably R-V88 in the Chadic project. It seems the administrator has intentionally or accidently restricted who can view the results of his project, but there are at least 3 new kits in process as of early July. Hopefully we can see these at some point.

vineviz
08-06-2012, 07:39 PM
I believe there are about 4 kits (out of 9 total) who are probably R-V88 in the Chadic project. It seems the administrator has intentionally or accidently restricted who can view the results of his project, but there are at least 3 new kits in process as of early July. Hopefully we can see these at some point.

It is always disappointing when DNA projects are completely invisible, but sometimes privacy concerns dictate it. We have one Chadic man and several Sudanese men in the R1b(xP297 project) but always welcome more. We can manage to make members anonymous if they wish to be.

ADW_1981
08-12-2012, 01:59 AM
It is always disappointing when DNA projects are completely invisible, but sometimes privacy concerns dictate it. We have one Chadic man and several Sudanese men in the R1b(xP297 project) but always welcome more. We can manage to make members anonymous if they wish to be.

Despite all of this, it looks like one of those new 3 kits turned out to be (highly likely ) R1b1 (prob. V88+) as that member joined the R1b public project.

TigerMW
11-01-2012, 09:50 PM
Here is what the structure of the R1b tree should be, down to the level of R-M73 and R-M269.

http://vizachero.com/R1b1/R1btreev2.png

Is L389 close to being added to the ISOGG tree?

TigerMW
04-18-2013, 11:05 PM
I try to keep this descendency tree graphic current. It is the Y DNA tree/phylogeny for the early branches of R1b, as best as I know it. R1b is marked by the SNP M343 so all R1b people have M343+. Please post any corrections or omissions here.


https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg

FTDNA's haplotree is behind so for source data for the graphic I use International Society of Genetic Genealogy's (ISOGG) Y hapgroup R tree at
http://isogg.org/tree/ISOGG_HapgrpR.html

I supplement that with data and new news from the following projects.

R1b1 Asterisk (M343+ P297-) [V88 people are in this]
http://www.familytreedna.com/public/R1b1Asterisk/default.aspx?section=yresults

R1b-ht35(M269+ P312- U106-) [L23* people are in this along with L51*, L11* and a few M269*]
http://www.familytreedna.com/public/ht35new/default.aspx?section=yresults

R1b-M73
http://www.familytreedna.com/public/r1b1b1/default.aspx?section=yresults

I generally defer to the project administrators of these projects as far as SNP status at the individual level. Some of the SNP testing for these people was done at non-FTDNA testing companies so their Y DNA SNP reports may not be entirely accurate.

Silesian
04-19-2013, 01:51 PM
I try to keep this descendency tree graphic current. It is the Y DNA tree/phylogeny for the early branches of R1b, as best as I know it. R1b is marked by the SNP M343 so all R1b people have M343+. Please post any corrections or omissions here.
Thanks for the R1b phylogeny. I was wondering if there are any similar chart's except with roughly calculated dates added from your data and Mjost calculations for all the branches?

alan
04-19-2013, 02:11 PM
I agree. Adding (even if with wide confidence intervals) date calculations based on sandwiching between inter and intra clades would be very useful. Personally I am pretty aware of the proposed dates for L51 and downstream but its the upstream dates that I am having trouble retaining.

TigerMW
04-19-2013, 03:32 PM
Thanks for the R1b phylogeny. I was wondering if there are any similar chart's except with roughly calculated dates added from your data and Mjost calculations for all the branches?

I hesitate to post TMRCA estimates on a chart I build as they can take us off on extensive tangent conversations. In other words, I don't feel comfortable defending any single TMRCA estimate as accurate. I think they should all be viewed with suspicion.

Now that I've said that, below are the R1b by clade age estimates that I pulled out Marko Heinila's analysis in 2011 along with Anatole Klyosov's summary estimates in his 2012 paper. Heinila has a different method. It's based on STRs still, but uses the "maximum likelihood" method rather than a pure variance based approach. Klyosov does do some checking to see if he feels he has a representative sample. Both were using long haplotypes and doing some STR selection/deselection based on linearity. You can see they are not that much different.


K years before present

Marko Heinila _ Anatole Klyosov

M343_ 14.0 __ 14.0

V88__ _9.5 __ _6.9
v88__ ____ __ _4.3 (Africa)
V69__ ____ __ _4.3

M73__ _7.2 __ _8.0

M269_ _5.7 __ _7.0
L23__ _5.7 __ _6.2
L51__ _4.9 __ _4.9
L11__ _4.8 __ _4.6
U106_ _4.5 __ _4.2
P312_ _4.2 __ _4.2
U152_ _4.2
L2___ _4.2
L21__ _4.2

The above are all based on germ-line mutation rates, but they seem to fit in with the Karafet 2008 SNP counting method of for R1, the MRCA of both R1b and R1a.

M173_ _18.5 <-- Karafet

We also have Vizachero's estimate for L389 of 16k ybp earlier in this thread but he says that is on limited STR knowledge.

Please note all of the above are NOT precise estimates, just best estimate (most likely) midpoints.

Klyosov's paper is at http://www.scirp.org/journal/PaperInformation.aspx?paperID=19567
Karafet's paper is at http://genome.cshlp.org/content/18/5/830.short

TigerMW
04-19-2013, 03:58 PM
...

K years before present

Marko Heinila _ Anatole Klyosov

M343_ 14.0 __ 14.0

V88__ _9.5 __ _6.9
v88__ ____ __ _4.3 (Africa)
V69__ ____ __ _4.3

M73__ _7.2 __ _8.0

M269_ _5.7 __ _7.0
L23__ _5.7 __ _6.2
L51__ _4.9 __ _4.9
L11__ _4.8 __ _4.6
U106_ _4.5 __ _4.2
P312_ _4.2 __ _4.2
U152_ _4.2
L2___ _4.2
L21__ _4.2

Other than the very young age of L11, which is close to 95% of Western and Central European R1b, I think the most noteworthy items are M269 and L23.

M269 early branches are typically found far from Western Europe but we see estimates (5.7 & 7.0k ybp) that are really barely Neolithic, especially back in the SW Asia/Near East region. The M269 MRCA didn't exist when the Neolithic took off, if these estimates are at all right. FTDNA's Chief Scientist, Mike Hammer, presented soon after the Karafet 2008 paper (co-authored by Hammer) that R1b-M269 was 4-8k ybp and moved into Western and Central Europe in a general east to west flow. He would have had knowledge of SNP counting as it relates to R1b at that time even though the Karafet paper didn't get down to anymore resolution than R1. I have no reason to think that R1b-M269 really is not in this age range.

Silesian
04-20-2013, 04:46 AM
Other than the very young age of L11, which is close to 95% of Western and Central European R1b, I think the most noteworthy items are M269 and L23.

M269 early branches are typically found far from Western Europe but we see estimates (5.7 & 7.0k ybp) that are really barely Neolithic, especially back in the SW Asia/Near East region. The M269 MRCA didn't exist when the Neolithic took off, if these estimates are at all right. FTDNA's Chief Scientist, Mike Hammer, presented soon after the Karafet 2008 paper (co-authored by Hammer) that R1b-M269 was 4-8k ybp and moved into Western and Central Europe in a general east to west flow. He would have had knowledge of SNP counting as it relates to R1b at that time even though the Karafet paper didn't get down to anymore resolution than R1. I have no reason to think that R1b-M269 really is not in this age range.

I don't quite understand something. When MJost compared my results with Nazarov his calculator came up with:


With only two haplotypes, I can only calcuate IntraClade Coalescence (n-1) Age of using Bird's q STRs (twenty five of 67 markers) results in a

7,761 +/-1,568 year before present with a max of 9,329 years for you two guys with SNP L150? But listed as R1b1a2a1.

223828 Nazarov Piotr Nazarov, b.1886, d.1932, Yaik Cossack clan Kazakhstan R1b1a2a1 12 21 14 11 11-15 12 12 12 13 14 28 17 9-10 11 11 25 15 19 28 15-15-16-18 11 11 19-23 16 16 17 17 37-42 12 12 11 9 15-16 8 10 10 8 10 11 12 21-22 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12
176123 A.K. Silesia/ Poland/Germany/Czech[ Shlesien,Śląsk1750] Poland R1b1a2a1 12 24 14 10 11-14 12 12 11 14 13 31 16 9-10 11 11 25 15 19 33 14-15-16-19 10 10 19-23 16 16 19 19 37-40 12 12 11 9 15-16 8 10 10 8 10 11 12 23-23 16 10 12 12 15 8 12 23 20 14 12 11 13 11 10 12 12

If we are both R-M269+ L23+ L150+ and L23 is 5.7 - 6.2 K before present according to Marko Heinila _ Anatole Klyosov how can we both be R1b1a2a1?

TigerMW
04-20-2013, 05:17 AM
I don't quite understand something. When MJost compared my results with Nazarov his calculator came up with:

If we are both R-M269+ L23+ L150+ and L23 is 5.7 - 6.2 K before present according to Marko Heinila _ Anatole Klyosov how can we both be R1b1a2a1?

Was the TMRCA estimate that Jost did use just two haplotypes? Statistical estimates down at the onesie, twosie level don't work well and would have very wide error ranges. Statistical methods are most useful when large data samples are available.

The mutation rates underpinning TMRCA estimates are just averages. On average, they may work very well, but in any individual situation that may be quite a ways off.

Silesian
04-20-2013, 06:50 AM
Was the TMRCA estimate that Jost did use just two haplotypes? Statistical estimates down at the onesie, twosie level don't work well and would have very wide error ranges. Statistical methods are most useful when large data samples are available.

The mutation rates underpinning TMRCA estimates are just averages. On average, they may work very well, but in any individual situation that may be quite a ways off.

Well it seems rather odd the base model for Bashkir's haplotype is 12 24 14 10 X X X 12 12 13 13 30 - 10. who had a common ancestor 500+/- ybp is closer to my numbers than Nazarov.

L23+

12 24 14 10 X X X 12 12 13 13 30 - 10. Bashkir base model
12 24 14 10 X X X 12 12 11 14 31-Poland
12 21 14 11 X X X 12 12 12 13 28- Khazakstan

MJost
04-20-2013, 07:02 AM
Marko H published those YBP numbers in 2011 but in 2012 he re-studied and calculated a entire new set of mutation rates with rate "calibration" for 111 marker.

Marko stated to me, "The fact that these mutation rates are somewhat higher than what I used before seems to be quit reasonable in the case of some deep genealogical clusters. The majority trees do not have that much structure, however. Some of the clearer cases are Scandinavian/Scottish R1a1a1/R1a1a1h (111 STR) and MacGregor Ian Cam in R-L21 (67 STR)."

These new 2012 mutation rates applied to your two haplotypes variances produced 7,761 - 1,568 = 6.193 (6.2k) which is right at the edge of 5.7 - 6.2 K numbers from AK's and Marko's earlier slower overall rates. If you took 100 more haplotypes that were mostly similar to one of you than the other one, the ages might get much smaller. We need a additional haplotypes to get a true Modal age. The numbers I provided were sampled Coalescence variances which would be younger than the Modal age.

You were questioning 'how can we both be R1b1a2a1?' not sure what you meant. You can re ask your question.

MJost

Silesian
04-20-2013, 02:40 PM
Marko H published those YBP numbers in 2011 but in 2012 he re-studied and calculated a entire new set of mutation rates with rate "calibration" for 111 marker.

Marko stated to me, "The fact that these mutation rates are somewhat higher than what I used before seems to be quit reasonable in the case of some deep genealogical clusters. The majority trees do not have that much structure, however. Some of the clearer cases are Scandinavian/Scottish R1a1a1/R1a1a1h (111 STR) and MacGregor Ian Cam in R-L21 (67 STR)."

These new 2012 mutation rates applied to your two haplotypes variances produced 7,761 - 1,568 = 6.193 (6.2k) which is right at the edge of 5.7 - 6.2 K numbers from AK's and Marko's earlier slower overall rates. If you took 100 more haplotypes that were mostly similar to one of you than the other one, the ages might get much smaller. We need a additional haplotypes to get a true Modal age. The numbers I provided were sampled Coalescence variances which would be younger than the Modal age.

You were questioning 'how can we both be R1b1a2a1?' not sure what you meant. You can re ask your question.
MJost

I was not taking into account +/- which brings the age in line with both AK's and Marko's model's. I'm curious when they have a presumbly newly discovered ancient lineage, from Africa like the one they found a little while back, do they use the same technique; that is, only using one sample and comparing it to a known cluster?

Can you also recommend a easy to use calculator online . I noticed that YHRD has common base model's however they have only 8-20 str's.
For example some samples from http://www.yhrd.org/YP745 where I can enter and compare with Nazarov?

Rathna
04-20-2013, 03:16 PM
For example some samples from http://www.yhrd.org/YP745 where I can enter and compare with Nazarov?

Which among these haplotypes would be R-L23?

N 19 389I 389II 390 391 392 393 385 438 439 437 448 456 458 635 YGATAH4 576 481 549 533 570 643
41 15 12 29 23 10 13 12 13,18 10 12 15 19 15 17 19 12 -1 -1 -1 -1 -1 -1
2 15 12 29 22 10 10 11 13,18 10 10 14 22 15 16 21 11 -1 -1 -1 -1 -1 -1
1 14 14 31 23 11 14 14 11,13 14 10 14 19 13 17 23 11 -1 -1 -1 -1 -1 -1
1 15 11 29 22 9 12 10 13,17 10 12 15 19 15 15 20 12 -1 -1 -1 -1 -1 -1
1 15 11 29 22 9 12 10 13,18 10 11 15 19 15 15 20 11 -1 -1 -1 -1 -1 -1
1 15 11 29 22 9 12 11 13,18 10 11 15 19 15 15 20 12 -1 -1 -1 -1 -1 -1
1 15 11 29 22 10 12 10 11,13 10 11 15 19 15 15 20 12 -1 -1 -1 -1 -1 -1
1 15 11 31 25 12 13 11 13,18 12 12 17 23 15 18 26 11 -1 -1 -1 -1 -1 -1
1 15 12 28 22 9 12 10 12,16 10 10 14 20 18 15 20 11 -1 -1 -1 -1 -1 -1
1 15 12 28 23 10 13 14 13,18 10 12 15 19 15 17 19 12 -1 -1 -1 -1 -1 -1

Silesian
04-20-2013, 04:14 PM
Which among these haplotypes would be R-L23?
If the distance between Nazarov and other L23+ in the region is 6.2K +/- I would like to calculate the age of Q and N found in the same region. For example is Q and N much older than L23+ in Kazahkstan region or are they in the same range.

Rathna
04-20-2013, 04:59 PM
If the distance between Nazarov and other L23+ in the region is 6.2K +/- I would like to calculate the age of Q and N found in the same region. For example is Q and N much older than L23+ in Kazahkstan region or are they in the same range.
Probably the most part of the above haplotypes are hg. O (perhaps someone hg. G) rather that N or Q.

TigerMW
04-20-2013, 06:21 PM
Well it seems rather odd the base model for Bashkir's haplotype is 12 24 14 10 X X X 12 12 13 13 30 - 10. who had a common ancestor 500+/- ybp is closer to my numbers than Nazarov.

L23+

12 24 14 10 X X X 12 12 13 13 30 - 10. Bashkir base model
12 24 14 10 X X X 12 12 11 14 31-Poland
12 21 14 11 X X X 12 12 12 13 28- Khazakstan

Estimates based on just nine STRs are also subject to greater risk as well as working with just a couple of haplotypes. In my personal case, I'm off 2 or 3 GD steps from by best match at the same markers you are showing above. However, at 111 markers we are only off 7 which is very good. He also has my surname so I feel he really is the best match. Our TMRCA estimates 9 markers would be very high but at 111 very low. You can drown crossing a river that is average only three feet deep. Averages are great for large numbers (populations) but down at the individual/singleton levels they could be misleading.

We also have to watch out for some markers. Some STRs' mustations are found to not have a linear relationship with time. I think one of the markers above is DYS449 (the last.) That's a bad one. DYS390 isn't too good either.

TigerMW
04-20-2013, 10:42 PM
If the distance between Nazarov and other L23+ in the region is 6.2K +/- I would like to calculate the age of Q and N found in the same region. For example is Q and N much older than L23+ in Kazahkstan region or are they in the same range.

You mentioned "in the region". I think you are wanting to compare Q and N in the same geographical region. I apologize in advance as I'm not intneding to imply you are not logical but to compare Q within a geography with N within the same geography is nonsensical.

All Q no matter where in the world is more closely related to all other Q and the same goes for N. First, one should determine the ages of all Q and all N and then compare upward in the descendency tree/phylogeny. There could be some convergence of STRs of folks in different haplogroups that end up giving us what Anatole Klyosov describes as phantom MRCAs. They are not real. All of this points to the value of interclade (vs intraclade) age estimates and building one layer of interclade age estimates upon another.

Silesian
04-21-2013, 03:07 AM
Estimates based on just nine STRs are also subject to greater risk as well as working with just a couple of haplotypes. In my personal case, I'm off 2 or 3 GD steps from by best match at the same markers you are showing above. However, at 111 markers we are only off 7 which is very good. He also has my surname so I feel he really is the best match. Our TMRCA estimates 9 markers would be very high but at 111 very low. You can drown crossing a river that is average only three feet deep. Averages are great for large numbers (populations) but down at the individual/singleton levels they could be misleading.

A lot of studies do not provide 111 markers, and many people cannot afford 111 marker test; perhaps more so in some Eastern areas where R1b might be found, so we have to work with what we have.



We also have to watch out for some markers. Some STRs' mustations are found to not have a linear relationship with time. I think one of the markers above is DYS449 (the last.) That's a bad one. DYS390 isn't too good either.

Sometimes YHRD sample base, will only provide a handful of markers, however they use DYS390.
If you could choose what are your favorite/most reliable markers?


You mentioned "in the region". I think you are wanting to compare Q and N in the same geographical region. I apologize in advance as I'm not intneding to imply you are not logical but to compare Q within a geography with N within the same geography is nonsensical.

You don't have to apologize . I think you misunderstand what I'm seeking. Anatole Klyosov shows the age of L23 in the region where Nazarov comes from[Khazakstan] as being quite old, and shows L23 migration going West. This is contrary to some who propose a Eastward migration of L23. I would like to compare the age of Q and N, or whatever other samples are found in the YHRD base or similar studies, with the age of L23 in the same region.

TigerMW
04-21-2013, 04:31 AM
A lot of studies do not provide 111 markers, and many people cannot afford 111 marker test; perhaps more so in some Eastern areas where R1b might be found, so we have to work with what we have.
Agreed, but we just have to accept that the less data we have to work with the less we can rely on the data.


Sometimes YHRD sample base, will only provide a handful of markers, however they use DYS390.
If you could choose what are your favorite/most reliable markers?
I will leave that up to the scientists. Busby, et al. made what appears to be a very feeble attempt, Marko Heinilla made a more significant attempt but did not not publish. Steven Bird published a paper on this which I believe is the latest and greatest.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048638
We should probably open a new thread on this.....
Remember, earlier I said I don't like to produce TMRCA estimates as we get lost in the woods rather quickly.

I set up a new thread here so we can further discuss TMRCA estimates. Hopefully, I can get Mark Jost over on this thread as he has been studying this issue.
http://www.anthrogenica.com/showthread.php?828-STR-Wars-GDs-TMRCA-estimates-Variance-Mutation-Rates-amp-SNP-counting



Anatole Klyosov shows the age of L23 in the region where Nazarov comes from[Khazakstan] as being quite old, and shows L23 migration going West. This is contrary to some who propose a Eastward migration of L23. I would like to compare the age of Q and N, or whatever other samples are found in the YHRD base or similar studies, with the age of L23 in the same region.
I don't necessarily agree with everything Klyosov says and he does change his position from time to time, but where is it specifically in his writings that you are referring to? In his 2012 paper on R1b he has R1b-L23 as 6.2k ybp. Also keep in mind that his communications style in English is a little not so sophisticated.

... but I do agree, based on long haplotype diversity from DNA projects (about 200) that L23xL51 seems older in Anatolia, Caucasus and the Near East than in Europe.

Silesian
04-21-2013, 03:22 PM
I don't necessarily agree with everything Klyosov says and he does change his position from time to time, but where is it specifically in his writings that you are referring to?In his 2012 paper on R1b he has R1b-L23 as 6.2k ybp. Also keep in mind that his communications style in English is a little not so sophisticated.

... but I do agree, based on long haplotype diversity from DNA projects (about 200) that L23xL51 seems older in Anatolia, Caucasus and the Near East than in Europe.

The most distant R1b haplotypes (those exhibiting the greatest mu-tational differences) from European R1b haplotypes, were found in Siberia and Middle Asia (a part of Central Asia) populations. Central Asian R1b haplotype bearers have the most ancient common ancestors with European R1b bearers, and those ancient common ancestors lived ~16,000 ybp in Cen-tral Asia. We do not know as yet whether in South Siberia or Middle Asia; however, the evidence will demonstrate that it was somewhere in that vast region.
In this endeavor both terms, “haplogroup”

R-L23 apparently arose on the eastern side of the Russian Plain, where Europe meets Asia, ~6200 ybp and migrated to the Caucasus and further South, to Anatolia and the Middle East. Another branch of L23 went westward, to Europe, approxi-mately 4500 ybp.
The most eastern

Nazarov does not appear to be part of the recent Bashkir common ancestor branch[Bashkir L23 branch has a common ancestor who lived only 575 ± 175 ybp.]

01. (BASHKIRS) R1b+M269
011. (BASHKIRS, COSSACKS, POLES) R1b+L150
http://www.familytreedna.com/public/Bashqort_Clans/default.aspx?section=yresults

29 of 10 marker haplotypes of subclade R-L23 of the Bashkirs were published (Myres et al., 2010), and their base haplotype is 12 24 14 10 X X X 12 12 13 13 30 - 10. This is a typical albeit slightly mu-tated L23 haplotype with its characteristic first allele DYS393 = 12. 26 haplotypes of those 29 were identical, as shown above, and the whole Bashkir L23 branch has a common ancestor who lived only 575 ± 175 ybp. However, this base haplotype differs from the European R-L23 base haplotype 12 24 14 10 X X X 12 12 13 14 29 - 11 by three mutations, which sets these two base haplotypes apart by 3/.018 = 167 → 200 conditional gen-erations—5000 years, and places their common ancestor at 5500 ybp.

http://www.scirp.org/journal/PaperInformation.aspx?paperID=19567

Klyosov used different calculation numbers from Mjosts.Both show a similar 6200YBP age range. Mjost's calculations[lower band] using 27 str's Poland - Nazarov-Khazakstan.

MJost
04-21-2013, 07:23 PM
I have done several reviews.

TMRCA Estimated Ages Summary Report R1b-Early Data Set.pdf
https://docs.google.com/file/d/0By9Y3jb2fORNeHcxYzFpMUVXYTg/edit?usp=sharing

IntercladeTMRCA-Gen111T_Estimator_M269treeSubclades_MJost10-23-2012
https://docs.google.com/file/d/0By9Y3jb2fORNMUVUTF83LW9HN28/edit?usp=sharing

Please note that I expect these same set of ages to increase overall using the better set of Linear STR as Bird has suggested by maybe 5 to 10%.

Just be aware that Intraclade sampling age is usually less than Modal. Larger differences is due to slow or bottleneck growth affects. Larger number of Haplotypes will provide more confidence. Since these reports I have started to show confidence intervals based on the confidence level selected as a validation of the data. Use my TMRCA spread sheet to check your own set of Haplotypes.

MJost

TigerMW
04-22-2013, 01:10 PM
Okay, I think I see where I didn't understand you or where either of us may misunderstand Klyosov.

