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Rathna
12-18-2013, 04:49 AM
Rootsi et al, Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites, Nature Communications 4, Article number: 2928 doi:10.1038/ncomms3928

http://www.nature.com/ncomms/2013/13...comms3928.html


At last we'll have the solution also for hg. R-Z2105, because they tested many Jewish R-Z2105 and we'll be able to see their relation with Europeans and with me too who are in that line.
Anyway the time of hg. R are what I have said: many thousands of years. We'll be able to count them exactly.

Rathna
12-18-2013, 06:07 AM
Then
from P to R about 4,000 y
from R to R1 about 3,200 y
from R1 to R-Z2105 and R-L11 about 10,700 y
from R-Z2105 to the line of these Jews 800 y
between this Kurdish Jew and an Assyrian about 4,500 y

P.S. The SNPs come from only 8,97Mbp not from the Full Y, thus the dates are higher, we don't know how much.

GTC
12-18-2013, 06:47 AM
http://www.nature.com/ncomms/2013/13...comms3928.html


I get "Error: page not found"

Rathna
12-18-2013, 06:52 AM
I get "Error: page not found"

I took the link from the posts of Generalissimo and Humanist. I have the paper and the Supplements. You can see Humanist on R1b, Others, Assyrians etc. where he publishes many interesting posts.

GTC
12-18-2013, 07:01 AM
I took the link from the posts of Generalissimo and Humanist. I have the paper and the Supplements. You can see Humanist on R1b, Others, Assyrians etc. where he publishes many interesting posts.

Here it is:

http://www.nature.com/ncomms/2013/131217/ncomms3928/full/ncomms3928.html

Abstract

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

Rathna
12-18-2013, 08:49 AM
Now we know that the Kurdish Jew (16881) is an R-Z2110, with the SNPs Z2103/Z2104/Z2105/Z2107 before the separation from the other 2 lines (Turkish Jew 16133 and Moroccan Jew 16886 by one side and the Assyrian 13750 on the other).
The mutations Z2106/Z2109/Z2110 should be on his line (together with many others of course). It would lack only the SNP Z2108, probably out of this 8,97Mbp.
But Z2110 has been found so far above all in East Europe till the Isles and perhaps in some Gypsy lines. Difficult to say if it is an ancient Jewish line or an introgressed one.

Rathna
12-18-2013, 09:09 AM
The Assyrian 13750 is an R-L584. Thus the other Jewish line (Turkish Jew 16133 and Moroccan Jew 16886) isn't either Z2110 nor L584.

Rathna
12-18-2013, 09:25 AM
The R-L584 should derive from the R-Z2103/Z2104/Z2105/Z2107 (we don't know about Z2108) but not Z2106. Then the Tuscan of 1KGP (NA20532) is on the line which brings to Z2110 but not to L584, where are probably Carnevali with its PF7580.

P.S. But if Z2108 is with Z2109 in NA20866, it is on the line which brings to Z2110.

smal
12-18-2013, 11:16 AM
And now the Z2103 tree is -

http://s006.radikal.ru/i213/1312/52/e682892e6abf.jpg (http://radikal.ru/fp/e1d9d2547d6144459d7ce169dc3c960e)

Rathna
12-18-2013, 11:20 AM
Great work, smal. I'll study it later.

Rathna
12-18-2013, 02:17 PM
These are the STRs of the Assyrian L-584 and the linked people, amongst them the Jew Silver (45475):

_b1a R1b1a2a2a1: L23+ L584+ L943+ L944? L945? & L946+? (Ashkenazi "Group C + Assyrian")
213562 Iraq R1b1a2
13 24 14 10 11-14 12 12 12 14 13 30 17 9-9 11 11 24 15 19 30 15-15-17-17 11 12 19-23 16 15 18 17 35-36 12 12 11 9 15-16 8 10 10 8 10 12 12 23-23 16 11 12 12 16 8 12 22 21 12 12 11 13 11 11 12 13
205749 Gulawi Be-Lachin, b. 1800 and d. 1880 Turkey R1b1a2
13 24 14 11 11-14 12 12 12 14 13 30 16 9-9 11 11 25 15 19 29 15-15-17-17 11 12 19-23 16 15 16 17 36-37 12 12 11 9 15-16 8 10 10 8 11 11 12 23-23 16 11 12 12 15 8 12 22 20 12 12 11 13 11 11 12 12 35 15 9 16 12 26 26 17 11 11 13 13 10 9 11 12 10 11 11 30 12 13 24 13 10 10 23 15 20 12 23 17 12 16 25 12 23 18 10 14 16 8 11 11
_b1a R1b1a2a2a1a: L23+ L584+ L943+ L944+ L945+ & L946+ (Ashkenazi "Group C")
45475 Louis Silver Lithuania R1b1a2a1
12 24 14 11 11-14 12 12 12 14 13 30 16 9-9 11 11 25 15 19 28 15-15-16-17 11 12 19-23 15 15 17 18 36-37 12 12 11 9 15-16 8 10 10 8 11 11 12 21-23 16 11 12 12 16 8 11 22 20 13 12 11 13 11 11 12 12

And these are the SNPs tested:

90492 Sekharya Barkho R1b1a2 R-M269 L584+, L943-
205749 Gulawi Be-Lachin, b. 1800 and d. 1880 R1b1a2 R-M269 L584+, L943+
258253 Musa Aliyev, 1903 -1995, Shahbuz, Nakhichevan R1b1a2 R-M269 L584+, Z2103+, L943-
213562 R1b1a2 R-M269 L943+

And these are the two L943-:

90492 Sekharya Barkho Turkey R1b1a2
12 24 13 10 11-14 12 12 12 14 13 30 17 9-10 11 11 26 16 19 30 15-16-16-17 11 11 19-22 16 16 16 16 35-39 12 12 11 9 15-16 8 10 10 8 11 11 12 23-23 16 10 12 12 14 8 12 22 20 14 12 11 13 11 11 12 12 258253 Musa Aliyev, 1903 -1995, Shahbuz, Nakhichevan Azerbaijan R1b1a2
12 24 14 11 11-14 12 11 12 13 13 29 15 9-10 11 11 25 15 19 28 15-15-16-18 11 11 19-23 16 16 17 16 36-37 11 11 11 9 15-16 8 10 10 8 11 11 10 23-23 17 11 12 12 15 8 13 22 20 13 12 11 13 10 11 12 12

Rathna
12-18-2013, 03:07 PM
If we count the separation between Silver and me:

45475 Louis Silver Lithuania R1b1a2a1
12 24 14 11 11-14 12 12 12 14 13 30 16 9-9 11 11 25 15 19 28 15-15-16-17 11 12 19-23 15 15 17 18 36-37 12 12 11 9 15-16 8 10 10 8 11 11 12 21-23 16 11 12 12 16 8 11 22 20 13 12 11 13 11 11 12 12

H1614 Antonio del Badia (1449-?) Castelfiorentino (Firenze) Italy R1b1a2
12 24 15 10 11-14 12 12 12 13 12 29 16 9-10 11 11 24 15 19 29 14-14-16-17 10 11 19-23 16 15 19 17 36-37 12 12 11 9 15-16 8 10 10 8 10 11 12 23-24 16 10 12 12 16 8 12 22 21 13 12 11 13 11 11 12 12 32 15 9 16 11 25 26 19 12 11 13 12 10 9 12 11 10 11 11 30 12 14 24 14 10 9 20 15 19 14 23 18 12 15 24 12 23 18 10 14 18 9 11 11

we have 23 mutations out of 67 markers.
(454x23): 134= 80 generations. As the years that separated my Z2105* from Silver are at least 4,500, thus every generation lasted at least 56 years. Perhaps this is a proof that both descend from Methuselah.

P.S. The mutations are 22, but a little changes.

smal
12-18-2013, 06:53 PM
The slightly updated Z2103 tree
http://s005.radikal.ru/i212/1312/cc/033ea2c00497.png (http://radikal.ru/fp/b2b889f517b649bf944637d149ca0336)

Humanist
12-18-2013, 07:44 PM
The slightly updated Z2103 tree

Thanks for the update, smal.

ADW_1981
12-18-2013, 08:44 PM
Who are those "green" folks in the other branches. Is there any relationship by religion or ethnicity to the various jewish groups? I'd also be interested in seeing where the Sephardic jews fall, both those in the diaspora and any Sephardic men who have oral history from Spain.

Joe B
12-18-2013, 08:54 PM
Who are those "green" folks in the other branches. Is there any relationship by religion or ethnicity to the various jewish groups? I'd also be interested in seeing where the Sephardic jews fall, both those in the diaspora and any Sephardic men who have oral history from Spain.
smal posted this on the R1b-PF7580 thread (http://www.anthrogenica.com/showthread.php?1586-From-R-L23-L150-to-R-PF7580&p=22598&viewfull=1#post22598)


And the Z2103 tree of the 1000 genomes (yellow) and Geno 2.0 (green) tested samples.

Rathna
12-18-2013, 09:39 PM
The slightly updated Z2103 tree
http://s005.radikal.ru/i212/1312/cc/033ea2c00497.png (http://radikal.ru/fp/b2b889f517b649bf944637d149ca0336)

smal, many thanks for the update, but we don't know if PF7580 and L584 are on the same plane. This has been demonstrated true for Goldschlager, but for what I know neither Carnevali nor Aghinitei, both PF7580 from Geno 2.0, has been tested for L584.
Silver is both PF7580 and L584 and L943/L944/L945/L946 and also CTS1848 and PF3449 and this should appear in the tree.
From the data I reported above about the Assyrians (and which aren't clear) it seems that they are positive only for L943 and not also for L945, but perhaps you have ascertained this for the Assyrian of the paper, but there should be a differentiation amongst them, and then these SNPs could be own of the Assyrian pool. By their STRs values they and Silver don't seem very close , but of course we'll be able to say something more careful only with more Full Y or also Big Y.

Rathna
12-18-2013, 09:51 PM
P.S. The mutations are 22, but a little changes.

Actually with 60 years as to 25 we would have that factor of about 2.5 for which I (and not I alone) am saying from many years that it is the difference between the germline mutation rate and that demonstrated by ancient DNA, and this shouldn't be a little.

smal
12-19-2013, 07:34 AM
we don't know if PF7580 and L584 are on the same plane. This has been demonstrated true for Goldschlager, but for what I know neither Carnevali nor Aghinitei, both PF7580 from Geno 2.0, has been tested for L584.
This is true. But when we have the different PF7580 and L584 results for a single sample we’ll change the tree.


Silver is both PF7580 and L584 and L943/L944/L945/L946 and also CTS1848 and PF3449 and this should appear in the tree.
That is strange, but I can’t find any + data for L943/L944/L945/L946 for Silver in Ftdna projects.


From the data I reported above about the Assyrians (and which aren't clear) it seems that they are positive only for L943 and not also for L945, but perhaps you have ascertained this for the Assyrian of the paper, but there should be a differentiation amongst them, and then these SNPs could be own of the Assyrian pool. By their STRs values they and Silver don't seem very close , but of course we'll be able to say something more careful only with more Full Y or also Big Y.
Unfortunately I didn’t see the real sequences of peoples from the Rootsi et al article. There is only a list of positive SNP. So it’s not possible to differ between negative and “no reads” data. Therefore, we couldn’t be sure that Assyrian 13750 is negative for L944, L946, CTS1848, PF3449.

Rathna
12-19-2013, 08:38 AM
That is strange, but I can’t find any + data for L943/L944/L945/L946 for Silver in Ftdna projects.


smal, the SNPs for which Silver is positive are given by the administrators of the "ht 35 FTDNA Project" and I posted them also above:
_b1a R1b1a2a2a1a: L23+ L584+ L943+ L944+ L945+ & L946+ (Ashkenazi "Group C")
Perhaps we should ask them.
Semargl.DNA gives positive for L943 the sample 205749 and no one for the others and these SNPs aren't reported either in the "Jewish R1b project" where Silver is an administrator.
But I have always known that they were discovered just from a WTY of the same Silver and that someone was tested for L943 demonstrates this. Perhaps we should ask Humanist, whether he wants to say something about that.

Humanist
12-19-2013, 08:44 AM
But I have always known that they were discovered just from a WTY of the same Silver and that someone was tested for L943 demonstrates this. Perhaps we should ask Humanist, whether he wants to say something about that.

That is my understanding as well.

smal
12-19-2013, 09:16 AM
That is my understanding as well.
Then I must correct the tree.
http://i064.radikal.ru/1312/a0/20f5090fcf48.jpg (http://radikal.ru/fp/840ee41825d744e0a9af9794f9e262bb)

AJL
12-24-2013, 03:28 AM
Who are those "green" folks in the other branches. Is there any relationship by religion or ethnicity to the various jewish groups? I'd also be interested in seeing where the Sephardic jews fall, both those in the diaspora and any Sephardic men who have oral history from Spain.

I have an ancestral Sephardi line with an Iberian-form surname from the Syrian/Turkish border area, from which a distant cousin has tested +L584 (and has not tested beyond that).

Joe B
12-24-2013, 06:07 PM
Who are those "green" folks in the other branches. Is there any relationship by religion or ethnicity to the various jewish groups? I'd also be interested in seeing where the Sephardic jews fall, both those in the diaspora and any Sephardic men who have oral history from Spain.

I have an ancestral Sephardi line with an Iberian-form surname from the Syrian/Turkish border area, from which a distant cousin has tested +L584 (and has not tested beyond that).
R1b-L584 is found in Sephardic and Ashkenazi Jewish populations. Most likely in Mizrahi Jews too since L584 seems endemic to the middle east. The story of the Sephardic Jews(Jews of the Spanish rite) of Aleppo illustrates how R1b-L584 and other haplogroups may have left the middle east in antiquity for Iberia and returned after the Alhambra Decree (http://en.wikipedia.org/wiki/Alhambra_Decree) of 1492.
JewishGen - The Jews of Aleppo (http://www.jewishgen.org/sefardsig/aleppojews.htm)

Many Jewish families settled in Aleppo, as it was an established center for great rabbinical learning. During the initial settlement period, the Spanish Jews who had emigrated from Spain, remained separate and apart from the indigenous Aleppan Jews. The Spanish Jews spoke Ladino, a mixture of Hebrew and Spanish that was not understood in Aleppo, where the population spoke Arabic and read Hebrew with an Arabic accent. Added to the mixture of native Syrians and Spanish Jews from Sepharad, were Italian Jews, who were commonly referred to as "Francos." It took several centuries, but eventually the two communities – the new Spanish Jews and the Jews indigenous to Aleppo, converged into one and the Ladino language of the Spanish Jews died out by the middle of the 18 th Century. Yet the surnames of the families - like Kassin and Labaton - lived on into the 21 st Century. EDIT:The Ladino language survived in many other places. (see #29 (http://www.anthrogenica.com/showthread.php?1727-R1b-phylogeny&p=24448&viewfull=1#post24448))

The migration settlement map of Spanish Jews combined with other expulsions over the centuries shows some of the complication.
Wikipedia
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ec/Sepharadic_Migrations.jpg/800px-Sepharadic_Migrations.jpg http://upload.wikimedia.org/wikipedia/commons/thumb/6/65/Expulsion_judios-en.svg/570px-Expulsion_judios-en.svg.png

AJL
12-24-2013, 06:13 PM
^ Yes it amazes me that this yDNA line seems to have returned more or less to its exact point of origin after perhaps as much as 1500 years!

Joe B
12-24-2013, 06:27 PM
^ Yes it amazes me that this yDNA line seems to have returned more or less to its exact point of origin after perhaps as much as 1500 years!
Hope all R1b-L584 and potential haplotypes are ready for some testing this year. With the Geno 2.0 PF7580>L584 confirmation and a L584 Big Y test result due soon, some neat discoveries are in the works for the R1b-L584 subclade.

Humanist
12-24-2013, 06:40 PM
^ Yes it amazes me that this yDNA line seems to have returned more or less to its exact point of origin after perhaps as much as 1500 years!

Hi AJ. Can you tell me if what is stated below is correct? I had never read that before, but given the high frequency of R1b among Alawites (30+ %), it would be an interesting development.

Wikipedia


Levite ancestry through history

Some Levites have adopted a related last name to signify their priestly status. Not necessarily all carriers of the downlisted surnames are descended from Levite tribe, but it is usually considered a good indication of genuine Levite ancestry through the ages. Because of diverse geographical locations, the names have several variations:

"Alouwi", Arabic variant, of Sephardic origin (Alawites of Lebanon and Syria)

AJL
12-24-2013, 07:29 PM
Hi AJ. Can you tell me if what is stated below is correct? I had never read that before, but given the high frequency of R1b among Alawites (30+ %), it would be an interesting development.

I'm not aware of any connection between Alawites and Levites: the word is generally assumed to be Arabic for "follower of Ali." My L584 line was Israelite in any case (i.e. non-Levite).

razyn
12-24-2013, 08:56 PM
I realize you quoted this from another source...


It took several centuries, but eventually the two communities – the new Spanish Jews and the Jews indigenous to Aleppo, converged into one and the Ladino language of the Spanish Jews died out by the middle of the 18 th Century.

And maybe that source was specific to Aleppo. But the Ladino language wasn't dead in the 18th century; it was widely spoken through the 19th (among other places, in Morocco), and I believe there are still those who understand it. A friend of ours, Flory Jagoda, has recorded several albums that include Ladino songs she learned as a child in Sarajevo. http://en.wikipedia.org/wiki/Flory_Jagoda

Joe B
12-24-2013, 09:54 PM
I realize you quoted this from another source...



And maybe that source was specific to Aleppo. But the Ladino language wasn't dead in the 18th century; it was widely spoken through the 19th (among other places, in Morocco), and I believe there are still those who understand it. A friend of ours, Flory Jagoda, has recorded several albums that include Ladino songs she learned as a child in Sarajevo. http://en.wikipedia.org/wiki/Flory_JagodaThe jewishgen.org source was referring only to the Aleppo community. The part of the article that was qouted is called The Convergence of Two Communities. Just wanted to show that it may be difficult to discern if R1b-L584 was part of the Jews from Spain community or not. Certainly surnames along with written and oral histories will help sort it out.
No intention on my part to do away with an entire language. I'm not worthy. Aleppo is a good example except for the language part.
The Ladino Language is alive and well! Made a note about Ladino in the original post. Thanks razyn.
The Jews of Aleppo (http://www.jewishgen.org/sefardsig/aleppojews.htm)
by Sarina Roffé
Sarina Roffé is a career journalist and holds a masters in Jewish Studies. She has researched numerous genealogies including the Kassin and Labaton rabbinic dynasties ans is considered an expert in Aleppan Jewry. She is a member of Brooklyn's Syrian Jewish community and the Jewish Genealogical Society, Inc. of New York.

razyn
12-24-2013, 11:55 PM
Made a note about Ladino in the original post. Thanks razyn.

You're welcome, and I'll tell Flory -- it's sort of her calling. She's now 88 and (being a tiny woman to begin with) can't really rock out with her accordion, anymore. But she's a fine musician, still sings and plays a (lightweight) classical guitar and performs, in Ladino and a few other languages. I actually met her through the Washington Balalaika Society orchestra, in which both of us have played for the past 20+ years... in itself, something of a melting pot.

I realize that's off topic, and will now hush.

seferhabahir
12-25-2013, 06:57 AM
I realize you quoted this from another source...

And maybe that source was specific to Aleppo. But the Ladino language wasn't dead in the 18th century; it was widely spoken through the 19th (among other places, in Morocco), and I believe there are still those who understand it. A friend of ours, Flory Jagoda, has recorded several albums that include Ladino songs she learned as a child in Sarajevo. http://en.wikipedia.org/wiki/Flory_Jagoda

Went to a Passover Seder two year ago at a friends house in California whose family was from Gibraltar. We all used a siddur that was in English, Hebrew, and Ladino. There is also a large Sephardic community in Seattle, many of whom came from Rhodes and Marmara. Last month, I watched as senior citizens at a Seattle SNF were happily entertained by a musician singing Hanukkah songs in Ladino (including "Ocho Kandelikas" written by Flory Jagoda). No doubt a lot of them can still speak Ladino.

Rathna
01-06-2014, 06:24 AM
What does it happen at Chromo2?

I ordered my Chromo2 on 13 september 2013, also paying 20Ł more, because I didn't find the site of the previous customers (my guilty).
After many weeks, more than those promised, I wrote a letter:

Hi Laura Marshall,
these are my data
Number Date Value
36054 13/09/2013 Ł129.00
and my kit arrived in the lab on 2 October. I ask why my results aren't available yet.
Regards, Gioiello Tognoni

No answer so far. In the same days Telfermagne, who was in the same batch of mine, after a letter received his results.
To-day they are 95 days that my kit arrived in the lab.
Of course I asked for my raw data and they cannot send me what they want. I am expecting some results very important for our R-Z2105 tree (see here the smal's tree).
I am very angry and disappointed.

GTC
01-06-2014, 07:14 AM
No answer so far.
... I am very angry and disappointed.

I assume you used the "support" email address?

Suggest either telephoning them (where they say you have to leave a message) or perhaps emailing their media person about your bad experience with her company. Perhaps Ms Moffat will investigate the no response situation on your behalf:

http://www.britainsdna.com/about/contact-us

Rathna
01-06-2014, 07:55 AM
I assume you used the "support" email address?

Suggest either telephoning them (where they say you have to leave a message) or perhaps emailing their media person about your bad experience with her company. Perhaps Ms Moffat will investigate the no response situation on your behalf:

http://www.britainsdna.com/about/contact-us

I thank you, but I've found on my account only this:

Our apologies, we are currently experiencing technical issues

Joe B
01-07-2014, 12:14 AM
I've decided to do some SNP testing with YSEQ DNA and to fill a complete row on the microplate. So 8 SNPs need to be chosen. They already have Z2110/CTS7822. Z2104 and Z2107 were just added to the catolog by someone else's request. That is good news because it means somebody else is testing these SNPs too. Thomas Krahn has hinted at testing CTS7959, CTS9230, CTS11767. We also have the question of PF7580 and if PF7580+, L584- is possible. There are obviously a lot of SNPs I don't know about and would dearly appreciate your phylogenetic thinking. My thinking is that it would be good to have some testing done by Sanger sequencing to compliment the SNP array testing most people are doing now.
Joe
Z2103+, Z2105+, L277-, L584-

Rathna
01-07-2014, 06:44 AM
I've decided to do some SNP testing with YSEQ DNA and to fill a complete row on the microplate. So 8 SNPs need to be chosen. They already have Z2110/CTS7822. Z2104 and Z2107 were just added to the catolog by someone else's request. That is good news because it means somebody else is testing these SNPs too. Thomas Krahn has hinted at testing CTS7959, CTS9230, CTS11767. We also have the question of PF7580 and if PF7580+, L584- is possible. There are obviously a lot of SNPs I don't know about and would dearly appreciate your phylogenetic thinking. My thinking is that it would be good to have some testing done by Sanger sequencing to compliment the SNP array testing most people are doing now.
Joe
Z2103+, Z2105+, L277-, L584-

Of course only after having received my Chromo2 I'll decide to test some of these SNPs. Being like you so far Z2105+ L277- L584- I could be both PF7580 (we already have Carnevali in Italy and he could be one to test for L584 to know if these SNPs are disjointed and this would be interesting for me and for the theory of an Italian/Western European origin of Z2105) and Z2110 or any intermediate SNP or like the Tuscan in 1KGP to be on the left line of the tree which brought to the two Jews.

Rathna
01-07-2014, 06:28 PM
At last my results arrived! It was worth it!
It seems I am R-Z2110*. Some doubts about my Z2103-, which would seem to break the two SNPs Z2103/Z2105, but we wouldn't understand why if I am of the subclade Z2110*.