... Anatole Klyosov shows the age of L23 in the region where Nazarov comes from[Khazakstan] as being quite old, and shows L23 migration going West. This is contrary to some who propose a Eastward migration of L23. ...


R-L23 apparently arose on the eastern side of the Russian Plain, where Europe meets Asia, ~6200 ybp

I interpret Klyosov's statement here as relating to R1b-L23 as a whole and the age of the whole branch is 6200 ybp, regardless of the origin region. He wasn't exactly clear but he generally lists the true age of each whole subclade in his papers somewhere (and I think this it) but it can be confusing because he also talks about non-SNP marked sub-branches as well.

When he said "arose on the eastern side of the Russian Plain" I don't think he is talking about a sub-branch of L23 but that R1b-L23 as a whole originated in that region. BTW, I don't necessarily agree with him but it is a possibility. His age of 6200 ybp seems reasonable to me, though, given what I've seen of the diversity of the haplotypes in L23xL51 and the placement of L23 above L51 and below M269.

Is why are you interested in the ages of Q and N because you have some ideas about Q and/or N may or may not have migrated with L23?

Silesian
04-22-2013, 03:30 PM
Okay, I think I see where I didn't understand you or where either of us may misunderstand Klyosov.




I interpret Klyosov's statement here as relating to R1b-L23 as a whole and the age of the whole branch is 6200 ybp, regardless of the origin region. He wasn't exactly clear but he generally lists the true age of each whole subclade in his papers somewhere (and I think this it) but it can be confusing because he also talks about non-SNP marked sub-branches as well.

When he said "arose on the eastern side of the Russian Plain" I don't think he is talking about a sub-branch of L23 but that R1b-L23 as a whole originated in that region. BTW, I don't necessarily agree with him but it is a possibility. His age of 6200 ybp seems reasonable to me, though, given what I've seen of the diversity of the haplotypes in L23xL51 and the placement of L23 above L51 and below M269.

Is why are you interested in the ages of Q and N because you have some ideas about Q and/or N may or may not have migrated with L23?

yes, I wanted to see what was the variance and possible age in that neck of the woods.

L23X51
12-21-14-11-[11/15]-12-12-12-13-14-28-Kazakhstan
12-24-11-11-[11/14]-12-12-13-13-13-30-Kazakhstan
12-25-14-11-[11/13]-12-12-12-13-13-29-Kazakhstan
12-24-14-10-[11/14]-12-12-12-13-13-29-Kazakhstan
12-24-14-10-[11/14]-12-13-12-13-13-30-Pakistan
R M207+ M173-/M124-
13-23-14-10-[13/22]-11-12-11-14-12-30-Pakistan
13-23-14-10-[14-20]-11-12-12-14-12-30-Tajikistan
Q M242
12-23-14-10-[13/15]-12-12-11-12-13-30-Tajikistan
13-25-13-10-[13/16]-12-14-13-13-13-29-Uzbekistan

TigerMW
04-22-2013, 03:35 PM
yes, I wanted to see want was happening it that neck of the woods.

L23X51
12-21-14-11-[11/15]-12-12-12-13-14-28-Kazakhstan
12-24-11-11-[11/14]-12-12-13-13-13-30-Kazakhstan
12-25-14-11-[11/13]-12-12-12-13-13-29-Kazakhstan
12-24-14-10-[11/14]-12-12-12-13-13-29-Kazakhstan
12-24-14-10-[11/14]-12-13-12-13-13-30-Pakistan
R M207+ M173-/M124-
13-23-14-10-[13/22]-11-12-11-14-12-30-Pakistan
13-23-14-10-[14-20]-11-12-12-14-12-30-Tajikistan
Q M242
12-23-14-10-[13/15]-12-12-11-12-13-30-Tajikistan
13-25-13-10-[13/16]-12-14-13-13-13-29-Uzbekistan

I don't think calculating intraclade TMRCA estimates for such small groups with limited STRs will be that useful.
I also don't think interclade TMRCA estimates between these subclades would be that meaningful either as they are only quite distantly related (according to the SNP based phylogenies.)

The Eastern Eurasian plains are huge. Do you have any distribution maps or tables that show possible correlations of these haplogroups across the various sub-regions?

Silesian
04-22-2013, 03:58 PM
I don't think calculating intraclade TMRCA estimates for such small groups with limited STRs will be that useful.
I also don't think interclade TMRCA estimates between these subclades would be that meaningful either as they are only quite distantly related (according to the SNP based phylogenies.)

The Eastern Eurasian plains are huge. Do you have any distribution maps or tables that show possible correlations of these haplogroups across the various sub-regions?

I agree, we really do not have enough data samples from the region to make any assumptions other than L23x51/R/Q , can be found in the same region. That is why I would hesitate to peg the oldest samples of L23x51 originating from the Middle East.

TigerMW
04-22-2013, 04:55 PM
I agree, we really do not have enough data samples from the region to make any assumptions other than L23x51/R/Q , can be found in the same region. That is why I would hesitate to peg the oldest samples of L23x51 originating from the Middle East.

If you are just talking about R1b-L23xL51/Z2103/5? and very broad regions, we do have considerably more data. We have about 200 67 STR haplotypes that Mark Jost has done calculations with. Quite a few of those are from Anatolia and Anatolia looks to be more diverse so it may well be older than, say, European L23xL51 but we do not that much data from SE Europe.

Maybe Mark can give us an update. I think he has looked at this both from both long haplotypes and short haplotypes/study data viewpoints.

There are many issues with using modern DNA and using STR diversity, for example the Armenian L23xL51 may actually have come from SE Europe along the west coast of the Black Sea at an earlier time.

Perhaps Mark can give us an update, but I feel comfortable saying that L23xL51, in toto, is of higher diversity and probably greater age than L11. We have found a lot of L23x51 right around the Black Sea, particularly Anatolia, so that is something to consider at the same time.

TigerMW
04-22-2013, 05:08 PM
If you are just talking about R1b-L23xL51/Z2103/5? and very broad regions, we do have considerably more data. We have about 200 67 STR haplotypes that Mark Jost has done calculations with. Quite a few of those are from Anatolia and Anatolia looks to be more diverse so it may well be older than, say, European L23xL51 but we do not that much data from SE Europe. ...

I don't think we have much long haplotype data from L23xL51 in Central Asia either, the same as SE Europe, even though we do for Anatolia.

If you look at the Myres frequency maps you can see why Klyosov is interested in the L23x51 out to the east. I presume that on short haplotypes he decided that was older. I guess we should go look at that part of the paper to see if that is the case or he is just trying to do some association of L23x51 in Asia with the fact that we have relative M73 out there too.
https://dl.dropboxusercontent.com/u/17907527/R1b-L23_Asterisk_Frequency_Map_by_Myres_2010.jpg

Silesian
04-22-2013, 05:40 PM
If you are just talking about R1b-L23xL51/Z2103/5? and very broad regions, we do have considerably more data. We have about 200 67 STR haplotypes that Mark Jost has done calculations with. Quite a few of those are from Anatolia and Anatolia looks to be more diverse so it may well be older than, say, European L23xL51 but we do not that much data from SE Europe.

R1b-L23XL51 extends to Z2103/Z2105>L277+>L584+ and L277-L584- What are the samples from the far East[Kazakhstan/Uzbekistan/Pakistan...etc] closer to the origins of Q or R1 for example, will they be Z2103+/- L277+/- L584+/-? It would be sure nice to get a idea what snp's are there; I already offered to help Nazarov from Khazakhstan, relayed through Mark.



Maybe Mark can give us an update. I think he has looked at this both from both long haplotypes and short haplotypes/study data viewpoints.

There are many issues with using modern DNA and using STR diversity, for example the Armenian L23xL51 may actually have come from SE Europe along the west coast of the Black Sea at a much earlier time.

Perhaps Mark can give us an update, but I feel comfortable saying that L23xL51, in total is of higher diversity and probably greater age than L11. We have found a lot of L23x51 right around the Black Sea, particularly Anatolia, so that is something to consider at the same time.

Both you and Mark/Richard R/JeanM/Alan, have done a terrific job for R1b projects, and or trying to find out exactly where ancestors originated from. So a big thank-you!
A sample set of 200 is great. However out of the 200 samples what percent % come from the farthest Eastern locations, like Kazakhstan/Pakistan, and all the way to say Siberia?
If Mark could give a general breakdown of collected samples[N] and what % of the 200, they comprise, with their geographic region? For example we might not being seeing the big picture, as various tribes were perhaps displaced, or were very mobile in the last [X] thousands of years. We might not even know what questions to ask without all the possible snp's involved and undiscovered; as the case with the branching of L150, Z2103/Z2105 back mutations or undiscovered snp's. We can only give a rough sketch at best, however without a solid starting point it becomes very difficult IMO.


L23x51 in Asia with the fact that we have relative M73 out there too.

Yes you are right M73 and more distant R2 are also of interest.

TigerMW
04-22-2013, 06:28 PM
... Both you and Mark/Rocco/JeanM/Alan, have done a terrific job for R1b projects, and or trying to find out exactly where ancestors originated from. So a big thank-you!
You are welcome, but it is more fun than fulfilling, at least at this point.


A sample set of 200 is great. However out of the 200 samples what percent % come from the farthest Eastern locations, like Kazakhstan/Pakistan, and all the way to say Siberia?
Not many at all. Most of the project L23xL51 data is from Anatolia. A lot of it, I assume, is Armenian immigrants to the US.

Peter H, the ht35 project administrator is a great guy for helping us understand L23xL51.

BTW, I see you go by Z2105. Somewhere I saw this subclade was being called Z2103 and I think the two have been thought of as phylogenetically equivalent. Is there any reason to think one is older than the other? or than one is more stable and a better "lead with" SNP? When I checked I saw more people Z2103+ and Z2105 ? than Z2105+ Z2103 ?

Silesian
04-23-2013, 04:44 AM
BTW, I see you go by Z2105. Somewhere I saw this subclade was being called Z2103 and I think the two have been thought of as phylogenetically equivalent. Is there any reason to think one is older than the other? or than one is more stable and a better "lead with" SNP? When I checked I saw more people Z2103+ and Z2105 ? than Z2105+ Z2103 ?

I only tested for Z2105+ currently I'm batched for Z2103.

Rathna
04-23-2013, 05:05 AM
R M207+ M173-/M124-
13-23-14-10-[13/22]-11-12-11-14-12-30-Pakistan
13-23-14-10-[14-20]-11-12-12-14-12-30-Tajikistan


These are very likely R2, like mine from India.

jsa
04-27-2013, 09:53 PM
These are very likely R2, like mine from India.

To date what is the ethnic make-up of z2105?

Thanks

Joe B
04-28-2013, 10:29 PM
To date what is the ethnic make-up of z2105?

Thanks
JSA,
Ethnic make-up is a subject fraught with danger. So let me say this first, I believe only in the scientific method.
Here is some raw data taken from a spread sheet Mike compiled called R1b-Early Haplotypes found on the R1b yahoo group. It is the most solid data I know of and is from last fall. L23* is diffuse and interesting in 39 old world countries with many ethnic groups and multiple migrations.
With nothing to distinguish Z2105 from L23/L150.1 everybody that L23* is included. N=282

By Country
Albania 2 Armenia 49 Belarus 1 Bulgaria 4
Croatia 1 Czech Rep 2 Egypt 1 England 12
France 4 Georgia 1 Germany 6 Greece 7
Hungary 7 India 2 Iran 13 Iraq 14
Ireland 3 Italy 16 Kazakhstan 2 Kosovo 1
Lebanon 1 Lithuania 8 Macedonia 1 Netherlands 2
Pakistan 1 Palestine 1 Poland 19 Russia 5
Saudi Arabia2 Scotland 3 Slovakia 1 Spain 5
Sweden 1 Switzerland 3 Syria 3 Turkey 46
Ukraine 5 U.A.E 2 zzCountry 25 Total 282

L23* listed in a project or other ethnic designation. N=126
Albanian 1 Arab name 1
Aramaic project 1 Armenia project 5
Armenian project 78 Assyrian project 14
Badakhshani ? 1 Dagestan Lak people 1
Jewish project 24 Total 126

The R1b Cohane Project has developed a modal that shows some promise as a guide for further modal work with L23. It kind of depends on the geography and/or endogamy of our ancestors to see if defining snps or strs will be found. The best way to get there will be by the scientific method. That is why I have ordered Z2103 and L277 snp tests to compliment my L584- result. With all the testing that has occurred this winter and spring, old assumptions will go and new hypotheses will result if history is any guide.

Mike, your data has been of great value. Do you have a preferred way to reference your work?

Thanks, Joe

TigerMW
05-02-2013, 06:34 PM
This belongs in this thread so I'm moving it. I would like to figure out the relationship of CTS1078 and CTS1083. Lawrence has checked out the details and it looks like ISOGG's tree and foot note are in error.



Ymap says that CTS1078 is exactly the same location as Z2103 (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7246135..7246135). CTS1083 is an entirely different location (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7248420..7248420).

The ISOGG tree appears to be mixed up. Its SNP page (http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html), however, correctly lists CTS1078 as equivalent to Z2103. (On that page it is the footnote that is wrong.)

seferhabahir
05-05-2013, 03:13 PM
Joe B suggested I might find some answers here regarding a cousin's Geno 2.0 test result showing L23- and L150+ and some new SNPs PF7558, PF7562 and PF7563 where he tested positive. Is it worth his money (or my money, since I doubt he would pay) to do more testing at FTDNA for STR markers or other new SNPs like Z2103 or Z2105? His result indicates that L150 should probably be above L23. I'm running out of money to do further testing of cousin DNA. Does his result support the notion that the other known L23- L150+ results are valid and not testing mistakes?

TigerMW
05-05-2013, 03:19 PM
Joe B suggested I might find some answers here regarding a cousin's Geno 2.0 test result showing L23- and L150+ and some new SNPs PF7558, PF7562 and PF7563 where he tested positive. Is it worth his money (or my money, since I doubt he would pay) to do more testing at FTDNA for STR markers or other new SNPs like Z2103 or Z2105? His result indicates that L150 should probably be above L23. I'm running out of money to do further testing of cousin DNA. Does his result support the notion that the other known L23- L150+ results are valid and not testing mistakes?

I'm very leery of L150. Please make sure to have FTDNA explain what type of L150 SNP mutation was found in this individual. I would also ask them to recheck their L23 result to make sure it is really an ancestral call and not some kind of no call or bad read. I'd wait to hear back.

L23xL51 individuals should be considering both Z2103 and Z2105 or possibly downstream L584 or L277 based on if they match STRs with people in L584 or L277.

I think everyone in R1b should go to 67 STRs.

seferhabahir
05-05-2013, 03:51 PM
Mike,

I only have the raw Geno 2.0 results for his test as below. Not sure what type of L150 the Geno 2.0 chip tests (there is only one location), but the FTDNA draft tree shows the L150 mutation as C -> T and the L23 mutation as G -> A so I think the results below are right.

L23 Y G G
L150 Y T T
PF7558 Y A A
PF7562 Y T T
PF7563 Y A A

seferhabahir
05-05-2013, 04:10 PM
I only have the raw Geno 2.0 results for his test as below. Not sure what type of L150 the Geno 2.0 chip tests (there is only one location), but the FTDNA draft tree shows the L150 mutation as C -> T and the L23 mutation as G -> A so I think the results below are right.

L23 Y G G
L150 Y T T
PF7558 Y A A
PF7562 Y T T
PF7563 Y A A

His paternal lineage is Ashkenazi with his father and grandfather living in Moscow. Before that, it is impossible to say. Could have been anywhere in the Pale.

Joe B
05-07-2013, 06:59 PM
This belongs in this thread so I'm moving it. I would like to figure out the relationship of CTS1078 and CTS1083. Lawrence has checked out the details and it looks like ISOGG's tree and foot note are in error.
Originally Posted by lgmayka
"Ymap says that CTS1078 is exactly the same location as Z2103 (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7246135..7246135). CTS1083 is an entirely different location (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7248420..7248420).
The ISOGG tree appears to be mixed up. Its SNP page (http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html), however, correctly lists CTS1078 as equivalent to Z2103. (On that page it is the footnote that is wrong.)"

We have a new kit in the ht35 project that is Geno 2.0 haplotype CTS7822 while FTDNA has haplotype L-150. Should we add CTS7822 to CTS1078 and CTS1083 for more information?

TigerMW
05-07-2013, 07:12 PM
Originally Posted by lgmayka
"Ymap says that CTS1078 is exactly the same location as Z2103 (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7246135..7246135). CTS1083 is an entirely different location (http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=ChrY%3A7248420..7248420).
The ISOGG tree appears to be mixed up. Its SNP page (http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html), however, correctly lists CTS1078 as equivalent to Z2103. (On that page it is the footnote that is wrong.)"

We have a new kit in the ht35 project that is Geno 2.0 haplotype CTS7822 while FTDNA has haplotype L-150. Should we add CTS7822 to CTS1078 and CTS1083 for more information?

Yes, we should watch CTS7822 also.

Rathna
05-07-2013, 07:41 PM
Yes, we should watch CTS7822 also.

It seems that CTS7822 is equivalent to Z2110, and was found firstly by Richard Rocca in the Italian Varipapa, actually a Calabrian of Arbereshe origin, and I thought that this was a Balkan cluster. But now CTS7822 is appearing in other R-L23 (for instance Shomo, Wade) and we don’t know how the administrators of the ht 35 FTDNA Project created lastly a new subclade based upon the back mutation of L150 and now we don’t understand upon what, but Wade has been put there and many are surely L150+.

[EDIT by moderator: fixed quotes]

R.Rocca
05-07-2013, 08:16 PM
Yes, we should watch CTS7822 also.

It seems that CTS7822 is equivalent to Z2110, and was found firstly by Richard Rocca in the Italian Varipapa, actually a Calabrian of Arbereshe origin, and I thought that this was a Balkan cluster. But now CTS7822 is appearing in other R-L23 (for instance Shomo, Wade) and we don’t know how the administrators of the ht 35 FTDNA Project created lastly a new subclade based upon the back mutation of L150 and now we don’t understand upon what, but Wade has been put there and many are surely L150+.

Just a reminder that of the two 1000 Genomes samples that were Z2110+, one was from Iberia and the other from Colombia. The highest level of the Z2110 branch is an undocumented SNP (hopefully we can create the primer) from Tuscany.

The single sample that is L23+Z2103+(L277-L584-Z2110 et al -) is a Han Chinese.


[EDIT by moderator: fixed quotes]

Rathna
05-07-2013, 09:36 PM
Just a reminder that of the two 1000 Genomes samples that were Z2110+, one was from Iberia and the other from Colombia. The highest level of the Z2110 branch is an undocumented SNP (hopefully we can create the primer) from Tuscany.

The single sample that is L23+Z2103+(L277-L584-Z2110 et al -) is a Han Chinese.

What do you mean for “highest”: the most “ancestral” or the most “derived”?
Probably the Chinese wasn’t a Han but a Hui and I supported the theory that he descended from a Roman soldier of the Crassus’ army defeated at Charrae on 53 BC and linked to me because there is another Hui on YHRD who matches me at the STRs level. Perhaps I should test myself too for these SNPs.

[EDIT by moderator: fixed quotes]

R.Rocca
05-08-2013, 12:04 PM
What do you mean for “highest”: the most “ancestral” or the most “derived”?
Probably the Chinese wasn’t a Han but a Hui and I supported the theory that he descended from a Roman soldier of the Crassus’ army defeated at Charrae on 53 BC and linked to me because there is another Hui on YHRD who matches me at the STRs level. Perhaps I should test myself too for these SNPs.

For the Tuscany sample, I mean that he is the least derived in his branch. As for the Hun Chinese from Beijing, I find it difficult to see how we can classify someone who is ancestral to anything found in Italy as being descended from a Roman Legion.

[EDIT by moderator: fixed quotes... let's all try to be careful with them so we aren't attributing a quote to the wrong person.]

Rathna
05-08-2013, 01:19 PM
For the Tuscany sample, I mean that he is the least derived in his branch. As for the Hun Chinese from Beijing, I find it difficult to see how we can classify someone who is ancestral to anything found in Italy as being descended from a Roman Legion.


I spoke about this the first time on Rootsweb in the Summer of 2007 when the paper about the “Romans in Liqian” was firstly published. After I have spoken of this in many forums.
When your group published the paper about the 1KGP, where there were a Tuscan and a Chinese (I remember a Hui more than a Han) who were R-L23 and Z2103 /Z2105+, I understood that probably I was Z2105+ too, seeing the Tuscan and the Hui who were so. Then they were classified so, and we didn’t know that they were the Tuscan Z2110 plus a downstrean SNP not yet identified and the Hui negative from Z2106 on. This probably is the argument of your actual research.
Why I think that this Hui is linked to me?

For this:

On Worldfamilies I wrote this:
“I make you note that another Hui gets my haplotype: 12,24,15,10,11-14,12,12,12,13,13 (my 12 is recent),29,”

Geno 2.0 and R-L23 and R-L51

Of course I should test Z2106-Z2110 and to find them negative. I bet they are.

R.Rocca
05-08-2013, 02:18 PM
I spoke about this the first time on Rootsweb in the Summer of 2007 when the paper about the “Romans in Liqian” was firstly published. After I have spoken of this in many forums.
When your group published the paper about the 1KGP, where there were a Tuscan and a Chinese (I remember a Hui more than a Han) who were R-L23 and Z2103 /Z2105+, I understood that probably I was Z2105+ too, seeing the Tuscan and the Hui who were so. Then they were classified so, and we didn’t know that they were the Tuscan Z2110 plus a downstrean SNP not yet identified and the Hui negative from Z2106 on. This probably is the argument of your actual research.
Why I think that this Hui is linked to me?

For this:

On Worldfamilies I wrote this:
“I make you note that another Hui gets my haplotype: 12,24,15,10,11-14,12,12,12,13,13 (my 12 is recent),29,”

Geno 2.0 and R-L23 and R-L51

Of course I should test Z2106-Z2110 and to find them negative. I bet they are.

He is classified as Han Chinese from Beijing. Please see here: http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18645

Rathna
05-08-2013, 02:45 PM
He is classified as Han Chinese from Beijing. Please see here: http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18645

Yes, he was classified so also before:

NA18645 Y R1b1a2a1*: M207+ L23+ L49.1+ L150+ L51- U152- P297- L584- /CHB/ “appears to be L277+"

We will see if this changes my hypotheses. R-L23 isn't so diffused in China, but it is more in Hui and North Western Chinese people (actually Uygurs).

Rathna
05-08-2013, 02:55 PM
We will see if this changes my hypotheses. R-L23 isn't so diffused in China, but it is more in Hui and North Western Chinese people (actually Uygurs).

Anyway also about this Chinese we are speaking of a subclade of a subclade of a subclade as to R-L23* from which R-L51. And that R-L51 were born in Italy rather than in China I think neither you doubt.

AJL
05-08-2013, 04:46 PM
that R-L51 were born in Italy rather than in China I think neither you doubt.

That's a false dilemma.

http://onegoodmove.org/fallacy/fd.htm

jsa
05-12-2013, 03:06 AM
Seems like Armenia, Turkey, Poland, Italy have the highest concentration of z2105. Interesting...