PF7580 CC negative
S334 GG negative (L277)
CTS7763 AA negative
CTS8966 GG negative
Z2103 CC negative
Z2105 AC positive
Z2109 GG positive
Z2110 TT positive
CTS9219 GG negative
CTS699 GG negative

P.S. If not the separation was just between Z2105 and Z2103, but there are any Z2110 tested for both these SNPs?

Joe B
01-07-2014, 06:39 PM
What would be the smart and targeted SNP wish list for filling in some of the unknowns with R1b-L23>L150>Z2103>? phylogeny that my haplotype can test for? Smal's advanced Z2103 tree has some of the SNPs and gaps that we are interested in. Are there more that we need to take a look at?
Eight SNPs are needed.

Based on the smal Z2103 tree.
Z2104
Z2107
CTS7822/Z2110
CTS9219
PF7580

YSEQ has suggested these three SNPs. I'm not sure where they fit on the phylogenetic tree
CTS7959
CTS9230
CTS11767

These SNPs L150+, L23+, Z2103+, Z2105+, L144-, L21-, L277-, L51-, L584-, P310-, P312-, U106- have been tested and it's #257842 if you must.




And the Z2103 tree of the 1000 genomes (yellow) and Geno 2.0 (green) tested samples.

The slightly updated Z2103 tree
http://s005.radikal.ru/i212/1312/cc/033ea2c00497.png (http://radikal.ru/fp/b2b889f517b649bf944637d149ca0336)

Joe B
01-07-2014, 06:40 PM
At last my results arrived! It was worth it!
It seems I am R-Z2110*. Some doubts about my Z2103-, which would seem to break the two SNPs Z2103/Z2105, but we wouldn't understand why if I am of the subclade Z2110*.

PF7580 CC negative
S334 GG negative (L277)
CTS7763 AA negative
CTS8966 GG negative
Z2103 CC negative
Z2105 AC positive
Z2109 GG positive
Z2110 TT positive
CTS9219 GG negative
CTS699 GG negative

P.S. If not the separation was just between Z2105 and Z2103, but there are any Z2110 tested for both these SNPs?
Yee Haw!! Tell me how I can compliment your results.
CTS7822/Z2110 TT positive
CTS9219 GG negative

Rathna
01-07-2014, 06:45 PM
Yee Haw!! Tell me how I can compliment your results.
CTS7822/Z2110 TT positive
CTS9219 GG negative

I have 15,000 SNPs to study. I'll let you know.

Rathna
01-07-2014, 06:54 PM
YSEQ has suggested these three SNPs. I'm not sure where they fit on the phylogenetic tree
CTS7959
CTS9230
CTS11767



I am
CTS7959 AA negative
CTS9230 CC negative
CTS11767 CC negative
Already posted my result for PF7580, which is negative of course.

Rathna
01-07-2014, 07:09 PM
PF1610 AA negative

This SNP was found positive in 26483.

Rathna
01-07-2014, 07:15 PM
Perhaps it is interesting all this series of positive PF SNPs:
PF2590 GG positive PF2592 AA positive PF259 GG negative PF2615 GG positive PF2617 AA positive PF2619 AG positive PF2621 AA positive PF2622 AA positive PF2624 GG positive PF2626 00 no_call PF2629 00 no_call PF2640 00 no_call PF2642 AG positive PF2651 AA positive PF2653 AA positive PF2655 GG positive PF2658 CC positive PF2660 AA positive PF2677 TT positive PF2679 AA positive PF2683 TT positive PF2684 GG positive PF2685 TT positive PF2688 AA positive PF2690 AA positive PF2700 GG positive PF2702 AA positive PF2704 AA positive PF2709 GG positive PF2716 CC positive PF2718 AA positive PF2722 GG positive PF2734 AA positive PF2736 GG positive PF2737 GG positive PF2739 GG positive PF2742 GG positive PF2743 00 no_call PF2747 GG positive PF2748 AA positive PF2760 AA positive PF2762 CC positive PF2775 GG positive

Rathna
01-07-2014, 07:23 PM
And also this:
PF6399 AA positive PF6409 AA positive PF6410 AA positive PF6419 CC positive PF6429 GG positive PF6430 AA positive PF6432 AA positive PF6434 GG positive PF6435 GG positive PF643 AA positive PF6443 AG positive PF6451 AA positive PF6463 AA positive PF6467 AG positive PF6469 GG positive PF6471 GG positive PF6475 AA positive PF6481 AA positive PF6484 AA positive PF6487 CC positive PF6492 AA negative PF6495 AA positive PF6497 CC positive PF6503 AA negative PF6506 AA positive PF6507 AA positive PF6510 00 no_call PF6512 00 no_call PF6524 GG positive PF6528 AA positive PF653 GG positive

Joe B
01-07-2014, 07:30 PM
PF1610 AA negative

This SNP was found positive in 26483.
Chris has him at the PF6404 level.

Rathna
01-07-2014, 07:43 PM
S136 00 no_call S13613 00 no_call S13614 00 no_call

This is interesting because, as I have said many times in the past, S136 is L50, but I have a deletion of 9bp in that region (found just from EthnoAncestry), around 7.012.028, and these no-calls demonstrate this.

smal
01-08-2014, 08:01 AM
At last my results arrived! It was worth it!
It seems I am R-Z2110*. Some doubts about my Z2103-, which would seem to break the two SNPs Z2103/Z2105, but we wouldn't understand why if I am of the subclade Z2110*.

PF7580 CC negative
S334 GG negative (L277)
CTS7763 AA negative
CTS8966 GG negative
Z2103 CC negative
Z2105 AC positive
Z2109 GG positive
Z2110 TT positive
CTS9219 GG negative
CTS699 GG negative

P.S. If not the separation was just between Z2105 and Z2103, but there are any Z2110 tested for both these SNPs?

Rathna, I can't undestand your results.

PF7580 C->A CC negative
S334 (L277) T->С GG negative ??
CTS7763 A->G AA negative
CTS8966 C->T GG negative ??
Z2103 G->C CC negative ?? positive
Z2105 C->A AC positive ?? heterozygous
Z2109 T->C GG positive ??
Z2110 A->T TT positive
CTS9219 G->A GG negative
CTS699 C->T GG negative ??

Rathna
01-08-2014, 08:20 AM
Rathna, I can't undestand your results.

PF7580 C->A CC negative
S334 (L277) T->С GG negative ??
CTS7763 A->G AA negative
CTS8966 C->T GG negative ??
Z2103 G->C CC negative ?? positive
Z2105 C->A AC positive ?? heterozygous
Z2109 T->C GG positive ??
Z2110 A->T TT positive
CTS9219 A->T GG negative ??
CTS699 C->T GG negative ??

Of course something doesn't fit, and also the three months in delaying them has some meaning. Anyway let's try to use them where it is possible. I have signaled that Z2103- and Z2110+ don't fit. This is written before my results:

"This is your Y chromosome raw data for the chromo2 chip. We only advise expert genetic genealogists to use this file, as almost all important information is distilled into the genetic signature and other results. The file is a tab-delimited text file which may be opened in a spreadsheet program. Each line corresponds to a single SNP and you will find three columns with respectively, the SNP name, your genotype and whether the result is positive (derived) or negative (ancestral). Alleles are called to the Illumina TOP strand. Where it was not possible to call the allele in your sample, a zero is given and the result is "no_call". We may from time to time update the raw data if it becomes possible to call markers which were initially problematic. While the Y chromosome is a single copy piece of DNA, the Illumina software used to call alleles is designed for autosomal markers which come in two copies. Hence when AA or GG are given, it means A or G, respectively. A small number of markers give apparent heterozygote calls, e.g. AG. As shown in the result column, these indicate a positive call. The reason they appear to be heterozygous is again because of limitations in the Illumina clustering software, which expects three clusters. If the true positive and negative clusters are too close together, it is not possible to force a homozygous call for the one variant, hence an AG call is allowed. Our downstream scripts register this as a positive call. In a few cases a marker might arise, for example, by the DNA letter A changing to C, then much later in time in someone with the C it changes back to an A again; this is called back-mutation. One such example is the marker S163: if you carry the ancestral A you are negative, if you carry the C it is shown as (positive) and if you carry the back-mutated A, it is shown as "back-mutated". We can tell the back-mutations from the ancestral variants using the other markers you carry".

smal
01-08-2014, 08:22 AM
YSEQ has suggested these three SNPs. I'm not sure where they fit on the phylogenetic tree
CTS7959
CTS9230
CTS11767


CTS7959 17,764,622 A->T
CTS9230 18,760,768 G->T
CTS11767 23,257,041 G->T

These three SNPs are on the same level as CTS9219. The HG01515 sample has all four SNPs that differ it from the others.

smal
01-08-2014, 08:54 AM
A small number of markers give apparent heterozygote calls, e.g. AG. As shown in the result column, these indicate a positive call.

OK. They explain the presence of heterozygotes. But how can we explain such results - S334 (L277) T->С GG negative ??

Rathna
01-08-2014, 09:07 AM
OK. They explain the presence of heterozygotes. But how can we explain such results - S334 (L277) T->С GG negative ??

We should be sure that S334 actually corresponds to L277!

Rathna
01-08-2014, 09:08 AM
PF1610 AA negative

This SNP was found positive in 26483.

Chromo2 doesn't test PF6404 which is put at the same level of L23/L49 (for which I was tested positive by 23andMe) and about Campbell (26483) I make you note how our SNPs near PF6404 (which are probably on the same level nearby L23) coincide:
mine
PF6399 AA positive PF6409 AA positive PF6410 AA positive PF6419 CC positive PF6429 GG positive PF6430 AA positive PF6432 AA positive PF6434 GG positive PF6435 GG positive PF643 AA positive PF6443 AG positive PF6451 AA positive PF6463 AA positive PF6467 AG positive PF6469 GG positive PF6471 GG positive PF6475 AA positive PF6481 AA positive PF6484 AA positive PF6487 CC positive PF6492 AA negative PF6495 AA positive PF6497 CC positive PF6503 AA negative PF6506 AA positive PF6507 AA positive PF6510 00 no_call PF6512 00 no_call PF6524 GG positive PF6528 AA positive PF653 GG positive
the Campbell's
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,

Rathna
01-08-2014, 09:56 AM
What to think about Campbell? He hasn't been tested for Z2103/Z2105 nor L277 and L584. It seems Z2110- (if he hadn't had a no-call there).
This is his 111 markers values:

26483 David Campbell (1819) United Kingdom R1b1a2a1
12 24 14 10 11-14 12 12 13 13 13 29 17 9-11 11 11 25 15 19 30 14-15-16-17 10 11 19-23 15 18 19 17 34-37 12 12 11 9 15-16 8 10 10 8 10 12 12 20-23 16 10 12 12 15 8 12 22 21 13 12 11 13 11 12 12 12 34 15 9 16 12 26 26 19 12 11 13 12 10 9 12 12 10 11 11 30 11 13 23 14 10 10 21 15 17 14 23 18 12 15 24 13 24 18 10 14 17 9 11 11
If we compare the two series:
Campbell:
8 10 10 8 10 12
11 13 11 12 12 12
mine:
8 10 10 8 10 11
11 13 11 11 12 12
he has two mutations, thus probably a separation between 4,000 and 8,000 years (this is my thinking).
This structure is unique and only in the first series coincides with others, even though we should put on account also a mutation of DYS511 from 11 to 10 and not to 12. It seems that this cluster has some links with Jewish haplotypes, thus I'd suggest to test him above all for L584, but before to see if his Geno 2.0 has PF7580 negative or if he had a no-call:

79073 Volkov or Kachko or Kachka, b. 1875 Ukraine R1b1a2a
12 24 14 10 11-15 10 12 12 13 14 28 16 9-10 11 11 26 15 19 28 15-15-16-18 10 13 20-23 16 16 17 17 35-37 11 12 11 9 15-16 8 10 10 8 10 12 10 24-24 16 10 12 13 15 8 12 21 20 13 12 11 13 11 11 12 12 35 15 9 16 12 29 26 19 11 11 13 12 11 9 12 12 10 11 11 30 13 13 24 13 10 9 22 15 19 12 24 20 13 15 24 12 23 18 9 14 17 9 11 11
101678 Vincencio Cano abt. 1770 Taumaulipas Mexico Unknown Origin R1b1a2a1
12 25 14 11 11-14 12 12 14 13 14 29 16 9-9 11 11 26 15 19 32 14-15-16-18 11 12 19-24 15 15 18 17 37-37 13 12 11 9 15-16 8 10 10 8 10 12 12 23-23 16 10 12 12 15 8 12 22 20 13 13 12 13 11 11 12 11
213562 Iraq R1b1a2
13 24 14 10 11-14 12 12 12 14 13 30 17 9-9 11 11 24 15 19 30 15-15-17-17 11 12 19-23 16 15 18 17 35-36 12 12 11 9 15-16 8 10 10 8 10 12 12 23-23 16 11 12 12 16 8 12 22 21 12 12 11 13 11 11 12 13

Rathna
01-08-2014, 10:34 AM
This is the PFseries near L23:
Campbell
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Seymour (Z2110+/L150-)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Silver (L584+, L943/L946+)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Kassabian (Z2103/Z2105+)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Soltz
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+
Sands (Z2110+)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
I Lakkis
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Carnevali (PF7580)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Burkholder (L277+)
PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+,
Bardiga (L269+/L150+/PF7558/62/63+)
PF6404-, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+

etc etc
mine (for linkage disequilibrium)
PF6399 AA positive PF6409 AA positive PF6410 AA positive PF6419 CC positive PF6429 GG positive PF6430 AA positive PF6432 AA positive PF6434 GG positive PF6435 GG positive PF643 AA positive PF6443 AG positive PF6451 AA positive PF6463 AA positive PF6467 AG positive PF6469 GG positive PF6471 GG positive PF6475 AA positive PF6481 AA positive PF6484 AA positive PF6487 CC positive PF6492 AA negative PF6495 AA positive PF6497 CC positive PF6503 AA negative PF6506 AA positive PF6507 AA positive PF6510 00 no_call PF6512 00 no_call PF6524 GG positive

Silesian
01-08-2014, 01:57 PM
What to think about Campbell? He hasn't been tested for Z2103/Z2105 nor L277 and L584. It seems Z2110- (if he hadn't had a no-call there).
This is his 111 markers values:

26483 David Campbell (1819) United Kingdom R1b1a2a1
12 24 14 10 11-14 12 12 13 13 13 29 17 9-11 11 11 2 5 15 19 30 14-15-16-17 10 11 19-23 15 18 19 17 34-37 12 12 11 9 15-16 8 10 10 8 10 12 12 20-23 16 10 12 12 15 8 12 22 21 13 12 11 13 11 12 12 12 34 15 9 16 12 26 26 19 12 11 13 12 10 9 12 12 10 11 11 30 11 13 23 14 10 10 21 15 17 14 23 18 12 15 24 13 24 18 10 14 17 9 11 11
If we compare the two series:
Campbell:
8 10 10 8 10 12
11 13 11 12 12 12
mine:
8 10 10 8 10 11
11 13 11 11 12 12
he has two mutations, thus probably a separation between 4,000 and 8,000 years (this is my thinking).
This structure is unique and only in the first series coincides with others, even though we should put on account also a mutation of DYS511 from 11 to 10 and not to 12. It seems that this cluster has some links with Jewish haplotypes, thus I'd suggest to test him above all for L584, but before to see if his Geno 2.0 has PF7580 negative or if he had a no-call:

79073 Volkov or Kachko or Kachka, b. 1875 Ukraine R1b1a2a
12 24 14 10 11-15 10 12 12 13 14 28 16 9-10 11 11 26 15 19 28 15-15-16-18 10 13 20-23 16 16 17 17 35-37 11 12 11 9 15-16 8 10 10 8 10 12 10 24-24 16 10 12 13 15 8 12 21 20 13 12 11 13 11 11 12 12 35 15 9 16 12 29 26 19 11 11 13 12 11 9 12 12 10 11 11 30 13 13 24 13 10 9 22 15 19 12 24 20 13 15 24 12 23 18 9 14 17 9 11 11
101678 Vincencio Cano abt. 1770 Taumaulipas Mexico Unknown Origin R1b1a2a1
12 25 14 11 11-14 12 12 14 13 14 29 16 9-9 11 11 26 15 19 32 14-15-16-18 11 12 19-24 15 15 18 17 37-37 13 12 11 9 15-16 8 10 10 8 10 12 12 23-23 16 10 12 12 15 8 12 22 20 13 13 12 13 11 11 12 11
213562 Iraq R1b1a2
13 24 14 10 11-14 12 12 12 14 13 30 17 9-9 11 11 24 15 19 30 15-15-17-17 11 12 19-23 16 15 18 17 35-36 12 12 11 9 15-16 8 10 10 8 10 12 12 23-23 16 11 12 12 16 8 12 22 21 12 12 11 13 11 11 12 13
Of course Campbell demonstrates Eastern European model.Combination of forensic marker DYS 464 ABCD {[14-15- 16-17]fast mutating marker}, plus DYS 392 {[13] slow mutating marker}, DYS 449 {[30-33] fast mutating marker}, and very, very slow DYS 426 {12 }

CX94E-R1b1b2a - L23EE Modal
http://www.ysearch.org

http://www.familytreedna.com/public/JewishR1b/default.aspx?section=yresults
Group A DYS-426 11 DYS-464ABCD15-15-16-16DYS-39214
Group B DYS-464-ABCD [SIZE=1]15-15-16-16DYS-392 14

These are separated by perhaps as much as 2-5 thousand years.

Rathna
01-08-2014, 04:33 PM
Of course Campbell demonstrates Eastern European model.Combination of forensic marker DYS 464 ABCD {[14-15- 16-17]fast mutating marker}, plus DYS 392 {[13] slow mutating marker}, DYS 449 {[30-33] fast mutating marker}, and very, very slow DYS 426 {12 }

CX94E-R1b1b2a - L23EE Modal
http://www.ysearch.org

http://www.familytreedna.com/public/JewishR1b/default.aspx?section=yresults
Group A DYS-426 11 DYS-464ABCD15-15-16-16DYS-39214
Group B DYS-464-ABCD [SIZE=1]15-15-16-16DYS-392 14

These are separated by perhaps as much as 2-5 thousand years.

Silesian, do you think that Campbell belong to the East European L23 cluster? But which would be its final SNP?
I have always thought that all they were Z2110, but it seems now that this would be also my final SNP, in spite of the uncertainties that there are about my Chromo2 test.
The Jewish clusters, those two of the "Jewish R1b project" (and I have explained this many times), are two different haplogroups, with only one ancestor each, with a recent origin, and have nothing to do one each other. They are put together (erroneously) by the presence of L150+, but the first is
R-M269/L150+/PF7558+/PF7562+/PF7563+ and of course L23-, L49-, PF6404-
the other is
R-L23+/L49+/Z2103+/Z2105+/L277+
i.e. they have two different origin.
The case of Volkov (I know and have studied from many years, and I found the unique haplotype close to him) is another cluster, probably a Z2103/Z2105+, I'd know willing which by a SNP test.
But you know that there are many secrets there.

Silesian
01-08-2014, 04:47 PM
Silesian, do you think that Campbell belong to the East European L23 cluster? But which would be its final SNP?
I have always thought that all they were Z2110, but it seems now that this would be also my final SNP, in spite of the uncertainties that there are about my Chromo2 test.
The Jewish clusters, those two of the "Jewish R1b project" (and I have explained this many times), are two different haplogroups, with only one ancestor each, with a recent origin, and have nothing to do one each other. They are put together (erroneously) by the presence of L150+, but the first is
R-M269/L150+/PF7558+/PF7562+/PF7563+ and of course L23-, L49-, PF6404-
the other is
R-L23+/L49+/Z2103+/Z2105+/L277+
i.e. they have two different origin.
The case of Volkov (I know and have studied from many years, and I found the unique haplotype close to him) is another cluster, probably a Z2103/Z2105+, I'd know willing which by a SNP test.
But you know that there are many secrets there.

Without question you do not belong to R1b Jewish/Arab/Assyrian, Semitic[Afro-Asian speaking] cluster. This can be easily seen comparing Benedictine Monastery of Podlažice- R1b model DYS 392 {[13] slow mutating marker}, very, very slow DYS 426 {12 } 1000 years. This is probably why my ancestors had a very strong Catholic tradition. To first compare your theory you need a model. Benedictine Monastery of Podlažice- R1b model is very simple, which you belong. Other projects do not provide model[if they do I have not seen them] so how can you compare?



Physical model (most commonly referred to simply as a model but in this context distinguished from aconceptual model)

Rathna
01-08-2014, 05:07 PM
Without question you do not belong to R1b Jewish/Arab/Assyrian, Semitic[Afro-Asian speaking] cluster. This can be easily seen comparing Benedictine Monastery of Podlažice- R1b model DYS 392 {[13] slow mutating marker}, very, very slow DYS 426 {12 } 1000 years. This is probably why my ancestors had a very strong Catholic tradition. To first compare your theory you need a model. Benedictine Monastery of Podlažice- R1b model is very simple, which you belong. Other projects do not provide model[if they do I have not seen them] so how can you compare?

Probably this EEL23 should have in its modal
DYS464=14-15-16-18
(and I'd add
DYS446=14 or more)
and probably this was also the thinking of lgmayka, who I think conceived it first.
Otherwise we don't explain because many have DYS464d=19.
I have always thought that 14-15-16-17 was a first mutation and my 14-14-16-17 a second mutation of DYS464b from 15 to 14.
But the series
8 10 10 8 10 11
11 13 11 11 12 12
put these haplotypes within 4,000 years.

Silesian
01-08-2014, 05:50 PM
Probably this EEL23 should have in its modal
DYS464=14-15-16-18
(and I'd add
DYS446=14 or more)
and probably this was also the thinking of lgmayka, who I think conceived it first.
Otherwise we don't explain because many have DYS464d=19.
I have always thought that 14-15-16-17 was a first mutation and my 14-14-16-17 a second mutation of DYS464b from 15 to 14.
But the series
8 10 10 8 10 11
11 13 11 11 12 12
put these haplotypes within 4,000 years.

lgmayka does a good job helping with Polish project he is also very knowledgeable, also genetic mathematician Ken Nortvedt might have been the one to notice DYS 464 fast mutating markers in the R1b Eastern European model.


You know that my thinking has always been the other way around: that Middle Easterner R1b haplotypes derived from the European ones

First you must provide a str model for Italy, and Middle Eastern[ Arab,Assyrian,Ashkenazi], then we can compare.

vettor
01-08-2014, 05:58 PM
lgmayka does a good job helping with Polish project he is also very knowledgeable, also genetic mathematician Ken Nortvedt might have been the one to notice DYS 464 fast mutating markers in the R1b Eastern European model.



First you must provide a str model for Italy, and Middle Eastern[ Arab,Assyrian,Ashkenazi], then we can compare.

I agree with you.
Also quoting DYS464 is unreliable as they are always placed in numerical order and not actually shown in there true founding order. I am "lucky" I have 11-11-11-11 :)

Rathna
01-08-2014, 06:10 PM
First you must provide a str model for Italy, and Middle Eastern[ Arab,Assyrian,Ashkenazi], then we can compare.

The three haplotypes confirmed R-Z2110* (Drakopoulos, Ware, Varipapa) bring all to the Balkans: Drakopoulos is a Greek, Ware an Englishman but I have always supposed of Gypsy origin of an haplogroup introgressed from Eastern Europe, Varipapa is an Italian but I have always said of Arbereshe origin).
Thus I think that so far a Balkan or a Central Asian origin is more and more likely.
So far R-Z2109* (thus Z2110-) is NA20866, thus an Indian it seems.

Rathna
01-08-2014, 06:21 PM
First you must provide a str model for Italy, and Middle Eastern[ Arab,Assyrian,Ashkenazi], then we can compare.

But if you want an Italian haplotype which could be the ancestor of all the EEL23 I could send you that of my relative Tognarelli (R-Z2105+/L277-/L584-)

211020 Italy R1b1a2
12 24 14 11 11-14 12 12 13 13 13 29 16 9-10 11 11 25 15 19 30 14-15-16-18 10 11 19-23 15 15 20 17 37-38 11 12

Silesian
01-08-2014, 06:37 PM
But if you want an Italian haplotype which could be the ancestor of all the EEL23 I could send you that of my relative Tognarelli (R-Z2105+/L277-/L584-)

211020 Italy R1b1a2
12 24 14 11 11-14 12 12 13 13 13 29 16 9-10 11 11 25 15 19 30 14-15-16-18 10 11 19-23 15 15 20 17 37-38 11 12

It's not Italian, Eastern European model, I'm waiting for. It is the model of Ashkenazi,Arabs, Assyrians, Alawites,Druze. They derive from the same region and speak the same language Semitic [Afro-Asiatic] it would make sense to have a basic model? For example L584+ L277+ model in 37 str basic format. Just provide a basic model for this region to compare with your Italian or Eastern European model, Western Europe, or even Khazakhstan.

Rathna
01-08-2014, 06:53 PM
It's not Italian, Eastern European model, I'm waiting for. It is the model of Ashkenazi,Arabs, Assyrians, Alawites,Druze. They derive from the same region and speak the same language Semitic [Afro-Asiatic] it would make sense to have a basic model? For example L584+ L277+ model in 37 str basic format. Just provide a basic model for this region to compare with your Italian or Eastern European model, Western Europe, or even Khazakhstan.

I apologize but I don't understand what you want. Markers values change forwards and backwards and are a little reliable. We are trying to understand which is the phylogeny by the SNPs (better to have the Big Y or the Full Y).
I have always said that L584+ presuppose PF7580, found so far in an Italian and a Romanian. If they will be L584-, it is clear that all the L584+, diffused above al in Middle East, are derived from Europeans.
I have always said that I have some doubt about L277+, because we haven't found so far an intermediate SNP between Z2105 and L277, and all the L277+ (all the Jewish cluster and many people from India to Western Europe) may be very ancient and close to the oirigin.
About Z2110 I have discussed above.
There is also a line on the left of the smal's tree which have two Jews but an ancestor in Tuscany (NA20532).
I think thus that the plays are open yet and you cannot deny that Tuscany and Italy is on the game.
Tognarelli is a Tuscan from Lunigiana, with links (by his haplotype) to Corsicans and overall in Western Europe. And to say all, if he too would belong to Z2110*, we two would have one of the highest variance of this subclade.

Silesian
01-08-2014, 07:17 PM
I apologize but I don't understand what you want. Markers values change forwards and backwards and are a little reliable. We are trying to understand which is the phylogeny by the SNPs (better to have the Big Y or the Full Y).
You have the most reliable chrom2 snp test, what can you show that ysearch can't? For example what are your top 5 matches on ysearch, Estruscan? Do the snp' match your top 10 Etruscan/Italian? If R1b L277+ is ancient it should be possible to have a model? Ht-35 project has a model why not R1b L277+?


There is also a line on the left of the smal's tree which have two Jews but an ancestor in Tuscany (NA20532).

If you have they ysearch number, I would like to see who there close matches are.

Humanist
01-08-2014, 07:31 PM
It's not Italian, Eastern European model, I'm waiting for. It is the model of Ashkenazi,Arabs, Assyrians, Alawites,Druze. They derive from the same region and speak the same language Semitic [Afro-Asiatic] it would make sense to have a basic model? For example L584+ L277+ model in 37 str basic format. Just provide a basic model for this region to compare with your Italian or Eastern European model, Western Europe, or even Khazakhstan.

Although Semitic, we in fact do not speak the same language as most others in the ME. Assyrians speaks E Aramaic. The great majority of other populations speak Arabic. I have even speculated that at least some of our R1b frequencies may be related to our adoption of Aramaic.


Well, we do speak an eastern variety of an originally NW Semitic language, so some western input should certainly be expected. I have speculated that this possible "western" input may be reflected (at least in part) by our elevated frequencies of R1b. Specifically, ancestral lines that may be connected to Syrian Alawites of NW Syria. Their modern homeland is situated in the area of the "Neo-Hittite," AKA, "Aramaean" kingdoms of the Iron Age.

https://upload.wikimedia.org/wikipedia/commons/f/fe/NeoHittiteStates.gif

Silesian
01-08-2014, 07:38 PM
Although Semitic, we in fact do not speak the same language as most others in the ME. Assyrians speaks E Aramaic. The great majority of other populations speak Arabic. I have even speculated that at least some of our R1b frequencies may be related to our adoption of Aramaic.
You have a lot of knowledge and data at your disposal. It should be with relative ease you can show a very basic model of Assyrian R1b, is the same/differs from R1b Arab/Ashkenazi/Alawites/ Druze. Where you can enter in a set of values and have Assyrians with similar type show up.

ysearch-Assyrian R1b model?

Joe B
01-08-2014, 09:09 PM
What role do you think DYS640=12 and DYF406S1=10 might play in the mix for 26483-Campbell? DYS449=30 seems intermediate between 31-33 eastern European and 29 far western European. Of course, 26483 also has a DYS511=12 that is interesting. One thing to keep in mind about modals in these subclades are the slow mutating markers that are off modal. Almost every R1b-Z2103 has at least one wierd STR marker that make things more difficult.

Joe B
01-08-2014, 10:34 PM
You have a lot of knowledge and data at your disposal. It should be with relative ease you can show a very basic model of Assyrian R1b, is the same/differs from R1b Arab/Ashkenazi/Alawites/ Druze. Where you can enter in a set of values and have Assyrians with similar type show up.

ysearch-Assyrian R1b model?
All you have to do is look at the various projects yourself. The modals are right there. This is a very complicated region where each of these groups may include members that are R1b-Z2103 L277+ or L584+ not to forget R1b-Z2103 L277- or L584-. Z2103 and the other known SNPs probably predate these groups and any arguments over language. Any STR haplotypes are most likey due to endogomey that these groups practiced for culture preservation.

Rathna
01-08-2014, 10:36 PM
I'll try to answer your questions.

Silesian

"You have the most reliable chrom2 snp test, what can you show that ysearch can't?"

We have discussed about my Chromo2, and, as smal let me note, it isn't reliable at all. There are many inconsistencies (see above a letter of smal). I don't know which results are reliable, perhaps that I am Z2110+ and CTS9219-, which would put me like an R-Z2110*, and this would be already something, but other results seem unreliable, so I wrote to Laura Marshall of Chromo2. We'll see if she will respond.
Once for all: markers values have many inconsistencies because mutate forwards and backwards and only SNPs should decide which are the closest links.

"For example what are your top 5 matches on ysearch, Etruscan?"

I posted many times which are the closest to me on YHRD, which is more important than ySearch, because tested all over the world. My haplotype is rare within R-Z2105, but my closest ones are in Western Europe and the closest one in Modena province, yes where Etruscans lived, unfortunately not contactable because tested on blind by Dr Ferri. Another close to me is a Hui from China I have always thought a descendant of a Roman soldier survived from the Charrae defeat. It is out of doubt that my haplotype is rooted in Italy or Central-Western Europe, but also about this will decide the SNPs more than the markers values.

"Do the snp' match your top 10 Etruscan/Italian?"

Unfortunately we have a few Italians SNPs tested or Geno 2.0/Chromo2 tested. Less Big Y or Full Y. We have the 1KGP which had 105 Tuscans and it gave us many important results, for instance my mtDNA K1a1b1e in one Tuscan out of 105, which demonstrated the Tuscan/Italian origin of my mt.

"If R1b L277+ is ancient it should be possible to have a model? Ht-35 project has a model why not R1b L277+?"

I have always written against the "modal" which is an artifice and the more an haplogroup is old the more a "modal" is absurd. You have a modal only for recent haplotypes, and that you have a modal of your EE-L23 cluster isn't in favor of its ancientness.

"If you have the[ir] ysearch number, I would like to see who their close matches are".

Of course we haven't the markers values of the 1KGP tested ones.


JoeB
"What role do you thing DYS640=12 and DYF406S1=10 might play in the mix for 26483-Campbell? DYS449=30 seems intermediate between 31-33 eastern European and 29 far western European. Of course, 26483 also has a DYS511=12 that is interesting. One thing to keep in mind about modals in these subclades are the slow mutating markers that are off modal. Almost every R1b-Z2103 has at least one wierd STR marker that make things more difficult".

As I have said to Silesian, we try to use the markers values to individuate a cluster when we lack the SNPs test, but the SNPs will always decide.
I have tried to individuate some series or singular marker, but, as I have always thought (and said) that there is a convergence to the modal as time passes etc., neither the slow mutating markers are completely sure. DYS511=12 of Campbell may be =10 of other clusters as 1 mutation from 11, which seems the "modal" of our cluster, then his haplotype could be linked to those with 10 as those with 12 I posted above. For this only the match by SNP should decide at last.

Joe B
01-09-2014, 03:09 AM
PF1610 AA negative

This SNP was found positive in 26483.PF1610 is seen in E1b, E1b1b1a1b-D-111, R1b, L21, U152, Z2103, J1 and maybe more. Hard to say if it is a good SNP in general.

Joe B
01-09-2014, 04:34 AM
CTS7959 17,764,622 A->T
CTS9230 18,760,768 G->T
CTS11767 23,257,041 G->T

These three SNPs are on the same level as CTS9219. The HG01515 sample has all four SNPs that differ it from the others.
That's really helpful to know. Based on that I am going to test for Z2104, Z2107 and Z2110/CTS7822 and see where that goes. YSEQ is offering a "test 7 SNPs and get one free" deal. That doesn't look like the best way to go in this situation.
Thanks

Rathna
01-09-2014, 06:04 AM
@ Silesian

Wow, we have the STRs values of the 1KGP:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140107_chrY_str_haplotypes/YSTRs_PowerPLexY23_1000Y_QA_20130107.txt
Population SampleID YHaplogroup
DYS576 DYS389I DYS448 DYS389II DYS19 DYS391 DYS481 DYS549 DYS533 DYS438 DYS437 DYS570 DYS635 DYS390 DYS439 DYS392 DYS643 DYS393 DYS458 DYS385a DYS385b DYS456 Y-GATA-H4

TSI NA20532 R1b
18 13 19 28 14 10/11 23 13 12 12 15 16 23 24 12 14 10 13 18 11 14 16 12

Reconstructed by the FTDNA format:
13 24 14 10/11 11-14 na na 12 13 14 28
just the sequence 13 14 28 found in many Jewish R1b, some certainly R-L277+. In this case the Tuscan NA20532 is the ancestor by SNPs of the two Jews: Turkish Jew 16133 and Moroccan Jew 16886.
Jews from Tuscans or Tuscans from Jews?

P.S. The other values are:
DYS458=18
DYS437=15
DYS448=19
DYS456=16
DYS576=18
DYS570=16
DYS438=12
DYS481=23
DYS549=13
DYS533=12
DYS635=23
DYS643=10
YGATAH4=12(-1)

Rathna
01-09-2014, 06:25 AM
GIH NA20866 R1b
19 13 19 29 14 11 22 13 12 12 15 18 23 24 12 13 10 13 16 11 14 16 13
Reconstructed bt the FTDNA format:
DYS576 DYS389I DYS448 DYS389II DYS19 DYS391 DYS481 DYS549 DYS533 DYS438 DYS437 DYS570 DYS635 DYS390 DYS439 DYS392 DYS643 DYS393 DYS458 DYS385a DYS385b DYS456 Y-GATA-H4
13 24 14 11 11-14 na na 12 13 13 29
458=16
459a na
459b na
455 na
454 na
447 na
437=15
448=19
449 na
It seems that the Indian R-Z2109* is just an AMH. From where?

P.S. The other values are close to the Western European Z2110:
DYS456=16
DYS576=19
DYS570=18
DYS481=22
DYS549=13
DYs533=12
DYS635=23
DYS643=10
YGATAH4=13(-1)

smal
01-09-2014, 09:41 AM
Reconstructed by the FTDNA format:
13 24 14 10/11 11-14 na na 12 13 14 28
just the sequence 13 14 28 found in many Jewish R1b, some certainly R-L277+. In this case the Tuscan NA20532 is the ancestor by SNPs of the two Jews: Turkish Jew 16133 and Moroccan Jew 16886.

1) Unfortunately, NA20532 has a gap in the DNA sequence (no reads) in the L277 region. It can have the L277+ haplotype. In this case we have a new snapshot of the Z2103 tree.

http://s47.radikal.ru/i115/1401/33/aedf679d5e5c.jpg (http://radikal.ru/fp/51f332615ba74c3186b5f9b054b87034)

2) I have added NA20532 (http://www.semargl.me/en/dna/ydna/kit/60264/) and NA20866 (http://www.semargl.me/en/dna/ydna/kit/60265/) into Semargl database.

Rathna
01-09-2014, 11:49 AM
1) Unfortunately, NA20532 has a gap in the DNA sequence (no reads) in the L277 region. It can have the L277+ haplotype. In this case we have a new snapshot of the Z2103 tree.

http://s47.radikal.ru/i115/1401/33/aedf679d5e5c.jpg (http://radikal.ru/fp/51f332615ba74c3186b5f9b054b87034)

2) I have added NA20532 (http://www.semargl.me/en/dna/ydna/kit/60264/) and NA20866 (http://www.semargl.me/en/dna/ydna/kit/60265/) into Semargl database.

Smal, it would be interesting to know if also the two Jews have been tested for L277, because I was probably the first to say that this sequence 13 14 28 was that of the L277+, and individuated like that the Jewish cluster. Unfortunately they do everything in secret, but I think that no one may escape my analysis. If the Tuscan and these Jews like all the others of the Jewish cluster were L277+ it would be very good for me. Also because I think having demonstrated that the two known Italian L277+ have the highest variance amongst the haplotypes known so far, and I have always expressed my theory about L277+, that it could be a very ancient subclade of Z2103/Z2105+.
Some doubt about the Indian I spoke about above: for his AMH he could be also of Western European descent (recent).
But have you something to do with Semargl? A person I esteem so much, but he is R1a and you R1b, you couldn't be the same person.

GTC
01-09-2014, 12:01 PM
If the Tuscan and these Jews like all the others of the Jewish cluster were L277+ it would be very good for me.

I can't help noticing your frequent references to Jews in your various posts. What is it about Jews, in particular, that interests you?

Rathna
01-09-2014, 12:25 PM
95875 Pietro Stasi, b 1854, Potenza, Italy Italy R1b1a2a1
12 23 14 11 11-14 12 12 13 14 14 29 17 9-10 11 11 25 15 19 31 14-15-16-18 11 12 19-23 15 16 19 17 35-37 12 12 11 9 15-16 8 10 10 8 10 10 12 21-24 15 10 12 12 15 8 11 22 20 13 13 11 13 11 11 12 12
Manno: Ysearch 5C2NP.
But at this poiint also Mattoli could be a candidate for L277+:
30885 Nicolo' Mattoli year 1475, Bevagna, Umbria, Italy Italy R1b1a2a1
12 26 14 11 11-15 12 12 13 12 15 27 15 9-10 11 11 26 15 19 29 15-16-16-18 11 11 19-23 16 15 19 18 35-37 13 12 11 9 15-16 8 10 10 8 10 11 12 23-23 17 10 12 12 15 8 11 22 20 13 12 11 13 11 11 12 12 37 15 9 16 12 25 26 19 11 11 13 12 10 9 12 12 10 11 11 30 13 12 25 13 10 10 22 15 19 13 25 17 12 15 23 12 23 19 10 14 18 9 11 11
and as Mangino is going to be tested for Geno 2.0 and whether he didn't use my donor of 50$, I ask Richard Rocca to test with those (and others if for Geno 2.0, but my money is enough for a SNP a la carte) also Mattoli, as he could be L277+, and we should have many Italians with the motives:
13 14 28
12 14 27
14 14 29
12 15 27

Rathna
01-09-2014, 12:31 PM
I can't help noticing your frequent references to Jews in your various posts. What is it about Jews, in particular, that interests you?

We began to discuss about this many years ago: R1b1* and subclades were born in Middle East and peopled Europe or were born in Europe (perhaps you know my theory of the Italian Refugium) and peopled Middle East, thus Jews with my mtDNA K and Y R1b and subclades are of European origin?

You will admit that I fought this scientific research with less means as to my opponents.

smal
01-09-2014, 12:35 PM
Smal, it would be interesting to know if also the two Jews have been tested for L277...

Unfortunately, there is only a list of SNP from Rootsi et al. I can't compare the actual sequences... So, we might only ask Rootsi about L277.



Some doubt about the Indian I spoke about above: for his AMH he could be also of Western European descent (recent).

His STR haplotype looks like AMH, but he is Z2103, Z2105. This is important, because we might have missed many AMH like Z2103 haplotypes.


But have you something to do with Semargl? A person I esteem so much, but he is R1a and you R1b, you couldn't be the same person.

Semargl gave me access to manage R1b in his database.

GTC
01-09-2014, 01:33 PM
We began to discuss about this many years ago: R1b1* and subclades were born in Middle East and peopled Europe or were born in Europe (perhaps you know my theory of the Italian Refugium) and peopled Middle East, thus Jews with my mtDNA K and Y R1b and subclades are of European origin?

So, you are equating a cluster of Jews in some project as representing the Middle East in general? Do they give places of origin, or is this the information that you say is not revealed?

Have you given thought to the opposite situation: namely that your own line, going back far enough, may be Jewish?

Yes, I think anybody who has read a Rathna post here or elsewhere will be familiar with "Italian Refugium theory" as a term. I asked you a while back when you intend publish a peer reviewed paper on your theory so that we can read in the one concise document your detailed arguments and see the data backing your conclusions. As you say that you are not a recognized academic in this field, I suggested the Journal of Genetic Genealogy.


You will admit that I fought this scientific research with less means as to my opponents.

For me it's not scientific research until it's published in a scientific journal, demonstrating recognizable scientific method. Until then, I'd consider it more an obsessive hobby that may bear fruit but that needs to be documented and presented in a scientific manner for scrutiny by others.

Silesian
01-09-2014, 02:28 PM
For me it's not scientific research until it's published in a scientific journal, demonstrating recognizable scientific method. Until then,
I'm sorry did I miss something? Was Kromsdorf R1b or King Tut closer to your line of R1b or Rathna's?

Silesian
01-09-2014, 04:44 PM
.. endogomey that these groups practiced for culture preservation.

There you go using big words again. It really does not take much to confuse me. However I would think that marrying within ones community would be ideal conditions for a modal haplotype.

Joe B
01-09-2014, 05:48 PM
There you go using big words again. It really does not take much to confuse me. However I would think that marrying within ones community would be ideal conditions for a modal haplotype.My guess is the longer the those haplotypes have time to develop in situ, the more unique those haplotypes will become. That would make it more difficult to connect some of these haplotypes to each other. A recent migration should be more apparent. Of course we need to consider that these are humans that do not alway follow custom, they mess around. Hope that explains the any exceptions to the rule. It's coming down to SNPs and hope you are thinking about that for yourself.

I always keep a tab open for googling big words.

Silesian
01-09-2014, 06:07 PM
My guess is the longer the those haplotypes have time to develop in situ, the more unique those haplotypes will become. That would make it more difficult to connect some of these haplotypes to each other. A recent migration should be more apparent. Of course we need to consider that these are humans that do not alway follow custom, they mess around. Hope that explains the any exceptions to the rule. It's coming down to SNPs and hope you are thinking about that for yourself.

I always keep a tab open for googling big words.

So how would you apply your theory of endogamy to the following 3 projects?

http://www.familytreedna.com/public/JewishR1b/default.aspx?section=yresults

http://www.familytreedna.com/public/Ashkenazi-Levite/default.aspx?section=yresults

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

Is it possible to apply your theory and create a general modal in the above projects?

Joe B
01-09-2014, 06:38 PM
So how would you apply your theory of endogamy and a possible model haplotype to the following 3 projects?

http://www.familytreedna.com/public/JewishR1b/default.aspx?section=yresults

http://www.familytreedna.com/public/Ashkenazi-Levite/default.aspx?section=yresults

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

Is it possible to apply your theory and create a general modal in the above projects?I called it a guess not worthy to be a theory. Thanks
When looking at these projects the first thing I would to do is treat them with respect.
What do you mean by possible modal haplotype? The Assyrian Heritage DNA Project has 29 modals. Do you want more?
What do you mean by a general modal?
Have you tried creating custom modals using Excel or Mike's R1b-Early spreadsheet?

STR modals have some real limitations without up-to-date SNP testing.

Silesian
01-09-2014, 07:26 PM
I called it a guess not worthy to be a theory. Thanks
When looking at these projects the first thing I would to do is treat them with respect.
What do you mean by possible modal haplotype? The Assyrian Heritage DNA Project has 29 modals. Do you want more?
What do you mean by a general modal?
Have you tried creating custom modals using Excel or Mike's R1b-Early spreadsheet?
STR modals have some real limitations without up-to-date SNP testing.

Okay I'll use my ysearch # as an example @ 67 str's and calculated generation, despite it's obvious limitations, to show what I mean by general modal.
Here are my some closest matches in the region, paternal ancestors come from, some of which match the region on my gedmatch[Eurogenes, Dodedad,MLDP] and 23andme result's[Ukraine/Russia matches]. There was a R1b E.E modal already in the system and my closest match around 1500+/-years so I'm very lucky.


CX94E-R1b1b2a -L23EE Modal Unknown Unknown Family Tree DNA 67-131500+/- years
DB9H7-Preußen/Prussia, Germany R1b1a2a1 (tested) Family Tree DNA 67-14
HW54G-Jászság, Hungary R1b1a2a1 (tested) Family Tree DNA 67 16
FGK82-Majer, Austro-Hungarian Empire R1b1a2 (tested) Family Tree DNA 67-15
XQE85-Unknown Unknown Family Tree DNA 67-16
CRQ37-Stehlik Unknown R1b1a2a1 (tested) Family Tree DNA 67-16
Z7AF9-Réca (in Slovak), Réte (in Hungarian), Slovakia R1b1a2 (tested) Family Tree DNA 67-16
P7U4J- Ukraine Unknown Family Tree DNA 67-15
2XHXQ-Kazakhstan Unknown Family Tree DNA 67-18

However some of the result's are conflicting like Jászság[ Ossets or Iranians?] and Khazakstan [Bashkirs?]

Joe B
01-09-2014, 09:15 PM
Okay I'll use my ysearch # as an example @ 67 str's and calculated generation, despite it's obvious limitations, to show what I mean by general modal.
Here are my some closest matches in the region, paternal ancestors come from, some of which match the region on my gedmatch[Eurogenes, Dodedad,MLDP] and 23andme result's[Ukraine/Russia matches]. There was a R1b E.E modal already in the system and my closest match around 1500+/-years so I'm very lucky.