JSA,
Ethnic make-up is a subject fraught with danger. So let me say this first, I believe only in the scientific method.
Here is some raw data taken from a spread sheet Mike compiled called R1b-Early Haplotypes found on the R1b yahoo group. It is the most solid data I know of and is from last fall. L23* is diffuse and interesting in 39 old world countries with many ethnic groups and multiple migrations.
With nothing to distinguish Z2105 from L23/L150.1 everybody that L23* is included. N=282

By Country
Albania 2 Armenia 49 Belarus 1 Bulgaria 4
Croatia 1 Czech Rep 2 Egypt 1 England 12
France 4 Georgia 1 Germany 6 Greece 7
Hungary 7 India 2 Iran 13 Iraq 14
Ireland 3 Italy 16 Kazakhstan 2 Kosovo 1
Lebanon 1 Lithuania 8 Macedonia 1 Netherlands 2
Pakistan 1 Palestine 1 Poland 19 Russia 5
Saudi Arabia2 Scotland 3 Slovakia 1 Spain 5
Sweden 1 Switzerland 3 Syria 3 Turkey 46
Ukraine 5 U.A.E 2 zzCountry 25 Total 282

L23* listed in a project or other ethnic designation. N=126
Albanian 1 Arab name 1
Aramaic project 1 Armenia project 5
Armenian project 78 Assyrian project 14
Badakhshani ? 1 Dagestan Lak people 1
Jewish project 24 Total 126

The R1b Cohane Project has developed a modal that shows some promise as a guide for further modal work with L23. It kind of depends on the geography and/or endogamy of our ancestors to see if defining snps or strs will be found. The best way to get there will be by the scientific method. That is why I have ordered Z2103 and L277 snp tests to compliment my L584- result. With all the testing that has occurred this winter and spring, old assumptions will go and new hypotheses will result if history is any guide.

Mike, your data has been of great value. Do you have a preferred way to reference your work?

Thanks, Joe

MJost
05-14-2013, 09:00 PM
If you are just talking about R1b-L23xL51/Z2103/5? and very broad regions, we do have considerably more data. We have about 200 67 STR haplotypes that Mark Jost has done calculations with. Quite a few of those are from Anatolia and Anatolia looks to be more diverse so it may well be older than, say, European L23xL51 but we do not that much data from SE Europe.

Maybe Mark can give us an update. I think he has looked at this both from both long haplotypes and short haplotypes/study data viewpoints.

There are many issues with using modern DNA and using STR diversity, for example the Armenian L23xL51 may actually have come from SE Europe along the west coast of the Black Sea at an earlier time.

Perhaps Mark can give us an update, but I feel comfortable saying that L23xL51, in toto, is of higher diversity and probably greater age than L11. We have found a lot of L23x51 right around the Black Sea, particularly Anatolia, so that is something to consider at the same time.

Yes the L23xL51 appears to have a tad higher variance.



R1b Early spreadsheet dataset


Using stable 67M(25used) Bird's q NO MCM's Used


IntraClade Coalescence

# w/ first tier subclades only

L23# n=212 Variance: 13.87

L23# xL51 n=186 Variance: 13.46

L23 w/ only L51 n=187 Variance: 14.34

L51* n=26 Variance: 13.29

L51* & L11* n=67 Variance: 11.99

L11* n=41 Variance: 10.33

TigerMW
05-14-2013, 10:41 PM
# w/ first tier subclades only
Thanks, Mark. What do you mean by "first tier subclades only"?

MJost
05-15-2013, 01:19 AM
Thanks, Mark. What do you mean by "first tier subclades only"?

The only including the first subclade below a specified clade. example L23 and L51 but not L11, no second deeper clades.

MJost

alan
05-16-2013, 11:17 PM
Yes the L23xL51 appears to have a tad higher variance.



R1b Early spreadsheet dataset


Using stable 67M(25used) Bird's q NO MCM's Used


IntraClade Coalescence

# w/ first tier subclades only

L23# n=212 Variance: 13.87

L23# xL51 n=186 Variance: 13.46

L23 w/ only L51 n=187 Variance: 14.34

L51* n=26 Variance: 13.29

L51* & L11* n=67 Variance: 11.99

L11* n=41 Variance: 10.33

If I am understanding the above correctly, this brings L51* closer in age to L23*, something I hadnt seen before.

TigerMW
05-17-2013, 03:50 AM
If I am understanding the above correctly, this brings L51* closer in age to L23*, something I hadnt seen before.

Yes, that's my interpretation too. In the past I've been getting L51xL11 as 10% or so more diverse than most of L11 and L23xL11 as 25-35% more but it looks like with the slower Bird's low q markers the gap narrows.... which is interesting as it makes the points between the Balkans SE France/NW Italy more critical to handle the closer ages.

I wish we had 100 or so L51xL11 long haplotypes and some without the 426=13 off-modal... and I'd feel better about diversity comparisons with it.

alan
05-17-2013, 11:38 PM
Yes, that's my interpretation too. In the past I've been getting L51xL11 as 10% or so more diverse than most of L11 and L23xL11 as 25-35% more but it looks like with the slower Bird's low q markers the gap narrows.... which is interesting as it makes the points between the Balkans SE France/NW Italy more critical to handle the closer ages.

I wish we had 100 or so L51xL11 long haplotypes and some without the 426=13 off-modal... and I'd feel better about diversity comparisons with it.

Yes it seems to make L51 far closer in age to L23 and about a third older than L11. People tend to put L11 in the 2500BC bracket and that would push L51 back to something like 4000BC. Both that age for a clade with that distribution and also a hiatus of 1500 years between L51 and L11 would require some pondering. Even if L51 is simply a parallel clade rather than ancestral to L11 then it would still require some discussion why an almost entirely western European clade is that old. Here is a thought. If L51 is nearly as old as L23, could that be the reason why ancestral true L23* is not being picked up? In other words if the L51 line quickly broke off the L23XL51 line then there wasnt much time for an ancestral L23* line for L51 to develop. That kind of logic would also really highlight the parallel rather than ancestral nature of most L23XL51 (something that of course is already well know) but it would explain things rather well. Also, if L51 really did occur soon after L23 then the distribution of L51 really makes one wonder if L23XL51 and L51* are two different stories dating to a similar time.

seferhabahir
05-25-2013, 11:24 PM
Joe B suggested I might find some answers here regarding a cousin's Geno 2.0 test result showing L23- and L150+ and some new SNPs PF7558, PF7562 and PF7563 where he tested positive. Is it worth his money (or my money, since I doubt he would pay) to do more testing at FTDNA for STR markers or other new SNPs like Z2103 or Z2105? His result indicates that L150 should probably be above L23. I'm running out of money to do further testing of cousin DNA. Does his result support the notion that the other known L23- L150+ results are valid and not testing mistakes?

I have the 37 marker results back now (kit N114224) and you can see them in the ht35 project. He is most closely matched to an Ashkenazi, Pesach Arcus b.1822 Minsk/Belarus (kit 101029), a 36/37 match.

Also, I found two other FTDNA kits with PF7558, PF7562, and PF7563 Geno 2.0 results with very different haplotypes than my cousin (both of these kits are listed as L150+ but also appear to be L23-, since L23 is not among the listed positive SNP results from Geno 2.0):

N92413 R1b1a2a1 12, 25, 14, 11, 10-15, 11, 12, 12, 14, 13, 30

N57861 R1b1a2a1 12, 25, 14, 11, 11-15, 11, 12, 12, 14, 13, 30

N114224 R1b1a2a1 12, 24, 14, 10, 11-13, 11, 12, 12, 13, 14, 29

MJost
05-26-2013, 12:11 AM
Yes it seems to make L51 far closer in age to L23 and about a third older than L11. People tend to put L11 in the 2500BC bracket and that would push L51 back to something like 4000BC. Both that age for a clade with that distribution and also a hiatus of 1500 years between L51 and L11 would require some pondering. Even if L51 is simply a parallel clade rather than ancestral to L11 then it would still require some discussion why an almost entirely western European clade is that old. Here is a thought. If L51 is nearly as old as L23, could that be the reason why ancestral true L23* is not being picked up? In other words if the L51 line quickly broke off the L23XL51 line then there wasnt much time for an ancestral L23* line for L51 to develop. That kind of logic would also really highlight the parallel rather than ancestral nature of most L23XL51 (something that of course is already well know) but it would explain things rather well. Also, if L51 really did occur soon after L23 then the distribution of L51 really makes one wonder if L23XL51 and L51* are two different stories dating to a similar time.

Here is the Generation calculations for the above posted variances using MarkoH's summed mutation rate for the Bird's Stable STRs used out of 67. As you can see, the number of generations is affected by which STRs have more or less variance in each group of HTs. And possibly, L23# and
L23# xL51 were bottle necked stunting the age (and its not due to a low sample size). You can split up the generations and give each portion their correct years per generation to come up with a suggest YBP.




Rate: 0.0947
L23#____________ Var 13.87________Gen 146.5
L23# xL51________Var 13.46________Gen 142.1
L23 w/ only L51____Var 14.34________Gen 151.4
L51*_____________Var 13.29________Gen 140.3
L51* & L11*_______Var 11.99________Gen 126.6
L11*_____________Var 10.33________Gen 109.1


MJost

alan
05-26-2013, 06:44 PM
Here is the Generation calculations for the above posted variances using MarkoH's summed mutation rate for the Bird's Stable STRs used out of 67. As you can see, the number of generations is affected by which STRs have more or less variance in each group of HTs. And possibly, L23# and
L23# xL51 were bottle necked stunting the age (and its not due to a low sample size). You can split up the generations and give each portion their correct years per generation to come up with a suggest YBP.






MJost

I just want to check your abbreviations. What does # mean? Also what does w/only mean? I am not sure I understand these.

MJost
05-26-2013, 08:15 PM
I just want to check your abbreviations. What does # mean? Also what does w/only mean? I am not sure I understand these.

L23 w/ only L51 was L23 with just L51 included only and no other subclades. The SNPs labled with the # is only includes the first subclade below a specified clade. example L23 and L51 but not L11, no second more recent subclades.

Including only one subclade below and not including the larger subclades at three or more below, seems to limit the overall saturation that would cause a washout of the older HTs (ratio's) giving it a younger age. Think of it as a sliding window variance method. If starting with a small ancestral Clade that was much younger, it might be less effected.

MJost

TigerMW
06-02-2013, 02:54 PM
I've got a tinyurl for the descendency tree now too. http://tinyurl.com/R1b-Tree


I try to keep this descendency tree graphic current. It is the Y DNA tree/phylogeny for the early branches of R1b, as best as I know it. R1b is marked by the SNP M343 so all R1b people have M343+. Please post any corrections or omissions here.


https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg

Rathna
06-02-2013, 03:21 PM
I've got a tinyurl for the descendency tree now too. http://tinyurl.com/R1b-Tree
By the recent Geno 2.0 of Raza, Varanasi, India, we have understood (actually the administrators of the project after than me) that L278 is on the same plane of M343 and M415 and upstream P25. This before someone may split M343/L278/M415.
There is also a new SNP, YSC0000224, between these three and P25.

dartraighe
06-02-2013, 06:22 PM
What is important about the SNP L389+?

Rathna
06-02-2013, 06:29 PM
What is important about the SNP L389+?

L388 and L389 define now R1b1*and subclades, then only this line is the ancestor of the subclades. It is cluster A of the R1b1 FTDNA Project, but, amongst them, I have always said that only those clades with YCAII=18-23 (and 18-22 found in Italian samples: Demao and Toniolo) are the possible ancestors of R-P297, then R-M73 and M269.

dartraighe
06-02-2013, 07:19 PM
I see it on my Geno2.0 results, L389+ along with a lot of other SNPs.

[[[ Mikewww/Moderator on 6/2/2013: This is all very nice, but if you are unfamiliar with what this means you should go to a newbie forum and ask questions. If that is the case, here is an option: http://groups.yahoo.com/group/DNA-NEWBIE/
However, I think you are an experienced poster on multiple forums so given your background this post appears to be devoid of content. Please only post if you have something meaningful and applicable in context of the discussion. ]]]

seferhabahir
06-03-2013, 03:45 PM
I've got a tinyurl for the descendency tree now too.

Mike,

You have much more latitude than ISOGG or FTDNA. Given the new evidence that PF7558, PF7562 and PF7563 seems to define an L23- group under L150.1, would you consider modifying your chart? I now count four known kits with these three SNPs that are L150+ and L23- (you could still put L150.1 in a cloud below M269 but above L23 and a new parallel box with the PF SNPs in it.

f126775 Moishe Bardiga, b. abt 1740 Berestechko, Ukraine Ukraine R1b1a2a1

N114224 Aleksandr Lifschitz, b. 1840, Russian Empire Belarus R1b1a2a1

N92413 R1b1a2a1

N57861 R1b1a2a1

TigerMW
06-03-2013, 07:37 PM
Mike,

You have much more latitude than ISOGG or FTDNA. Given the new evidence that PF7558, PF7562 and PF7563 seems to define an L23- group under L150.1, would you consider modifying your chart? I now count four known kits with these three SNPs that are L150+ and L23- (you could still put L150.1 in a cloud below M269 but above L23 and a new parallel box with the PF SNPs in it.

f126775 Moishe Bardiga, b. abt 1740 Berestechko, Ukraine Ukraine R1b1a2a1
N114224 Aleksandr Lifschitz, b. 1840, Russian Empire Belarus R1b1a2a1
N92413 R1b1a2a1
N57861 R1b1a2a1

Here is an attempt. Is this what you are talking about? Generally I try to use clouds for SNP positioning that is not validated or are otherwise unclear or private.

https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg

Can the R1b-M269+ U106- P312- (R1b ht35) project admin, Peter Hrechdakian, confirm how we should position L150.1? It seems quite uncertain at this point. ISOGG still lists L150.1 as equivalent to L23.
• • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349, L150.1/PF6274.1

I just wonder if L150 is too unstable to use at all.

Rathna
06-03-2013, 07:59 PM
Can the R1b-M269+ U106- P312- (R1b ht35) project admin, Peter Hrechdakian, confirm how we should position L150.1? It seems quite uncertain at this point. ISOGG still lists L150.1 as equivalent to L23.
• • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349, L150.1/PF6274.1

I just wonder if L150 is too unstable to use at all.

We have discussed a lot about L150 in the past, but probably it isn’t true that it is unstable, as all the people tested also by Geno 2.0 demonstrate that it is largely stable. The solution I gave I think is reliable: every haplogroup is L150-. L23 has the mutation to L150+. Amongst these only two so far (Romitti and Seymour) had a back mutation to L150-. Amongst the R-M269*, which is L150-, there is clade (all the Jews/R-M269* but also Gashi now) who had a mutation to L150+ independent from the mutations happened amongst the L23. I think that everything is clear now and L150 is stable and important.

To Mikewww: perhaps you lacked a post of mine: L278 isn’t at the same level of P25, but on the line of M343 and M415. P25 defines now R1b1* upstream L388/L389 and V88. This is demonstrated by the Geno 2.0 of Raza from Varanasi (India).

MJost
06-03-2013, 08:20 PM
Isogg
http://isogg.org/tree/ISOGG_HapgrpR.html

R1b1 = L278, M415/PF6251, P25.1, P25.2, P25.3 <<< up to .3 in various other non-R subclades

and
in the R list notes
Added .1 to L150, .1 to PF6274; added L150.2!, PF6274.2! (!=back mutation), CTS1078/Z2103, Z2105 to tree on 24 March 2013

MJost

TigerMW
06-03-2013, 08:35 PM
We have discussed a lot about L150 in the past, but probably it isn’t true that it is unstable, as all the people tested also by Geno 2.0 demonstrate that it is largely stable. The solution I gave I think is reliable: every haplogroup is L150-. L23 has the mutation to L150+. Amongst these only two so far (Romitti and Seymour) had a back mutation to L150-. Amongst the R-M269*, which is L150-, there is clade (all the Jews/R-M269* but also Gashi now) who had a mutation to L150+ independent from the mutations happened amongst the L23. I think that everything is clear now and L150 is stable and important.

To Mikewww: perhaps you lacked a post of mine: L278 isn’t at the same level of P25, but on the line of M343 and M415. P25 defines now R1b1* upstream L388/L389 and V88. This is demonstrated by the Geno 2.0 of Raza from Varanasi (India).

So L278 is below M343 and above P25, right?

My baseline on this charts is ISOGG. I only add to this when we have pretty good reason, like the citizen-sciencist R1b1a2 paper that has updates that ISOGG hasn't been able to validate yet.

As of now, ISOGG http://isogg.org/tree/ISOGG_HapgrpR.html has
• • • R1b1 L278, M415/PF6251, P25_1, P25_2, P25_3

Can the appropriate R1b x297 administrators confirm that L278 should be moved up?


As of now, ISOGG http://isogg.org/tree/ISOGG_HapgrpR.html has
• • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349, L150.1/PF6274.1

Are you saying L150.1+ is above L23 and below M269 by "(all the Jews/R-M269* but also Gashi now) who had a mutation to L150+ independent from the mutations happened amongst the L23" ? I wasn't clear on if this is a third mutation or just evidence that L150.1 happened before L23.

Has Thomas Krahn got a different positioning in his draft tree for L150.1 and L150.2? Can the R1b ht35 project administrators confirm how to handle L150?

I'm not a project administrator for these early branching subclades so I'd like to get confirmation from people who are doing this.

Rathna
06-03-2013, 08:43 PM
So L278 is below M343 and above P25, right?

My baseline on this charts is ISOGG. I only add to this when we have pretty good reason, like the citizen-sciencist R1b1a2 paper that has updates that ISOGG hasn't been able to validate yet.

As of now, ISOGG http://isogg.org/tree/ISOGG_HapgrpR.html has
• • • R1b1 L278, M415/PF6251, P25_1, P25_2, P25_3

Can the appropriate R1b x297 administrators confirm that L278 should be moved up?


As of now, ISOGG http://isogg.org/tree/ISOGG_HapgrpR.html has
• • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349, L150.1/PF6274.1

Are you saying L150.1+ is above L23 and below M269 by "(all the Jews/R-M269* but also Gashi now) who had a mutation to L150+ independent from the mutations happened amongst the L23" ? I wasn't clear on if this is a third mutation or just evidence that L150.1 happened before L23.

Has Thomas Krahn got a different positioning in his draft tree for L150.1 and L150.2? Can the R1b ht35 project administrators confirm how to handle L150?

I'm not a project administrator for these early branching subclades so I'd like to get confirmation from people who are doing this.

267597 Raza Varanasi R1b R-M343 CTS10168+, CTS10362+, CTS109+, CTS11358+, CTS11575+, CTS11726+, CTS125+, CTS12632+, CTS1996+, CTS2134+, CTS3135+, CTS3331+, CTS3358+, CTS3431+, CTS3536+, CTS3654+, CTS3662+, CTS3868+, CTS3996+, CTS4364+, CTS4368+, CTS4437+, CTS4443+, CTS4740+, CTS5318+, CTS5457+, CTS5532+, CTS5884+, CTS6135+, CTS6383+, CTS6800+, CTS6907+, CTS7922+, CTS7933+, CTS8243+, CTS8980+, CTS9828+, F1046+, F115+, F1209+, F1302+, F1320+, F1329+, F1704+, F1714+, F1753+, F1767+, F180+, F2048+, F2075+, F211+, F212+, F2142+, F2155+, F2302+, F2402+, F2482+, F2587+, F2688+, F2710+, F2837+, F29+, F295+, F2985+, F2993+, F3111+, F313+, F3136+, F33+, F332+, F3335+, F344+, F3556+, F356+, F359+, F3599+, F3692+, F378+, F4+, F47+, F506+, F556+, F63+, F640+, F647+, F652+, F671+, F719+, F82+, F83+, F93+, L132+, L15+, L16+, L278+, L350+, L468+, L470+, L471+, L498+, L506+, L566+, L721+, L747+, L768+, L779+, L781+, L82+, M139+, M168+, M207+, M235+, M294+, M343+, M415+, M42+, M45+, M526+, M89+, M94+, P128+, P131+, P132+, P135+, P136+, P138+, P14+, P141+, P145+, P146+, P148+, P151+, P158+, P159+, P160+, P166+, P187+, P207+, P225+, P226+, P228+, P229+, P230+, P232+, P233+, P235+, P236+, P237+, P238+, P240+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P295+, PAGES00083+, PF1016+, PF1029+, PF1031+, PF1040+, PF1046+, PF1061+, PF1092+, PF1097+, PF110+, PF1203+, PF1269+, PF1276+, PF15+, PF192+, PF210+, PF212+, PF223+, PF234+, PF258+, PF2591+, PF2593+, PF2599+, PF2600+, PF2608+, PF2611+, PF2615+, PF2624+, PF263+, PF2631+, PF2643+, PF272+, PF2745+, PF2747+, PF2748+, PF2749+, PF2770+, PF278+, PF292+, PF316+, PF325+, PF342+, PF500+, PF5465+, PF5466+, PF5468+, PF5471+, PF5851+, PF5853+, PF5854+, PF5865+, PF5869+, PF5871+, PF5882+, PF5886+, PF5887+, PF5888+, PF5953+, PF5956+, PF5957+, PF5964+, PF5965+, PF5982+, PF6007+, PF601+, PF6063+, PF6145+, PF6246+, PF6250+, PF6270+, PF6272+, PF667+, PF719+, PF720+, PF725+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF844+, PF892+, PF937+, PF951+, PF954+, PF970+, V186+, V189+, V205+, V52+, V9+, YSC0000067+, YSC0000075+, YSC0000176+, YSC0000179+, YSC0000182+, YSC0000186+, YSC0000201+, YSC0000205+, YSC0000207+, YSC0000227+, YSC0000230+, YSC0000232+, YSC0000233+, YSC0000251+, YSC0000270+, YSC0000279+, YSC0000288+, Z486+

Yes, Geno 2.0 doesn’t test P25 and we don’t know if Raza is positive or negative. Anyway he is negative for YSC0000224+, present both in L389+ and V88+, who are positive for P25.

TigerMW
06-03-2013, 10:00 PM
267597 Raza Varanasi ... L278+ ... M343+, M415+
...
Yes, Geno 2.0 doesn’t test P25 and we don’t know if Raza is positive or negative. Anyway he is negative for YSC0000224+, present both in L389+ and V88+, who are positive for P25.

I'm probably missing some other information you have. If we don't know his P25 value we can't say L278 is upstream of P25. Has Krahn or anyone looked at YSC0000224? Is it stable? Are you looking at Varanasi's raw Geno2 file?

The project admins should be tracking L278 and YSC0000224, right? I don't see this in the subgroupings. Can we get one of the project admins or the ISOGG person who covers this to give us an update.

seferhabahir
06-04-2013, 12:34 AM
Are you saying L150.1+ is above L23 and below M269 by "(all the Jews/R-M269* but also Gashi now) who had a mutation to L150+ independent from the mutations happened amongst the L23" ? I wasn't clear on if this is a third mutation or just evidence that L150.1 happened before L23.

Has Thomas Krahn got a different positioning in his draft tree for L150.1 and L150.2? Can the R1b ht35 project administrators confirm how to handle L150?

I think Rathna and I disagree about whether L150 had two separate positive mutations, one under L23 and one that was part of the M269xL23 group. It looks to me that L150.1+ is above L23 and below M269 and is the reason that we find a bunch of L23- people (either Sanger tested for L23 which I think Bardiga was, or Geno 2.0 tested for L23 which would be all the other three kits with the positive PF trio) that are L150.1+ because I am looking for a M269xL23 that is L150.1- and haven't seen one. If there is one, perhaps someone can point it out. And if there really were three different L150 mutations (two independent positive mutations and a third back mutation, it really is not a good SNP to make heavy use of).

Thomas Krahn has L150 below L23 in his draft tree, which I think is incorrect. If it was my chart (but it's not, it is yours so I defer to you and you shouldn't feel obligated until someone with more expertise can weigh in), I would tend to put L150.1 in a cloud above L23 and below M269 and the three PF SNPs in a cloud below L150.1 but parallel to L23. I haven't seen anyone with PF7558, PF7562, and PF7563 test negative for L150 to date. All four are L150+ (at least from their Geno 2.0 results). We don't know whether Gashi has the PF SNPs, but he appears to also be L150+ and L23- from his tests. If these PF SNPs become available, we could test Gashi for them.

R.Rocca
06-04-2013, 01:41 AM
I think Rathna and I disagree about whether L150 had two separate positive mutations, one under L23 and one that was part of the M269xL23 group. It looks to me that L150.1+ is above L23 and below M269 and is the reason that we find a bunch of L23- people (either Sanger tested for L23 which I think Bardiga was, or Geno 2.0 tested for L23 which would be all the other three kits with the positive PF trio) that are L150.1+ because I am looking for a M269xL23 that is L150.1- and haven't seen one. If there is one, perhaps someone can point it out. And if there really were three different L150 mutations (two independent positive mutations and a third back mutation, it really is not a good SNP to make heavy use of).

Thomas Krahn has L150 below L23 in his draft tree, which I think is incorrect. If it was my chart (but it's not, it is yours so I defer to you and you shouldn't feel obligated until someone with more expertise can weigh in), I would tend to put L150.1 in a cloud above L23 and below M269 and the three PF SNPs in a cloud below L150.1 but parallel to L23. I haven't seen anyone with PF7558, PF7562, and PF7563 test negative for L150 to date. All four are L150+ (at least from their Geno 2.0 results). We don't know whether Gashi has the PF SNPs, but he appears to also be L150+ and L23- from his tests. If these PF SNPs become available, we could test Gashi for them.

So the PF SNPs seem to be the real important SNPs and L150 may or may not be stable enough, right?

seferhabahir
06-04-2013, 03:33 AM
So the PF SNPs seem to be the real important SNPs and L150 may or may not be stable enough, right?

Well, I think it looks that way. Showing up with an L150+ result now doesn't really say much. FWIW, Geno 2.0 lists PF7558 as the terminal SNP. I don't really know if there is a hierarchy for the three. They may be phylogenetically equivalent, as all four kits showed up with all three positive. If FTDNA can offer one or all of them, then perhaps we can get some other M269* looking for a home to test. These PF SNPs are broader in scope than just the M269xL23 Ashkenazi cluster, given what I see in the 12 marker STRs for kits N92413 and N57861.

Rathna
06-04-2013, 04:04 AM
So the PF SNPs seem to be the real important SNPs and L150 may or may not be stable enough, right?

That R-M269* is L150- is possible to see on the “Adriano Squecco spreadsheet” where there are many R-M269 and are negative. L150 has been so long debated, but if the administrators of the “ht 35 project” admitted it like a back mutation in L23 (at the beginning only for Romitti and Seymour, after for many others but who are L150+: I asked clarification about this), I don’t understand why the same L150 couldn’t be taken in consideration for those R-M269* with L150+, whereas all the others of the same haplogroup are clearly – (negative) like all the other haplogroups. This may be seen on the “Adriano Squecco spreadsheet”.
It is clear that these PF SNPs are very important, because they define a R-M269 subclade where there are all the R-M269 Jews and these other two: a Greek and an anonymous American linked to the Greek by his STRs values.
If you, Richard Rocca, give a glance to all the Geno 2.0 published, you can see that L150 is reliable, because all the subclades of R-L23 are + (positive).

PS. I have written a lot about Gashi, above all on Worldfamilies, and it seems to me he is positive and is R-M269*, then he would be linked to the Jewish cluster and to the other two, who, being from Greece, let me think that this subclade comes from the Balkan.

E16492 Hysen Gashi, b. 19xx R1b1a2a1 R-L150 L150+, L23-, L49-, L51-, M269+, P312-, U106-

AJL
06-04-2013, 05:11 AM
That R-M269* is L150- is possible to see on the “Adriano Squecco spreadsheet” where there are many R-M269 and are negative.

The Squecco spreadsheet clearly reads in the Comments colum: "L150 (R1b1a2a1) [WARNING: v2/v3 inconsistent results]." This might mean a flippy SNP, or a stable second instance, or it might mean that the 23andme reads are garbage. You'll have to rely on actual Sanger sequencing, not just chip technology, to sort this out.

Rathna
06-04-2013, 05:56 AM
The Squecco spreadsheet clearly reads in the Comments colum: "L150 (R1b1a2a1) [WARNING: v2/v3 inconsistent results]." This might mean a flippy SNP, or a stable second instance, or it might mean that the 23andme reads are garbage. You'll have to rely on actual Sanger sequencing, not just chip technology, to sort this out.

For V2 (that I did) 23andme is reliable. Anyway Gashi has been tested by FTDNA:

E16492 Hysen Gashi, b. 19xx R1b1a2a1 R-L150 L150+, L23-, L49-, L51-, M269+, P312-, U106-

and I bet with you that he will get these three Sardinian (you asked who said this: me) SNPs.

TigerMW
06-04-2013, 01:32 PM
Thanks, all, for the informative discussion. For the current time, I'm going to stick close to the vest (be conservative) and follow ISOGG but try to denote that there are inconsistencies with L150. It appears that testing for PF7558, PF7562 and PF7563 is critical to better understand this. Hopefully the R1b ht35 project is considering how to explore this.

https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg

Rathna
06-04-2013, 07:09 PM
I have seen that, finally, the administrators of the “ht 35 FTDNA Project” decided to form this cluster:

_a. R1b1a2: L150.?+ L23- L51- L11- (also possibly PF7558+, PF7562+ & PF7563+)

N114224 Aleksandr Lifschitz, b. 1840, Russian Empire Belarus R1b1a2a1

226720 Dov Ber Fabrikant b.c. 1810 Vetka, Belarus Belarus R1b1a2a1

126775 Moishe Bardiga, b. abt 1740 Berestechko, Ukraine Ukraine R1b1a2a1

E16492 Hysen Gashi, b. 19xx Albania

N92413 Greece R1b1a2a1

seferhabahir
06-04-2013, 09:36 PM
...the administrators of the “ht 35 FTDNA Project” decided to form this cluster:

_a. R1b1a2: L150.?+ L23- L51- L11- (also possibly PF7558+, PF7562+ & PF7563+)

N114224 Aleksandr Lifschitz, b. 1840, Russian Empire Belarus R1b1a2a1
226720 Dov Ber Fabrikant b.c. 1810 Vetka, Belarus Belarus R1b1a2a1
126775 Moishe Bardiga, b. abt 1740 Berestechko, Ukraine Ukraine R1b1a2a1
E16492 Hysen Gashi, b. 19xx Albania
N92413 Greece R1b1a2a1

Everyone involved is now at the same level of understanding, including the owners of the above kits.

So, if any further tests get similar results, they can be placed in the same cluster. :D

seferhabahir
07-04-2013, 03:56 PM
Everyone involved is now at the same level of understanding, including the owners of the above kits.

So, if any further tests get similar results, they can be placed in the same cluster. :D

I see that PF7558, PF7562 and PF7563 are now available as standalone SNP tests from FTDNA at $39 apiece. According to Thomas Krahn, PF7563 is probably the best bet (the least ambiguous test result) since the other two SNPs have very similar regions on the X chromosome. E16492 (Gashi) should order these three to see what happens and how broad these SNPs might be. Certainly it encompasses the Jewish M269xL23 group but maybe/probably also Gashi and anyone else that tests as L23- L150+.

Joe B
07-23-2013, 08:34 PM
For the current time, I'm going to stick close to the vest (be conservative) and follow ISOGG but try to denote that there are inconsistencies with L150.

Thanks for making the easy to read phylogenetic trees and I agree with being conservative and following ISOGG.
With an eye to the future, this paper may be worth a look.
An experimental computer-generated Y-chromosomal phylogeny, leveraging public Geno 2.0 results and the current ISOGG tree Chris Morley, 17th July 2013.
It is refreshing that the author seems to be rather humble about his project.
This is a large .pdf document.
http://ytree.morleydna.com/ExperimentalGenoPhylogeny.pdf

An example from the Morley tree.
R1b1a2a, L150/PF6274, L23/PF6534/S141, L49/S349,
R1b1a2a–1, L448, PF6404
R1b1a2a1, M412/L51/PF6536/S167
R1b1a2a1–1, CTS6889, PF7589
R1b1a2a2, CTS1083, Z2103/CTS1078, Z2105
R1b1a2a2b, L277
R1b1a2a2c, L150/PF6274
R1b1a2a2–1, CTS7763, CTS8966
R1b1a2a2–2, between R1b1a2a2–2 and R1b1a2a2a: CTS1848, PF3449, PF7580
R1b1a2a2a, L584
R1b1a2a–1–1, CTS7822
R1b1a2a–1–1–1, CTS1219
R1b1a2a–2, PF7558, PF7562, PF7563

[[[ Mikewww/Moderator on 7/23/2013: Thanks, Joe. I haven't used it yet. I noticed there is a thread on this under Y chromosome under "Other". I am interested in the tool, but I think over here is the right place to discuss the tool. : http://www.anthrogenica.com/showthread.php?1132-C-Morley-s-Y-DNA-phylogeny-Geno-2-0-ISOGG-integration&p=10392&viewfull=1#post10392 ]]]

TigerMW
10-07-2013, 03:33 AM
Humanist has updated me on L943 so I'm adding it to the descendency tree chart.
Hi Mike. Did you create the above graphic? If so, how about adding a spot for L943 below L584? I do not see much discussion on the forums about it. From the scant testing to date, two Assyrian R-L584 men are derived for L943, and one Assyrian R-L584 man is ancestral.

http://i1178.photobucket.com/albums/x372/paulgiva78/passover/l943_gd-1.jpg

Here is the new version:
https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg

TigerMW
10-24-2013, 01:04 AM
....
An experimental computer-generated Y-chromosomal phylogeny, leveraging public Geno 2.0 results and the current ISOGG tree Chris Morley, 17th July 2013.
...
An example from the Morley tree.
....
R1b1a2a1, M412/L51/PF6536/S167
...

I want to make sure I have L51 correctly. Is PF6536 physically identical to L51 or phylogenetically equivalent and does that still remain consistent?



Z2103 CTS1078 Z2103 7246135 7186135
Z2104 PF7575 Z2104 12677962 14167962
Z2105 14256826 15747432
Z2106 12723646 14213646
Z2107 CTS7340 Z2107 15938378 17428984
Z2108 12176901 13716901
Z2109 CTS1843 Z2109 12601439 14091439
Z2110 CTS7822 Z2110 16194093 17684699

Z2111 3323086 3263086
Z2112 4652104 4592104
Z2113 6028320 5968320
Z2114 13757450 15248056
Z2115 CTS5981 Z2115 15101312 16591918
Z2116 CTS10379 Z2116 17936652 19427258
Z2117 7544708 7484708
Z2118 PF7589 Z2118 8127783 8067783
Z2119 CTS7153 Z2119 15833558 17324164
Z2120 12332081 13822081

My understanding, from Vince V. I think, is that all L51xL11 was probably Z2113+ ? Is that still true?

I saw this today from Richard R on another thread. I notice Rathna had referred to Z2115 also.

Of interest in the GoNL data, the counts show that there are two L51(xL11) samples that are not derived for Z2115, which has been found in every L51(xL11) sequence in the 1KG, PGP and Francalacci datasets (Tuscany, Sardinia, Puerto Rico, and USA). http://www.anthrogenica.com/showthread.php?1489-A-deeper-think-about-beakers-in-Britain-and-R1b-DNA-quot-from-the-West-quot&p=17086&viewfull=1#post17086

Is that just a typo... Z2115 or is it is Z2113 or are the two equivalent phylogenetically in some way?

R.Rocca
10-24-2013, 01:24 AM
I want to make sure I have L51 correctly. Is PF6536 physically identical to L51 or phylogenetically equivalent and does that still remain consistent?




My understanding, from Vince V. I think, is that all L51xL11 was probably Z2113+ ? Is that still true?

I saw this today from Richard R on another thread. I notice Rathna had referred to Z2115 also.
http://www.anthrogenica.com/showthread.php?1489-A-deeper-think-about-beakers-in-Britain-and-R1b-DNA-quot-from-the-West-quot&p=17086&viewfull=1#post17086

Is that just a typo... Z2115 or is it is Z2113 or are the two equivalent phylogenetically in some way?

Based on the Francalacci and PGP data, it looks like Z2115 is the highest level SNP in the L51(xL11) group.

Rathna
10-24-2013, 05:07 AM
Based on the Francalacci and PGP data, it looks like Z2115 is the highest level SNP in the L51(xL11) group.

To be Z2115-, whereas all the others tested so far are + and that this is (so far) the final SNP of the series (that known so far) doesn't mean anything about the origin of R-L51.
We have a R-L51 in the "ht 35 FTDNA Project":

143613 Abraham van Tielroe m. 1639 Domburg, NL Netherlands R1b1a2a1a
13 23 14 11 11-14 13 12 12 13 13 28 20 9-10 11 11 24 15 19 30 15-16-17-18 10 12 19-23 15 15 18 19 36-37 12 12 11 9 15-16 8 10 10 8 10 9 12 22-23 16 10 12 12 15 8 12 20 20 14 12 11 13 11 11 12 12
He is in the range of the R-L51 haplotypes, but with some weird values (DYS458=20, DYS511=9, DYS481=20), which may demonstrate that he belongs to a different clade amongst the paragroup R-L51, which will have many different subclades which have to be tested for all these SNPs.

Also for R-L11 we have two Dutches in the"ht 35 FTDNA project":

142454 Jacob Jobse 1551/1626 Ouddorp NL Netherlands R1b1a2a1a1
13 24 14 11 11-12 12 12 12 12 14 29 16 9-10 11 11 25 15 19 30 15-15-17-18 11 11 19-23 15 15 17 16 38-41 12 12
128054 Dirk Gerritsz van der Mij, 1615 Noordwijk Netherl Netherlands R1b1a2a1a1
13 24 14 11 11-14 12 12 12 12 14 28 16 9-10 11 11 25 15 19 30 15-15-17-19 11 11 19-23 16 15 17 17 37-38 12 12 11 9 15-16 8 10 10 8 10 10 12 23-23 18 10 12 12 14 8 12 21 20 15 12 11 14 11 11 12 12 35 15 9 16 12 27 26 19 12 12 15 12 11 9 12 12 10 11 10 30 12 13 24 14 10 10 22 15 20 13 23 17 11 15 25 12 23 18 10 14 17 9 13 11

They belong clearly to the same haplotype with DYS392=14, and, because the second is tested for 111 markers, he has also DYS461=13, whereas the modal is 12 and also R-P312 and R-U106 have 12. I'd say that Netherlands has a cluster of the paragroup (because also L11 is a paragroup) the farthest one from the line which generated the subclades.

Humanist
10-24-2013, 04:48 PM
Humanist has updated me on L943 so I'm adding it to the descendency tree chart.

Thank you!

R.Rocca
10-25-2013, 02:53 PM
To be Z2115-, whereas all the others tested so far are + and that this is (so far) the final SNP of the series (that known so far) doesn't mean anything about the origin of R-L51.

First, I didn't say anything about where L51 originated, I just simply stated a fact...the GoNL dataset contains two L51+ derived results more than L11 derived results, therefore there are two unaccounted for L51+ L11- samples. There are no Z2115+ derived samples in their dataset. Therefore, we can assume that the dataset contains two L51+ Z2115- samples.

Secondly, we've seen you post for years about "the most ancestral" haplotypes. Don't you think that having an L51+ Z2115- sample to compare future L51+ Z2115+ samples to is extremely important, regardless of STR signature?

TigerMW
10-26-2013, 06:30 PM
We have a R-L51 in the "ht 35 FTDNA Project":

143613 Abraham van Tielroe m. 1639 Domburg, NL Netherlands

Also for R-L11 we have two Dutches in the"ht 35 FTDNA project":

142454 Jacob Jobse 1551/1626 Ouddorp NL Netherlands
128054 Dirk Gerritsz van der Mij, 1615 Noordwijk Netherl

I have all of these guys in the R1b-Early_Haplotypes spreadsheet and have tried to classify them by off-modal STR pattern. I know you don't like spreadsheets but you can download one for free from openoffice.org. The usefulness of any one STR is not that great. It is recurrent patterns that can be helpful in comparison with other people. The more the merrier, both STRs and other people (number of haplotypes.)

Rathna
10-26-2013, 07:45 PM
I have all of these guys in the R1b-Early_Haplotypes spreadsheet and have tried to classify them by off-modal STR pattern. I know you don't like spreadsheets but you can download one for free from openoffice.org. The usefulness of any one STR is not that great. It is recurrent patterns that can be helpful in comparison with other people. The more the merrier, both STRs and other people (number of haplotypes.)

It isn't true I don' like spreadsheet. I like them very much and I'd use them willing, only if I were able to upload them and only to see them. Unfortunately I often am not able to do so. For years I wasn't able to see the "Adriano Squecco spreadsheet" because it was linked with DNA-forums and when I was banned someone forbade me the access and this has lasted for years by my PC. Only to-day I have look at the "Itai Perez spreadsheet" because I have upload Office for proof (for free) and I have seen the data of DeMao I had by him and did know his mutation in PF7481.
Often it is a problem of programs.

Joe B
12-16-2013, 05:05 AM
Thanks, all, for the informative discussion. For the current time, I'm going to stick close to the vest (be conservative) and follow ISOGG but try to denote that there are inconsistencies with L150. It appears that testing for PF7558, PF7562 and PF7563 is critical to better understand this. Hopefully the R1b ht35 project is considering how to explore this.

https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg
Hey Mike,

Would you consider adding Geno 2.O terminal SNPs CTS7822 and PF7580 to the Early R1b tree? That way the Geno 2.0 folks can visually find their place on the tree and know if L277 or L584 should be tested.

A Phylogenetic Guess

PF7558* R-M269>L150>PF7558 PF7558+/PF7562+/PF7563+, L23-, Z2103-
Z2103*(Z2105*) R1b-M269>L23>Z2103>Z2105 L277-, L584-
L277* R1b-M269>L23>Z2103>Z2105>L277
CTS7822* R1b-M269>L23>Z2103>Z2105>CTS7822 CTS9219-
CTS9219* R1b-M269>L23>Z2103>Z2105>CTS7822>CTS9219
L584* R1b-M269>L23>Z2103>Z2105>PF7580>L584 L943-
L943* R1b-M269>L23>Z2103>Z2105>PF7580>L584>L943*
CTS1848 and PF3449 placement is unclear. Could this be the order? L584>CTS1848>PF3449>L943*?)

L23+, L478+, L49+, PF6404+ seem to be on the same level.

Except for the PF7558 level, L150 seems to be of no value.
smal has a nice Z2103 mini-tree that shows it better than I can explain it. http://www.anthrogenica.com/showthread.php?1586-From-R-L23-L150-to-R-PF7580&p=22598&viewfull=1#post22598
Thanks

Rathna
12-16-2013, 06:44 AM
Except for the PF7558 level, L150 seems to be of no value.


Joe B, for saying this, i.e. that L150- is worth only under Z2110, we have to see a Geno 2.0 or a Chromo 2 or something else of Romitti, who is the other L23 with L150-. I think having demonstrated that he doesn't belong to the cluster of Seymour and we don't either know if he is Z2110+. Thus L150- has probably happened also elsewhere in the tree.
Beyond this we have always to see some R-M269* which is L150-. It is presupposed, but I haven't seen anyone so far: all the R-M269 tested are L150+ and PF7558/PF7562/PF7563+.

Joe B
04-30-2014, 06:56 PM
A new and detailed R1b-Z2103 Phylogenetic Tree is up and posted to the R1b1a2 (P312- U106-) DNA Project (aka ht35 Project) (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults). Just scroll down to the second tree. This Z2103 tree was hand crafted by smal. Impressive as usual. Thanks to smal and Peter for getting this posted to the project homepage.

brygian
04-30-2014, 07:57 PM
A new and detailed R1b-Z2103 Phylogenetic Tree is up and posted to the R1b1a2 (P312- U106-) DNA Project (aka ht35 Project) (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults). Just scroll down to the second tree. This Z2103 tree was hand crafted by smal. Impressive as usual. Thanks to smal and Peter for getting this posted to the project homepage.

A big thank you. Hopefully my YSEQ tests will bring even more clarity. I ordered Z2103, Z2104, Z2105, CTS9416, PF7585, Z2106, Z2109, Z2110 and CTS9219 from YSEQ. When the results are out I will also order Y6687319, Y14629851, S20902, S17864 and S12460. Unfortunately Z2107 and Z2108 are not offered by YSEQ. It is strange that other people have been tested for Z2107 and Z2108 at YSEQ but they told me the SNPs cannot be ordered. At the same time they seem to be having a hard time with Z2106 but it is in their catalog.

Geolocke
05-01-2014, 12:17 AM
A new and detailed R1b-Z2103 Phylogenetic Tree is up and posted to the R1b1a2 (P312- U106-) DNA Project (aka ht35 Project) (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults). Just scroll down to the second tree. This Z2103 tree was hand crafted by smal. Impressive as usual. Thanks to smal and Peter for getting this posted to the project homepage.

Many thanks to Smal, Peter & JoeB for this updated information!

Paulie
05-01-2014, 04:13 AM
A new and detailed R1b-Z2103 Phylogenetic Tree is up and posted to the R1b1a2 (P312- U106-) DNA Project (aka ht35 Project) (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults). Just scroll down to the second tree. This Z2103 tree was hand crafted by smal. Impressive as usual. Thanks to smal and Peter for getting this posted to the project homepage.

Now we wait for a little update on the left side of those charts. :)

http://www.anthrogenica.com/showthread.php?2370-R1b-L51-Results-discussion&p=38764&viewfull=1#post38764

Joe B
10-03-2014, 06:14 AM
An updated R1b1b2 (P312- U106-) DNA Project advanced phylogenetic tree has just been posted thanks to smal. Please note that 203564 Big Y results add a new new level to R1b-CTS9219. 169774 belongs to the S6868 branch which is quite a few levels downstream of R-L11. The Z2109 level is getting very interesting with at least three independent lines.
Thanks smal for your analysis and our very current haplotree.
As a reminder, please go to the R1b1b2 (P312- U106-) DNA Project for a correct haplotree and recommended SNPs.
https://www.familytreedna.com/public/ht35new/

Joe B
10-07-2014, 04:08 PM
R-YSC0000072 is not a good haplogroup and YSC0000072 is not a good SNP test. Geno 2.0 is positive while Sanger sequencing is negative for YSC0000072. FTDNA has this bad SNP scheduled for removal from their Y-tree. Next update to that tree is unknown.
If anybody has a question about what SNP to order, your best bet is to consult the trees and subgroups in the R1b1b2 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/). Or just ask.

smal
10-12-2014, 06:24 AM
The R1b1a2/ht35 project tree (https://www.familytreedna.com/public/ht35new/default.aspx) was updated. I have added following samples:
1) 226720 (Faber) and N60445 (Chevallier) belonging to L150+ L23- PF7562+ PF7563+ branch;
2) N125449 (Schliessmann) belonging to Z2103+ L584+ branch;
3) 352440 (Wilson), B5296 (Shaw) and ? (Oehler) belonging to P311+ CTS4528+ branch.

brygian
10-12-2014, 07:11 AM
smal, where do you have the L943+, L945+ data from for kits N125449 and 45475?

smal
10-12-2014, 07:44 AM
smal, where do you have the L943+, L945+ data from for kits N125449 and 45475?

The L943, L944, L945 and L946 SNPs were discovered in the 45475 kit. They are available in the BigY report and in his BAM file. But as you can see from the R1b1a2/ht35 project tree the N125449 sample does not have such SNPs.

ballardgen
10-13-2014, 07:33 PM
S1194 under P311??