CX94E-R1b1b2a -L23EE Modal Unknown Unknown Family Tree DNA 67-131500+/- years
DB9H7-Preußen/Prussia, Germany R1b1a2a1 (tested) Family Tree DNA 67-14
HW54G-Jászság, Hungary R1b1a2a1 (tested) Family Tree DNA 67 16
FGK82-Majer, Austro-Hungarian Empire R1b1a2 (tested) Family Tree DNA 67-15
XQE85-Unknown Unknown Family Tree DNA 67-16
CRQ37-Stehlik Unknown R1b1a2a1 (tested) Family Tree DNA 67-16
Z7AF9-Réca (in Slovak), Réte (in Hungarian), Slovakia R1b1a2 (tested) Family Tree DNA 67-16
P7U4J- Ukraine Unknown Family Tree DNA 67-15
2XHXQ-Kazakhstan Unknown Family Tree DNA 67-18

However some of the result's are conflicting like Jászság[ Ossets or Iranians?] and Khazakstan [Bashkirs?]That's the same problem most of us R1b-Z2103 types are running into. Nobody really close. Maybe STR signatures are the way to go instead of genetic distance. STR signatures have limitations too.
The Ossets and Bashkirs really look like they have a recent founder effect or suffered from recent genetic bottlenecks. They really need some more SNP and STR testing. #259814 and #236257 interesting as they seem close at 12 STRs but really diverge after that.

The Iranian possibilties are just too broad as it is a big country with lots of different groups.

Could Armenian merchants be responsible for some of the spread of R1b-Z2103 in the last 500 years or so?

This may upset a few people, but I don't buy a lot of these age calculations with our subclade. Many of the slow STRs don't act so slow.

RobertCasey
01-09-2014, 11:13 PM
So how would you apply your theory of endogamy to the following 3 projects?

http://www.familytreedna.com/public/JewishR1b/default.aspx?section=yresults

http://www.familytreedna.com/public/Ashkenazi-Levite/default.aspx?section=yresults

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

Is it possible to apply your theory and create a general modal in the above projects?

I have done a lot of work with YSTR patterns and have found two conclusions (based on known YSNP predictors):

1) There are combinations of YSTR marker values that unique to older YSNPs. This is because YSTRs are similar to water
flowing down a river - the markers that are common (in the middle of the river) have little meaning. However, finding
those rare combinations of YSTR values allow YSNP predictors to predict very old YSNPs but generally do not work
more recent that 5,000 to 10,000 years old with 67 markers (rare marker values like water on the very edge of
the river).

2) There is another method for YSNP prediction that only works for more recent YSNPs that only works well from
1,000 to 2,000 years old. This is the true limitation of YSTRs for finding YSTR patterns. Binary Logistic Regression
works very well in this timeframe for 67 markers around 90 % of the time (sometimes some YSNPs just do not
mutate enough (YSTR wise) to create reliable prediction at 67 markers and 111 markers or more would be required.

3) If you start looking at YSNPs in the 2,000 to 4,000 year range such as Z253, son of DF13 and grandson
of L21, there are already over a dozen signatures (YSTR patterns) that have survived today. These patterns
are great for locating a potential for discovering new YSNPs since YSTRs track YSNPs very well back
to 1,000 to 2,000 years ago. Since you are looking at Jewish projects, L583 is primarily Jewish submissions
but L21 probably only has 1 or 2 % Jewish submissions - so these people probably had ancestors that
converted to the Jewish faith 500 to 1,500 years ago (the relative age of L583):

http://www.rcasey.net/DNA/R_L21/Analysis/R_L21_Analysis_L583.html

For around 50 L21 YSNPs that are younger than 2,000 years, my L21 YSNP predictor tool
has around 98 % accuracy for prediction according to statistical tools:

http://www.rcasey.net/DNA/R-L21_SNP_Predictor_Intro.html

Silesian
01-10-2014, 06:55 AM
STR signatures have limitations too.
The Ossets and Bashkirs really look like they have a recent founder effect or suffered from recent genetic bottlenecks. They really need some more SNP and STR testing. #259814 and #236257 interesting as they seem close at 12 STRs but really diverge after that.

The Iranian possibilties are just too broad as it is a big country with lots of different groups.

Shaken not stirred question?
Which R1b cluster do you think will have the highest ANE reading?

Group 1. North Osset region.
276867 North Ossetia R1b R-M343 M343+, M269-
R1b Z2105 North Ossetians
http://www.familytreedna.com/public/Ossetian/default.aspx?section=ysnp

Group 2. Georgians
216826 Georgia R1b1 R-P25 M343+, P25+, M18-, M269-, M335-, M73-, P297-, V88-
250742 R1b1a2 R-M269 [R1b 2105?]
http://www.familytreedna.com/public/georgia/default.aspx?section=ysnp

Group 3. Bashkirs
223828 Yaik Cossack clan Kazakhstan R1b1a2a1- L277+
254638 Bashkir Monash-Buryjan clan Russian Federation R1b1a2[2105*]?
262276 Qangli-Kipchak Karakalpak , Uzbekistan R1b1a1 R1b M73+
http://www.familytreedna.com/public/Bashqort_Clans/default.aspx?section=yresults

Group 4. Native Siberians/Uralians-region
238998 R1b R-M343 M343+, M269-
177944 R1b1 R-P25 P25+, M269-
186198 R1b1a1 R-M73
120014 R1b1a2 R-M269 R1b[z2105?]
http://www.familytreedna.com/public/SiberiaTransbaikalia/default.aspx?section=yresults

Group 5 KZ region.
R1b1a1-M73

178045-Kazakhstan R1b1a1
R/R1b/R1b Z2105 ? cluster
172373-Kazakhstan R1b1a2 R1b Z2105*?
267285-Kazakhstan R1b1a2 R1b Z2105*?
236567-Kazakhstan R1b*?
225439-Kazakhstan R?
http://www.familytreedna.com/public/alash/default.aspx?section=yresults



Group 6. Iran region.
R1b* Kurds from Khazakstan/Azebaijan

Rathna
01-10-2014, 09:07 AM
Group 1.
276867 North Ossetia R1b R-M343 M343+, M269-
R1b Z2105 North Ossetians
http://www.familytreedna.com/public/Ossetian/default.aspx?section=ysnp


What about these Ossetians?
276867 is R-M73
276935 is classified R-M269
All the others are an unique haplotype of recent origin belonging to the EE-L23, probably Z2105/Z2110/CTS9219+.
Certainly Ossetians aren't at the origin of these haplotypes, all introgressed from elsewhere.

Silesian
01-10-2014, 02:39 PM
What about these Ossetians?
276867 is R-M73
276935 is classified R-M269
All the others are an unique haplotype of recent origin belonging to the EE-L23, probably Z2105/Z2110/CTS9219+.
Certainly Ossetians aren't at the origin of these haplotypes, all introgressed from elsewhere.

What about JoeB theory that many R1b Z2105 are Armenian merchants, For example the branch your family comes from Etruscan, is it possible that they derive from Armenian merchants? Also what branch are the Ukrainian R1b found by Cruciani et al ?


R1b1*, like R1b* is rare. As mentioned above, examples are described in older articles, for example two in a sample from Turkey,[4]]Cruciani et al. in the large 2010 study found 3 cases amongst 1173 Italians , 1 out of 328 West Asians and 1 out of 156 East Asians.[23] ]Varzari found 3 cases in the Ukraine, in a study of 322 people from the Dniester-Carpathian region, who were P25 positive, but M269 negative.Cruciani et al , [4

Are Cruciani et al R1b samples from Dniester-Carpathian region, who were P25 positive, but M269 negative, close to Ossetian or Georgians? Or is this a completely different mutated branch?

Rathna
01-10-2014, 03:06 PM
What about JoeB theory that many R1b Z2105 are Armenian merchants, For example the branch your family comes from Etruscan, is it possible that they derive from Armenian merchants?

1) I couldn't this morning study all your samples, but 'll do it next. It is clear that Georgians have more haplotypes and more variance than Ossetians.
2) That the R-Z2105-s in the Caucasian region are mostly of Armenian origin isn't said only by JoeB. I am saying that from many years, and, because Armenians are Indo-Europeans speaking an Indo-European language close to Greek and come probably from the Balkans, that Z2105 came from the Balkans is a likely possibility.
3) In Turkey weren't only Armenian merchants. There were at least 80,000 Italic merchants and their families, whose killing provoked the wars against Mithridate VI and his defeat. Imagine how many merchants may have come from Italy and elsewhere in the following centuries. Of course only deep studies will be able to understand the origin of our Y: mine, yours etc.
3) These tests (above all Big Y and Full Y) will respond also this.

Silesian
01-10-2014, 03:16 PM
1) I couldn't this morning study all your samples, but 'll do it next. It is clear that Georgians have more haplotypes and more variance than Ossetians.
2) That the R-Z2105-s in the Caucasian region are mostly of Armenian origin isn't said only by JoeB. I am saying that from many years, and, because Armenians are Indo-Europeans speaking an Indo-European language close to Greek and come probably from the Balkans, that Z2105* came from the Balkans is a likely possibility.
3) In Turkey weren't only Armenian merchants. There were at least 80,000,000 Italic merchants and their families, whose killing provoked the wars against Mithridate VI and his defeat. Imagine how many merchants may have come from Italy and elsewhere in the following centuries. Of course only deep studies will be able to understand the origin of our Y: mine, yours etc.
3) These tests (above all Big Y and Full Y) will respond also this.
Thanks. It seems very likely Armenians and Balkan connection. I also wanted your opinion on the Kurd phylogeny, since the oldest Iranian groups also carry R1b Z2105* L277+ L584+. However the Kurds from Kazakh and the Kurds from Armenian border in Azebaijan carry R1b* what do you make of this branch R1b*?

R1b* (that is R1b with no subsequent distinguishing SNP mutations) is extremely rare. The only population yet recorded with a definite significant proportion of R1b* are the Kurds of southeastern Kazakhstan with 13%.[7] However, more recently, a large study of Y-chromosome variation in Iran, revealed R1b* as high as 4.3% among Persian sub-populations.....However, more recently, a large study of Y-chromosome variation in Iran, revealed R1b* as high as 4.3% among Persian sub-populations[18]
Are these two separate branch of R1b* 343+ Iranian Kurds or do they derive from one source?

Rathna
01-10-2014, 03:16 PM
Also what branch are the Ukrainian R1b found by Cruciani et al ?
Are Cruciani et al R1b samples from Dniester-Carpathian region, who were P25 positive, but M269 negative, close to Ossetian or Georgians? Or is this a completely different mutated branch?

This is the problem of R1b1* I have written tons of letters about and I think having demonstrated the highest variance in Italy and that Cruciani found three samples in Italy is very meaning. You should know that Indian R1b1 are L389-, thus not our ancestors. I am asking from years that the Caucasian R1b1 are tested for L389, but in vain . They are ascribed to L389+, but are tested only for P25, which is only upstream.
Anyway Mangino is going to be tested by Geno 2.0, one person that FTDNA and Vizachero, against all my letters from many years, put amongst the M269*. I bet he is R1b1*. We'll see next.

Silesian
01-10-2014, 03:49 PM
This is the problem of R1b1* I have written tons of letters about and I think having demonstrated the highest variance in Italy and that Cruciani found three samples in Italy is very meaning. You should know that Indian R1b1 are L389-, thus not our ancestors. I am asking from years that the Caucasian R1b1 are tested for L389, but in vain . They are ascribed to L389+, but are tested only for P25, which is only upstream.
Anyway Mangino is going to be tested by Geno 2.0, one person that FTDNA and Vizachero, against all my letters from many years, put amongst the M269*. I bet he is R1b1*. We'll see next.

More questions. What about the very different R1b Z2105* in KZ project, they look very different from our branch?

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

R1b1a1-M73

178045-Kazakhstan R1b1a1
R/R1b/R1b Z2105 ? cluster
172373-Kazakhstan R1b1a2 R1b Z2105*?
267285-Kazakhstan R1b1a2 R1b Z2105*?
236567-Kazakhstan R1b*?
225439-Kazakhstan R?

Rathna
01-10-2014, 03:56 PM
Thanks. It seems very likely Armenians and Balkan connection. I also wanted your opinion on the Kurd phylogeny, since the oldest Iranian groups also carry R1b Z2105* L277+ L584+.

I have found only these samples in the "Iranian FTDNA project", but certainly I put much much more of them from SMGF to Ysearch:
Assyrian
205003 Iran R1b1a2
13 24 14 10 11-14 12 12 12 14 13 30
Azeri
258253 Musa Aliyev, 1903 -1995, Shahbuz, Nakhichevan Azerbaijan R1b1a2
12 24 14 11 11-14 12 11 12 13 13 29 15 9-10 11 11 25 15 19 28 15-15-16-18 11 11 19-23 16 16 17 16 36-37 11 11 11 9 15-16 8 10 10 8 11 11 10 23-23 17 11 12 12 15 8 13 22 20 13 12 11 13 10 11 12 12
Persian
N16373 Iran R1b1a2a
12 24 14 11 11-14 12 12 12 13 14 29

Of course Aliyev has a high variance. Azeris are turkyfied Iranians, and Iranians and Kurds speak an Indo-European language, thus some of them will have come from the Balkans or Eastern Europe. But I should study their haplotypes more deeply.

P.S. Aliyev is R-L584+ (258253 Musa Aliyev, 1903 -1995, Shahbuz, Nakhichevan R1b1a2 R-M269 L584+, Z2103+, L943-), thus if it will be demonstrated that they descend from the European PF7580, neither these haplotypes were born there.

Rathna
01-10-2014, 04:49 PM
More questions. What about the very different R1b Z2105* in KZ project, they look very different from our branch?

172373-Kazakhstan R1b1a2 R1b Z2105*?
267285-Kazakhstan R1b1a2 R1b Z2105*?
236567-Kazakhstan R1b*?
225439-Kazakhstan R?

We could begin to put together these haplotypes:
172373 Altynbai Assilbekov KZ, к.ю.н.,Ph D tolegetai,matai14c.,Asylbek18c.,Pernebai20c.,kazak Kazakhstan R1b1a2
12 24 11 11 11-14 12 12 13 13 13 30 16 9-9 11 11 24 15 20 29 16-16-16-16 11 13 19-23 15 16 17 17 38-38 11 12

240714 Tleybayev KZ Kazakhstan R1b1a2
12 24 14 11 11-14 12 12 12 13 13 29 16 9-9 11 11 24 15 20 29 16-16-16-16 11 13 19-23 15 16 17 17 36-36 11 12

232777 Тойланбаев Tortkhara tribe, Nayman el Kazakhstan R1b1a2a1
12 24 14 11 11-14 12 12 12 13 13 30 16 9-9 11 11 24 15 20 29 16-16-16-16 11 13 19-23 15 16 17 17 36-36 11 12

In spite of multistep mutations (172373: DYS19 from 14 to 11), two mutations (172373: DYS439 from 12 to 13 or vice versa, and 240714: DYS389II from 30 to 29 or vice versa) and perhaps two recLOH in CDY from 36-38: very strange two recLOH!), this is clearly a very recent haplotype of R-Z2105. It would be interesting to know which subclade).
In YHRD format:
14 13-30 (29) 24 11 13 12 11-14 12 12 (13) 15 20 15 16 na 14 (13+1)
thus it isn't so different from the Western European R-Z2105, if not for having developed autonomously for some thousands of years, but it could have been brought there by the Tocharians or other Indo-European peoples.

Rathna
01-10-2014, 05:09 PM
With two values closer to the modal we have already three haplotypes:
14 13 29 24 11 13 12 11,14 12 12 15 19 15 16 14 2 >>
14 13 29 24 11 13 12 11,14 12 12 15 20 15 16 13 1 >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 15 16 23 14 18 21 12 11 18 10 - >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 15 16 25 14 -1 -1 -1 -1 -1 -1 - >>
1 of 191 Northern Greece, Greece [Greek] Eurasian - European - South-Eastern European Europe
1 of 105 Athens, Greece [Greek] Eurasian - European - South-Eastern European Europe
1 14 13 29 24 11 13 12 11,14 12 12 15 20 15 16 23 13 -1 -1 -1 -1 -1 -1 -
1 of 50 Alpujarra de la Sierra, Spain [Spanish] Eurasian - European - Western European Europe

Do you think that Greeks and Spaniards came from Kazakhstan?

Joe B
01-10-2014, 05:45 PM
Shaken not stirred question?
Which R1b cluster do you think will have the highest ANE reading?

Group 1. North Osset region.
276867 North Ossetia R1b R-M343 M343+, M269-
R1b Z2105 North Ossetians
http://www.familytreedna.com/public/Ossetian/default.aspx?section=ysnp

Group 2. Georgians
216826 Georgia R1b1 R-P25 M343+, P25+, M18-, M269-, M335-, M73-, P297-, V88-
250742 R1b1a2 R-M269 [R1b 2105?]
http://www.familytreedna.com/public/georgia/default.aspx?section=ysnp

Group 3. Bashkirs
223828 Yaik Cossack clan Kazakhstan R1b1a2a1- L277+
254638 Bashkir Monash-Buryjan clan Russian Federation R1b1a2[2105*]?
262276 Qangli-Kipchak Karakalpak , Uzbekistan R1b1a1 R1b M73+
http://www.familytreedna.com/public/Bashqort_Clans/default.aspx?section=yresults

Group 4. Native Siberians/Uralians-region
238998 R1b R-M343 M343+, M269-
177944 R1b1 R-P25 P25+, M269-
186198 R1b1a1 R-M73
120014 R1b1a2 R-M269 R1b[z2105?]
http://www.familytreedna.com/public/SiberiaTransbaikalia/default.aspx?section=yresults

Group 5 KZ region.
R1b1a1-M73

178045-Kazakhstan R1b1a1
R/R1b/R1b Z2105 ? cluster
172373-Kazakhstan R1b1a2 R1b Z2105*?
267285-Kazakhstan R1b1a2 R1b Z2105*?
236567-Kazakhstan R1b*?
225439-Kazakhstan R?
http://www.familytreedna.com/public/alash/default.aspx?section=yresults



Group 6. Iran region.
R1b* Kurds from Khazakstan/AzebaijanI still think that these ancient admixtures more related to geography and ethnicity. Any relationship to R1b-Z2103 phylogeny is coincidental. IMO

Silesian
01-10-2014, 07:21 PM
I still think that these ancient admixtures more related to geography and ethnicity. Any relationship to R1b-Z2103 phylogeny is coincidental. IMO
Exactly as you have pointed out the Assyrians practiced endogamy and have 67 ydna signatures. Humanist has shown they have high level of R1b and come from the most ancient of Semitic language people. R1b comes from ancient Aramaic. To top it the Assyrians have very little R1a 2% I think is what newtoboard quoted.


Although Semitic, we in fact do not speak the same language as most others in the ME. Assyrians speaks E Aramaic. The great majority of other populations speak Arabic. I have even speculated that at least some of our R1b frequencies may be related to our adoption of Aramaic.


That's what makes your ancient admixtures more related to geography and ethnicity theory so intriguing when applied to the R1b Z2105* L277+ L584+ Assyrians who practiced endogamy and originate from Aramaic semitic speaking people, yet have two mixtures in the ANE tests, not one. Where did ANE [7.02___ANE[/] in Assyrians come from?

We can use Humanist result he is 100% Assyrian.

99.44__EEF
-6.45__WHG
7.02___ANE

Rathna
01-11-2014, 03:53 AM
About Aliyev's haplotype I let you judge from these data. Of course by YHRD it is difficult to ascertain all its particularities:
DYD388=11 from 12
DYS438=11 from 12
DYF406S1=11 from 10
DYS557=17 from 16
DYS594=11 from 10
DYS572=10 from 11


14 13 29 24 11 13 12 11,14 12 15 19 16 16 12 5 >>
3 14 13 29 24 11 13 12 11,14 12 12 15 19 16 16 23 12 -1 -1 -1 -1 -1 -1 - >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 16 16 23 12 19 22 12 13 18 9 - >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 16 16 24 12 17 21 13 12 17 10 - >>
2 of 601 Rostock, Germany [German] Eurasian - European - Western European Europe
1 of 760 Rio de Janeiro, Brazil [Admixed] Admixed Latin America
1 of 832 Sverdlovsk Region, Russian Federation [Russian] Eurasian - European - Eastern European Asia
1 of 77 Manaus, Brazil [Admixed Brazilian] Admixed Latin America

14 13 29 24 11 13 12 11,14 12 15 19 15 15 12 2 >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 15 15 23 12 -1 -1 -1 -1 -1 -1 - >>
1 14 13 29 24 11 13 12 11,14 12 12 15 19 15 15 24 12 20 22 14 11 16 10 - >>
1 of 163 Israel & Palestinian Authority Area [Arab] Afro-Asiatic - Semitic Asia
1 of 104 Ljubljana, Slovenia [Slovenian] Eurasian - European - Eastern European Europe

14 13 29 24 11 13 12 11,14 12 16 19 16 15 12 1 >>
1 14 13 29 24 11 13 12 11,14 12 12 16 19 16 15 23 12 18 20 13 12 17 10 - >>
1 of 260 Freiburg, Germany [German] Eurasian - European - Western European Europe

R.Rocca
01-12-2014, 02:32 AM
Kit no. 274480 from Elena, Bebrovo, Bulgaria is L150+, M269+, Z2103-, Z2105-. Given the uncertainty of L150, it would be good to see if he is L23+. If so, he would be the first L23+ L51- Z2103- Z2105-, correct?

Too bad, but it looks like the ht35 project has not been maintained in months.

Joe B
01-12-2014, 03:16 AM
Kit no. 274480 from Elena, Bebrovo, Bulgaria is L150+, M269+, Z2103-, Z2105-. Given the uncertainty of L150, it would be good to see if he is L23+. If so, he would be the first L23+ L51- Z2103- Z2105-, correct?

Too bad, but it looks like the ht35 project has not been maintained in months.
Thanks Richard. 274480 looks like a L150.? or L23-, L150+ (PF7558+, PF7562+, PF7563+, Geno2.0) and they all have DYS426=11 so far.
It has been a long time since since we have seen changes to the ht35 project. Hopefully everything is alright and they know they have supportive members in that project....that need help and are willing to help.

Rathna
01-12-2014, 04:24 AM
Kit no. 274480 from Elena, Bebrovo, Bulgaria is L150+, M269+, Z2103-, Z2105-. Given the uncertainty of L150, it would be good to see if he is L23+. If so, he would be the first L23+ L51- Z2103- Z2105-, correct?

Too bad, but it looks like the ht35 project has not been maintained in months.

We have discussed a lot of this case on eng.molgen and, as I predicted, he is R-M269+/L150+/PF7558/62/63+.

R.Rocca
01-12-2014, 04:53 AM
We have discussed a lot of this case on eng.molgen and, as I predicted, he is R-M269+/L150+/PF7558/62/63+.

So he had a Geno 2.0 test or an individual L23 test?

Rathna
01-12-2014, 05:14 AM
So he had a Geno 2.0 test or an individual L23 test?

For what I know he is doing Geno 2.0 from 2 December 2013 and is going to do Big Y, but if you had to bet upon his haplogroup, what would you bet about?