From Memory I believe I found S1194 in a P311 sample for Wilson

smal
10-13-2014, 08:08 PM
S1194 under P311??
From Memory I believe I found S1194 in a P311 sample for Wilson

S1194 is known from the Chromo2 tested samples; 16 S1194+ (2 CTS4528-, 14 CTS4528+). Unfortunately, FTDNA does not report S1194 in BigY matches. And I do not have BAM files from this branch to check the status of S1194 directly. So, I've included this marker in the tree as questionable.

VinceT
10-13-2014, 08:49 PM
HG00148 from the 1KGP data-set is P311/PF6545/S128+ S1194+ CTS4528/S1200+ S14328+ S1196+ DF100/S1203+

ballardgen
10-14-2014, 10:17 AM
S1194 is known from the Chromo2 tested samples; 16 S1194+ (2 CTS4528-, 14 CTS4528+). Unfortunately, FTDNA does not report S1194 in BigY matches. And I do not have BAM files from this branch to check the status of S1194 directly. So, I've included this marker in the tree as questionable.

Sorry should have said "But negative for CTS4528 /DF100" and of course negative for P312 and U106

smal
10-14-2014, 11:04 AM
Sorry should have said "But negative for CTS4528 /DF100" and of course negative for P312 and U106

ballardgen, do you study BAM files?

ballardgen
10-14-2014, 08:13 PM
ballardgen, do you study BAM files?

Hi smal - I study anything CTS4528 DF100 related, I have compared several BIG Y samples up to P311 but did not get to looking at BAM files as I now have no FTDNA project access to gather further testers and data anymore, my old R1b-L11* project now being defunct/closed.

My study is private because FTDNA gave the R1b-DF100 project to somebody else they believed to be more deserving, and as I protested at the time, I have seen no progress in that project to merit being put aside.

I have 50 plus CTS4528 / DF100 samples/contacts and some relevant P311 same.

I dont do much study until the winter months and my main interest are Genealogy but would offer any help on taking my and my groups subclade forward if I can be of assistance.

smal
10-15-2014, 07:50 AM
Hi smal - I study anything CTS4528 DF100 related, I have compared several BIG Y samples up to P311 but did not get to looking at BAM files as I now have no FTDNA project access to gather further testers and data anymore, my old R1b-L11* project now being defunct/closed.

My study is private because FTDNA gave the R1b-DF100 project to somebody else they believed to be more deserving, and as I protested at the time, I have seen no progress in that project to merit being put aside.

I have 50 plus CTS4528 / DF100 samples/contacts and some relevant P311 same.

I dont do much study until the winter months and my main interest are Genealogy but would offer any help on taking my and my groups subclade forward if I can be of assistance.

Hi ballardgen,
Unfortunately, the FTDNA project administrators do not have an access to the BAM files of project members. I can see only the information provided by FTDNA through the BigY matching utility. That is why there are many unsolved problems hindering the development of the correct tree. One example of this is S1194. There is no positive or negative information about S1194 in FTDNA reports.
I have to communicate with each person and ask to send me raw data (BAM file) for analysis. I would be appreciated if you were able to convince the BigY tested members of your group to send me their data. This information will be used only for the project tree development and the correct subdividing of the big CTS4528 group.

ballardgen
10-15-2014, 01:21 PM
smal

using cromo2 position data - can you not search these in novel variants ??

i.e. S1194 position 14668524 ref A alt G

Search BIG Y - Novel Variant "14668524"


Cant try it myself...... NO access to FTDNA data.

I will be in touch with my members recommending they contact you regards .BAM files submission

smal
10-15-2014, 02:05 PM
smal
using cromo2 position data - can you not search these in novel variants ??
i.e. S1194 position 14668524 ref A alt G
Search BIG Y - Novel Variant "14668524"
Cant try it myself...... NO access to FTDNA data.
I will be in touch with my members recommending they contact you regards .BAM files submission

Of course, I know the position of S1194. It is not available among Novel Variants. If SNP is not available among Novel Variants, this can means:
1. SNP is negative;
2. SNP is positive, but FTDNA set too hard threshold and failed to find it;
3. SNP is unknown, BigY test does not cover this region of genome;
4. SNP is unknown, in this sample there are “no reads”.
To select between these variants we should study raw data (BAM files).

ballardgen
10-19-2014, 10:23 PM
smal

not sure if this can help you I cant double check results because i no longer have a FTDNA project
but taken from the search facility of my facebook group back in June 2014, I made this statement.

UPDATE - Yfull are predicting S14328 as a brother to CTS4528/DF100 - I found this mutation upstream in P311 quite a while ago so its no brother !! - S14328 - 13647616 - C.A (Crome2)
(P311+ sample Wilson S14328+ & negative for DF100-)

If the P310 Wilson, that's in the HT35 project is connected to the Sinclair samples then that may be the sample to check Kit # 216606 Wilson ??

Good Luck

VinceT
10-20-2014, 03:22 AM
Just to be clear, I don't know if the DF100/S1203 probe on Chromo2 is working as expected, and may be reporting false negatives.

smal
10-20-2014, 12:37 PM
smal

not sure if this can help you I cant double check results because i no longer have a FTDNA project
but taken from the search facility of my facebook group back in June 2014, I made this statement.

UPDATE - Yfull are predicting S14328 as a brother to CTS4528/DF100 - I found this mutation upstream in P311 quite a while ago so its no brother !! - S14328 - 13647616 - C.A (Crome2)
(P311+ sample Wilson S14328+ & negative for DF100-)

If the P310 Wilson, that's in the HT35 project is connected to the Sinclair samples then that may be the sample to check Kit # 216606 Wilson ??

Good Luck

ballardgen,

1) 352440 Wilson is CTS4528+ DF100? S14328+
2) 216606 Wilson is DF100- and he is really connected to Sinclair
3) In my tree Hinkel's position must be changed, he is S14328+.
4) I've studied the first CTS4528 BAM file (Adams), S1194 is unknown, there are "no reads".

ballardgen
10-21-2014, 09:50 AM
ballardgen,

1) 352440 Wilson is CTS4528+ DF100? S14328+
2) 216606 Wilson is DF100- and he is really connected to Sinclair
3) In my tree Hinkel's position must be changed, he is S14328+.
4) I've studied the first CTS4528 BAM file (Adams), S1194 is unknown, there are "no reads".

Thanks smal

I have asked Steve Sinclair of the "Sinclair Project" to ask Wilson 20166 to join HT35, I believe from memory this is where the answer is, we will wait and see.

ballardgen
10-21-2014, 10:18 AM
253994 Oehler

Lawson Baker?,

b. 1805 NC; d. 1870 Nodaway Cty, MO

R-CTS4528

13 24 14 11 11-14 12 12 13 13 12 29 18 9-10 11 11 24 15 19 30 15-15-15-17 11 10 19-22 16 15 19 17 36-40 12 12 11 9 15-16 8 10 10 8 10 10 12 23-23 16 10 12 12 17 8 12 22 20 13 12 11 13 11 11 12 12 32 15 9 16 13 27 26 19 12 12 12 12 10 9 12 13 10 11 11 30 12 13 24 13 10 11 21 15 18 13 24 17 12 15 24 12 23 18 10 14 17 10 12 11

ballardgen
10-21-2014, 06:16 PM
278944 Ballard
258423 Ballard

are cousins and share the same Y

smal
11-03-2014, 08:30 AM
The R1b1a2/ht35 project tree was updated. I've added 5 new BigY tested samples.

1) 330027 (Contrisciane) belonging to Z2103>L277 branch. He shares one marker, A753, with Stacy, but I am not sure that it is a good marker;
2) 283558 (Haroutinian -Tchatalian) belonging to the Z2103>L584 branch. There are no new shared markers under L584;
3) -? (Vettoretto) belonging to L51>PF7589 branch. The R-PF7589 branch was reformatted significantly.
4) -? (St. Clair) belonging to the R-P311* branch. We have 23 non-private SNPs in this line now. Unfortunately, S1194 is unknown.
5) 60637 (Meyer) belonging to the R-CTS4528 branch. His terminal marker is S1211.

ballardgen
11-04-2014, 11:00 AM
The R1b1a2/ht35 project tree was updated. I've added 5 new BigY tested samples.


4) -? (St. Clair) belonging to the R-P311* branch. We have 23 non-private SNPs in this line now. Unfortunately, S1194 is unknown.
5) 60637 (Meyer) belonging to the R-CTS4528 branch. His terminal marker is S1211.

smal, I have sent you an email

Regards

smal
11-10-2014, 06:22 PM
There is a next update of the R1b1a2/ht35 project (https://www.familytreedna.com/public/ht35new/default.aspx) tree. I've added 2 new BigY and 2 PGP samples.

1) 329814 (Villanueva Garcia) belonging to M269>PF7562 branch.
2) 147232 (Miller) belonging to CTS7822+ CTS9219- branch. There are no new shared markers under CTS7822;
3) PGP124 belonging to the R-CTS4528 branch. He is close to 16296 (Foster).
4) PGP45 belonging to R-CTS4528 branch. PGP45 and Oehler's BAM file help me to correct the S1211 branch.

ballardgen
11-10-2014, 06:45 PM
There is a next update of the R1b1a2/ht35 project (https://www.familytreedna.com/public/ht35new/default.aspx) tree. I've added 2 new BigY and 2 PGP samples.

1) 329814 (Villanueva Garcia) belonging to M269>PF7562 branch.
2) 147232 (Miller) belonging to CTS7822+ CTS9219- branch. There are no new shared markers under CTS7822;
3) PGP124 belonging to the R-CTS4528 branch. He is close to 16296 (Foster).
4) PGP45 belonging to R-CTS4528 branch. PGP45 and Oehler's BAM file help me to correct the S1211 branch.




Thanks for your work smal

Pillar_of_fire
11-11-2014, 02:42 PM
There is a next update of the R1b1a2/ht35 project (https://www.familytreedna.com/public/ht35new/default.aspx) tree. I've added 2 new BigY and 2 PGP samples.

1) 329814 (Villanueva Garcia) belonging to M269>PF7562 branch.
2) 147232 (Miller) belonging to CTS7822+ CTS9219- branch. There are no new shared markers under CTS7822;
3) PGP124 belonging to the R-CTS4528 branch. He is close to 16296 (Foster).
4) PGP45 belonging to R-CTS4528 branch. PGP45 and Oehler's BAM file help me to correct the S1211 branch.

There is a new match to Nochev - Sobol, dated Nov, 10th.

Pillar_of_fire
11-11-2014, 02:44 PM
There is a new match to Nochev - Sobol, dated Nov, 10th.
He seem to group with Hollandsworth

smal
11-11-2014, 04:44 PM
He seem to group with Hollandsworth

Sobol belongs to the BY250+ BY251+ branch.

TigerMW
11-11-2014, 06:27 PM
Thank you for your work on this tree.

This is the current version, right?
https://www.familytreedna.com/public/ht35new/

Which of these branches appear largest? Are there geographic affinities?

I need to do some updating in the R1b general forums and it starts at the top.

Joe B
11-11-2014, 07:13 PM
Thank you for your work on this tree.

This is the current version, right?
https://www.familytreedna.com/public/ht35new/

Which of these branches appear largest? Are there geographic affinities?

I need to do some updating in the R1b general forums and it starts at the top.
Hey Mike,

The trees for the R1b-M269 (P312- U106-) DNA Project are very current due to the hard work of smal. Sometimes the project tree is updated twice a week. The more general descendancy tree shows valid SNPs that can be ordered from FTDNA. The FTDNA tree should be ignored.

It's hard to say which branches are actually the largest because of the better sampling in Europe versus Southwest Asia. The Balkans and Asia Minor are certainly still key areas. In Europe, the predominant branch is R1b-CTS7822/Z2110 and the son, R1b-CTS9219. R1b-CTS9219 includes the R1b-Z2103 : CTS7822+ CTS9219+, L23EE Type subgroup in the Polish DNA Project. In general, the distribution of CTS7822 and CTS9219 in Europe is diffuse. R1b-L277 and R1b-L584 are more common in Southwest Asia, Armenian, Assyrian, Sephardic and Ashkenazi populations. Perhaps the same can be said for the PF7558, PF7562, PF7563 (L150+, L23-) group. The L51 branches are mostly seen in Europe based on sampling.

The truth about this project is....we still have a lot to learn! As far as this forum is concerned CTS7822, CTS9219 and L584 should have the most discussion.

Joe B
12-01-2014, 09:43 PM
The R1b-M269 (P312- U106-) Project (https://www.familytreedna.com/public/ht35new/default.aspx) has added six SNPs to the recommended list.
Z2106 is downstream of the R1b-L277.1 and R1b-L584 branches and upstream to the R1b-CTS7763+ and R1b-CTS7822/Z2110 branches. Z2106 will only be available for the Sanger seqencing test at YSEQ because of it's location on a long STR.
Z2109/CTS1843 is just upstream of R1b-CTS7822/Z2110. For those who tested CTS7822/Z2110-, Z2109 might be worth checking out. We are expecting Z2109+, CTS7822/Z2110- to represent another branch.

On the R1b-L11 branch, several SNPs are now recommend downstream of the CTS4528 DF100 level.
S14328 is just after CTS4528 DT100, followed by S1211 and then CTS7141 F4036.

But hey, it's easier just to look at the phylogenetic trees at the R1b-M269 (P312- U106-) Project (https://www.familytreedna.com/public/ht35new/default.aspx).

ballardgen
12-01-2014, 10:13 PM
The R1b-M269 (P312- U106-) Project (https://www.familytreedna.com/public/ht35new/default.aspx) has added six SNPs to the recommended list.
Z2106 is downstream of the R1b-L277.1 and R1b-L584 branches and upstream to the R1b-CTS7763+ and R1b-CTS7822/Z2110 branches. Z2106 will only be available for the Sanger seqencing test at YSEQ because of it's location on a long STR.
Z2109/CTS1843 is just upstream of R1b-CTS7822/Z2110. For those who tested CTS7822/Z2110-, Z2109 might be worth checking out. We are expecting Z2109+, CTS7822/Z2110- to represent another branch.

On the R1b-L11 branch, several SNPs are now recommend downstream of the CTS4528 DF100 level.
S14328 is just after CTS4528 DT100, followed by S1211 and then CTS7141 F4036.

But hey, it's easier just to look at the phylogenetic trees at the R1b-M269 (P312- U106-) Project (https://www.familytreedna.com/public/ht35new/default.aspx).

Thanks Joe we will try to keep up with you ;-)

https://www.familytreedna.com/public/R1b-S14328Genealogy

lgmayka
12-01-2014, 11:28 PM
Z2106 is downstream of the R1b-L277.1 and R1b-L584 branches and upstream to the R1b-CTS7763+ and R1b-CTS7822/Z2110 branches.
You mean that Z2106 is a sibling of L277.1 and L584. Z2106 is downstream from Z2103.

Joe B
12-02-2014, 02:10 AM
You mean that Z2106 is a sibling of L277.1 and L584. Z2106 is downstream from Z2103.L277.1+ and L584+ haplotypes are Z2106 negative. R1b-CTS7763+ and R1b-CTS7822/Z2110+ haplotypes are Z2106 positive.
Sorry for any confusion.

smal
12-08-2014, 09:33 PM
The R1b1a2/ht35 project tree was updated. There are 3 new BigY tested samples:

1) 83 (Falk/Israel) belonging to M269>PF7562 branch;
2) ? (Sobol) belonging to the BY250, BY251 branch;
3) 44808 (James) belonging to the R-P311*. He has some common markers with 38215 (Fox) and 348499 (Burke). But I need BAM file to be sure.

Then, I found that the new article,
The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades (http://mbe.oxfordjournals.org/content/early/2014/11/26/molbev.msu327.short?rss=1&utm_source=dlvr.it&utm_medium=tumblr),
will have a significant impact on our project tree and have integrated 13 samples (H2014-red colour) from this article in the project tree.

This allows me to find
1. second PF7566, PF7569 sample in the PF7562 branch
2. new marker in the CTS7763, CTS8966 branch. This branch is very strange. Now we have a sample from Butan (!).
3. 8 markers in Nochev's line
4. new subclade in the EE cluster.

Silesian
12-09-2014, 06:40 AM
....... new marker in the CTS7763, CTS8966 branch. This branch is very strange. Now we have a sample from Butan (!).......

What are the odds R1B-L277+ and R1b-CTS8966+ found in same region Bulgaria/Romania and again in R1b L277 + in Kolkata, West Bengal, India; and R1b-CTS8966+Bhutan?

brygian
12-09-2014, 08:18 AM
If I remember correctly, the Bulgarian/Romanian CTS8966+ individual is of Turkish origin. The Turkic people inhabit Central Asia all the way to China. The Uighurs actually live in China.

brygian
12-09-2014, 07:03 PM
If I remember correctly, the Bulgarian/Romanian CTS8966+ individual is of Turkish origin. The Turkic people inhabit Central Asia all the way to China. The Uighurs actually live in China.

I was corrected on another forum that the person in question is actually of Gagauz (https://en.wikipedia.org/wiki/Gagauz_people) origin.

Silesian
12-09-2014, 07:30 PM
I was corrected on another forum that the person in question is actually of Gagauz (https://en.wikipedia.org/wiki/Gagauz_people) origin.
Thanks for investigating the Gagauz origin. It's not very common, to show up in Bhutan and have a possible Gagauz connection is very interesting. Perhaps Eurasian Steppe connection? R1b L277 is also found around Steppe regions.

Chad Rohlfsen
12-14-2014, 12:31 AM
Hey Mike,

The trees for the R1b-M269 (P312- U106-) DNA Project are very current due to the hard work of smal. Sometimes the project tree is updated twice a week. The more general descendancy tree shows valid SNPs that can be ordered from FTDNA. The FTDNA tree should be ignored.

It's hard to say which branches are actually the largest because of the better sampling in Europe versus Southwest Asia. The Balkans and Asia Minor are certainly still key areas. In Europe, the predominant branch is R1b-CTS7822/Z2110 and the son, R1b-CTS9219. R1b-CTS9219 includes the R1b-Z2103 : CTS7822+ CTS9219+, L23EE Type subgroup in the Polish DNA Project. In general, the distribution of CTS7822 and CTS9219 in Europe is diffuse. R1b-L277 and R1b-L584 are more common in Southwest Asia, Armenian, Assyrian, Sephardic and Ashkenazi populations. Perhaps the same can be said for the PF7558, PF7562, PF7563 (L150+, L23-) group. The L51 branches are mostly seen in Europe based on sampling.

The truth about this project is....we still have a lot to learn! As far as this forum is concerned CTS7822, CTS9219 and L584 should have the most discussion.

Where is the highest variance in the pre-L-23 branch? How many SNPs and STRs are you using?

Chad Rohlfsen
12-14-2014, 07:08 AM
MJost,
Do you have a variance map or spreadsheet for m-269* Do you know which appears to have the older STRs or SNPs?

MJost
12-14-2014, 03:34 PM
MJost,
Do you have a variance map or spreadsheet for m-269* Do you know which appears to have the older STRs or SNPs?
I did some Busby 2011 haplotypes and had some R1b-Early from around Oct 2012 and put some results into a few PDFs. I also moved the 2012 67 marker haplotypes from the R1b-Early and placed them into my latest version of my TMRCA spreadsheet and zipped them all and placed them on my Google Documents linked here
https://drive.google.com/file/d/0By9Y3jb2fORNYlpLU19NTzk0bTg/view?usp=sharing

You may derive what ever info you wish from them. The loaded TMRCA Estimator has 280 67marker HTs. I have everything set for 67 using Bird's select markers. The sum of variance produces
YrsPerGen* Count Intraclade Founder's Modal Age Modal Gen Age StdDevInGen YBP +OR-YBP Max-YBP Modal FVAR Modal FSD SD CONFIDENCE CI SD GenModal CI +OR-YBP
30 N=280 Clade A: 194.0 45.3 5,821.5 1,358.0 7,179.5 18.377 4.287 95.45% 99.43 2,982.8

MJost

George Chandler
12-14-2014, 07:06 PM
MJost,
Do you have a variance map or spreadsheet for m-269* Do you know which appears to have the older STRs or SNPs?

I don't advise trusting any age estimate for an SNP using STR's. When you look at the S1051 group we are all separate lines descending from a single common SNP and yet when you run STR age estimates the TMRCA varies by up to 1200 years or more..and again they should all have the same TMRCA.

George

MJost
12-14-2014, 07:22 PM
I disagree.
I don't advise trusting any age estimate for an SNP using STR's. When you look at the S1051 group we are all separate lines descending from a single common SNP and yet when you run STR age estimates the TMRCA varies by up to 1200 years or more..and again they should all have the same TMRCA.

George

George Chandler
12-14-2014, 07:43 PM
I disagree.

Anything under or around 1,000 years isn't bad but when see the FGC5496 Wigand STR analysis coming back with a TMRCA 1,000 years earlier to me than the 9919A1's.. who I share a MRCA with at least 1,000 years after DF13 using SNP testing there is an obvious problem with the STR analysis.

The evidence speaks for itself.

George

Chad Rohlfsen
12-14-2014, 07:45 PM
MJost,
Very interesting. Do you have m-269* variance for Bulgaria? Also, just using Ukraine, without Czechs. Czechs may be killing that percentage. It's strange to see Italy up there so high. Maybe that is from mainland Greeks and Ionians. Do you have STR variance for pre-L23, or an m-269(xL23)? Unless that was included here. Thanks!

alan
12-14-2014, 08:01 PM
I did some Busby 2011 haplotypes and had some R1b-Early from around Oct 2012 and put some results into a few PDFs. I also moved the 2012 67 marker haplotypes from the R1b-Early and placed them into my latest version of my TMRCA spreadsheet and zipped them all and placed them on my Google Documents linked here
https://drive.google.com/file/d/0By9Y3jb2fORNYlpLU19NTzk0bTg/view?usp=sharing

You may derive what ever info you wish from them. The loaded TMRCA Estimator has 280 67marker HTs. I have everything set for 67 using Bird's select markers. The sum of variance produces
YrsPerGen* Count Intraclade Founder's Modal Age Modal Gen Age StdDevInGen YBP +OR-YBP Max-YBP Modal FVAR Modal FSD SD CONFIDENCE CI SD GenModal CI +OR-YBP
30 N=280 Clade A: 194.0 45.3 5,821.5 1,358.0 7,179.5 18.377 4.287 95.45% 99.43 2,982.8

MJost


Would you interpret that as M269 dating to around 4000BC?

alan
12-14-2014, 08:03 PM
MJost,
Very interesting. Do you have m-269* variance for Bulgaria? Also, just using Ukraine, without Czechs. Czechs may be killing that percentage. It's strange to see Italy up there so high. Maybe that is from mainland Greeks and Ionians. Do you have STR variance for pre-L23, or an m-269(xL23)? Unless that was included here. Thanks!

From memory the peak in Italy is just opposite Albania, another peak. The two things are probably linked

Joe B
12-14-2014, 09:16 PM
The Arbëreshë may be the cause of that Southern Italian spike especially around Calabria.

kostop
12-15-2014, 10:37 AM
Also, Calabria has always been a place with heavy Greek presence, with continuous migrations from Greece dating from the 8th century BC since the Byzantine times.
I have visited villages where they still speak a Greek dialect (griko).
http://en.wikipedia.org/wiki/Griko_people
http://en.wikipedia.org/wiki/Calabrian_dialect_(Greek)

MJost
12-15-2014, 02:14 PM
Anything under or around 1,000 years isn't bad but when see the FGC5496 Wigand STR analysis coming back with a TMRCA 1,000 years earlier to me than the 9919A1's.. who I share a MRCA with at least 1,000 years after DF13 using SNP testing there is an obvious problem with the STR analysis.

The evidence speaks for itself.

GeorgeThe evidence speaks for itself? I think a more detailed information is needed to be discussed. TMRCA numbers need to be taken in context.

ALL DF13 subclades would have the their first founder STR and SNP mutation around 3600 ybp. Not all DF13 subclade haplogroups will produce an effective TMRCA due to missing, low counts, or a migration founder effects.

FGC5494 with 194 non-duplicated HTs show

IntraClade Coalescence (n-1) Age <<<<<< this is the point in time where this group has a
MRCA node which is always at or lower than Founders age.
Mean Generations StdDevInGen YBP +OR-YBP
95.7 31.8 2,869.5 953.4


Intraclade Founder's Modal Age<<<<< this is the point where all haplotypes
roll back to the founders original (modal) haplotype.
Modal Gen Age StdDevInGen YBP +OR-YBP
112.7 34.5 3,380.1 1,034.8

Anatole Klyosov's Linear Method
Generations 98>109

MJost

George Chandler
12-15-2014, 03:27 PM
The evidence speaks for itself? I think a more detailed information is needed to be discussed. TMRCA numbers need to be taken in context.

ALL DF13 subclades would have the their first founder STR and SNP mutation around 3600 ybp. Not all DF13 subclade haplogroups will produce an effective TMRCA due to missing, low counts, or a migration founder effects.

FGC5494 with 194 non-duplicated HTs show

IntraClade Coalescence (n-1) Age <<<<<< this is the point in time where this group has a
MRCA node which is always at or lower than Founders age.
Mean Generations StdDevInGen YBP +OR-YBP
95.7 31.8 2,869.5 953.4


Intraclade Founder's Modal Age<<<<< this is the point where all haplotypes
roll back to the founders original (modal) haplotype.
Modal Gen Age StdDevInGen YBP +OR-YBP
112.7 34.5 3,380.1 1,034.8

Anatole Klyosov's Linear Method
Generations 98>109

MJost

The founder age for DF13 being 3,600 years is flat out wrong..it's close but it's still wrong. Once the testing of ancient remains becomes public you'll understand. I told this to Anatole years ago when he was arguing that L21 was no more than 2,200 years to the founder. Take the S1051 lines and you can see we all share 5 common ancient SNP's below DF13 and yet most of us branch from that point into completely different SNP lines. That's approximately 3,700 years ago and there are another 5 SNP's above them unique in our line under DF13. You don't have to believe me that's fine it's up to you but run a TMRCA for each of those lines and include the Wigand 9919 FGC5496 to see what you get. The math is flawed - don't drink the cool-aid.

George

MJost
12-15-2014, 04:07 PM
The founder age for DF13 being 3,600 years is flat out wrong..it's close but it's still wrong. Once the testing of ancient remains becomes public you'll understand. I told this to Anatole years ago when he was arguing that L21 was no more than 2,200 years to the founder. Take the S1051 lines and you can see we all share 5 common ancient SNP's below DF13 and yet most of us branch from that point into completely different SNP lines. That's approximately 3,700 years ago and there are another 5 SNP's above them unique in our line under DF13. You don't have to believe me that's fine it's up to you but run a TMRCA for each of those lines and include the Wigand 9919 FGC5496 to see what you get. The math is flawed - don't drink the cool-aid.

George
3600 is the date for most of the first tier DF13 subclades. DF13 is around 3750 ypb. [email protected] 4250 and P312/u106 @ 4560.

>Anatole years ago when he was arguing that L21 was no more than 2,200 years to the founder.
You mean he said 2200bc?

>include the Wigand 9919 FGC5496

Please explain what are you doing here.

My the cool-aid. is just fine, thank you.

MJost

MJost
12-15-2014, 04:29 PM
Would you interpret that as M269 dating to around 4000BC?
My old STR data for M269 (280 67marker HTs.) was 5,821.5 SD+- 1,358.0. Thus at the max SD = 7, 179.5 ybp (or 5180bc).

Since I have been recalibrating using my SNPs back to DF13 and adding back all ancestral SNPs known, M269 was spawned around 7233ybp (or 5233bc).

Using my estimated 129 years per mutation dating SNP blocks above DF13 at 3750 ybp (my suggested DF13 age) working backwards similar to Wei Wei, Qasim Ayub, [...], and Chris Tyler-Smith's results.

R1b1a2 - M269 - (903 yrs in this block of unordered seven SNPs to L23) = Max 7233 (5233bc)

block of unordered SNPs - max ages
L23 6330 ybp (4300bc)
L51 5943 ybp (3943bc)
L11 5427 ybp (3427bc)
P312 4524 (2524bc)
L21 4266 (2266bc)

MJost

jdean
12-15-2014, 04:29 PM
3600 is the date for most of the first tier DF13 subclades. DF13 is around 3750 ypb. [email protected] 4250 and P312/u106 @ 4560.

>Anatole years ago when he was arguing that L21 was no more than 2,200 years to the founder.
You mean he said 2200bc?

>include the Wigand 9919 FGC5496

Please explain what are you doing here.

My the cool-aid. is just fine, thank you.

MJost

Iain McDonald recently estimated DF49 to be 2095 BC (2717 BC - 1606 BC) using Big Y SNP counting

This was based on
one SNP created every 137.2 years (95% confidence interval: 122 to 157 years/SNP


This rate is defined by a combination of literature studies (Xue/Poznik/Mendez/Scozzari/Francalacci et al.)

MJost
12-15-2014, 04:53 PM
Iain McDonald recently estimated DF49 to be 2095 BC (2717 BC - 1606 BC) using Big Y SNP counting

This works out to be 29.8 mutations back to DF49 (including DF49?). I have 29 validated SNPs (out of 70) back to DF13 (counting FGC55494) but I use 129 years per mutation to arrive at 3600 ybp for the age of FGC5494. We are close, 8.2 years diff. between us. For Iain's has 95% confidence interval: 122 to 157 years/SNP.

And he is using 33 Ave. Years per GEN. Changing my 29 SNPs to 137.2 years per SNP instead of 129 = 2024bc.


MJost

jdean
12-15-2014, 05:14 PM
This works out to be 29.8 mutations back to DF49 (including DF49?). I have 29 validated SNPs (out of 70) back to DF13 (counting FGC55494) but I use 129 years per mutation to arrive at 3600 ybp for the age of FGC5494. We are close, 8.2 years diff. between us. For Iain's has 95% confidence interval: 122 to 157 years/SNP.

And he is using 33 Ave. Years per GEN. Changing my 29 SNPs to 137.2 years per SNP instead of 129 = 2024bc.


MJost

I'm not sure of the rest but from memory the Xue study used a known tree negating the need to estimate yrs/gen ?

alan
12-15-2014, 10:39 PM
My old STR data for M269 (280 67marker HTs.) was 5,821.5 SD+- 1,358.0. Thus at the max SD = 7, 179.5 ybp (or 5180bc).

Since I have been recalibrating using my SNPs back to DF13 and adding back all ancestral SNPs known, M269 was spawned around 7233ybp (or 5233bc).

Using my estimated 129 years per mutation dating SNP blocks above DF13 at 3750 ybp (my suggested DF13 age) working backwards similar to Wei Wei, Qasim Ayub, [...], and Chris Tyler-Smith's results.

R1b1a2 - M269 - (903 yrs in this block of unordered seven SNPs to L23) = Max 7233 (5233bc)

block of unordered SNPs - max ages
L23 6330 ybp (4300bc)
L51 5943 ybp (3943bc)
L11 5427 ybp (3427bc)
P312 4524 (2524bc)
L21 4266 (2266bc)

MJost

Yep the devil's in the detail but at least the more eastern stuff is coming in around the relatively early copper age there while the western P312 forms seems to start around what is the later copper age although early coppe age in terms of NW Europe. So the term copper age seems a decent short hand for the spread of R1b clades down to P312 relative to their regions of dominance.

It shows that M269 is old but not old enough to be linked to the first waves of European farmers. The SNP looks like it may pre-date any intrusions from the steppes by 1000 years. So it may have been dwelling in the steppes because it and its immediate ancestor had to be somewhere and should already have turned up among farmers and their early copper using kin if they carried it.

L23 appears to potentially date to around the time of the first steppe intrusions. A couple of things you confirm that has been emerging for some time is that L51 branched off surprisingly early which is interesting given the present distribution of L51* which is broadly speaking south Alpine. This is interesting as it initially suggests a limited spread in the Alpine zone was all that was achieved for a considerable time. However it may simply have been erased in areas to the east where there was a big population change as the Tyrol study seems to indicate by its disappearance along the Romance-Slavic placenames division. So it may have had a presence further east once.

Its also interesting to see the relatively big gap in time between L51 and L11 and L11 and P312. This is interesting as it removes the concern about the strong contrast between the two main L11 branches -P312 and U106 if they had been separated for up to 500 years before the clade defining SNPs of the main surviving subclades occurred. Now we could perhaps think of L11 as existing in the latter half of the 4th millennium before either corded ware of beaker arose and a long L11* period stretching from several centuries before corded ware and 1000 years before beaker.

Chad Rohlfsen
12-15-2014, 10:55 PM
MJost,
Do you have variance numbers for individual populations in the Caucasus and Eastern Europe, for m-269? Is it also possible to tell whom has the oldest m-269 markers? Thanks!

MJost
12-16-2014, 03:51 AM
MJost,
Do you have variance numbers for individual populations in the Caucasus and Eastern Europe, for m-269? Is it also possible to tell whom has the oldest m-269 markers? Thanks!

No, only what I just had in the spreadsheet link I posted in
http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=61688&viewfull=1#post61688

MJost

Chad Rohlfsen
12-16-2014, 04:24 AM
No, only what I just had in the spreadsheet link I posted in
http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=61688&viewfull=1#post61688

MJost

Thank you. I did go through that. Lots of good info. How about L11 and L51? Do you have a variance map or table on that? Thank you, again!

MJost
12-16-2014, 04:32 AM
Yep the devil's in the detail but at least the more eastern stuff is coming in around the relatively early copper age there while the western P312 forms seems to start around what is the later copper age although early coppe age in terms of NW Europe. So the term copper age seems a decent short hand for the spread of R1b clades down to P312 relative to their regions of dominance.

It shows that M269 is old but not old enough to be linked to the first waves of European farmers. The SNP looks like it may pre-date any intrusions from the steppes by 1000 years. So it may have been dwelling in the steppes because it and its immediate ancestor had to be somewhere and should already have turned up among farmers and their early copper using kin if they carried it.

L23 appears to potentially date to around the time of the first steppe intrusions. A couple of things you confirm that has been emerging for some time is that L51 branched off surprisingly early which is interesting given the present distribution of L51* which is broadly speaking south Alpine. This is interesting as it initially suggests a limited spread in the Alpine zone was all that was achieved for a considerable time. However it may simply have been erased in areas to the east where there was a big population change as the Tyrol study seems to indicate by its disappearance along the Romance-Slavic placenames division. So it may have had a presence further east once.

Its also interesting to see the relatively big gap in time between L51 and L11 and L11 and P312. This is interesting as it removes the concern about the strong contrast between the two main L11 branches -P312 and U106 if they had been separated for up to 500 years before the clade defining SNPs of the main surviving subclades occurred. Now we could perhaps think of L11 as existing in the latter half of the 4th millennium before either corded ware of beaker arose and a long L11* period stretching from several centuries before corded ware and 1000 years before beaker.Using more of a time line basis to get perspective of changes.
DF13 = 3750 ybp



L21(516)
P312(258)
L11(903)
L51(516)
L23(387)
M269(903)
|_____|_|________|___|__|_________|_
3750(1.75bc) Max 7233(5.23bc)

MJost
12-16-2014, 04:53 AM
Thank you. I did go through that. Lots of good info. How about L11 and L51? Do you have a variance map or table on that? Thank you, again!
Sorry no. There are L51 and L11 HTs in the same spreadsheet that you could work through. And you should read this thread
http://www.anthrogenica.com/archive/index.php/t-994.html

MJost

VinceT
12-16-2014, 08:55 AM
IIRC, Iain's currently down to about 135 years/SNP for BigY, putting U106 slightly over 4500 ybp, where "present" = 1945 CE (http://en.wikipedia.org/wiki/Before_Present).

As the SNPs between P310, L11 etc. to DF13 have all been identified using broad-coverage sequencing from sources such as 1KGP, Full Genomes Corp., one could conceivably use the shorter associative mutation rate of approximately 80-85 years per mutation for those specifically. but it will never be an apples-for-apples comparison, because the coverage for BigY is non-random, as it was was deliberately designed to favor regions containing certain SNPs over others.

alan
12-16-2014, 01:27 PM
I definitely think the various dating techniques are in the right ballpark - M269 post-dates the early farmer waves (even LBK had already spread by the time it existed) and almost certainly most of it is copper age at the earliest. That fits nicely with ancient DNA so far and I dont think that will change. Of course it seems likely that the first M269 guys were not in the farming world and the M269* clade as it survives may not have spread into the Balkans etc until L23xL51 was around too. It seems very likely to me that the spread into the Balkans and east of the farming world didnt much predate 4000BC and it seems that L11 probably didnt spread much until 3000BC was being approached and P312 may indeed have been spread by beaker people. We still of course from both archaeological and genetic perspectives have that uncertainly of how the earlier more eastern branches sent of offshoots to the west but it seems to have happened in the period 3500-2500BC which makes a lot of sense and again agrees with ancient DNA. I think teasing out more detail will require a significant amount more ancient DNA dating to the copper age across Europe. It hard not to be drawn to Corded Ware as an option for L11* or at least a part of it as a vector for the spread of L11 as it as a culture does included north, east-central and west-central/Alpine Europe and its earlier dating suggests a long existence in pre-beaker times.

alan
12-16-2014, 01:57 PM
These dates

L51 5943 ybp (3943bc)
L11 5427 ybp (3427bc)

would leave us with a number of choices becaue they are predominantly found west of eastern Europe

1.The dates are too old
2. Later movements have erased most traces of these in the east
3. There was a copper age movement west in the pre-Yamnaya period

All are not impossible IMO. There were of course pre-Yamanaya steppe intrusions into the Balkans and Hungary. Regardless, with L11* having such a long period of existence prior to P312 and U106 it really must have had a pre-beaker home and central Europe seem most likely to me given the locations of where L11 was shed branches other than P312 and U106. This and the timescale of 3400-2500BC indicates to me, allowing for a margin of error, that L11 was likely present in corded ware which occupied most of central and northern Europe across the period 3000-2600BC. I am not saying it had to be exclusively corded ware but it is the big culture of the period and its distibution would account for a lot of L11*. I still retain the suspicion that L51* looks like it could have had a role in the Remedello network somehow. Both these cultures have been earmarked as potentially having steppe influences by shorty after 3000BC and jointly cover a significant chunk of Europe from the east to Switzerland and SE France within a century or so of 2900BC so do provide a vector for moving R1b fairly far west by the period 2900-2750BC which puts it close to the start of the beaker period in Iberia. I think that both cultures bear a strong sibling similarity to beaker is undeniable.

MitchellSince1893
12-16-2014, 02:04 PM
I've been following the various date estimates using SNPs over the last few month and have seen P312 range from 4524 - 6265 YBP (2514 - 4251 BC), based on different SNP dating methods.

I'm interested in this date as I, like many others, am trying to determine the approximate age of my current terminal branch.

Without causing a heated debate, is it currently possible to narrow this date range based on other factors...is there consensus that it's definitely between x and y dates?

E.g. based on archaeology/genetics it can be no earlier/later than date x?

Can we say, with any degree of certainty that P312 is ____years old +/- _____years.

Or is 4524 - 6265 YBP all we can do at this point?

MJost
12-16-2014, 03:05 PM
IIRC, Iain's currently down to about 135 years/SNP for BigY, putting U106 slightly over 4500 ybp, where "present" = 1945 CE (http://en.wikipedia.org/wiki/Before_Present).

As the SNPs between P310, L11 etc. to DF13 have all been identified using broad-coverage sequencing from sources such as 1KGP, Full Genomes Corp., one could conceivably use the shorter associative mutation rate of approximately 80-85 years per mutation for those specifically. but it will never be an apples-for-apples comparison, because the coverage for BigY is non-random, as it was was deliberately designed to favor regions containing certain SNPs over others.

Vince, as always, you have the pulse on the SNP aging situations. Thank for pointing them out.

1) I totally agree with the apples to oranges comparison. There could be a conversion algorithm but subject to the second, third and forth items.
2) The coverage for BigY is non-random. It does appear that not everyone gets the same segment tested for what ever reason.
3) I have considered using different mutation rates for different parts of the tree, possibly, based on type of coverage 'sequencing',
example, most of the existing tree has been PCR sequenced with very successful amplification with an SNP-specific primers
eliminating false positives for what ever reason such as recombination events resulting in a possible slower rate calculation vs
broad-coverage (NGS) sequencing which raises the amount of SNP uncovered have but can we assume a derived SNP found in specific areas such as X-transpose & X-degrading zones of the ChrY is a 'Gold' product when Sanger sequencing, scored by a human, shows this low confidence?
4) If broad-coverage NGS is accepted, Thomas K states, "even if we're able to isolate the ChrY portion for sequencing there will be X to Y recombination's in this region sooner or later." What then?

MJost

MitchellSince1893
12-16-2014, 03:22 PM
...
3) I have considered using different mutation rates for different parts of the tree...

MJost

That's what I tried. As FGC stated that BigY was finding 47.8% of the private SNPs that FGC found, I was using one mutation rate for private SNPs found by BigY, and another for the established SNPs.

Based on what others had posted there were two different rates.

One used 173 years for private/novel BigY SNPs and 112 years for the established SNPs. The other used 120 years for private/novel BigY SNPs and 80 years for the established SNPs.

Using these methods with my own BigY results returned 6265 ybp and 4834 ybp for the age of P312.
However, I know there is great risk in doing this as the number of private SNPs identified can vary person to person, even if they are on the same branch.

Having said that, looking at 4 different branches below U152>L2>Z49>Z142; they range from 26 to 34 SNPs below this level. So there seems to be some consistency in this part of the tree at this point.

MJost
12-16-2014, 04:08 PM
I'm not sure of the rest but from memory the Xue study used a known tree negating the need to estimate yrs/gen ?

I used this Xue mutation referenced in the Wei study:

A calibrated human Y-chromosomal phylogeny based on resequencing

Wei Wei, Qasim Ayub, [...], and Chris Tyler-Smith
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561879/

Here is the reference to Xue study:
""estimate this number from the sequences of the three-generation
family... observation of two germline mutations in two transmissions of
8.97 Mb is consistent with the expectation of ∼0.6 mutations in two
transmissions (0.3 variants observed per meiosis in 10.5 Mb)"(Xue et al.
2009)."

My next post will be on my calc using this info for dating.

MJost

MJost
12-16-2014, 04:25 PM
I've been following the various date estimates using SNPs over the last few month and have seen P312 range from 4524 - 6265 YBP (2514 - 4251 BC), based on different SNP dating methods.

I'm interested in this date as I, like many others, am trying to determine the approximate age of my current terminal branch.

Without causing a heated debate, is it currently possible to narrow this date range based on other factors...is there consensus that it's definitely between x and y dates?

E.g. based on archaeology/genetics it can be no earlier/later than date x?

Can we say, with any degree of certainty that P312 is ____years old +/- _____years.

Or is 4524 - 6265 YBP all we can do at this point?

Ok, back in Oct 14 over on the [email protected]

forum I posted this info. I will go with my previous posted ages of the M269 subclades
considering blocks of SNPs.

""Lets run some numbers.

The aim to generate individual Y-chromosomal sequences with adequate
coverage. The need is to have these results appropriately filtered to
generate validated Y-SNP calls, including using PCR and Sanger
Sequencing. There are currently both FGS and BigY kits with SNP calls
that were ranked as High Quality which were retested and produced a
reduced number of validated SNPs.

A calibrated human Y-chromosomal phylogeny based on resequencing
Wei Wei, Qasim Ayub, [...], and Chris Tyler-Smith
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561879/

"estimate this number from the sequences of the three-generation
family... observation of two germline mutations in two transmissions of
8.97 Mb is consistent with the expectation of ∼0.6 mutations in two
transmissions (0.3 variants observed per meiosis in 10.5 Mb)"(Xue et al.
2009)."

Let say we have a point in time of 4000 ybp with 33 year generations
(ypg) equates to 121.1 generations. At 0.3 variants observed per meiosis,
calculates to 36.3 mutations that would occur.

At 3750 ybp (my suggested DF13 age) with 33 year generations equates to
113.6 generations. At 0.3 variants observed per meiosis, calculates to
34.1 mutations. 250 years less {Added this post 'from L21'} has 6 to 7
generations difference.

The one father who has an increased age at the point of meiosis may
increase the fractional number of variants observed just for the one
generation. But even if everyone was 40 years old at meiosis, at 4000 ybp
it only has 40 SNPs occurred.

Even at 5k ybp, as some prefer for DF13, same 33 ypg is 151.5 gens, 45.5
SNPs."

When asked why I used about the above methods, I wrote:
"I am showing the alternate studies that result in similar results. Check
out Ray Banks' comments (He is has light years more understanding of
these processes).
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2012-
11/1352614028
Ray used the info for the total SNPs discovered (not just validated
ones), that "a new detectable SNP arises every 55 yrs (or a little
less)."

So my 70 (approx.) Full Genome SNPs under DF13 using 55 years per SNP
equates to 3850 ybp. (my personal estimate of DF13 is around 3750.) You
mentioned 60 SNPs, so recalibrated would be 64 years per SNP. My deeper
shared SNPs plus my Sanger'ed list of (totaling 29 of the 70) SNPs would
be {close to others} 133 years per SNP, close to my estimated 129 years per mutation.
Initially it was shown the average of 33 BigY SNPs would be 116 years per
meiosis.""

MJost

alan
12-16-2014, 05:06 PM
I've been following the various date estimates using SNPs over the last few month and have seen P312 range from 4524 - 6265 YBP (2514 - 4251 BC), based on different SNP dating methods.

I'm interested in this date as I, like many others, am trying to determine the approximate age of my current terminal branch.

Without causing a heated debate, is it currently possible to narrow this date range based on other factors...is there consensus that it's definitely between x and y dates?

E.g. based on archaeology/genetics it can be no earlier/later than date x?

Can we say, with any degree of certainty that P312 is ____years old +/- _____years.

Or is 4524 - 6265 YBP all we can do at this point?

I suppose without ancient DNA the only inferences can be inferred from clade age range, current geography and archaeology within that date range. The date range is as you mentioned above. The geography of P312 is pretty much concentrated in western, central and northern Europe - if that is not misleading due to later evens wiping out its eastern end. If you ask me when within that date range in that geography I can see new movements into central, northern and part of western Europe I would have to say post-3000BC. I dont know of any widely accepted east to west movement that could have brought something brand new into the heart of Europe in the period 4300-3000BC so I would definitely tend to narrow P312 into the 3000-2500BC bracket. I think that would be uncontroversial to say that whether it be looking at Yamnaya, corded ware, Remedello 2, bell beaker (somehow) etc, none of these cultures pre-date 3000BC west of the Black Sea. If it does fall into the period 4200-3000BC then its certainly unexpected from an archaeological point of view and very low visibility.