274480 Bebrovo, Elena municipality, Bulgaria R1b1a2a1 R-L150 L150+, M269+, Z2103-, Z2105-
12 25 14 11 10-15 11 12 12 14 13 30 16 10-10 11 11 24 15 19 30 15-16-16-17 10 10 19-23 15 14 19 18 37-38 12 12 11 9 15-16 8 10 10 8 11 9 12 23-23 15 11 12 12 15 8 13 22 20 13 13 11 13 11 11 12 12
N92413 Greece R1b1a2a1
12 25 14 11 10-15 11 12 12 14 13 30
N92413 R1b1a2a1 R-L150
CTS10168+, CTS10362+, CTS10834+, CTS109+, CTS11358+, CTS11468+, CTS11575+, CTS11726+, CTS11985+, CTS12478+, CTS125+, CTS12632+, CTS1996+, CTS2134+, CTS2664+, CTS3063+, CTS3135+, CTS3331+, CTS3358+, CTS3431+, CTS3536+, CTS3575+, CTS3654+, CTS3662+, CTS3868+, CTS3996+, CTS4244+, CTS4364+, CTS4368+, CTS4437+, CTS4443+, CTS4740+, CTS5318+, CTS5457+, CTS5532+, CTS5577+, CTS5884+, CTS6135+, CTS623+, CTS6383+, CTS6800+, CTS6907+, CTS7400+, CTS7659+, CTS7922+, CTS7933+, CTS8243+, CTS8591+, CTS8665+, CTS8728+, CTS8980+, CTS9828+, F1046+, F115+, F1209+, F1302+, F1320+, F1329+, F1704+, F1714+, F1753+, F1767+, F1794+, F180+, F2048+, F2075+, F211+, F212+, F2142+, F2155+, F2402+, F2587+, F2688+, F2710+, F2837+, F29+, F295+, F2985+, F2993+, F3111+, F313+, F3136+, F33+, F332+, F3335+, F344+, F3556+, F356+, F359+, F3692+, F378+, F4+, F47+, F506+, F556+, F63+, F640+, F647+, F652+, F671+, F719+, F82+, F83+, F93+, L132+, L15+, L150+, L16+, L265+, L278+, L350+, L388+, L389+, L407+, L468+, L470+, L471+, L482+, L483+, L498+, L500+, L502+, L506+, L566+, L585+, L721+, L747+, L752+, L754+, L761+, L768+, L773+, L774+, 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+, P297+, 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+, PF6091+, PF6145+, PF6246+, PF6249+, PF6250+, PF6263+, PF6265+, PF6270+, PF6271+, PF6272+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+, PF667+, PF719+, PF720+, PF725+, PF7558+, PF7562+, PF7563+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF844+, PF892+, PF937+, PF951+, PF954+, PF970+, s10+, s3+, V186+, V189+, V205+, V52+, V9+, YSC0000067+, YSC0000072+, YSC0000075+, YSC0000166+, YSC0000176+, YSC0000179+, YSC0000182+, YSC0000186+, YSC0000194+, YSC0000201+, YSC0000203+, YSC0000205+, YSC0000207+, YSC0000213+, YSC0000219+, YSC0000224+, YSC0000225+, YSC0000227+, YSC0000230+, YSC0000232+, YSC0000233+, YSC0000251+, YSC0000269+, YSC0000270+, YSC0000279+, YSC0000288+, YSC0000294+

R.Rocca
01-12-2014, 12:53 PM
Do you know if all M269(xL23) that have tested with Geno 2.0 have also been PF7558+, PF7562+, PF7563+?

Rathna
01-12-2014, 01:01 PM
Do you know if all M269(xL23) that have tested with Geno 2.0 have also been PF7558+, PF7562+, PF7563+?

All the published ones I know, yes. For this I asked if there are someone different, and those I know are also L150+, and I asked if there is someone L150-. Probably Federighi with DYS462=12 is like these, but perhaps it would be interesting to test someone with DYS462=11 or the Italians with YCAII=17-23 etc.

Rathna
01-12-2014, 01:09 PM
This Italian (Ysearch 79UHC) has DYS462=11 and I am in contact with his American relatives by 23andMe.

Rathna
01-12-2014, 01:25 PM
Here you have some interesting haplotypes, but now I must go to Leghorn for the Messa di gloria of Pietro Mascagni:
79UHC Filandro Italy
12 26 14 11 11 14 11 12 11 13 13 29 16 9 10 11 11 25 15 19 30 15 15 15 16 10 11 19 23 15 12 12 11 11 12 23 10 13 14 12 13 30 24
56D68 Anonymous Iranian Natanz Esfahan, Iran
12 24 14 11 12 15 11 12 11 13 13 30 18 9 10 11 11 25 15 19 30 14 14 16 16 11 11 19 23 16 12 12 11 11 13 23 10 13 12 12 14 30 24
6A5HQ Anonymous Benin Benin
12 24 14 10 11 14 11 12 12 13 14 30 17 9 10 11 11 25 15 19 30 15 15 16 16 10 10 19 23 16 12 12 11 12 12 23 10 13 12 12 13 30 24
796ME Donato Italy
12 24 14 11 12 14 11 12 11 13 13 29 17 9 10 11 11 25 15 20 29 15 15 16 17 10 12 17 23 16 13 12 12 11 12 23 10 13 13 13 14 30 24
G5CCP Jlelati Lebanon
12 25 14 10 12 14 11 12 11 13 13 29 16 9 10 11 11 24 15 20 30 15 15 16 18 10 10 17 23 16 13 11 12 11 12 23 10 13 13 12 14 30 24
MHK97 Federighi Santa Maria a Monte, Pisa, Italy
12 25 14 10 11 14 11 12 11 13 13 29 16 9 10 11 11 24 15 20 29 15 15 16 16 10 10 19 23 16 12 12 11 12 12 23 10 13 12 12 13 30 24
RQ7K2 Rodrigues Soledade, Rio Grande do Sul, Brazil
12 26 14 11 11 14 11 12 11 13 13 29 16 9 10 11 11 25 15 19 29 15 15 15 16 10 11 19 23 15 12 12 11 11 12 23 10 13 14 12 13 30 24
SRPAM Anonymous Unknown
12 26 14 11 11 14 11 12 12 13 13 29 16 9 10 11 11 26 15 19 32 15 15 16 17 10 10 19 23 16 12 12 11 12 13 23 10 13 12 12 14 31 24
TJKDA Ciaschini San Costanzo, Pesaro e Urbino, Italy
12 25 14 11 11 14 11 12 11 13 13 29 17 9 10 11 11 24 15 19 28 15 15 16 17 10 11 19 22 16 12 12 12 11 12 24 10 13 12 12 13 30 24
URZC3 Revelli Cafasse, Torino, Italy
12 24 14 11 12 14 11 12 12 13 13 29 16 9 10 11 11 25 15 19 31 15 15 16 18 11 11 19 23 15 12 12 10 11 12 23 10 13 13 12 13 30 24
X3HFU Zebary Iraq
12 24 14 11 11 14 11 12 11 13 13 29 17 9 10 11 11 25 15 19 28 14 15 15 17 10 11 19 23 15 13 12 11 12 12 23 10 13 12 12 13 28 24

Rathna
01-13-2014, 02:21 PM
95875 Pietro Stasi, b 1854, Potenza, Italy Italy R1b1a2a1
12 23 14 11 11-14 12 12 13 14 14 29 17 9-10 11 11 25 15 19 31 14-15-16-18 11 12 19-23 15 16 19 17 35-37 12 12 11 9 15-16 8 10 10 8 10 10 12 21-24 15 10 12 12 15 8 11 22 20 13 13 11 13 11 11 12 12
Manno: Ysearch 5C2NP.
But at this poiint also Mattoli could be a candidate for L277+:
30885 Nicolo' Mattoli year 1475, Bevagna, Umbria, Italy Italy R1b1a2a1
12 26 14 11 11-15 12 12 13 12 15 27 15 9-10 11 11 26 15 19 29 15-16-16-18 11 11 19-23 16 15 19 18 35-37 13 12 11 9 15-16 8 10 10 8 10 11 12 23-23 17 10 12 12 15 8 11 22 20 13 12 11 13 11 11 12 12 37 15 9 16 12 25 26 19 11 11 13 12 10 9 12 12 10 11 11 30 13 12 25 13 10 10 22 15 19 13 25 17 12 15 23 12 23 19 10 14 18 9 11 11
and as Mangino is going to be tested for Geno 2.0 and whether he didn't use my donor of 50$, I ask Richard Rocca to test with those (and others if for Geno 2.0, but my money is enough for a SNP a la carte) also Mattoli, as he could be L277+, and we should have many Italians with the motives:
13 14 28
12 14 27
14 14 29
12 15 27

It merits to test Mattoli for L277 also because we have another Italian with the motive: 13 15 28:
BKXNU Brigano Calabria, Italy
12 24 14 11 11 14 12 12 13 13 15 28 17 9 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 12 12 11 11 13 23 10 13 12 12 13 30 24

Rathna
01-13-2014, 06:13 PM
Many thanks for your answer, Angelika. Of course I suspected that some results were due to a reading of the reverse strand, but also so it seemed to me that there were some incosistencies, above all my Z2103 ancestral and it is the first time that this happens in my haplogroup and this forces us to make another tree.
Hope to can publish your letter on "Anthrogenica", not only because it is very useful for us all, but also for BritainsDNA, I have always defended against other companies.

Kind Regards, Gioiello Tognoni

Dear Gioiello,

My colleague has forwarded your request to me.
Please see the header of your raw data file, which explains the issues that you appear to have with your results:

"This is your Y chromosome raw data for the chromo2 chip. We only advise expert genetic genealogists to use this file, as almost all important information is distilled into the genetic signature and other results. The file is a tab-delimited text file which may be opened in a spreadsheet program. Each line corresponds to a single SNP and you will find three columns with respectively, the SNP name, your genotype and whether the result is positive (derived) or negative (ancestral). Alleles are called to the Illumina TOP strand. Where it was not possible to call the allele in your sample, a zero is given and the result is "no_call". We may from time to time update the raw data if it becomes possible to call markers which were initially problematic. While the Y chromosome is a single copy piece of DNA, the Illumina software used to call alleles is designed for autosomal markers which come in two copies. Hence when AA or GG are given, it means A or G, respectively. A small number of markers give apparent heterozygote calls, e.g. AG. As shown in the result column, these indicate a positive call. The reason they appear to be heterozygous is again because of limitations in the Illumina clustering software, which expects three clusters. If the true positive and negative clusters are too close together, it is not possible to force a homozygous call for the one variant, hence an AG call is allowed. Our downstream scripts register this as a positive call. In a few cases a marker might arise, for example, by the DNA letter A changing to C, then much later in time in someone with the C it changes back to an A again; this is called back-mutation. One such example is the marker S163: if you carry the ancestral A you are negative, if you carry the C it is shown as (positive) and if you carry the back-mutated A, it is shown as "back-mutated". We can tell the back-mutations from the ancestral variants using the other markers you carry."

In terms of the SNPs you have sent us - I have checked these, and can add the following:

1) For the 4 SNPs below, we are reading off the same strand as the reference, and you do indeed just carry one allele (C, A, G and T respectively), even though it is reported as "homozygous", which is an artefact of the genotyping software:
PF7580 C->A CC negative --> you carry the C allele (negative)
CTS7763 A->G AA negative --> you carry the A allele (negative)
CTS9219 G->A GG negative --> you carry the G allele (negative)
Z2110 A->T TT positive --> you carry the T allele (positive)

2) For the 4 SNPs below, we are reading off the other strand, so if you want to convert to the strand that genbank is using, you have to swap C to G and A to T (and vice versa):
CTS699 C->T GG negative --> you carry the C allele (negative)
Z2109 T->C GG positive --> you carry the C allele (positive)
Z2103 G->C CC negative --> you carry the C allele (negative)
CTS8966 C->T GG negative --> you carry the C allele (negative)

Note that we use the superior TOP strand designation of Illumina for the Y raw file. It allows unequivocal assignment of alleles, unlike the FORWARD strand which can change.

3) For Z2105 we have chosen to use the heterozygous cluster to represent the positive cluster (as we obtain better results this way) - so the AC is because of this; you carry the A allele.
Z2105 C->A AC positive --> you carry the A allele (positive)


4) For S334, we have now updated our clusters (and thank you for drawing our attention to this SNP, which is very rare), and the clusters will now be AG = negative and GG = positive (again, this is because of limitations in the Illumina SNP calling software, and actually represents A = negative and G = positive, which means we are again reading off the complementary strand to that which genbank is using).
S334 (L277) T->С AG negative --> you carry the A allele (negative)

In terms of negative (ancestral) vs positive (derived) we used three samples from different deep branches in the A paragroup to determine the direction of evolution empirically. This is more reliable than any other method as most of these SNPs had never been tested in for example the A0 branch, and hence the true ancestral allele was not known. Back mutations across the full depth of the tree are not so rare when you are dealing with >14000 SNPs!

I hope this answers your queries - feel free to get in touch with me directly if you have any others. We regularly update the Y chromosome clusters and results given out, as and when we notice that a SNP is not clustered correctly (which then have to be fixed) or does not make phylogenetic sense (in which case we also remove them, even though the genotying calls are likely correct, there is little value in the information) so we value all customer feedback in this regard.

Best wishes,
Angelika



From: Gioiello Tognoni <[email protected]>
Date: Wednesday, 8 January 2014 19:18
To: Laura Marshall <[email protected]>
Subject: Inconsistencies

Hi Laura,
I thank you for my results, but I noted some inconsistencies :
PF7580 C->A CC negative
S334 (L277) T->С GG negative ??
CTS7763 A->G AA negative
CTS8966 C->T GG negative ??
Z2103 G->C CC negative ?? positive
Z2105 C->A AC positive ?? heterozygous
Z2109 T->C GG positive ??
Z2110 A->T TT positive
CTS9219 G->A GG negative
CTS699 C->T GG negative ??
May you explain why? Thanks, Gioiello Tognoni


--
Dr. Angelika Kritz
Senior Scientist
ScotlandsDNA

R.Rocca
01-13-2014, 06:43 PM
Many thanks for your answer, Angelika. Of course I suspected that some results were due to a reading of the reverse strand, but also so it seemed to me that there were some incosistencies, above all my Z2103 ancestral and it is the first time that this happens in my haplogroup and this forces us to make another tree.
Hope to can publish your letter on "Anthrogenica", not only because it is very useful for us all, but also for BritainsDNA, I have always defended against other companies.

I don't think a new tree is needed. Either Z2103 is really negative in your sample and it is unstable due to a back mutation (unlikely) or the chip has an issue with this SNP and you are really Z2103+ (likely).

Silesian
01-13-2014, 06:45 PM
Many thanks for your answer, Angelika. Of course I suspected that some results were due to a reading of the reverse strand, but also so it seemed to me that there were some incosistencies, above all my Z2103 ancestral and it is the first time that this happens in my haplogroup and this forces us to make another tree.
Hope to can publish your letter on "Anthrogenica", not only because it is very useful for us all, but also for BritainsDNA, I have always defended against other companies.

Kind Regards, Gioiello Tognoni

Thank you for posting this. Do you have any theories on how this will change smal's tree if you really are Z2103-?

Rathna
01-13-2014, 06:51 PM
I don't think a new tree is needed. Either Z2103 is really negative in your sample and it is unstable due to a back mutation (unlikely) or the chip has an issue with this SNP and you are really Z2103+ (likely).

Richard, I thank you for your answer, but some days ago I asked if all the Z2110+ were tested for both Z2105 and Z2103, this to see if Z2103 could be before the other subclades, but not before Z2110.
Only this was my doubt. BritainsDNA seems to me very reliable, also in testing my 9bp deletion in the L50 region (around 7,012,023), in fact there are many no-calls, and this confirms also my hypothesis that the S SNPs are in series.

Rathna
01-13-2014, 06:52 PM
Thank you for posting this. Do you have any theories on how this will change smal's tree if you really are Z2103-?

See my answer above to Richard Rocca.

smal
01-13-2014, 07:31 PM
Read this (http://www.google.by/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CCkQFjAA&url=http%3A%2F%2Fres.illumina.com%2Fdocuments%2Fpr oducts%2Ftechnotes%2Ftechnote_topbot.pdf&ei=7zrUUrrPMea84ASFo4DgDg&usg=AFQjCNH0M8J2cuBs8kGgcwdFKvGlaJhD9A&bvm=bv.59026428,d.Yms) document to understand this sentence:



Note that we use the superior TOP strand designation of Illumina for the Y raw file. It allows unequivocal assignment of alleles, unlike the FORWARD strand which can change.



Rathna, you should verify your Z2103- result in FTDNA. It is not possible to explan the Z2103- Z2109+ Z2110+ result.

Rathna
01-13-2014, 07:54 PM
Read this (http://www.google.by/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CCkQFjAA&url=http%3A%2F%2Fres.illumina.com%2Fdocuments%2Fpr oducts%2Ftechnotes%2Ftechnote_topbot.pdf&ei=7zrUUrrPMea84ASFo4DgDg&usg=AFQjCNH0M8J2cuBs8kGgcwdFKvGlaJhD9A&bvm=bv.59026428,d.Yms) document to understand this sentence:




Rathna, you should verify your Z2103- result in FTDNA. It is not possible to explan the Z2103- Z2109+ Z2110+ result.

At this point I think that my Z2103 + or - is a little worth. Probably I am Z2103+, seen that Seymour (Z2110+) is Z2103+ and Z2105+. I think that it would be more interesting that Richard Rocca, like administrator of the "Italy FTDNA Project", does test Mattoli for L277. He already has my 50$, and if it will be demonstrated that Italy has R-L277+ with these variance
13 14 28
12 14 27
14 14 29
12 15 27
13 15 28
whereas the Jewish ones have only
13 14 28
I think it would be difficult not to agree with my theory of the "Italian Refugium".

palamede
01-13-2014, 09:39 PM
I don't understand what Angelika wrote about Z2103
"For the 4 SNPs below, we are reading off the other strand, so if you want to convert to the strand that genbank is using, you have to swap C to G and A to T (and vice versa):
CTS699 C->T GG negative --> you carry the C allele (negative)
Z2109 T->C GG positive --> you carry the C allele (positive)
Z2103 G->C CC negative --> you carry the C allele (negative)"

For CTS699 and Z2109 , needs to swap G by C, this involves CTS699- and Z2109+ . I understand.
But for Z2103 , She should say "you carry the G allele (negative)" . I suppose I wanted to write G and I wrote C.

Correction on 01/14 : I wanted to write :
"I suppose she wanted to write G and she wrote C".
Very sorry.

Rathna
01-14-2014, 01:10 AM
I don't understand what Angelika wrote about Z2103
"For the 4 SNPs below, we are reading off the other strand, so if you want to convert to the strand that genbank is using, you have to swap C to G and A to T (and vice versa):
CTS699 C->T GG negative --> you carry the C allele (negative)
Z2109 T->C GG positive --> you carry the C allele (positive)
Z2103 G->C CC negative --> you carry the C allele (negative)"

For CTS699 and Z2109 , needs to swap G by C, this involves CTS699- and Z2109+ . I understand.
But for Z2103 , She should say "you carry the G allele (negative)" . I suppose I wanted to write G and I wrote C.

Palamede, I thank you for having given a glance to my results, but Angelika is right. If we consider the other strand, we should write:

Z2103 G->C becomes Z2103 C->G

and my C is negative and G would be positive. Of course a back mutation (unlikely Rocca says) or an error is always possible. The unique thing to do is to test me for Z2103 by FTDNA or by Krahn's new company, but, as I have said above, this has a little importance to me now, because it doesn't change my tree, and I am R-Z2110*, i.e. ancestral to the most part of this subclade and found so far in Italy and the Balkans. It would be interesting to test also Romitti, L150- like Seymour, but with a different haplotype from those people put in that absurd subclade of the "ht 35 FTDNA project" under L150-, actually only of Seymour and Romitti and happened for independent mutations.

P.S. To test Romitti not for Z2103/Z2105, because he and his son have been tested for these SNPs and are positive. To test Romitti for Z2110 and for the SNP of Seymour under Z2110: F672.

R.Rocca
01-14-2014, 01:23 AM
At this point I think that my Z2103 + or - is a little worth. Probably I am Z2103+, seen that Seymour (Z2110+) is Z2103+ and Z2105+. I think that it would be more interesting that Richard Rocca, like administrator of the "Italy FTDNA Project", does test Mattoli for L277. He already has my 50$, and if it will be demonstrated that Italy has R-L277+ with these variance
13 14 28
12 14 27
14 14 29
12 15 27
13 15 28
whereas the Jewish ones have only
13 14 28
I think it would be difficult not to agree with my theory of the "Italian Refugium".

Let me know if that's the person you want to apply the funds to and I will contact him.

Rathna
01-14-2014, 01:34 AM
Let me know if that's the person you want to apply the funds to and I will contact him.

This is the person of the "Italy FTDNA project". Of course we cannot contact Brigano, I found on SMGF, or the Tuscan NA20532 of the 1KGP.

30885 Nicolo' Mattoli year 1475, Bevagna, Umbria, Italy Italy R1b1a2a1
12 26 14 11 11-15 12 12 13 12 15 27 15 9-10 11 11 26 15 19 29 15-16-16-18 11 11 19-23 16 15 19 18 35-37 13 12 11 9 15-16 8 10 10 8 10 11 12 23-23 17 10 12 12 15 8 11 22 20 13 12 11 13 11 11 12 12 37 15 9 16 12 25 26 19 11 11 13 12 10 9 12 12 10 11 11 30 13 12 25 13 10 10 22 15 19 13 25 17 12 15 23 12 23 19 10 14 18 9 11 11

Rathna
01-14-2014, 02:14 AM
Hope that also this letter is useful (and interesting) for the readers of the "R1b Phylogeny" thread:

Dear Gioiello,
I am glad I could clear things up, and feel free to post my reply on Anthrogenica. We appreciate your public support - thank you!

I am not sure if Jim mentioned this to you - but we have decided to release the anonymised YDNA results of 1000 random male chromo2 customers. This will be in the form of an excell spreadsheet, with one column per customer (BD# removed) and 1 row per SNP. We will also indicate the inferred subtype. I am working on this at the moment but it might be a week or so before it is released.

I will also send you your updated Y raw file once I have completed my SNP updates.

Best wishes,
Angelika

Rathna
01-22-2014, 04:54 PM
It seems that in the PF SNPs series I am positive for PF2642 (found also in I1-Z140), which seems a good SNP, and also for PF7499.


PF2642 11670264 13210264 no no no no no C -> T
PF7499 13494051 14984657 no no no no no G -> A

Whereas I haven’t this SNP (i.e I am ancestral):
PF4432 15106043 16596649 no no no no no C -> G

Silesian
01-22-2014, 05:37 PM
It seems that in the PF SNPs series I am positive for PF2642 (found also in I1-Z140), which seems a good SNP, and also for PF7499.


PF2642 11670264 13210264 no no no no no C -> T
PF7499 13494051 14984657 no no no no no G -> A

Whereas I haven’t this SNP:
PF4432 15106043 16596649 no no no no no C -> G

Is this another branch?

Rathna
01-22-2014, 10:12 PM
Is this another branch?
If they will be confirmed, yes, it is. Of course every subclade is a paragroup, which will get its own mutations, and by this point of view I shouldn't say that my haplotype is the "ancestor" of others. They are all on the same plane, and only the Full Y will be able to say who descends from whom.

Rathna
01-23-2014, 06:13 PM
I am on hurry, and I'll study them this night, but by comparing my Chromo2 with an R-U106/Z156*, I find this mismatches:
CTS11150, L1052, L1143,[I have to control from S10738 to S20315], S3023, S3530, S629, S6814, S8628, S8670, S8706, S8714, S8726, Z612 beyond the PF and Z SNPs I have already signaled.

Rathna
01-23-2014, 07:05 PM
I am on hurry, and I'll study them this night, but by comparing my Chromo2 with an R-U106/Z156*, I find this mismatches:
CTS11150, L1052, L1143,[I have to control from S10738 to S20315], S3023, S3530, S629, S6814, S8628, S8670, S8706, S8714, S8726, Z612 beyond the PF and Z SNPs I have already signaled.
Perhaps L1052 is L1053, and the first three SNPs are in R-L21 (it seems) but the others not.

EDIT: L1052 AA negative L1053 AA positive

Rathna
01-24-2014, 03:47 AM
Other possible SNPs to add: S10358 AG positive S12460 AG positive S13077 AG positive


Thus the SNPs to investigate for my R-Z2110* should be these ones:
PF2642, PF7499, S10358, S12460, S13077, S3023, S3530, S629, S6814, S8628, S8670, S8706, S8714, S8726, Z612

Rathna
01-24-2014, 04:01 PM
It merits to test Mattoli for L277 also because we have another Italian with the motive: 13 15 28:
BKXNU Brigano Calabria, Italy
12 24 14 11 11 14 12 12 13 13 15 28 17 9 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 12 12 11 11 13 23 10 13 12 12 13 30 24

This is another Italian very close to Mattoli:

118515 Italy Italy R1b1a2
12 26 14 10 12-14 12 12 13 12 15 27 17 9-10 11 11 25 15 19 30 15-16-16-18 11 11 19-23 15 16 19 18 36-37 12 12

And interesting, even though far as to the haplotype, this Armenian:

299810 Armenia R1b1a2
12 23 14 11 11-16 12 12 12 13 15 28 17 9-10 11 11 25 15 19 27 15-15-16-19 10 11 19-22 16 16 18 18 36-39 11 12 11 9 15-17 8 10 10 8 10 10 12 23-23 16 10 13 12 15 8 12 22 20 13 12 11 13 11 11 12 12

Rathna
01-25-2014, 04:20 AM
Another collection of probable R-L277 which links Italy and Middle East and another Italian (I have already posted a Brigano) with DYS392=15:

B5QG9 Mattoli Bevagna, Umbria, Italy
12 26 14 11 11 15 12 12 13 12 15 27 15 9 10 11 11 26 15 19 29 15 16 16 18 11 11 19 23 16 15 19 18 35 37 13 12
5T2JM öztürk Turkey
12 24 14 10 11 15 12 12 13 12 14 27
ABVDQ Tuttle Tharston County, Norfolk, England
12 24 14 11 11 15 12 12 13 13 14 28
BZ5A8 Pera Iran
12 26 14 11 11 14 12 12 13 13 14 29
EC479 Brigano Calabria, Italy
12 24 14 11 11 14 12 12 13 13 15 28
G7N7S Vartanian Armenia
12 24 14 11 11 15 12 12 13 13 14 28
GQPPT Nishanian Turkey
12 24 14 11 11 15 12 12 13 13 14 28
KKBTE öztürk Turkey
12 24 14 10 11 15 12 12 13 12 14 27
U6R94 Contrisciane Castlealto, Abruzzo, Italy
12 26 14 11 11 14 12 12 12 12 14 27
VCDW4 öztürk Turkey
12 24 14 10 11 15 12 12 13 12 14 27
ZBBBK Marks Italy
12 26 14 10 12 14 12 12 13 12 15 27

Rathna
01-25-2014, 11:25 AM
There is also someone who prefers to remain anonymous:

EC479 Brigano Calabria, Italy
12 24 14 11 11 14 12 12 13 13 15 28
BKXNU Brigano Calabria, Italy
12 24 14 11 11 14 12 12 13 13 15 28 17 9 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 12 12 11 11 13 23 10 13 12 12 13 30 24
JRTHH unknown Unknown
12 24 14 11 11 14 12 12 13 13 15 28 17 9 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 12 12

Rathna
01-26-2014, 10:23 AM
Hi smal, as I have hinted some time ago, it is very likekly that L277, that in your map isn't linked to the center of Z2103/Z2105, is actually not on the right of your map but on the left, under the Tuscan NA20532 and of the two Jews downstream. I make you note that this Tuscan has DYS393=13 like Burkholder from Switzerland, who is tested L277+, and of course in my theory Swiss haplogroups came from the Italian Refugium, not only for this haplogroup, or the Italian Refugium was actually Alpine thus common to they all.
We are waiting for the test of Mattoli about L277. Meanwhile I ask you if there are some SNP in common between these two branches or if there are SNPs negative (ancestral) which may exclude this link.

smal
01-26-2014, 05:16 PM
Hi smal, as I have hinted some time ago, it is very likekly that L277, that in your map isn't linked to the center of Z2103/Z2105, is actually not on the right of your map but on the left, under the Tuscan NA20532 and of the two Jews downstream. I make you note that this Tuscan has DYS393=13 like Burkholder from Switzerland, who is tested L277+, and of course in my theory Swiss haplogroups came from the Italian Refugium, not only for this haplogroup, or the Italian Refugium was actually Alpine thus common to they all.
We are waiting for the test of Mattoli about L277. Meanwhile I ask you if there are some SNP in common between these two branches or if there are SNPs negative (ancestral) which may exclude this link.

Hi Rathna, we have already discussed this possibility here (http://www.anthrogenica.com/showthread.php?1727-R1b-phylogeny&p=26401&viewfull=1#post26401). Like you I think that the Tuscan NA20532 sample belongs to the L277 branch. There were not found any specific SNPs in Geno 2.0 microarray for L277 branch. So, we need to test these (http://www.anthrogenica.com/showthread.php?1722-R1b-L277-1*-R1b-M269-gt-L23-gt-L150-gt-Z2103-gt-Z2105-gt-L277-1*-2014&p=26688&viewfull=1#post26688) SNPs to prove that the Tuscan NA20532 line and the Burkholder line from Switzerland belong to the same L277 branch.

Rathna
01-26-2014, 05:56 PM
Hi Rathna, we have already discussed this possibility here (http://www.anthrogenica.com/showthread.php?1727-R1b-phylogeny&p=26401&viewfull=1#post26401). Like you I think that the Tuscan NA20532 sample belongs to the L277 branch. There were not found any specific SNPs in Geno 2.0 microarray for L277 branch. So, we need to test these (http://www.anthrogenica.com/showthread.php?1722-R1b-L277-1*-R1b-M269-gt-L23-gt-L150-gt-Z2103-gt-Z2105-gt-L277-1*-2014&p=26688&viewfull=1#post26688) SNPs to prove that the Tuscan NA20532 line and the Burkholder line from Switzerland belong to the same L277 branch.

Yes, I thank you, but it would be worth also the other way around, that some L277+ is tested for these SNPs, from Z2104/PF7575 to all those tested by Rootsy et alii. It is strange that no one of the L277+ has done this test. Anyway so far we don't know, isn't it true?

smal
01-26-2014, 06:30 PM
There is no easy way to test for these new SNPs. FTDNA does not offer such possibility except for BigY. It is only possible to order new analysis in YSEQ...

Joe B
01-26-2014, 10:08 PM
Yes, I thank you, but it would be worth also the other way around, that some L277+ is tested for these SNPs, from Z2104/PF7575 to all those tested by Rootsy et alii. It is strange that no one of the L277+ has done this test. Anyway so far we don't know, isn't it true?
There is no easy way to test for these new SNPs. FTDNA does not offer such possibility except for BigY. It is only possible to order new analysis in YSEQ...Dr. Krahn mentioned a few SNPs in correspondence with him. Does anybody know about the phylogeny of SNPs Z8127 to Z8159? CTS9906 is another one mentioned that is a little more difficult because of many proximal repeats but doable.
YSEQ (http://www.yseq.net/) has Z2104/PF7575 and Z2107/CTS7340 in the catalog (http://shop.yseq.net/) and ready to go. A dry sample is submitted which should make it very easy to send in from any country.

smal
01-27-2014, 07:27 AM
Dr. Krahn mentioned a few SNPs in correspondence with him. Does anybody know about the phylogeny of SNPs Z8127 to Z8159? CTS9906 is another one mentioned that is a little more difficult because of many proximal repeats but doable.
Could you tell me chromosome positions for SNPs Z8127 to Z8159?
CTS9906 is private for HG01515 (CTS9212).


YSEQ (http://www.yseq.net/) has Z2104/PF7575 and Z2107/CTS7340 in the catalog (http://shop.yseq.net/) and ready to go. A dry sample is submitted which should make it very easy to send in from any country.
At the moment Z2104 and Z2107 are on the same level as Z2105 and Z2103.

Rathna
01-27-2014, 08:08 AM
CTS9906 is private for HG01515 (CTS9212).


Perhaps CTS9219.

Rathna
01-27-2014, 08:10 AM
Could you tell me chromosome positions for SNPs Z8127 to Z8159?

I am surprised from the high number of these SNPs. I don't know if they actually exist.

Joe B
01-27-2014, 08:38 AM
Could you tell me chromosome positions for SNPs Z8127 to Z8159?
CTS9906 is private for HG01515 (CTS9212).


At the moment Z2104 and Z2107 are on the same level as Z2105 and Z2103.
Wish I could tell you anything about SNPs Z8127 to Z8159. They were mentioned as a area to look for good primers. I couldn't find anything about them. If I have it right, CTS9906 goes with the CTS7959, CTS9230, CTS11767 also found in HG01515 (CTS9212).
I'm betting my Z2104, Z2107 and Z2110 results won't change the tree.

Rathna
01-29-2014, 11:55 AM
I have just received this letter from BritainsDNA. I'll provide next to post my final results I am extracting from the raw data (Z2103 negative has been confirmed):

Hi Gioiello,
As promised, please find attached your updated Y raw file. The file I mentioned in my previous email (of anonymised results of 1500 customers) is ready but too big to send by email - I will let you know when our IT department has got a download link for this working.
Best wishes,
Angelika

Dr. Angelika Kritz
Senior Scientist
ScotlandsDNA

Rathna
01-29-2014, 03:14 PM
CTS10149+, CTS11150+, CTS11468+, CTS11575+, CTS11948+, CTS11991+, CTS12057+, CTS12633+, CTS12773+, CTS1738+, CTS2134+, CTS2254+, CTS2480+, CTS2569+, CTS2664+, CTS3229+, CTS3315+, CTS3316+, CTS3358+, CTS3654+, CTS3818+, CTS3844+, CTS4293+, CTS4437+, CTS4740+, CTS4944+, CTS5139+!, CTS5248+, CTS543+, CTS6327+, CTS6376+, CTS6383+, CTS6445+, CTS7301+, CTS7604+, CTS7659+, CTS7922+, CTS7941+, CTS8627+, CTS8728+, CTS9200+, CTS9556+, CTS9760+, F1794+, L1002+, L1013+, L1053+, L1084+, L1098+, L1118+, L1123+, L1129+, L1130+, L1137+, L1143+, L1145+, L1150+, L1179+, L1220+, L132+, L1345+, L1350+, L1352+, L265+, L278+, L320+, L352+, L438+, L440+, L468+, L470+, L479+, L498+, L508+, L543+, L58+, L604+, L741+, L752+, L757+, L768+, L773+, L822+, L82+, L875+, L882+, L969+, M213+, M235+, M294+, M299+, M415+, M42+, M523+, M526+, M74+, P128+, P131+, P135+, P139+, P140+, P141+, P142+, P143+, P151+, P158+, P159+, P160+, P163+, P224+, P225+, P226+, P229+, P230+, P232+, P233+, P234+, P236+, P239+, P242+, P244+, P245+, P280+, P282+, P284+, P285+, P294+, P295+, P297+, P305+, PAGE081+, PAGE083+, PF1067+, PF1081+, PF1252+, PF1253+, PF1416+, PF1695+, PF1911+, PF2590+, PF2592+, PF2615+, PF2617+, PF2619+, PF2621+, PF2622+, PF2624+, PF2642+, PF2651+, PF2653+, PF2655+, PF2658+, PF2660+, PF2677+, PF2679+, PF2683+, PF2684+, PF2685+, PF2688+, PF2690+, PF2700+, PF2702+, PF2704+, PF2709+, PF2716+, PF2718+, PF2722+, PF2734+, PF2736+, PF2737+, PF2739+, PF2742+, PF2747+, PF2748+, PF2760+, PF2762+, PF2775+, PF3495+, PF3500+, PF5459+, PF5461+, PF5480+, PF5495+, PF5857+, PF5861+, PF5865+, PF5869+, PF5870+, PF5872+, PF5873+, PF5885+, PF5887+, PF5893+, PF5898+, PF5908+, PF5912+, PF5914+, PF5917+, PF5918+, PF5923+, PF5927+, PF5936+, PF5940+, PF5941+, PF5945+, PF5949+, PF5953+, PF5957+, PF5958+, PF5964+, PF5966+, PF5977+, PF5980+, PF5981+, PF5982+, PF6016+, PF6040+, PF6047+, PF6055+, PF6056+, PF6063+, PF6065+, PF6079+, PF6082+, PF6114+, PF6115+, PF6116+, PF6129+, PF6136+, PF6143+, PF6145+, PF6242+, PF6246+, PF6249+, PF6252+, PF6258+, PF6263+, PF6265+, PF6267+, PF6269+, PF626+, PF6271+, PF6272+, PF6399+, PF6409+, PF6410+, PF6419+, PF6429+, PF6430+, PF6432+, PF6434+, PF6435+, PF643+, PF6443+, PF6451+, PF6463+, PF6467+, PF6469+, PF6471+, PF6475+, PF6481+, PF6484+, PF6487+, PF6495+, PF6497+, PF6506+, PF6507+, PF6524+, PF6528+, PF653+, PF679+, PF733+, PF744+, PF7499+, PF825+!, PF834+, PF869+, PF948+, S10358+, S11330+!, S11638+, S12460+, S12547+!, S13077+, S138+, S1572+, S19777+, S1984+!, S19862+!, S1+, S2003+, S2017+, S20246+, S20315+, S20902+, S26361+, S3023+, S349+, S351+, S3530+, S3848+, S3+, S4276+, S4888+, S4+, S629+, S6378+, S8235+, S8628+, S8670+, S8706+, S8709+, S8726+, S8889+, S9158+, S959+, SRY10831+!, V102+, V104+, V126+, V168+, V186+, V187+, V221+, V226+, V231+, V241+, V244+, V29+, V41+, V52+, V9+, YSC0167+, YSC0186+, YSC0203+, YSC0227+, YSC1297+, Z1244+, Z2103-, Z2105+, Z2109+, Z2110+, Z612+.

Joe B
01-29-2014, 04:46 PM
I have just received this letter from BritainsDNA. I'll provide next to post my final results I am extracting from the raw data (Z2103 negative has been confirmed):

Hi Gioiello,
As promised, please find attached your updated Y raw file. The file I mentioned in my previous email (of anonymised results of 1500 customers) is ready but too big to send by email - I will let you know when our IT department has got a download link for this working.
Best wishes,
Angelika

Dr. Angelika Kritz
Senior Scientist
ScotlandsDNA
I wonder how they confirmed the Z2103- result. Was it by another testing method?
Consider that two Z2110/CTS7822 haplotypes have tested Z2103+.

Rathna
01-29-2014, 04:56 PM
Two of the previous SNPs aren't confirmed:
S6814 AA positive
has become
S6814 GG negative
and
S8714 AG positive
has disappeared.
Thus my SNPs under investigation are these:
PF2642, PF7499, S10358, S12460, S13077, S3023, S3530, S629, S8628, S8670, S8706, S8726, Z612.

Rathna
01-29-2014, 05:05 PM
I wonder how they confirmed the Z2103- result. Was it by another testing method?
Consider that two Z2110/CTS7822 haplotypes have tested Z2103+.

We have discussed a lot about this and we did some hypotheses. One of these could be that there had been a mistake in the reading of the primers, i.e. that a computer had done a mistake between a reading forwards or reverse, because the mutations is a transversion from G to C and the mistake could be in the reading, but now that they have checked again my results (in fact they have corrected some mistakes: two in my new SNPs I posted above), I tend to think that the result is correct and to think to a back-mutation in a SNP recognized not so stable.
This could be a case like that of L150, but for my line could be meaningful, of course in a short time.
As I have posted above, the test has recognized also my deletion of 9bp in the region of L50/S136, deletion ascertained just from EthnoAncestry also on my far relative Giancarlo Tognoni (MRCA during the 15th century).

Joe B
01-29-2014, 05:40 PM
We have discussed a lot about this and we did some hypotheses. One of these could be that there had been a mistake in the reading of the primers, i.e. that a computer had done a mistake between a reading forwards or reverse, because the mutations is a transversion from G to C and the mistake could be in the reading, but now that they have checked again my results (in fact they have corrected some mistakes: two in my new SNPs I posted above), I tend to think that the result is correct and to think to a back-mutation in a SNP recognized not so stable.
This could be a case like that of L150, but for my line could be meaningful, of course in a short time.
As I have posted above, the test has recognized also my deletion of 9bp in the region of L50/S136, deletion ascertained just from EthnoAncestry also on my far relative Giancarlo Tognoni (MRCA during the 15th century).
Hopefully it is a SNP array problem and not Z2103. It will take some time to understand Chromo 2. That will especially be true for a small clade such as R1b-Z2103. We're still trying to figure out Geno 2.0 and that's over a year old.
When 108347 tested L150- by both Sanger sequencing and SNP array, that made L150 worthless. Z2103 looked like a good clade defining SNP to replace L150. Time and more testing will determine if Z2103 is valid. I'm not ready to rip up the phylogenetic tree yet.

Rathna
01-30-2014, 01:33 AM
Hopefully it is a SNP array problem and not Z2103. It will take some time to understand Chromo 2. That will especially be true for a small clade such as R1b-Z2103. We're still trying to figure out Geno 2.0 and that's over a year old.
When 108347 tested L150- by both Sanger sequencing and SNP array, that made L150 worthless. Z2103 looked like a good clade defining SNP to replace L150. Time and more testing will determine if Z2103 is valid. I'm not ready to rip up the phylogenetic tree yet.

I don't say that Z2103 isn't valid, as I have supported the validity of L150, pretty against the most part of people. The fact that only two persons so far amongst many thousands have been found negative amongst the L23 and that there is a subclade of M269 where all the tested so far are positive where scholars would have expected a negative result doesn't make this SNP useless, only less reliable than others.
As to Z2103 will see. So far only one person (me) has been found Z2105+ and Z2103-. We'll see by next tests what will happen, but already when these SNPs were discovered I remember that even Vincent Vizachero suggested to test Z2105 rather than Z2103.
I wouldn't give any importance to this, having on the same plane a reliable SNP like Z2105, and above all we have the phylogeny now.

Joe B
01-30-2014, 03:32 AM
I don't say that Z2103 isn't valid, as I have supported the validity of L150, pretty against the most part of people. The fact that only two persons so far amongst many thousands have been found negative amongst the L23 and that there is a subclade of M269 where all the tested so far are positive where scholars would have expected a negative result doesn't make this SNP useless, only less reliable than others.
As to Z2103 will see. So far only one person (me) has been found Z2105+ and Z2103-. We'll see by next tests what will happen, but already when these SNPs were discovered I remember that even Vincent Vizachero suggested to test Z2105 rather than Z2103.
I wouldn't give any importance to this, having on the same plane a reliable SNP like Z2105, and above all we have the phylogeny now.Thanks for your perspective and experience with the Z2103-Z2110 SNPs. It will be interesting to see if Chrome 2 yields more Z2103-, Z2105+ results. We would have a better chance of finding out if it were Italy's Chromo 2.

Rathna
01-30-2014, 05:18 AM
Thanks for your perspective and experience with the Z2103-Z2110 SNPs. It will be interesting to see if Chrome 2 yields more Z2103-, Z2105+ results. We would have a better chance of finding out if it were Italy's Chromo 2.

Joe B, as I have said above, I wouldn't give much importance to this, because where there is a phylogeny a single SNP is worth less: it may have suffered a back mutation, above all if it is less stable than others. It may be used only for short lineage. But in mine I already have the 9bp deletion, so far found only in Giancarlo Tognoni (thus at least from the 15th century), but it could be also a little older.
What is interesting to me is that these rare back mutations may have happened in this R-Z2110* haplogroup if it will be demonstrated that also Romitti (the other L150-) belongs to this haplogroup, and the closeness to the other British cluster of Seymour lets me think so. It could be due to its ancientness or to other reasons. My deletion could be a sign.

Rathna
02-03-2014, 06:27 AM
A good news for our haplogroup: Matthew Ware is having his Big Y. Results for the end of February. This I have just written to him:

Matthew, this is a great news, because from Big Y your Y will be tested for at least 9Mbp, I think similar to those tested by the team who tested many Jewish Levites for their R1a, but also some R1b have been tested and their data have been published. We have a forty SNPs in the line of our haplogroup, and your data will be able to be compared with them.
I did only Chromo2 because more less expensive and have 13 new SNPs (two in the series PF: Paolo Francalacci, who is a friend, have to write me about them; one is Z612, just found in the hg. J2b, and 10 in the series S of the BritainsDNA, whose we don't know the collocation, but they said they are going to publish a spreadsheet).
Your data will be very useful to deepen our tree and to understand how your English line is linked to the Italian one (Romitti, Tognarelli and me) and to the line found so far in the Balkans,

Many thanks, Gioiello

Rathna
02-19-2014, 09:08 PM
BritainsDNA at last has released 2000 samples of the people tested so far. I am not there, but there are many interesting samples of our haplogroup.
First of all there are 18 R-L23/S141: amongst them:
R-Z2105 and subclades:
10 are Z2110 (Z2103 is unreliable)
588: CTS9219, S3844, S8889
589: CTS9219, PF2642 (I too, but probably it is a little reliable)
590: CTS9219
592: CTS9219, CTS4122, S13125
593
595:
1556: CTS9219
1588: CTS9219
1839: CTS9219
1996: CTS3849, CTS7206, L128, S4269
---------
The following are R-L23 (xL277, Z2110, PF7580)
584
585
586
587
594: S7721
There is 1 R-L277
1928: S334/L277
There is 1 R-L51 (Z2113, Z2118)
591: S1157, S1161, S1260, S3282, S8889
There is 1 R-L11
583: S128/P311

16 are R-M269: amongst them
R1b-S1194: 569-582, 1626, 1944: amongst them R-S1196: 571, 574,577,579,581,582.

Rathna
02-20-2014, 05:16 AM
Posted also in another thread:

Quote Originally Posted by Rathna View Post
Of course I did my inquire without a computer program, by watching every line, and did some mistakes, I'll correct next on "R1b phylogeny" (for instance it seems that 584, 585, 586, 587 beyond 591 are R-L51) and that the 10 Z2110 have also the SNPs S12460, S17864, S20900, but I have to verify.

The Morley's tree, if run completely, would be useful also to understand the position of the S SNPs, many resulted unreliable because present everywhere, but many others seem good.


S12460 could be the link between my R-Z2110 and all the BritainsDNA tested for this SNP and could demonstrate the link of my Z2110* with the British Z2110* and all the subclades CTS9219. If confirmed, this could be a great discover.

Corrected version:

BritainsDNA at last has released 2000 samples of the people tested so far. I am not there, but there are many interesting samples of our haplogroup.
First of all there are 18 R-L23/S141: amongst them:
R-Z2105 and subclades:
10 are Z2110 (Z2103 is unreliable) and S12460, S17864, S20902 (these 3 SNPs are upstream also Z2105 and L277)

588: CTS9219, S3844, S8889
589: CTS9219, PF2642 (I too, but probably it is a little reliable)
590: CTS9219
592: CTS9219, CTS4122, S13125
593
595:
1556: CTS9219
1588: CTS9219
1839: CTS9219
1996: CTS3849, CTS7206, L128, S4269
---------
The following is R-L23 (xL277, Z2109, Z2110, PF7580)
594: Z2105*, S7721
There is 1 R-L277
1928: S334/L277
There are 5 R-L51 (Z2113, Z2118)
584
585: P15
586: P15
587
591: S1157, S1161, S1260, S3282, S8889
There is 1 R-L11
583: S128/P311

16 are R-M269: amongst them
R1b-S1194: 569-582, 1626, 1944: amongst them R-S1196: 571, 574,577,579,581,582.