If we accept it cannot much predate 3000BC then its only a short step to saying that the bell beaker distribution correlation with P312 is a big part of it. Whether the first P312 person was bell beaker is less clear. If it wasnt bell beaker then there is a pretty short list of candidates of cultures it could have sat in in 3000-2500BC with the biggest being corded ware and of course other smaller late pre-beaker copper age cultures with suggested steppic influences like Remedello. If I absolutely had to bet I would say that L11 arose in corded ware around 3000BC and P312 arose in beaker c. 2800-2500BC but there are other options. I just dont think any of those options would pre-date 3000BC or even 2900BC. So IMO P312 must have arisen in the 3000-2500BC time range. Again I dont think too many people would disagree that that is highly probable. My feeling is that it arose close to the western Alps/French eastern border area where both corded ware and Remedello 2 (the two prime candidates for kurgan influences outside eastern Europe) were converging just a pass or two away from each other around 2759-2800BC. The fact both reached their western extremes around the western fringes of the Alps -one north avoids having to make a choice for now.

The timing is very close to the appearance of beaker in Iberia too. I certainly have a preference for any into Iberia movement of ultimate steppic origin being in that time frame rather than associated with the earlier initial spread of copper along the Med. and southern Alps c. 3600-3100BC. The problem has been and remains that the into Iberia movement - which must have happened to explain all that DF27 and some other P312- isnt exactly scorching in terms of its traces. However, I was very taken by that comment in the paper than Jean posted a link to that suggested the single graves in Iberian beaker were essentially burials following a corded ware traditions although the boldness of that statement surprised me. Let me put a scenario based on that. What if a male-only band of corded ware people went seeking Eldorado? They would have brought traditions but they wouldnt have brought their women who made their pots. So, they might have asked their local wives to make approximates. Maybe they did stumble soon on the tail ends of the pre-beaker Iberian copper network and followed it towards source. Maybe when they got there they performed a useful service through their mobility allowing the copper to reach out to further lands where it was even more valuable. It could have been a useful relationship, if perhaps a dangerous one. There is no question that somewhere around 2600BC Iberian metal was able to spread far further than pre-beaker Iberian copper had. The difference appears to be an added factor of mobility on an epic scale. Where did that added mobility come from? People with horses and ability to survive travelling across large distances? It did strike me too that perhaps the beaker archery kit had another use other than warfare and status symbol. Being able to hunt would have been a very useful option, over and above any cattle you were driving, to people moving over large distances.

As far as I am aware the only popular and fairly widely held significant movements within that period that enter central,northern and parts of western Europe are corded ware and to a much lesser degree Remedello 2 seems to hint at this too. I suppose you could add Globular Amphorae but its a pretty poor match for P312 to say the least. Of course corded ware for example only overlaps with the central and northern European part of P312 but at least it does significantly overlap. Obviously corded ware is not enough to explain P312 which ultimately does have its best fit with beaker. However, I wouldnt totally rule out a beginning of P312 in corded ware although I do think L11 is more likely. Anyway I am digressing - its hard not too with so many unknowns - but I would say I find a pre-3000BC date for P312 very hard to believe and I also find a post-2500BC date almost impossible to believe so that is a pretty tight timeframe IMO.

vettor
12-16-2014, 05:27 PM
I suppose without ancient DNA the only inferences can be inferred from clade age range, current geography and archaeology within that date range. The date range is as you mentioned above. The geography of P312 is pretty much concentrated in western, central and northern Europe - if that is not misleading due to later evens wiping out its eastern end. If you ask me when within that date range in that geography I can see new movements into central, northern and part of western Europe I would have to say post-3000BC. I dont know of any widely accepted east to west movement that could have brought something brand new into the heart of Europe in the period 4300-3000BC so I would definitely tend to narrow P312 into the 3000-2500BC bracket. I think that would be uncontroversial to say that whether it be looking at Yamnaya, corded ware, Remedello 2, bell beaker (somehow) etc, none of these cultures pre-date 3000BC west of the Black Sea. If it does fall into the period 4200-3000BC then its certainly unexpected from an archaeological point of view and very low visibility.

If we accept it cannot much predate 3000BC then its only a short step to saying that the bell beaker distribution correlation with P312 is a big part of it. Whether the first P312 person was bell beaker is less clear. If it wasnt bell beaker then there is a pretty short list of candidates of cultures it could have sat in in 3000-2500BC with the biggest being corded ware and of course other smaller late pre-beaker copper age cultures with suggested steppic influences like Remedello. If I absolutely had to bet I would say that L11 arose in corded ware around 3000BC and P312 arose in beaker c. 2800-2500BC but there are other options. I just dont think any of those options would pre-date 3000BC or even 2900BC. So IMO P312 must have arisen in the 3000-2500BC time range. Again I dont think too many people would disagree that that is highly probable. My feeling is that it arose close to the western Alps/French eastern border area where both corded ware and Remedello 2 (the two prime candidates for kurgan influences outside eastern Europe) were converging just a pass or two away from each other around 2759-2800BC. The fact both reached their western extremes around the western fringes of the Alps -one north avoids having to make a choice for now.

The timing is very close to the appearance of beaker in Iberia too. I certainly have a preference for any into Iberia movement of ultimate steppic origin being in that time frame rather than associated with the earlier initial spread of copper along the Med. and southern Alps c. 3600-3100BC. The problem has been and remains that the into Iberia movement - which must have happened to explain all that DF27 and some other P312- isnt exactly scorching in terms of its traces. However, I was very taken by that comment in the paper than Jean posted a link to that suggested the single graves in Iberian beaker were essentially burials following a corded ware traditions although the boldness of that statement surprised me. Let me put a scenario based on that. What if a male-only band of corded ware people went seeking Eldorado? They would have brought traditions but they wouldnt have brought their women who made their pots. So, they might have asked their local wives to make approximates. Maybe they did stumble soon on the tail ends of the pre-beaker Iberian copper network and followed it towards source. Maybe when they got there they performed a useful service through their mobility allowing the copper to reach out to further lands where it was even more valuable. It could have been a useful relationship, if perhaps a dangerous one. There is no question that somewhere around 2600BC Iberian metal was able to spread far further than pre-beaker Iberian copper had. The difference appears to be an added factor of mobility on an epic scale. Where did that added mobility come from? People with horses and ability to survive travelling across large distances? It did strike me too that perhaps the beaker archery kit had another use other than warfare and status symbol. Being able to hunt would have been a very useful option, over and above any cattle you were driving, to people moving over large distances.

As far as I am aware the only popular and fairly widely held significant movements within that period that enter central,northern and parts of western Europe are corded ware and to a much lesser degree Remedello 2 seems to hint at this too. I suppose you could add Globular Amphorae but its a pretty poor match for P312 to say the least. Of course corded ware for example only overlaps with the central and northern European part of P312 but at least it does significantly overlap. Obviously corded ware is not enough to explain P312 which ultimately does have its best fit with beaker. However, I wouldnt totally rule out a beginning of P312 in corded ware although I do think L11 is more likely. Anyway I am digressing - its hard not too with so many unknowns - but I would say I find a pre-3000BC date for P312 very hard to believe and I also find a post-2500BC date almost impossible to believe so that is a pretty tight timeframe IMO.


can you map this remedello2 area in western alps !......as Remedello is central italian alpine area , north and east of remedello is polada culture ................otzi, polada person with remedello weapons.

Chad Rohlfsen
12-17-2014, 03:51 AM
Single graves aren't just a steppe thing. Don't get hung up on it. The earliest elite single grave with prestige items is in Varna. It is more likely linked to that Danubian chalcolithic, than any steppe culture.

Joe B
01-10-2015, 02:43 AM
A new R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx) phylogenetic research tree is up. Everybody's dedication to testing is making a huge impact on this part of the R1b tree. Yet we need more people to test. smal has been very busy sorting SNPs resulting in greater definition to the branches.
There are many significant changes in all parts of the R1b1a2/ht35 tree. Enjoy )).
9 BigY tested samples
2 FGC tested samples
8 HGDP samples from Lippold et al. 2014

A searchable .pdf link has been added to the background page because of the large number of haplotypes included in the project research tree.

Abou
01-10-2015, 05:56 AM
Wonderful and a special thanks to smal for his immense efforts in this project. The tree looks more consistent and I am sure it will be more refined with the help of new samples. One tiny thing that is puzzling me, my PF2642 is positive (SDDQH) and the same thing goes for Tognoni (LDGHP) and BDNA-589. Notice that three of us are in different subbranches although belonging to the same CTS7822+ main branch.

smal
01-10-2015, 07:56 AM
Wonderful and a special thanks to smal for his immense efforts in this project. The tree looks more consistent and I am sure it will be more refined with the help of new samples. One tiny thing that is puzzling me, my PF2642 is positive (SDDQH) and the same thing goes for Tognoni (LDGHP) and BDNA-589. Notice that three of us are in different subbranches although belonging to the same CTS7822+ main branch.


PF2642 is ancestral. All our samples are positive and have "T" like Reference sequence.
PF2642 from BDNA is a result of the incorrect scoring in Chromo2 chip.

smal
01-10-2015, 10:31 AM
A placement of the Balkan cluster has to be corrected. It will be moved to Seguer's branch.

Joe B
01-10-2015, 08:15 PM
A placement of the Balkan cluster has to be corrected. It will be moved to Seguer's branch.
The Balkan correction to the R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new) phylogenetic research tree is published!

Chad Rohlfsen
01-22-2015, 12:52 AM
Mark,
I think those dates you gave me for 5200BCE was your m269, correct? Can you go back to P25 and M343?

BTW guys,
They analyzed 5 of the 10 El Portalon guys in Spain. All clustered with Sardinians. All dated from 3000-2000BCE. I am sticking to my guns that R1b and ANE entered Spain at 2000BCE at the earliest.

TigerMW
01-22-2015, 01:38 AM
Mark,
I think those dates you gave me for 5200BCE was your m269, correct? Can you go back to P25 and M343?

BTW guys,
They analyzed 5 of the 10 El Portalon guys in Spain. All clustered with Sardinians. All dated from 3000-2000BCE. I am sticking to my guns that R1b and ANE entered Spain at 2000BCE at the earliest.

I would not be too specific with a date, but if (which I think is the case) a large portion of the Yamnaya descendant tribes that moved up the Danube River and into the Hungarian Plains had R1b, it would make sense that majority of R1b only reached Iberia in a mid to latter phase of the Bell Beaker cultures, at the earliest.

This would nicely align with R1b-P312 patterns and align with a different kind of metallurgy that brought a more productive furnace smelting rather than crucible smelting.

MJost
01-22-2015, 02:06 AM
Mark,
I think those dates you gave me for 5200BCE was your m269, correct? Can you go back to P25 and M343?

BTW guys,
They analyzed 5 of the 10 El Portalon guys in Spain. All clustered with Sardinians. All dated from 3000-2000BCE. I am sticking to my guns that R1b and ANE entered Spain at 2000BCE at the earliest.

http://www.anthrogenica.com/showthread.php?3643-L23-gt-gt-DF13-Up-The-Danube-River-by-SNPs-and-Origin-Variance&p=64804&viewfull=1#post64804
yes, M269 - block of 7 SNP over 903 yrs in block, 6330 to 7233 (4330 to 5233bc) or there abouts.

MJost

Chad Rohlfsen
01-22-2015, 02:07 AM
Yes, clearly these are different people with a taste for horse meat. There are other elements of the culture that are foreign to Iberia. This whole pots thing is as pointless as claiming that Corded Ware is just TRB/Globular Amphora, because of the pottery. There are parallels here... New people with some native women continuing pottery, and some with chords.

Chad Rohlfsen
01-22-2015, 02:08 AM
Mark,
Can you go back as far as L389 and M343, for an age?

MJost
01-22-2015, 02:56 AM
Mark,
Can you go back as far as L389 and M343, for an age?

I did them in a block but here are each nodes age.


R1b-M343/PF6242 8007 (6007bc)

(2) M415/PF6251 * L278 ---- add 258 years or 7878 (5878bc)

(1) L389/PF6531 ----- add 129 years or 7620 (5620bc)

(2) P297/PF6398 * L320/PF6092 ---- add 258 years or 7491 (5491bc)

M269 Max ybp = 7233 (5233bc)

MJost

Chad Rohlfsen
01-22-2015, 03:17 AM
That m343 seems awfully young. That is the base of R1b, which should go back to 12-14kya. Are you certain of the number?

MJost
01-22-2015, 03:42 AM
That m343 seems awfully young. That is the base of R1b, which should go back to 12-14kya. Are you certain of the number?

You keep asking and I am still using the same SNPs to calculate. How would you calculate this tree?
MJost

Chad Rohlfsen
01-22-2015, 03:48 AM
You keep asking and I am still using the same SNPs to calculate. How would you calculate this tree?
MJost

How does your method differ from say, Klyosov, Myers, and others? Why are they getting such an older date? I can't remember if that was solely on STR's. I didn't go over the details of his work. Did he have statistical error? That is what I am wondering. Thanks!

parasar
01-22-2015, 05:01 AM
How does your method differ from say, Klyosov, Myers, and others? Why are they getting such an older date? I can't remember if that was solely on STR's. I didn't go over the details of his work. Did he have statistical error? That is what I am wondering. Thanks!

It was solely STR based.

Ebizur
01-22-2015, 05:50 AM
According to Hallast et al. 2014 recalibrated on the basis of Fu et al. 2014, R1b1-L278 should most likely be somewhere between 20,000 and 25,000 years old.

On the other hand, the extant diversity of R1b1a2-M269 (including that found among the Basques) really does seem to be only about 7,500 years old, which would mean that all R-M269 carriers share the same direct patrilineal ancestor who has lived around 5,500 BCE.

How old is that example of R1b that has been obtained from ancient DNA of a specimen from Germany? Is it M269+?

Leeroy Jenkins
01-22-2015, 06:12 AM
How old is that example of R1b that has been obtained from ancient DNA of a specimen from Germany? Is it M269+?

R1b-M269 (xU106) 2600-2500 BCE

alan
01-22-2015, 09:43 AM
R1b-M269 (xU106) 2600-2500 BCE

They really could have answered a lot of questions if they had been able to test for more SNPs. All we know is they were not U106.

alan
01-22-2015, 10:31 AM
Certainly the autosomal level DNA is staking up to suggest that there was an influx of genes on a significant scale from the east into the west after the Neolithic , despite a certainly element of mystery as to the exact process west of the Rhine. I would characterise R1b in the same way - clearly a post-Neolithic influx from the east that is archaeologically confusing in the west of Europe. I have no doubt the two things are one and the same. Given that there is no fade off of the ANE levels in Celtic fringes - the opposite in fact - I think this group who carried ANE and almost certainly P312 was established early in the process in the isles and is not a consequence of later Germanic movements into the west. As the continental Iron Age seems to have had only limited impact in places like Ireland and much of Scotland I think we can be certain that this took place in the Bronze and copper ages.

My current feeling is beaker has confused us. I believe L11 and P312 was present in western corded ware and that a barely visible small offshoot into Iberia c. 2700BC led to the arising of proto-beaker culture. Things then get confusing when the latter then refluxed along southern France and into the Alps by 2600BC where it then is in a position to influence and intermarry with its distant cousins who were also P312 derived. Something along these lines would explain the confusion about the whole P312 beaker things and directions.

A our knowledge of phylogeny and dating has improved its been clear that there was an INTO Iberia movement of P312 or perhaps DF27 alone. If, as beaker pot dates seem to suggest, beaker is oldest in Iberia then beaker per se does not provided an INTO Iberia scenario. So, its clear something that was not beaker but was ancestral to it is some way must have entered Iberia along with P312 or DF27. I personally think the most likely scenario is this happened immediately pre-beaker in the late 2700sBC and that beaker was a 2nd generation outcome of this intrusions. The intruders brought the individualised burial tradition and the basic shape of the beaker pots from in and adjacent to the corded ware world.

I personally think this was major change in Iberia and so was the beaker network that then extended from Iberia to the Alps c. 2600BC. If you look at pre-beaker copper age culture in Iberia the trade network was completely differently focused and showed little or no interest in the areas to the east of Iberia. The way copper was used was peculiar to Iberia and very different from its use in beaker and AFAIK they did not have individualised burial traditions. So, I believe there was a totally new element in Iberia c. 2700BC or so. I also believe this need not have been entirely unwelcome to the locals. The beaker network which sprung up seemed to focus on and opened up an very different zone of interaction than the pre-beaker copper age groups. One way I think an intrusive element into Iberia who contributed to the genesis of beaker may have benefited from the locals is maritime skill. The vast majority of central Europeans were landlocked except along the North Sea coast. So most likely that any intruders into Iberia in the immediate pre-beaker period were lacking in maritime skills compared to the local copper age groups who had a sophisticated trade network that included north Africa. If you look at beaker concentrations and dating it seems clear they used the seas to leapfrog areas to go from nodal point to nodal point and there remained large unsettled areas in between. That looks very like maritime travel to me.

Chad Rohlfsen
01-22-2015, 11:29 AM
Alan,
There is no ANE in the el Portalon farmers from 3000-2000BCE. Neither R1b, nor Corded entered.

Silesian
01-29-2015, 06:00 PM
Regions within Caucasus with elevated levels of R1b L23[51]/Z2103 and ANE[Ancient North Eurasion [24,000k+/-]
Derived from

ADMIXTURE in supervised mode, with the 24,000 year-old MA-1 or Mal'ta boy genome from South Siberia as one of the reference sample

http://eurogenes.blogspot.ca/2014/03/ancient-north-eurasian-ane-levels.html
https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit?pli=1#gid=62882571

Map of Caucasus languages adjacent Kartvelian language.
http://www.britannica.com/EBchecked/topic/100251/Caucasian-languages/75099/Vocabulary#ref604620
http://lingvarium.org/maps/caucas/1-all.gif
http://lingvarium.org/raznoe/publications/caucas/alw_cau_content.shtml

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_populations_of_the_Caucasus
Bagvalins 67.9+/-% Yunusbaev 2006
Lezgins (Axtynskiy District)29.6+/-% Balanovsky, Dibirova et al. 2011[4]
Tabassarans 39.5+/-% Yunusbaev2006

Eupedia @
http://www.eupedia.com/forum/threads/30763-New-map-of-Ancient-Eurasian-%28ANE%29-admixture

http://en.wikipedia.org/wiki/Caucasian_Albania#mediaviewer/File:Ancient_countries_of_Transcaucasia.jpg

alan
01-29-2015, 09:17 PM
Alan,
There is no ANE in the el Portalon farmers from 3000-2000BCE. Neither R1b, nor Corded entered.

The problem with that date range is its so wide it covers the end of the Neolithic, the early copper age, the late copper age/beaker period and the Early Bronze Age. The abstract description of 4000 years old Neolithic farmer doesnt makes sense. It would also be useful to know the cultural background. If it was beaker it would surely have said. So, until this is clarified I cannot really comment on it. Personally I suspect the population of Iberia was of largely Neolithic farmer stock, albeit with non-ANE Med copper working elements until at least 2750BC and they would have surely remained a large majority for centuries. I honestly would not expect ANE or R in Iberia until around the time of the first beakers around 2750BC and they would have been a patchy minority for centuries. So its would not surprise me in the least if there were many groups who were still largely of ENF stock at the time of El Portalón - although the date given is hopelessly vague. Also although I am no expert Burgos is sort of north-central Spain and from what I recall its not an especially early beaker area. I dont know where the best most up to date beaker map is for Iberia. I think there could have been pockets of mainly ENF descended populations for a long time.

smal
02-02-2015, 10:31 AM
A new R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx) phylogenetic research tree is up. 4 new BigY-tested samples were added:

1) 320190 (Laz, Mehmet) belonging to the PF7562+ PF7563- branch. At the moment this sample is most diverse from all M269+ BigY tested samples.
2) 16910 (Robinson) belonging to the CTS7822>CTS7556>FGC29330 branch.
3) N112689 (Ilinov) and
4) 99230 (Breske) belonging to the EE cluster of the CTS9219>Y5587 branch.

icebreaker
02-02-2015, 11:30 PM
It's nice to be on top :) (I'm 320190)

Chad Rohlfsen
02-03-2015, 01:53 AM
Full package Beakers arrived with the Bronze Age. That is just after the El Portalon samples. That is where I think R1b entered no earlier than 2000BCE.

jeanL
02-03-2015, 03:33 AM
Full package Beakers arrived with the Bronze Age. That is just after the El Portalon samples. That is where I think R1b entered no earlier than 2000BCE.

So basically according to your hypothesis then the individuals from SJAPL (http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CEgQFjAJ&url=http%3A%2F%2Feaa.elte.hu%2FFERNANDEZ.pdf&ei=H0HQVN74HcvroATDtIC4CQ&usg=AFQjCNFieAMp1izZMkD5EgXyHfRlS6hGCQ) should have no R1b-P312 derived clades in them? Interesting!!!

Chad Rohlfsen
02-03-2015, 04:20 AM
So basically according to your hypothesis then the individuals from SJAPL (http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CEgQFjAJ&url=http%3A%2F%2Feaa.elte.hu%2FFERNANDEZ.pdf&ei=H0HQVN74HcvroATDtIC4CQ&usg=AFQjCNFieAMp1izZMkD5EgXyHfRlS6hGCQ) should have no R1b-P312 derived clades in them? Interesting!!!

There is no R1b in nearly 30 samples from France, dating 3000-2725BCE. That should be telling.

jeanL
02-03-2015, 01:48 PM
There is no R1b in nearly 30 samples from France, dating 3000-2725BCE. That should be telling.

True! However I wouldn't use those samples to parallel the situation in SJAPL, given that those 30 samples are all C/C for the lactose tolerance gene, thus all lactose intolerant, while the folks from SJAPL drawn from the same time period appear to have ~30% Lactose tolerance based on the presence of the allele T−13910.

rms2
02-03-2015, 07:21 PM
SJAPL is interesting. Are there any plans to try to get y-dna from any of those remains?

I do not know, but I would be surprised if there is any R1b among them, mainly because it seems a trifle too early. Of course, I've been surprised before.

I know the Lichtenstein Cave site dates to about 2000 years after SJAPL, but there the one R1b guy was evidently lactose intolerant (CC at 13910), while all or most of the I2 remains and both the R1a sets of remains were LP (I don't remember right offhand how many were heterozygous and how many were homozygous).

Do we know if the people at SJAPL belonged to an identifiable culture? Beyond the mere date (c. 3000 BC), was it a Neolithic site, or were the people still living as hunter-gatherers?

jeanL
02-04-2015, 12:01 AM
SJAPL is interesting. Are there any plans to try to get y-dna from any of those remains?

I do not know, but I would be surprised if there is any R1b among them, mainly because it seems a trifle too early. Of course, I've been surprised before.

I know the Lichtenstein Cave site dates to about 2000 years after SJAPL, but there the one R1b guy was evidently lactose intolerant (CC at 13910), while all or most of the I2 remains and both the R1a sets of remains were LP (I don't remember right offhand how many were heterozygous and how many were homozygous).

Do we know if the people at SJAPL belonged to an identifiable culture? Beyond the mere date (c. 3000 BC), was it a Neolithic site, or were the people still living as hunter-gatherers?

I think they might have been part of the Megalithic Culture in the Basque Country, they are right from about that time. I spoke to the people who published their mt-DNA results not long ago, and they mentioned they had tried to obtain to Y-haplogroup stuff from a couple of older sites to no avail, not sure if they will(or have tried) try with these remains. One thing is for sure, it has a whopping 338 human remains in it, it is the biggest human burial in the Ebro Valley region in the Chalcolithic era, and many of them show signs of violence, and we also see the dichotomy of the lactate persistence, so hopefully somebody will sequence it in the future.

smal
02-09-2015, 06:56 AM
The R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx) phylogenetic tree was updated. 4 new BigY-tested samples were added:

1) 329814 (Burns) and
2) FTDNA-? (Spataro) belonging to the PF7562+ PF7563+ branch.
3) N9484 (Caceres) belonging to the L584 branch. This is a first non-positive PF7580 sample from the L584+ branch.
4) 317656 (Strozier) belonging to the CTS6889 branch.