P.S As to my data: I have a no call in S17864. "S20902 AG positive".

Rathna
03-05-2014, 01:44 AM
The positions of my SNPs are these:
PF2642=13,210,064
PF7499=14,984,657
S10358=7,568,055
S12460=9,762,847
S13077=10,036,994
S3023=4,190,976
S3530=CTS111=2,736,407
S629=21,691,570
S6814=14,326,011
S8628=3,713,309
S8670=3,715,431
S8706=3,717,921
S8714=3,718,514
S8726=3,718,895
Z612=17,509,602

P.S. The mutation S17864, where I have a no_call, but which is linked for Linkage disequilibrium to the other two (S12460, S20902) and I thought upstream Z2105, is Y16,050,529 from T to G. The paper of Rootsy et al on the Levites R1a gives it downstream Z2103/Z2104/Z2105/Z2107.
It would be very interesting because from Chromo2 it would seem that also L277 would be downstream, but of course something doesn't fit.
Of course I lacked to publish S20902= Y18,383,837.

Rathna
03-07-2014, 05:25 PM
Good to know that this SNP is on the same plane of Z2110 in the smal's tree:

16050529 S17864 S17864 SNP T G

Rathna
03-07-2014, 05:36 PM
It would be very interesting because from Chromo2 it would seem that also L277 would be downstream, but of course something doesn't fit.


L277 is negative. Everything OK.

Joe B
03-10-2014, 04:49 AM
How is BritainsDNA Chromo 2 doing with SNP coverage for Z2103/Z2105 haplotypes that are not Z2110/CTS7822+? Or is it too early to tell?

Rathna
03-10-2014, 08:35 AM
How is BritainsDNA Chromo 2 doing with SNP coverage for Z2103/Z2105 haplotypes that are not Z2110/CTS7822+? Or is it too early to tell?
For what I know Chromo2 doesn't test any of these SNPs downstream Z2105 till Z2109 and CTS7763, CTS8966, probably because these intermediate SNPs weren't important when Jim Wilsom designed Chromo2. Now they are important for our haplogroup. Of course only Big Y or Full Y could say something about this, but Chromo2 could have said something about the three SNPs I put on the same plane of Z2105 and above all about my PF, S SNPs and Z612 not collocated so far.
Otherwise we should test Big Y or Full y. But to test one SNPs after another risks to be more expensive and not resolutive.

Joe B
03-10-2014, 05:39 PM
For what I know Chromo2 doesn't test any of these SNPs downstream Z2105 till Z2109 and CTS7763, CTS8966, probably because these intermediate SNPs weren't important when Jim Wilsom designed Chromo2. Now they are important for our haplogroup. Of course only Big Y or Full Y could say something about this, but Chromo2 could have said something about the three SNPs I put on the same plane of Z2105 and above all about my PF, S SNPs and Z612 not collocated so far.
Otherwise we should test Big Y or Full y. But to test one SNPs after another risks to be more expensive and not resolutive.
On the other hand, waiting for these companies to get everything on one test is risky too. Sanger sequencing is still considered the gold stardard for SNP testing. All these other testing methods need to be validated by Sanger sequencing.

A main pillar of the scientific method is replication. The highest degree of confidence is replicated data with a convergence of evidence from different sources, consilience. That's how we figured out that the Z2103 primer on Chromo 2 was not working.

To get Z2110/CTS7822 on the ISOGG tree, SNP array results need to be validated by Sanger sequencing. My Z2110- can be part of the application.

Long before Chromo 2, a certain Tuscan was a big advocate for testing "all the Z's" and sensed they may be phylogenetically important. Hopefully, the next generation of SNP array tests will do a better job with our subclade.

CTS7763, CTS8966 are interesting and an individual from Turkey tested positive via Geno 2.0. Glad to see Chromo 2 has primers for them too.

Rathna, thanks for the great phylogenetic information you provide about our subclade.

P.S. The cost of targeted SNP testing is very reasonable. I've only spent about half the cost of a SNP array test so far.

Rathna
03-10-2014, 06:10 PM
CTS7763, CTS8966 are interesting and an individual from Turkey tested positive via Geno 2.0. Glad to see Chromo 2 has primers for them too.


164226, Garabed Kassabian, ~ 1850 ~1950, Konya, Turkey
The Turk is actually an Armenian from his surname. We always find Armenians, and perhaps "icebreaker" is right in saying that they are the most tested around the Caucasus, but we'll answer our questions when we discover where they came from, whether from Caucasus or from the Balkans, where their language brings us. And perhaps you know that in my theory Balkan people came out from the Italian Refugium, or North Adriatic if you like.
Anyway your Z2105* is interesting and could be linked to a North European ancient diffusion from the same Refugium. We'll see next, but I am afraid that we all shall do a Full Y for knowing that.

P.S. No doubt that Armenians came from the Balkans. Who hasn't linguistic studies in his curriculum may follow this conference on "Dienekes' Anthropology blog":

The place of the Armenian language in the Indo-European family

TigerMW
03-10-2014, 09:59 PM
I don't think a new tree is needed. Either Z2103 is really negative in your sample and it is unstable due to a back mutation (unlikely) or the chip has an issue with this SNP and you are really Z2103+ (likely).

I've found this problem for two of my derived SNPs. Both Geno 2 and Chromo 2 misreads them for some reason. Thomas Krahn and David Reynolds put them on the Geno 2 blacklist long ago. I think this level of Illumina technology has some challenges so a number of SNPs have to be suspect. Hopefully, the HiSeq2000 Illumina stuff has more reliable technology. In any event, I can see why Thomas Krahn recommends Sanger sequencing.... so I second Joe B's comments.

Rathna
03-11-2014, 05:04 AM
I've found this problem for two of my derived SNPs. Both Geno 2 and Chromo 2 misreads them for some reason. Thomas Krahn and David Reynolds put them on the Geno 2 blacklist long ago. I think this level of Illumina technology has some challenges so a number of SNPs have to be suspect. Hopefully, the HiSeq2000 Illumina stuff has more reliable technology. In any event, I can see why Thomas Krahn recommends Sanger sequencing.... so I second Joe B's comments.

Of course we now know that Z2103 in Chromo2 is unreliable, but after the publication of the 1999 people tested, and some other SNPs are unreliable, but I'd say very few amongst the about 15,000 tested ones. I'd say that the link costs-benefits is very good, because a SNPs costs like a grain of sands as to 35, 39 or 49 $ of FTDNA and Yseq. Having we a "phylogeny", we may understand when a SNP is reliable and my Z2103, as I said in my letters, wasn't relevant, having I Z2105, Z2109, Z2110 positive. In Chromo 2 are reliable also difficult SNPs like S334/L277 and so on (I paid 49$ for Marchesi c/o FTDNA, and, if my money were c/o BritainsDNA, I could have tested him for 15,000 SNPs with a little more).
For the linkage disequilibrium we may also understand the status of some no_calls, like my S17864/Y16050529.

Rathna
03-28-2014, 06:34 PM
We are always waiting for L277 test of Mattoli from 1.17.2014. Anyway it seems that his haplotype is deeply rooted in Italy:

B5QG9 Mattoli Bevagna, Umbria, Italy
12 26 14 11 11 15 12 12 13 12 15 27 15 9 10 11 11 26 15 19 29 15 16 16 18 11 11 19 23 16 15 19 18 35 37 13 12

ZBBBK Marks Italy
12 26 14 10 12 14 12 12 13 12 15 27

U6R94 Contrisciane Castellalto, Abruzzo, Italy
12 26 14 11 11 14 12 12 12 12 14 27

Rathna
04-10-2014, 03:31 AM
We are always waiting for L277 test of Mattoli from 1.17.2014. Anyway it seems that his haplotype is deeply rooted in Italy:

B5QG9 Mattoli Bevagna, Umbria, Italy
12 26 14 11 11 15 12 12 13 12 15 27 15 9 10 11 11 26 15 19 29 15 16 16 18 11 11 19 23 16 15 19 18 35 37 13 12

ZBBBK Marks Italy
12 26 14 10 12 14 12 12 13 12 15 27

U6R94 Contrisciane Castellalto, Abruzzo, Italy
12 26 14 11 11 14 12 12 12 12 14 27

We are waiting for Mattoli's test for L277 from FTDNA from 17.1.2014, but the closest haplotype to him, Marks W2V9F, is sharing his 23andMe with me and he has been tested L277+. Thus bet won. I think I'll be able to demonstrate also that this Ashkenazi Jew derives his Y from a person who lived in Italy around BSQG9 (Mattoli) and PX2JB, an Anonymous from Pomigliano d'Arco (Naples).

brygian
04-10-2014, 07:13 PM
To get Z2110/CTS7822 on the ISOGG tree, SNP array results need to be validated by Sanger sequencing. My Z2110- can be part of the application.

How much does a test like this cost? Where could I take one if that would help with the application? Has anybody with CTS9219 ever had such a test?

Joe B
04-10-2014, 08:24 PM
How much does a test like this cost? Where could I take one if that would help with the application? Has anybody with CTS9219 ever had such a test?
Hi bygian,
The YSEQ DNA Origins Project (http://www.yseq.net/) is the only place at this time to order SNPs Z2110/CTS7822 (http://shop.yseq.net/product_info.php?manufacturers_id=34&products_id=172) or CTS9219 (http://shop.yseq.net/product_info.php?manufacturers_id=34&products_id=678). The price is $35.00 per SNP ordered plus shipping. It's a dry sample so international postal shipping should be simple. Turn around time should be very fast too. Weeks instead of months for results.
I'm not sure if anybody has comfirmed CTS9219 by Sanger sequencing yet.
From ISOGG Ybrowse:
ISOGG YBrowser CTS9219 http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/?name=ChrY%3A18755279..18755279
CTS9219 Details http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse_details/chrY?ref=ChrY;start=18755279;end=18755279;name=CTS 9219;class=Sequence;feature_id=50344;db_id=chrY%3A database

Name: CTS9219
Type: snp
Source: point
Position: ChrY:18755279..18755279 (+ strand)
Length: 1
ISOGG_haplogroup: R1b1a2a
YCC_haplogroup: Approx. hg: R1b-L23
allele_anc: G
allele_der: A
comments: Syn. with CTS7822
count_derived: 0
count_tested: 0
mutation: G to A
primer_f: CTS9219_F GGCCATAAATGGGCAGG
primer_r: CTS9219_R CTGGCAAGACAGGACACCA
ref: Chris Tyler-Smith (2011)
primary_id: 50344
gbrowse_dbid: chrY:database
It would be pretty neat to see CTS7822/Z2110 and CTS9219 on the ISOGG tree.

Rathna
04-11-2014, 07:57 AM
U6R94 Contrisciane Castellalto, Abruzzo, Italy
12 26 14 11 11 14 12 12 12 12 14 27

Seen that after my post the place of origin on Ysearch has been rightly corrected in "Castellalto", also the original Italian surname should be : Contrisciani.

brygian
04-11-2014, 06:49 PM
Is ISOGG going to automatically get the data from YSEQ or how does it work?

Joe B
04-12-2014, 12:15 AM
Is ISOGG going to automatically get the data from YSEQ or how does it work?
Good questions. Hopefully someone with experience submitting SNPs to ISOGG will give us some advise....please. There was some discussion of a standard form.
The ISOGG Listing Criteria (http://www.isogg.org/tree/ISOGG_SNP_Requirements.html) requires a third party(one of us) to make a SNP submission for phylogenetic tree(cladogram) placement.
YSEQ has a general group that you can join to make your results reviewable. We can create one for the R1b early subclades very easily too. The bottom line is the data will be available to the ISOGG committee for review.
We are very fortunate to have Bulgarian delegation join in.

GTC
04-12-2014, 12:53 AM
Good questions. Hopefully someone with experience submitting SNPs to ISOGG will give us some advise....please. There was some discussion of a standard form.
The ISOGG Listing Criteria (http://www.isogg.org/tree/ISOGG_SNP_Requirements.html) requires a third party(one of us) to make a SNP submission for phylogenetic tree(cladogram) placement.
YSEQ has a general group that you can join to make your results reviewable. We can create one for the R1b early subclades very easily too. The bottom line is the data will be available to the ISOGG committee for review.
We are very fortunate to have Bulgarian delegation join in.

I gather that a draft of new ISOGG submission/listing rules is currently under review among the ISOGG administrators.

Joe B
04-12-2014, 02:08 AM
I gather that a draft of new ISOGG submission/listing rules is currently under review among the ISOGG administrators.Hope that doesn't slow things up as CTS7822/Z2110>CTS9219 are past due for submission. Those rules may be under review for a while if they are comparing the different testing methods.
With data from the 1000 Genomes Project, Geno 2.0, Chromo 2 and Big Y, it shouldn't take much validation by Sanger sequencing. Is the preponderance of data for CTS7822/Z2110>CTS9219 close enough for "Provisional BP" placement right now?
Some ISOGG submission/listing rules discussion.
http://www.anthrogenica.com/showthread.php?2207-Submitting-SNP-placment-requests-to-ISOGG
http://www.anthrogenica.com/showthread.php?791-R1b-L21-Phylogeny-%28SNP-based-family-tree%29&p=32018&viewfull=1#post32018


Where could I take one if that would help with the application? We will have to look at your STRs to make sure you meet the ISOGG criteria (http://www.isogg.org/tree/ISOGG_SNP_Requirements.html). Hope so.
iv. If 74 markers (or fewer) are compared, the minimum genetic distance to meet the diversity requirement is 7.
v. If 75 (or more) markers are compared, the diversity requirement is a minimum of 10%, computed by dividing the genetic distance by the number of markers compared, and rounding to the nearest integer value.



:beerchug: To GTC for moderating

brygian
04-12-2014, 09:45 AM
If I have understood the guidelines for submission, the following prerequisites have to be met:

1. At least two persons must have tested positive. Do we have a second CTS7822 or CTS9219 positive person with Sanger sequencing results?

2. STRs need to be provided. As of now I have just 25 STRs exposed at FTDNA but am going to order an upgrade to Y111 next week or so. Will this solve the STR issue?

3. The current ISOGG tree lists only CTS1078/Z2103, Z2105. If I interpret the template correctly, the link of the subgroup to the super group need to be proven. Does this mean that I have to test Z2103 or Z21005 and all the SNPs downstream to CTS9219? In that case I don't find all of these SNPs at YSEQ http://shop.yseq.net/index.php?manufacturers_id=34

Pillar_of_fire
04-12-2014, 10:18 AM
There is BIG Y for N112116 --> CTS7822+ and CTS9219- and Y67

brygian
04-12-2014, 10:34 AM
There is BIG Y for N112116 --> CTS7822+ and CTS9219- and Y67

As far as I know Big Y utilizes next generation sequencing and not Sanger sequencing. Isn't that a problem?

Pillar_of_fire
04-12-2014, 12:19 PM
CTS7822 is not yet available for order at FTDNA.

eastara has submitted requeste to be added - see post
http://eng.molgen.org/viewtopic.php?f=85&t=1480

Joe B
04-12-2014, 04:14 PM
CTS7822 is not yet available for order at FTDNA.

eastara has submitted requeste to be added - see post
http://eng.molgen.org/viewtopic.php?f=85&t=1480Thank eastara for requesting CTS7822/Z2110 for addition to the FTDNA SNP menu. It's critical that FTDNA make this SNP available in order to get adequate numbers tested. Vince and Mike made the Z2110/CTS7822 SNP request last fall and FTDNA has done nothing to this point. Let me qoute myself from last November.

Just wanted to say thanks to Vince T. and Mike for responding to our Z2110/CTS7822 request. They responded promptly last week. Project Managers do matter.
Hopefully it is not out of school to say that Vince mentioned some issues with the Z2110 region and Sanger sequencing when it was looked at last year. Thanks for sharing that.
Vince also mentioned something about Z2106-Z2110 being near or around L277.1 and wouldn't we like to find out. Let's hope these SNPs become a routine part of the next round of SNP array testing. It looks like Chromo 2 test for them now.
Whatever the outcome of your inquiries with FTDNA thanks looking at Z2110.
Four months and four SNP tests from YSEQ not offered by FTDNA. Why can't FTDNA do that unless they don't want to because of business reasons?

Joe B
04-12-2014, 04:59 PM
As far as I know Big Y utilizes next generation sequencing and not Sanger sequencing. Isn't that a problem?
The Big Y and other NGS data should be vital to the data package that is submitted. Because NGS and SNP array testing are new, the results need to be validated. That's true for any technology. Sanger sequencing is the gold standard, but not always because of the difficulties in sequencing some regions. The advantage SNPs CTS7822/Z2110 and CTS9219 have right now are results from multiple testing methods. We just about have consilience and hopefully ISOGG will take that under consideration.

If I have understood the guidelines for submission, the following prerequisites have to be met:

1. At least two persons must have tested positive. Do we have a second CTS7822 or CTS9219 positive person with Sanger sequencing results?

2. STRs need to be provided. As of now I have just 25 STRs exposed at FTDNA but am going to order an upgrade to Y111 next week or so. Will this solve the STR issue?

3. The current ISOGG tree lists only CTS1078/Z2103, Z2105. If I interpret the template correctly, the link of the subgroup to the super group need to be proven. Does this mean that I have to test Z2103 or Z21005 and all the SNPs downstream to CTS9219? In that case I don't find all of these SNPs at YSEQ http://shop.yseq.net/index.php?manufacturers_id=34
I don't think you will have to test for Z2103 and Z2105 since we have other kits that have proven that Z2110/CTS7822 are downstream. FTDNA has Z2103 and Z2105 available. Someone would have to make a request for them at YSEQ. Thomas Krahn could probably make the Z2103 and Z2105 primers in his sleep.

Your STR upgrade to Y-111 is awesome. Platinum level is more than good enough. Thanks!

Only one has admitted to testing for CTS7822/Z2110 by Sanger Sequencing. Wonder who that is?
CTS7822 Details (http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse_details/chrY?ref=ChrY;start=17684699;end=17684699;name=CTS 7822;class=Sequence;feature_id=45287;db_id=chrY%3A database)
ISOGG YBrowse CTS7822/Z2110 (http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/?name=ChrY%3A17684699..17684699)

Rathna
04-13-2014, 11:10 AM
I let you note that this sample from Poland of CTS7822+, CTS9219+, with DYS459a=8 and DYS446=14, could be the intermediate haplotype between the Western/Eastern European CTS9219+ and the "Balkan cluster" (it too CTS9219+), which had the RecLOH in DYS385 from 11-14 to 11-11.

N14933 Walenty Straszewski, b. 1731, Waldowo Szlacheckie Poland R1b1a2a
12 24 14 11 11-14 12 12 11 13 13 29 15 8-10 11 11 25 15 19 31 14-15-15-16 11 11 19-23 15 15 19 19 36-38 12 12 11 9 15-16 8 10 10 8 10 11 12 23-23 16 10 12 12 16 8 13 21 21 14 12 11 13 11 11 12 12

brygian
04-13-2014, 05:07 PM
I let you note that this sample from Poland of CTS7822+, CTS9219+, with DYS459a=8 and DYS446=14, could be the intermediate haplotype between the Western/Eastern European CTS9219+ and the "Balkan cluster" (it too CTS9219+), which had the RecLOH in DYS385 from 11-14 to 11-11.

N14933 Walenty Straszewski, b. 1731, Waldowo Szlacheckie Poland R1b1a2a
12 24 14 11 11-14 12 12 11 13 13 29 15 8-10 11 11 25 15 19 31 14-15-15-16 11 11 19-23 15 15 19 19 36-38 12 12 11 9 15-16 8 10 10 8 10 11 12 23-23 16 10 12 12 16 8 13 21 21 14 12 11 13 11 11 12 12

DYS446=14 seems to be common to all CTS9219+. https://drive.google.com/file/d/0BwfJVM510qocQng4c1p2NExGcTA/edit?usp=sharing

Joe B
04-17-2014, 07:51 PM
DYS446=14 seems to be common to all CTS9219+. https://drive.google.com/file/d/0BwfJVM510qocQng4c1p2NExGcTA/edit?usp=sharingDYS446=14 and CTS9219+ compared to DYS446=13 or 15 for CTS7822/Z2110+, CTS9219- is an interesting observation. DYS446=14 is seen with L584 and L277 too, so it's usefulness will be limited to Z2110/CTS7822 folks. STRs continue to surprise so with the low sample counts, we will have to see if DYS446=14 stays true for R1b>M269>L23>Z2103>Z2110/CTS7822>CTS9219.
The Polish FamilyTree DNA Project (https://www.familytreedna.com/public/polish/default.aspx?vgroup=polish&section=ycolorized) has a section towards the end of the Y-DNA Colorized Chart called R1b1a2a1 (L23+) - L23EE Type, Z2103+ Predicted that look like prime CTS9219 candidates. Also check out the Oziemblowski & Odrowaz DNA Surname Project (https://www.familytreedna.com/public/oziemblowski/default.aspx?section=ycolorized), Probasco/Bartoszewski/Bartos DNA Study (https://www.familytreedna.com/public/probasco-bartoszewski-bartos/default.aspx?section=yresults), Robbins DNA Project (https://www.familytreedna.com/public/robins/default.aspx?section=ycolorized) and Blair DNA Project (https://www.familytreedna.com/public/blair/default.aspx?section=yresults) as they may have good candidates for testing CTS9219.

Mike W did us a big favor compiling and analyzing data on these more rare R1b subclades. It's worth a look.

I maintain a R1b-Early_haplotypes spreadsheet of all the confirmed haplotypes that I can find from public projects. Its found under the Links section of the R1b-YDNA Yahoo group under "Haplotype Data for R1b Early Branches." The Links section is under the More drop down menu arrow on the main page.
http://groups.yahoo.com/groups/R1b-YDNA/
http://www.anthrogenica.com/showthread.php?1469-R1b-Early-Subclades-Haplotypes-Spreadsheet

Joe B
04-25-2014, 03:48 PM
The new FTDNA tree recommends/predicts an incorrect SNP for my haplotype L23. YSC0000072 in haplogroup J. This SNP is also known as PF6426 which is listed as haplogroup R.

It may be best to wait until the dust settles on this new FTDNA tree and stick with smal's very accurate tree from January. http://www.anthrogenica.com/showthread.php?1727-R1b-phylogeny&p=26401&viewfull=1#post26401

ISOGG Y Browse
http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/?name=ChrY%3A7766712..7766712
Name: YSC0000072
Type: snp
Source: point
Position: ChrY:7766712..7766712 (+ strand)
Length: 1
ISOGG_haplogroup: not listed
YCC_haplogroup: Not verified (J-L147)
allele_anc: C
allele_der: T
comments: Found in a hg J-L147 person (454 Y enrichment)
count_derived: 2
count_tested: 2
mutation: C to T
primer_f: TBD
primer_r: TBD
ref: Thomas Krahn (FTDNA)
primary_id: 14411
gbrowse_dbid: chrY:database

Name: PF6426
Type: snp
Source: point
Position: ChrY:7766712..7766712 (+ strand)
Length: 1
ISOGG_haplogroup: not listed
YCC_haplogroup: Approx. hg: R
allele_anc: T
allele_der: C
comments: Extracted from genome study of Sardinian samples
count_derived: 0
count_tested: 0
mutation: T to C
primer_f: TBD
primer_r: TBD
ref: Paolo Francalacci (2011)
primary_id: 14410
gbrowse_dbid: chrY:database

seferhabahir
04-25-2014, 04:03 PM
The new FTDNA tree recommends an incorrect SNP for haplogroup L23. YSC0000072 in haplogroup J. This SNP is also known as PF6426 which is listed as haplogroup R.


Even worse, my cousin who is in the PF7558/PF7562/PF7563 group of people (presumed L150+ L23-) is now categorized as having R-YSC0000072 as his Y-DNA terminal SNP identification. They still list this as underneath L23 and still equate L150 with L23 when we have all shown that this is probably not the case and that L150 is unreliable and even it it were, it is probably above L23. I'm sure their server will crash any minute now, with all the people logging in to see their new tree and Y-DNA designations. I'm sure they will get it all ironed out one of these days, but I don't think it will be soon. I give them kudos for trying, though.

brygian
04-25-2014, 04:19 PM
They have put eight SNPs below CTS9219. They are not there on smal's tree. Any comments on this?

Joe B
04-25-2014, 04:28 PM
They have put eight SNPs below CTS9219. They are not there on smal's tree. Any comments on this?Thanks B, Could you please list those SNPs, they may only be visible to your R1b-CTS9219 haplogroup. They need to be verified as belonging to the correct haplogroup.

Careful, smal is capable of drowning us in SNPs.:biggrin1:

brygian
04-25-2014, 04:44 PM
Thanks B, Could you please list those SNPs, they may only be visible to your R1b-CTS9219 haplogroup. They need to be verified as belonging to the correct haplogroup.

Carefull, smal is capable of drowning us in SNPs.:biggrin1:

The SNPs in questions are CTS11767 (with CTS9230, CTS7959 and CTS9906), L25, CTS9940, PF3928, F2610, CTS1039, CTS2791 and CTS8563. I checked my Geno 2.0 raw data and I have been tested for all of these and since I am not reported to be positive on FTDNA, I assume that I am negative for these.

smal
04-25-2014, 05:31 PM
You can congratulate me and many others. We are now R-M73 :( But there are good news. It is now possible to order some interesting SNPs.

Joe B
04-25-2014, 06:13 PM
You can congratulate me and many others. We are now R-M73 :( But there are good news. It is now possible to order some interesting SNPs. Is one of those interesting SNPS M269 for you? Does this mean R-M73 will be in your next R-Z2103 tree?
There could be some wild and crazy SNPs recommended if this is based just on 37 STRs for the R1b-Z2103 haplogroup.

Joe B
04-25-2014, 07:21 PM
The SNPs in questions are CTS11767 (with CTS9230, CTS7959 and CTS9906), L25, CTS9940, PF3928, F2610, CTS1039, CTS2791 and CTS8563. I checked my Geno 2.0 raw data and I have been tested for all of these and since I am not reported to be positive on FTDNA, I assume that I am negative for these.Thanks for listing those SNPs. You are probably right and negative for those SNPs from Geno 2.0. A good way to get information on a SNP is the ISOGG Y Browser (http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/). Just type in a SNP like L25 in the Landmark or Region box and hit search. Near the bottom, the different SNP names will appear. L25, PF5345 and S399 in this case. If you click one of the SNPs listed, the SNP detail will appear. Turns out that PF5345 is ISOGG_haplogroup: J2a1h2. Confused, so am I.
http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/
http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse_details/chrY?ref=ChrY;start=19136822;end=19136822;name=PF5 345;class=Sequence;feature_id=56446;db_id=chrY%3Ad atabase

This is from earlier in the year.

ISOGG SNP Compendium - Z2110/CTS7822
SNP Name(s).. GRCh37 Y-Pos (hg19).. Mutation

CTS7822 Z2110... 17684699................ A->T
CTS9219............ 18755279................ G->A
Future Research
CTS7959............ 17764622................. A->T
CTS9230............ 18760768................. G->T
CTS11767.......... 23257041................. G->T

ISOGG SNP Compendium Spreadsheet/Y-DNA SNP Index - 2014 (http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html)

brygian
04-25-2014, 07:53 PM
Thanks for listing those SNPs. You are probably right and negative for those SNPs from Geno 2.0. A good way to get information on a SNP is the ISOGG Y Browser (http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/). Just type in a SNP like L25 in the Landmark or Region box and hit search. Near the bottom, the different SNP names will appear. L25, PF5345 and S399 in this case. If you click one of the SNPs listed, the SNP detail will appear. Turns out that PF5345 is ISOGG_haplogroup: J2a1h2. Confused, so am I.
http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/
http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse_details/chrY?ref=ChrY;start=19136822;end=19136822;name=PF5 345;class=Sequence;feature_id=56446;db_id=chrY%3Ad atabase

This is from earlier in the year.

I checked my Geno 2.0 results for those markers in the ISOGG Y Browser and I am negative. L25 (http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse_details/chrY?ref=ChrY;start=19136822;end=19136822;name=L25 ;class=Sequence;feature_id=56447;db_id=chrY%3Adata base) is J2a1h2.

Interestingly, I am negative for PF7585 which is in between L23 and Z2110 (for which two I am positive) on smal's tree.

brygian
04-25-2014, 07:56 PM
You can congratulate me and many others. We are now R-M73 :( But there are good news. It is now possible to order some interesting SNPs.

They have also changed the shorthand nomenclature. I was R1b1a2a1 but now I am R1b1a1a4a.

Geolocke
04-25-2014, 08:54 PM
My terminal SNP remains at M269, however FT-DNA is recommending 2 SNP upgrades, one for L23 and the other for CTS7822 (Z2110). The new branches below M269 are spread out so far apart in the tree that I got tired of scrolling up and down, so I created a condensed version of the new branches below M269. After reviewing the condensed tree, there are three things that became apparent to me.

1) There is a new SNP below P312 and U106. Both of these are required to be tested Negative as one of the conditions of membership in the HT35 new project. I wonder if the inclusion of this new SNP (CTS4528) will change anything in that project.

2) I have tested positive for Z2103, but I don't see Z2103 or Z2105 in the new Y-tree. Does CTS7822 (Z2110) supersede those SNPs?

3) This morning when I checked my place on the new Y-Tree, FT-DNA had only recommended 1 new SNP upgrade (L23) but this afternoon when I went back to look again, FT-DNA had included the second suggestion (CTS7822). So I'm wondering if there is some on-going analysis or refinement of the Tree even as we all log in and check ourselves out.

At this point I'm inclined to wait a day or two before ordering any upgrades through the sale, just to see if any more suggestions pop up. Comments or suggestions are welcome. I can't seem to insert or attach the picture of my condensed Y-tree below M269. if anyone is interested in seeing it, drop me a note and I'll forward it to you.

-geo
M173+, M269+, M343+, M207+, P25+, M269+, Z2103+, P107-, U106-, U152-, U198-, P312-, P66-, SRY2627-, M222-, M37-, M65-, M73-, M18-, M126-, M153-, M160-

Joe B
04-25-2014, 09:35 PM
My terminal SNP remains at M269, however FT-DNA is recommending 2 SNP upgrades, one for L23 and the other for CTS7822 (Z2110). The new branches below M269 are spread out so far apart in the tree that I got tired of scrolling up and down, so I created a condensed version of the new branches below M269. After reviewing the condensed tree, there are three things that became apparent to me.

1) There is a new SNP below P312 and U106. Both of these are required to be tested Negative as one of the conditions of membership in the HT35 new project. I wonder if the inclusion of this new SNP (CTS4528) will change anything in that project.

2) I have tested positive for Z2103, but I don't see Z2103 or Z2105 in the new Y-tree. Does CTS7822 (Z2110) supersede those SNPs?

3) This morning when I checked my place on the new Y-Tree, FT-DNA had only recommended 1 new SNP upgrade (L23) but this afternoon when I went back to look again, FT-DNA had included the second suggestion (CTS7822). So I'm wondering if there is some on-going analysis or refinement of the Tree even as we all log in and check ourselves out.

At this point I'm inclined to wait a day or two before ordering any upgrades through the sale, just to see if any more suggestions pop up. Comments or suggestions are welcome. I can't seem to insert or attach the picture of my condensed Y-tree below M269. if anyone is interested in seeing it, drop me a note and I'll forward it to you.

-geo
M173+, M269+, M343+, M207+, P25+, M269+, Z2103+, P107-, U106-, U152-, U198-, P312-, P66-, SRY2627-, M222-, M37-, M65-, M73-, M18-, M126-, M153-, M160-
CTS7822/Z2110 is down stream from Z2103. The recommended SNP's from the new FTDNA tree are crazy right now. Z2103 and Z2105 were too new for the Geno 2.0 test and did not make the new tree. Getting Locke and Bennett families to test for CTS7822/Z2110 would be a good thing to rule in or out. CTS7822/Z2110 was not in the advanced SNP catalog as of a few minutes ago. So it's Geno 2.O, Chromo 2, Big Y or as a single SNP test at YSEQ. As far as I know, you are a member of the R1b-L23 FTDNA haplogroup by testing Z2103+ and that makes you are a member of the HT35 project. Best proof there is.
R1b-M269>L23>L150>Z2103>Z2105>Z2110/CTS7822>CTS9219

Geolocke
04-25-2014, 10:21 PM
Thanks Joe. FT-DNA has CTS7822 available as a SNP for testing right on the new Y-Tree. I am assuming this is the same as Z2110/CTS7822, but is that a correct assumption?

Joe B
04-25-2014, 10:37 PM
Thanks Joe. FT-DNA has CTS7822 available as a SNP for testing right on the new Y-Tree. I am assuming this is the same as Z2110/CTS7822, but is that a correct assumption?Yes it is. Here is the R1b-Z2103 made by smal that most of us are working off of. It includes data from several sources. http://www.anthrogenica.com/showthread.php?1727-R1b-phylogeny&p=26401&viewfull=1#post26401 There is nothing to say that you will be CTS7822+, it is just turning out to be an important new subclade for R1b-Z2103 in Europe. You may be close to 108347 Seymour who is CTS7822+, Geno2.0 and L150-, L23+, Z2103+, Z2105+, L277-, L584-. He's the best proof to ignore L150.
If CTS7822 turns out to be available for single SNP testing, that would be important to know.

Geolocke
04-25-2014, 10:51 PM
Joe, I've put a copy of my Condensed new Y-tree below M269 on a shared G-Drive. It can be accessed at the following link. Take a look and let me know if I am seeing things correctly. Note: my sketch only shows the new SNPs below M269. I excluded all existing SNPs except for the one relevant to the conditions for HT35.

https://drive.google.com/file/d/0ByEiKHkVDZBBLXZIOHpSVHlxWmM/edit?usp=sharing

-geo

Joe B
04-25-2014, 11:47 PM
Joe, I've put a copy of my Condensed new Y-tree below M269 on a shared G-Drive. It can be accessed at the following link. Take a look and let me know if I am seeing things correctly. Note: my sketch only shows the new SNPs below M269. I excluded all existing SNPs except for the one relevant to the conditions for HT35.

https://drive.google.com/file/d/0ByEiKHkVDZBBLXZIOHpSVHlxWmM/edit?usp=sharing

-geoThis is Goldschlager's who is Geno 2.0, Big Y and R1b-Z2105>L584+ tested. His screen shot is exacly the same as mine, except mine is in blue for ordering and has a remove button on the right. The question is can you order a single SNP(CTS7822) or does it make you order Geno 2.0?

Please enlighten me: the current FTDNA Y tree labels me as R_YSC0000072 (old one was R-L150). But the main puzzle is the L584 for which I tested +, is not shown any longer in my SNP list ? See attached the FTDNA and Morley (kit 271988) trees.

Thanks
G
http://www.anthrogenica.com/showthread.php?1586-From-R-L23-L150-to-R-PF7580-amp-L584&p=38376#post38376

Geolocke
04-26-2014, 12:53 AM
The price at the bottom of the page is the single SNP sale price, so I am assuming that Geno2 is no longer required for CTS7822.

Geolocke
04-26-2014, 01:00 AM
Luckily in our Locke Surname project we only had one individual who's hg was changed by this new tree.He had been Deep-clade tested back in 2008 and found to be R1a1a but is now listed as BT-SRY10831. His test kit now says that this is the only SNP he has tested for, so we are a bit confused. Any clue what BT stands for? It is a confusing case and we will be asking the help desk about this one.

Joe B
04-26-2014, 04:08 AM
The price at the bottom of the page is the single SNP sale price, so I am assuming that Geno2 is no longer required for CTS7822.Found all those SNPs including CTS7822/Z2110 for sale. Not sure if this was just added or I didn't see it before. Follow the little lines down to near the bottom of the tree, like you would for the ISOGG tree.
1778

Pillar_of_fire
04-26-2014, 05:15 AM
Just to share - N112116 has been identified by the new tree as R-Z47. This is an outright mistake since:

He is tested Sanger sequence : Z2105+ Z2103+ L21- U152- L584- L277-

He is tested BIG Y - he is negative for all SNP down the line L51L11P31P312 U152  - possitive only for L47

while he is positive for CTS7822

So I wrote to help desk to look into the way the results are read and haplogroups assigned.

Geolocke
04-26-2014, 12:19 PM
Joe, that's why I made my "condensed tree". It's a long scroll down to the bottom of that tree. I wish we could collapse branches in the new Y-tree like in the ISOGG tree.

smal
04-26-2014, 05:08 PM
There is virtually no information about new FTDNA branches.
1) The HG01515 sample from 1KGP is positive for CTS7822, CTS9219 and CTS11767, CTS9230, CTS7959 and CTS9906.
2) The HG01277 sample from 1KGP is positive for CTS7822 and CTS699.
3) The NA18645 sample from 1KGP is positive for CTS7763, CTS8966 and CTS2791/S2910. This is strange because the FTDNA shows CTS2791 as a subclade of CTS9219.
4) We know CTS1848 as a subclade of L584.
And I don’t find anything about PF3252, P53, L25, CTS9940, PF3928, F2610, CTS1039, CTS8563, F2107, Z1862, CTS6937, M64. Many of those SNPs were found in other haplogroups but this does not mean that they could not arise in our R1b branches.

Joe B
04-26-2014, 05:09 PM
Joe, that's why I made my "condensed tree". It's a long scroll down to the bottom of that tree. I wish we could collapse branches in the new Y-tree like in the ISOGG tree.
Geo, Thanks for helping a slow dude and everybody else figure that new system out. The main thing learned is that they have provided a whole bunch of SNPs for testing. Having CTS7822/Z2110, CTS9219, CTS699 and CTS7763 are good to have. Z2103, Z2105, L277, L584 and perhaps L943-L946 should have been moved from the advanced testing menu to the new tree for ordering. Where is PF7580?

Joe B
04-26-2014, 05:15 PM
There is virtually no information about new FTDNA branches.
1) The HG01515 sample from 1KGP is positive for CTS7822, CTS9219 and CTS11767, CTS9230, CTS7959 and CTS9906.
2) The HG01277 sample from 1KGP is positive for CTS7822 and CTS699.
3) The NA18645 sample from 1KGP is positive for CTS7763, CTS8966 and CTS2791/S2910. This is strange because the FTDNA shows CTS2791 as a subclade of CTS9219.
4) We know CTS1848 as a subclade of L584.
And I don’t find anything about PF3252, P53, L25, CTS9940, PF3928, F2610, CTS1039, CTS8563, F2107, Z1862, CTS6937, M64. Many of those SNPs were found in other haplogroups but this does not mean that they could not arise in our R1b branches.
What SNPs from the new FTDNA tree would say are worth recommending? A safe list. Like you said, many of these SNP are found in haplogroup J among others.

smal
04-26-2014, 06:00 PM
What SNPs from the new FTDNA tree would say are worth recommending? A safe list. Like you said, many of these SNP are found in haplogroup J among others.

The most interesting SNPs are CTS7822, CTS9219 and CTS7763. The CTS7822+ CTS9219- kits can be tested for CTS699. The CTS9219+ can be cheked for CTS11767. SNPs can arose independently in the J and R haplogroups but we have no examples to predict those new SNPs for STR haplotypes.

Joe B
05-02-2014, 07:03 PM
Even worse, my cousin who is in the PF7558/PF7562/PF7563 group of people (presumed L150+ L23-) is now categorized as having R-YSC0000072 as his Y-DNA terminal SNP identification. They still list this as underneath L23 and still equate L150 with L23 when we have all shown that this is probably not the case and that L150 is unreliable and even it it were, it is probably above L23. I'm sure their server will crash any minute now, with all the people logging in to see their new tree and Y-DNA designations. I'm sure they will get it all ironed out one of these days, but I don't think it will be soon. I give them kudos for trying, though.
The R1b1b2 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults) should have everybody PF7558/PF7562/PF7563 in the right group and people that should test for PF7558/PF7562/PF7563 in the _a. R1b-M269: L23- L51- L11- group. The new project trees supercede FTDNA's and should be consulted.

@seferhabahir Since you really are the one who led in this area, is PF7563 still the preferred SNP to test? It would be nice to eliminate L150 from the equation and test for PF7563 . This branch really looks interesting once L150 is gone.

seferhabahir
05-03-2014, 07:01 AM
The R1b1b2 (P312- U106-) DNA Project (https://www.familytreedna.com/public/ht35new/default.aspx?/publicwebsite.aspx%3Fsection=yresults) should have everybody PF7558/PF7562/PF7563 in the right group and people that should test for PF7558/PF7562/PF7563 in the _a. R1b-M269: L23- L51- L11- group. The new project trees supercede FTDNA's and should be consulted.

@seferhabahir Since you really are the one who led in this area, is PF7563 still the preferred SNP to test? It would be nice to eliminate L150 from the equation and test for PF7563 . This branch really looks interesting once L150 is gone.

I never did have these three SNPs Sanger tested in my cousin (his results are from Geno 2.0), but here is the advice I received from Thomas Krahn last year about them, so I would assume if someone was going to test one of them, then it should be PF7563.

"I have just designed primers for those 3 PF markers. They are on my order list. PF7563 is probably the best bet since the other two have very similar regions on the X chromosome."

When I last looked at this, my conclusion was that if someone was R-M269* then they were more than likely going to turn out to be PF7558/PF7562/PF7563. The R1b1b2 (P312- U106-) DNA Project has eliminated any reference to L150 in their new chart and now shows what I had said last year that PF7558/PF7562/PF7563 represents the branch off of M269 that has people who are not L23. It would be interesting to find out if there really are any R-M269* people at all (someone that will test negative for L23, PF7558, PF7562, PF7563).

Ogmion
06-18-2014, 01:11 AM
I am interested in what you make of this information regarding Silver 45475 and my Big Y sample compared to theirs kit 95673 FTDNA Austin but am new to the forum and am not sure how to provide an xls spreadsheet.
regards
Nick

brygian
07-16-2014, 05:29 PM
There is virtually no information about new FTDNA branches.
1) The HG01515 sample from 1KGP is positive for CTS7822, CTS9219 and CTS11767, CTS9230, CTS7959 and CTS9906.
2) The HG01277 sample from 1KGP is positive for CTS7822 and CTS699.
3) The NA18645 sample from 1KGP is positive for CTS7763, CTS8966 and CTS2791/S2910. This is strange because the FTDNA shows CTS2791 as a subclade of CTS9219.
4) We know CTS1848 as a subclade of L584.
And I don’t find anything about PF3252, P53, L25, CTS9940, PF3928, F2610, CTS1039, CTS8563, F2107, Z1862, CTS6937, M64. Many of those SNPs were found in other haplogroups but this does not mean that they could not arise in our R1b branches.

There is one person who is CTS9940+. This is kit M8867 from the Arab Tribes - Y-DNA (https://www.familytreedna.com/public/arab%20tribes/default.aspx?section=ysnp) and other projects. His data is very strange:


M181+, M112+, 50f2(P)+, CTS10362+, CTS10826+, CTS10834+, CTS109+, CTS11358+, CTS11468+, CTS11575+, CTS11716+, CTS11912+, CTS125+, CTS12632+, CTS1388+, CTS1996+, CTS2134+, CTS2179+, CTS2668+, CTS294+, CTS3186+, CTS3349+, CTS3431+, CTS346+, CTS3490+, CTS3536+, CTS3608+, CTS3609+, CTS3662+, CTS3868+, CTS3996+, CTS4364+, CTS4437+, CTS4443+, CTS4740+, CTS503+, CTS5064+, CTS5311+, CTS5318+, CTS5457+, CTS5532+, CTS5541+, CTS5552+, CTS5577+, CTS5599+, CTS5702+, CTS5884+, CTS5986+, CTS6135+, CTS623+, CTS6369+, CTS6383+, CTS6800+, CTS6907+, CTS7400+, CTS7653+, CTS7659+, CTS8243+, CTS8393+, CTS8591+, CTS8665+, CTS8980+, CTS9828+, CTS9940+, L104+, L147+, M112+, M181+, M182+, M192+, M249+, M299+, M42+, M94+, P108+, P305+, P85+, P90+, PAGES00026+, PAGES00072+, PAGES00081+, PF1016+, PF1029+, PF1040+, PF1046+, PF1061+, PF1092+, PF1097+, PF1203+, PF210+, PF212+, PF223+, PF258+, PF263+, PF272+, PF278+, PF292+, PF316+, PF325+, PF342+, PF3561+, PF500+, PF667+, PF719+, PF725+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF892+, PF937+, PF951+, PF970+, PK1+, SRY10831+, V220+, V221+, V234+, V237+, V241+, V250+, V85+, YSC0000207+, YSC0000227+, Z599+

Putting this in Morley's predictor (http://ytree.morleydna.com/predict) returns haplogroup R1b1a. FTDNA has not assigned haplogroup for this kit. The kit ID is strange too - what kind of kits start with the letter M?

brygian
07-16-2014, 09:42 PM
There is one person who is CTS9940+. This is kit M8867 from the Arab Tribes - Y-DNA (https://www.familytreedna.com/public/arab%20tribes/default.aspx?section=ysnp) and other projects. His data is very strange:

Putting this in Morley's predictor (http://ytree.morleydna.com/predict) returns haplogroup R1b1a. FTDNA has not assigned haplogroup for this kit. The kit ID is strange too - what kind of kits start with the letter M?

He has a very strange haplotype: 13 24 15 10 10-15 11 12 10 13 11 28 14 8-9 11 12 18 15 21 37 14-16-16-18 11 10 19-19 15 14 18 18 35-35 12 10 11 8 16-16 8 11 10 8 13 10 12 21-21 19 9 12 10 15 7 13 28 23 14 12 11 15 10 12 11 12

If I start entering these values in http://www.stevemorse.org/dna/hapest.php the numbers go crazy. At about 25 markers I get 100% E1b1 but adding just a couple of values more it goes back to 0% and this happens multiple times with multiple haplogroups.

smal
09-22-2014, 04:18 AM
We've updated the R1b1a2/ht35 tree on the project site (https://www.familytreedna.com/public/ht35new/default.aspx).

VinceT
01-02-2015, 06:27 AM
We've updated the R1b1a2/ht35 tree on the project site (https://www.familytreedna.com/public/ht35new/default.aspx).

Sample BDNA-583 (S8507, S12025, S15526, etc.) is actually in R-U106, confirmed by known S21+ Chromo2 testers, FGC and BigY; see also BDNA-1054 and BDNA-1060.

brygian
01-05-2015, 11:24 AM
The following two SNPs have been named and added to the ISOGG human Y-chromosome browser:

Y:16818973 (A/G) ZS5822
Y:18583831 (C/T) CTS8966

Joe B
01-05-2015, 04:52 PM
The following two SNPs have been named and added to the ISOGG human Y-chromosome browser:

Y:16818973 (A/G) ZS5822
Y:18583831 (C/T) CTS8966
SNP CTS8966 is under R1b-Z2103. What branch does ZS5822 belong to?

brygian
01-06-2015, 12:46 PM
SNP CTS8966 is under R1b-Z2103. What branch does ZS5822 belong to?

ZS5822 is below R1b1a2b PF7558, PF7562, PF7563.