Humanist
02-10-2015, 09:31 PM
The R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx) phylogenetic tree was updated. 4 new BigY-tested samples were added...

Interesting. I had not noticed that the Kurdish Jew was Z2106. I guess we can reasonably expect some Assyrians, particularly those from the Chaldean Catholic Church to also belong to Z2106.

Joe B
02-11-2015, 12:00 AM
Interesting. I had not noticed that the Kurdish Jew was Z2106. I guess we can reasonably expect some Assyrians, particularly those from the Chaldean Catholic Church to also belong to Z2106. Not only is he Z2106+, he is CTS699+. R1b-CTS699 rare son of R1b>CTS7822/Z2110. CTS699 is on the FTDNA tree. R1b-M269>L23>Z2103>Z2106>CTS7822>CTS699+
Might be a good time to contact Peter H. about systematic SNP testing for West Asia.

Abou
02-14-2015, 03:27 PM
Dear All,

please read my post on "The Out-of Maghreb Hypothesis for Western-R1b" at the following thread:

http://www.anthrogenica.com/showthread.php?3831-The-Out-of-Maghreb-Hypothesis-for-Western-R1b&p=69520#post69520

Enjoy
Abou

smal
02-18-2015, 09:36 AM
The R1b-M269 (P312- U106-) DNA Project tree (https://www.familytreedna.com/public/ht35new/default.aspx) was updated. 3 new BigY-tested samples were added:

1) 181183 Burzian-Bashkir. The R-Z2108, Z2109 Bashkirian line is available in tree now.
2) N110808 (Morrison) and
3) E15287 (Schlegel) belonging to the CTS4528 branch.

Humanist
02-18-2015, 09:55 AM
The R1b-M269 (P312- U106-) DNA Project tree (https://www.familytreedna.com/public/ht35new/default.aspx) was updated. 3 new BigY-tested samples were added:

1) 181183 Burzian-Bashkir. The R-Z2108, Z2109 Bashkirian line is available in tree now.
2) N110808 (Morrison) and
3) E15287 (Schlegel) belonging to the CTS4528 branch.

Thank you for the update, smal. Can you, by any chance, estimate the age of the L943/L945 branch? Or are there not enough results as of yet to estimate the age with any precision?

ballardgen
02-18-2015, 10:48 AM
smal do you need the .BAM for N110808 (Morrison)

smal
03-02-2015, 08:52 AM
Estonian Biocentre has presented several high quality R1b samples sequenced by CG (see 307 high coverage human Y chromosome sequences (http://evolbio.ut.ee/))

Tajik1 (Tajiks) R1b15 L278+ L389-
Mong4 (Mongols) R1b13 M73 M478
Bashk3 (Bashkirs) R1b13 M73 M478
Avar9 (Avars) R1b11 Z2103*
Tabas17 (Tabasarans) R1b11 Z2106*
Armen1 (Armenians) R1b11 L584*
UkrnW1 (Ukrainians) R1b8 U106
CArab2 (Christian-Arabs-Israel) R1b1 U152
ISR38 (Ashkenazi-Jews) R1b1 U152
Ger3 (Germans) R1b3 DF27
Mord1 (Mordvins) R1b3 DF27
AndT7 (Colla) R1b3 DF27
AndT13 (Colla) R1b3 DF27

Israel43 (Kurdistan-Jews), Israel48 (Moroccan-Jews), ISR31 (Turkey-Jews), Assyr3 (Assyrians) were already published by Rootsi at al. 2013 earlier. They are available in the R1b1a2/ht35 project tree.

Avar9 (Avars) , Tabas17 (Tabasarans) and Armen1 (Armenians) will be added in the R1b1a2/ht35 project tree.

smal
03-02-2015, 09:07 AM
The R1b1a2/ht35 project tree (http://www.kumbarov.com/ht35/R1b1a2_ht35%20project%20tree_13_03_01_2015.pdf) was updated. There are 6 new BigY tested samples:

1. 257597 (Keledjian) L277. It seems I’ve found a first subclade in L277.
2. 351312 (Hellgren/Östensson) L584+ PF7580-
3. 235098 (Kurilo) L584+ PF7580+
4. FTDNA-? (Mr.) Unknown sample from the CTS7763 line.
5. N113118 (Sabo/Szabo) belonging to third Z2109 line. This sample shares several markers with 257842 (Bork).
6. N128191 (Franz O.) Y5587+.

and 3 samples from Estonian Biocentre (see above (http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=72108&viewfull=1#post72108)). They are very interesting!

7. GS000018404-Avar9 (Avars, Dagestan_Gergebil) Z2103* This sample belongs to the Z2103+ but L277-, L584- and Z2106- line! It shares a single SNP (PF331) with HGDP00060 (Balochi, Pakistan). Unfortunately, the quality of HGDP00060 is low.

8. GS000018396-Tabas17 (Tabasarans, Dagestan_Makhachkala) Z2106* ( Z2106+ but Z2109- Z2108- CTS7763-, CTS8966-). This is the most distant Z2106+ sample at the moment.

9. GS000035452-Armen1 (Armenians, Vardenis) L584* (L584+ but PF7580- and PH1639-, PH4150-) Again, this is the most distant L584+ sample at the moment.

R.Rocca
03-02-2015, 01:10 PM
The R1b1a2/ht35 project tree (http://www.kumbarov.com/ht35/R1b1a2_ht35%20project%20tree_13_03_01_2015.pdf) was updated. There are 6 new BigY tested samples:

1. 257597 (Keledjian) L277. It seems I’ve found a first subclade in L277.
2. 351312 (Hellgren/Östensson) L584+ PF7580-
3. 235098 (Kurilo) L584+ PF7580+
4. FTDNA-? (Mr.) Unknown sample from the CTS7763 line.
5. N113118 (Sabo/Szabo) belonging to third Z2109 line. This sample shares several markers with 257842 (Bork).
6. N128191 (Franz O.) Y5587+.

and 3 samples from Estonian Biocentre (see above (http://www.anthrogenica.com/showthread.php?820-R1b-Early-Branching-Phylogeny-(SNP-based-family-tree)&p=72108&viewfull=1#post72108)). They are very interesting!

7. GS000018404-Avar9 (Avars, Dagestan_Gergebil) Z2103* This sample belongs to the Z2103+ but L277-, L584- and Z2106- line! It shares a single SNP (PF331) with HGDP00060 (Balochi, Pakistan). Unfortunately, the quality of HGDP00060 is low.

8. GS000018396-Tabas17 (Tabasarans, Dagestan_Makhachkala) Z2106* ( Z2106+ but Z2109- Z2108- CTS7763-, CTS8966-). This is the most distant Z2106+ sample at the moment.

9. GS000035452-Armen1 (Armenians, Vardenis) L584* (L584+ but PF7580- and PH1639-, PH4150-) Again, this is the most distant L584+ sample at the moment.

These samples are priceless given how under-sampled some of these areas/populations have been at the full genome level. I know it is not related to R1b1a2, but could you add M73 to the M478 branch on the tree as most know it by that name?

TigerMW
03-02-2015, 01:15 PM
Mord1 (Mordvins) R1b3 DF27

I'm a little surprised to see a DF27+ person all the way over with the Mordvins from the middle Volga River region. It is my understanding they speak a Uralic language.

smal
03-02-2015, 05:23 PM
I'm a little surprised to see a DF27+ person all the way over with the Mordvins from the middle Volga River region. It is my understanding they speak a Uralic language.

Yes, this is not usual. I know only he belongs to Mokshas people.
Based on YFull tree I can further position this sample in the R1b-P312>DF27>Z195>Z198>Z292* branch.

TigerMW
03-02-2015, 05:51 PM
Yes, this is not usual. I know only he belongs to Mokshas people.
Based on YFull tree I can further position this sample in the R1b-P312>DF27>Z195>Z198>Z292* branch.

Thank you, Smal. That means he is from an early branch just prior to SRY2627. SRY2627 is found across Germany, the Low Countries, England, France and Spain with a heavy dose in the Pyrenees. I don't have a time estimate for SRY2627 but I would think we must be talking about 3500-4000 years ago.

ADW_1981
03-02-2015, 05:58 PM
I wonder if all these guys P312+ types, including the U152 Bashkirs are just integrated Volga Germans during that resettlement period.

Humanist
03-02-2015, 06:10 PM
2. 351312 (Hellgren/Östensson) L584+ PF7580-

Any idea when PF7580 will be available for order at FTDNA?

Joe B
03-02-2015, 06:36 PM
Any idea when PF7580 will be available for order at FTDNA?
FTDNA has the request so hopefully PF7580 will be available for order very soon.

smal
03-02-2015, 06:36 PM
Any idea when PF7580 will be available for order at FTDNA?

It was requested, but FTDNA is not in a hurry.

Chad Rohlfsen
03-02-2015, 09:32 PM
http://www.anthrogenica.com/showthread.php?3643-L23-gt-gt-DF13-Up-The-Danube-River-by-SNPs-and-Origin-Variance&p=64804&viewfull=1#post64804
yes, M269 - block of 7 SNP over 903 yrs in block, 6330 to 7233 (4330 to 5233bc) or there abouts.

MJost

Here's a new mutation rate!!! What do you get for m343 through p312 and u106, with this?

http://dienekes.blogspot.com/2015/03/y-chromosome-mutation-rate-082x10-9.html?m=1

lgmayka
03-03-2015, 12:02 AM
Here's a new mutation rate!!! What do you get for m343 through p312 and u106, with this?
Chuckle. Don't you recognize the authors' names? Владимир Таганкин and Вадим Урасин run YFull! You can just look at the latest YFull tree to get the numbers you want.

But watch out for M269. An R1b-M478 man (#277808) just got his Big Y results, and he tested positive for a few of the SNPs that both FTDNA and YFull were associating with M269--namely:
CTS10834
CTS623
PF6477
PF6479
PF6520

The simplest explanation is that these belong at the P297 level, or perhaps they form a new level downstream from P297 but upstream from M269 and M478.

Chad Rohlfsen
03-03-2015, 12:46 AM
Chuckle. Don't you recognize the authors' names? Владимир Таганкин and Вадим Урасин run YFull! You can just look at the latest YFull tree to get the numbers you want.

But watch out for M269. An R1b-M478 man (#277808) just got his Big Y results, and he tested positive for a few of the SNPs that both FTDNA and YFull were associating with M269--namely:
CTS10834
CTS623
PF6477
PF6479
PF6520

The simplest explanation is that these belong at the P297 level, or perhaps they form a new level downstream from P297 but upstream from M269 and M478.

Interesting. I didn't know who ran yfull.

MJost
03-03-2015, 01:35 AM
Here's a new mutation rate!!! What do you get for m343 through p312 and u106, with this?

http://dienekes.blogspot.com/2015/03/y-chromosome-mutation-rate-082x10-9.html?m=1I wonder if the paper is in English and no fee? Its not listed on his web site http://aklyosov.home.comcast.net/~aklyosov/

MJost

VinceT
03-03-2015, 05:15 AM
Nothing to do with Anatole Klyosov.

Vladimir Tagankin and Vadim Urasin are also involved with running molgen.org. Vadim wrote the Y-haplogroup predictor at http://predictor.ydna.ru/

They also have a hand in running www.semargl.me.

brygian
03-07-2015, 03:42 PM
News from YFull.com

Terminal subclade events:
terminal haplogroup of sample NA20532 renamed from R1b1a2a2b to R-L277.1

new sample YF02832 in subclade R-V2986
new sample YF02873 in subclade R-Z2110*

Y-Tree changing:
subclade R1b1a2a renamed to R-L23 and added SNP L478/PF6403
subclade R1b1a2a1 renamed to R-L51
subclade R1b1a2a1a renamed to R-L151
subclade R1b1a2a2 renamed to R-Z2103
subclade R1b1a2a2b renamed to R-L277.1
at subclade R-Z2103 added SNPs Y12536, Y12537
at subclade R-Z2106 added SNP Y12538
parent of subclade R-CTS1450 changed from R-Z2110 to R-CTS7556
subclade R-CTS1450 renamed to R-CTS7556

The three new SNPs which they report have the following definitions:

Y12536 6687319 G->A
Y12537 9431931 C->T
Y12538 19016560 G->T

smal
03-07-2015, 09:16 PM
The three new SNPs which they report have the following definitions:

Y12536 6687319 G->A
Y12537 9431931 C->T
Y12538 19016560 G->T

They are not new, we know them from 1KGP.

Z8127 = Y12536
Z8129 = Y12537
Z8131 = Y12538

There are very few tested samples (CG} because generally BigY test does not cover these regions.

smal
03-09-2015, 09:00 PM
There is one interesting sample sequenced by Estonian Biocentre


(see 307 high coverage human Y chromosome sequences (http://evolbio.ut.ee/))
Tajik1 (Tajiks) R1b15 L278+ L389-


I found it forms new subclade under L278. It shares several SNPs with
FTDNA-267597 (Raza/Varanasi, India) and
bhu-0984 (Bhutan) from Hallast et al. 2014 (http://mbe.oxfordjournals.org/content/early/2014/12/13/molbev.msu327.full).

http://s018.radikal.ru/i509/1503/60/f16c78b0e14f.png (http://www.radikal.ru)

See the detaled tree here. (https://www.dropbox.com/s/j04q5ivx7iah9h4/R1b%20Y-DNA%20tree.pdf?dl=0)

smal
03-19-2015, 07:49 PM
Here is an updated version of the R1b early subclades tree based on recently published data:
Hallast et al. 2014,
Lippold et al. 2014,
Karmin et al. 2015,
sequences from 1000 Genomes Project
and few FTDNA samples.

Link (https://www.dropbox.com/s/j04q5ivx7iah9h4/R1b%20Y-DNA%20tree.pdf?dl=0)

TigerMW
04-06-2015, 05:24 PM
Here is an updated version of the R1b early subclades tree based on recently published data:
Hallast et al. 2014,
Lippold et al. 2014,
Karmin et al. 2015,
sequences from 1000 Genomes Project
and few FTDNA samples.

Link (https://www.dropbox.com/s/j04q5ivx7iah9h4/R1b%20Y-DNA%20tree.pdf?dl=0)
Smal, you show a block of SNPs led by CTS10107/V3949 as a peer to P297. This is just underneath of L389.

However, the R1b1 (xP297) project has M335 in that position and I don't see M335 in that list of equivalents led by CTS10107.
https://www.familytreedna.com/public/R1b1Asterisk/

Do we know how M335 fits into the picture?

I don't see M73 either. M73 should fit in or beside the M478 block of SNPs, brother to M269. [EDIT: I see FTDNA has M478 as downstream of M73.]

smal
04-07-2015, 07:18 AM
Smal, you show a block of SNPs led by CTS10107/V3949 as a peer to P297. This is just underneath of L389.

However, the R1b1 (xP297) project has M335 in that position and I don't see M335 in that list of equivalents led by CTS10107.
https://www.familytreedna.com/public/R1b1Asterisk/

Do we know how M335 fits into the picture?

I don't see M73 either. M73 should fit in or beside the M478 block of SNPs, brother to M269. [EDIT: I see FTDNA has M478 as downstream of M73.]

Mikewww, it's clear M335 and M73 mark clades branched out somewhere between P25 <-> P297 and P297 <-> M269, respectively. But in order to position them correctly in the comprehensive SNP tree we should have NGS sequenced samples for these clades.

TigerMW
04-07-2015, 02:35 PM
Mikewww, it's clear M335 and M73 mark clades branched out somewhere between P25 <-> P297 and P297 <-> M269, respectively. But in order to position them correctly in the comprehensive SNP tree we should have NGS sequenced samples for these clades.
How many people have the phylogenetic equivalent block led by CTS10107?
If they are NGS tested, are we saying M335 was not covered in the NGS test? Can you see the call for M335, was it ancestral?

smal
04-07-2015, 05:00 PM
How many people have the phylogenetic equivalent block led by CTS10107?

There is only a single NG-sequenced L389+ P297- sample, HG00640. The two Geno2 tested samples, N26020 Segarra and 14851 Espada, probably belong to the same branch (they are CTS5330+, CTS6189+, CTS7124+).


If they are NGS tested, are we saying M335 was not covered in the NGS test? Can you see the call for M335, was it ancestral?

M335 is covered by NGS tests, it is negative in all NG-sequenced samples. M335+ samples were not sequenced yet.

TigerMW
04-07-2015, 05:40 PM
There is only a single NG-sequenced L389+ P297- sample, HG00640. The two Geno2 tested samples, N26020 Segarra and 14851 Espada, probably belong to the same branch (they are CTS5330+, CTS6189+, CTS7124+).



M335 is covered by NGS tests, it is negative in all NG-sequenced samples. M335+ samples were not sequenced yet.

Okay, so it is possible that M335 could be downstream of the CTS5330+, CTS6189+, CTS7124+ block or parallel to this block, but not upstream.

TigerMW
04-10-2015, 02:56 PM
I've tried to update my old draft "big picture" look at R1b. I do try to show the early branching on this. Tell me what you think. It's on this thread.

http://www.anthrogenica.com/showthread.php?4288-R1b-Big-Picture-Descendants-Tree

Joe B
04-10-2015, 06:07 PM
I've tried to update my old draft "big picture" look at R1b. I do try to show the early branching on this. Tell me what you think. It's on this thread.

http://www.anthrogenica.com/showthread.php?4288-R1b-Big-Picture-Descendants-TreeIt's not an easy task to create a "big picture look to an increasingly complicated tree. Here are a few items to consider depending on the target audience.

Some of the SNPs that are listed under Z2103 are FTDNA haplogroups looking for a result. Small has them listed with a N/A instead of a sample number for the individual haplotype.
PF3252 N/A
P53 N/A
F2107 N/A
Z1862 N/A
CTS6937 N/A
Same for F2863 under L23.
F2863, YSC0000072- N/A
And for PF6714 under P310, L11.
PF6714 N/A

Under L51 PF7589/Z2118 are the same SNP and FTDNA uses R-PF7589

I've borrowed the idea of a descendancy cladogram from you. This cladogram lists the SNPs that are available for individual SNP testing from FTDNA except for Z2106 which is from YSEQ Sanger sequencing or NGS testing. https://www.familytreedna.com/groups/ht-3-5new/about/goals
The attention grabbing SNPs under R1b-Z2103 are L277 and L584.
R1b-M269>L23>Z2103>L277.1
R1b-M269>L23>Z2103>L584

Under R1b-Z2106 it's SNPs CTS7763, Z2109, CTS7822 and CTS9219 that people are looking for, especially CTS7822 and CTS9219.
R1b-M269>L23>Z2103>Z2106>CTS7763
R1b-M269>L23>Z2103>Z2106>Z2109
R1b-M269>L23>Z2103>Z2106>Z2109>CTS7822
R1b-M269>L23>Z2103>Z2106>Z2109>CTS7822>CTS9219

lgmayka
04-10-2015, 07:20 PM
Under R1b-Z2106 it's SNPs CTS7763, Z2109, CTS7822 and CTS9219 that people are looking for, especially CTS7822 and CTS9219.
Downstream from CTS9219, Slavs are interested in Y5587 and Y5586 (http://yfull.com/tree/R-Y5587/), both of which are individually testable at FTDNA.

morrisondna
04-15-2015, 04:50 PM
New Big Y Results are in for 155535 Berry placing him with Westbrooke and Schoenwalder on the L51xL11 SNP Tree at www.geneticousins.com/L51xL11/SNPTree.htm . All three of these lines fit in a separate A636/A626/A614 block under CTS11824. It was hoped that Berry and Westbrooke might show a closer connection in the south of England, but Big Y results place the connection over 4000 years ago in Europe.

smal
04-20-2015, 02:00 PM
The R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/groups/ht-3-5new/about/results) tree was updated. 4 new BigY-tested samples were added:

164226 (Kassabian) CTS7763
74013 (Robbins) Z2109>CTS3937>M64
? (Tillet) CTS9219*
223671 (Berry) CTS6889

and 19 Sardinian samples from Francalacci et al. 2013.

icebreaker
04-20-2015, 03:18 PM
There is a new M269* on Y-FULL

YF03278 new

Is there any information available about his ethnicity?

ballardgen
04-20-2015, 03:38 PM
Hi smal, did you get the last samples I sent from BDNA?

under CTS4528 > S14328,

I noticed you had not added them.









https://www.familytreedna.com/groups/r-1b-s14328-genealogy/about/background

smal
04-23-2015, 10:11 AM
Hi smal, did you get the last samples I sent from BDNA?
under CTS4528 > S14328,
I noticed you had not added them.

Hi ballardgen, I will do.

ChrisR
04-23-2015, 12:25 PM
The R1b-M269 (P312- U106-) DNA Project (https://www.familytreedna.com/groups/ht-3-5new/about/results) tree was updated.
Great work smal!!!
Please keep al versions of your tree in an archive, maybe a mirror on Google Drive etc.
This is groundbreaking citizen scientist research.

smal
05-18-2015, 04:51 AM
The R1b-M269 (P312- U106-) DNA Project tree (http://www.kumbarov.com./ht35/R1b1a2_ht35_project_tree_15_05_17_2015.pdf) was updated. It was added:

4 BigY tested samples:
FTDNA-B8903 (Myers) L584
FTDNA-148406 (Finney) CTS6889
FTDNA-40779 (Brown) CTS4528
FTDNA-319861 (Cruz) CTS4528

3 Chromo2 tested samples:
BDNA-42465/FTDNA-258432 (Ballard) CTS4528
BDNA-40292/FTDNA-373624 (Tuft) CTS4528
BDNA-41989 (Dawkins) CTS4528

1 sample from Underhill et al. 2015
U2015-PG1806 (Sephardic) L277

And
an updated data set for the 19 Sardinian samples from Francalacci et al. 2015.

ballardgen
05-18-2015, 10:45 AM
Thanks Small, :-)


I have reported S1187 & S1199 to BDNA, presumably these SNP's will be discontinued at BDNA like DF100 until they develop a functioning test for them.

and of course as you are aware - The combined results of Morrison, Schlegal, Meyer show that SNP, S1187-14054143 - Under R-S1211, is a random mutation, so of no use in any case.

smal
05-18-2015, 01:01 PM
and of course as you are aware - The combined results of Morrison, Schlegal, Meyer show that SNP, S1187-14054143 - Under R-S1211, is a random mutation, so of no use in any case.

I am not agree that S1187 is a random mutation. In this case, there are problems of an interpretation.

Unfortunately, I have only 3 S1211+ BAM files.
There are the following results for S1187 in the S1211+ samples:
....................FTDNA analysis.........BAM file analysis
319861 Cruz..............+..........................N/A
60637 Meyer..............?..........................N/A
PGP45.....................N/A........................+ (21G/1T)
N110808 Morrison.......+..........................+ (9G)
E15287 Schlegel.........?..........................N/A
253994 Oehler............?..........................+ (2G)
N24160 Pergrem.........?..........................+ (1G)
B5296 Shaw..............?..........................N/A

All Chromo2 tested samples are positive
BDNA-42465/FTDNA-258432 (Ballard) +
BDNA-574 +
BDNA-579 +
BDNA-581 +
BDNA-40292/FTDNA-373624 (Tuft) +
BDNA-571 +

Conclusions
If FTDNA do not report 14054143 (S1187) among Novel Variants it does not mean that a sample is really negative. It can have “no reads” or even be positive after the independent BAM file analysis. That is why it is so important to analyse the BAM file independently.

ballardgen
05-18-2015, 03:23 PM
smal what S1211 - .BAM files do you need?