L21: L159.2 and L69.4 parallel SNPs

[secherbernard]

I received an interesting mail from Thomas Krahn about L159.2 and L69.4 SNPs:

Technically the L159 test also reads the L69 allele because it is only
2bp next to it.
The order for the L69.4 marker only needs to be implemented into the
order system which gets increasingly difficult at such flipflop markers.
Maybe we should separate tests like this into a haplogroup independent
curiosity panel.

Those FTDNA customers who have a L159(.2) result can simply send me an
e-mail and ask for their L69 status for now. Please note your kit # in your request so
that it doesn't take much time to look it up.

So anybody who have been tested L21+ L159- have just to send an email to Thomas Krahn with kit number, to know if he is L69+.
For those who have already tested for L159, it is free (thanks Thomas).

Bernard

[Mikewww]

On another forum, a WTY participant said "The participant who tested L69.4 positive is from France".  Do you know if that is true?

[secherbernard]

On another forum, a WTY participant said "The participant who tested L69.4 positive is from France".  Do you know if that is true?

Yes, it is me.

Bernard

[Mikewww]

On another forum, a WTY participant said "The participant who tested L69.4 positive is from France".  Do you know if that is true?

Yes, it is me.
Bernard

Thank you for the update, Bernard.  I assumed that all of the other (than yourself) R-L21* WTY participants did not have this.

However, I've also been told that the primers changed so perhaps L69.4 was not evaluated in all of the R-L21* WTY participants.

Does anyone know anything more about that?  If you are an R-L21* WTY testee, please make sure you ask Dr. Krahn to confirm if you have L69.4+ or not or if they even know.  Of course, as noted, anyone who tested L159.2- (single SNP order) should ask Dr. Krahn to check their L69.4 status.

[Mark Jost]

I am also L69- as per Thomas K as I was L159 negative.

[vtilroe]

On another forum, a WTY participant said "The participant who tested L69.4 positive is from France".  Do you know if that is true?

Yes, it is me.
Bernard

Thank you for the update, Bernard.  I assumed that all of the other (than yourself) R-L21* WTY participants did not have this.

However, I've also been told that the primers changed so perhaps L69.4 was not evaluated in all of the R-L21* WTY participants.

Does anyone know anything more about that?  If you are an R-L21* WTY testee, please make sure you ask Dr. Krahn to confirm if you have L69.4+ or not or if they even know.  Of course, as noted, anyone who tested L159.2- (single SNP order) should ask Dr. Krahn to check their L69.4 status.

No, I do believe the primers used for L159 and L69 were always good and have provided good reads for WTY.  It was the ones that were used for the segment L226 was found on which had trouble in the past and were changed.  I can double-check the L21 WTY guys tomorrow, though - at least the ones that have their data on Finch2.

[Mikewww]

On another forum, a WTY participant said "The participant who tested L69.4 positive is from France".  Do you know if that is true?

Yes, it is me.

Are you GRC 000511 ?

[secherbernard]

Are you GRC 000511 ?

No, I am GRC 014326

Bernard

[rms2]

I understand L159.2 is more like an STR than an SNP. Is that true? What makes it an SNP then?

What of L69.4? Same thing?

[Mikewww]

Bernard posted this on another forum.  I also saw a letter where Dr. Krahn described the stability/unstability of L159.    I believe it is the same event (although parallel and separate) on the Hg I side and I think they treat it SNP-like... or technically speaking Unique Event Polymorphism(UEP)-like.  I'll look for that letter.

As you are L159+, you are L69-.
It is impossible to be L159+ and L69+ because :

In the case of L69+ the poly G is shortened from 6 to 4 bases and the
dinucleotid repeat gains one unit.
In the case of L159+ the poly G is elongated from 6 to 8 bases and the
dinucleotid repeat looses one unit.

This alignment of sequences may make this clearer:

AAACTGGGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L159+)
AAACTGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (HUGO and most others)
AAACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L69+)

[Mikewww]

I understand L159.2 is more like an STR than an SNP. Is that true? What makes it an SNP then?
What of L69.4? Same thing?

Here is the letter I was looking for it.  It is a posting by a WTY administrator.  She cites Dr. Krahn's communications.

We now have WTY results for our Leinster cluster participant, and a SNP mutation that had previously been detected in a Haplogroup I-M26 participant was also detected in our participant. Other Haplogroup I and R-L21 WTY participants have not been found positive for this SNP, so we know that there have been two parallel mutations giving rise to this SNP in the two different groups. This raises the possibility that this SNP may not be completely reliable, but Thomas Krahn says it is possible that this SNP will prove to be reliable enough to identify a branch of the Y chromosome tree. The SNP in question, L159, is in the same area as the similar SNP L69, which is also known to have been created by more than one mutation, and there is a technical explanation for a tendency toward mutations at the L69 and L159 positions that I have not had the time to review. I do recall seeing discussion of L69 on the Genealogy-DNA list, so for those who want to dig deeper right away, a search of the archives of that list should prove fruitful.

Thomas has recommended that we start by encouraging men whose haplotypes are very similar to the haplotype of our participant to order testing of the L159 SNP. I have already contacted surname project administrators for two of his closest matches, and the participant and I will discuss the possibility of recruiting one or more men of his surname to test, too. Most of our members should probably heed the advice of Thomas and see what happens with this first round of L159 tests before deciding whether to order this test for their lines.

There are a few of you that I have considered contacting to suggest testing. If you are wondering whether you may be one of these borderline cases and want to talk about testing now or later, feel free to e-mail me.

I have a message from Thomas that explains just a little about the situation with the L159 SNP, and it contains a link to more information. I will forward that message later.

[Mikewww]

I understand L159.2 is more like an STR than an SNP. Is that true? What makes it an SNP then?

What of L69.4? Same thing?

On the Beatty-Brynes forum, an Hg I guy with this L159+ commented that he felt like L159 seems reliable as a UEP.

I am in I-M26 myself, and we have tested several people both in I-M26
and other branches of I2a for the L159 SNP, and so far the results
were completely consistent and no problems with L159. But it seems to
be equivalent to M26 for us, so we haven't been focusing on it as much
as the new L160 SNP which divides I-M26 in a very interesting way.

My assessment of the information is that L69.4 is in the same boat as L159.2 as far as reliability goes.   Neither are conclusively UEP's, but I'm not sure anyone can prove anything is a UEP.   It looks like a pretty decent indicator though, at least within the confines of R-L21*.

Of course, it only looks good now because it doesn't look bad yet - our understanding of this is limited to about 15 or so haplotypes in R-L21*.

[vtilroe]

I looked at the raw sequences for L69 and L159 for the L21* guys that have their WTY data on Finch2 so far:

GRC#	Kit#	L69	L159
GRC011196	14738	G-	G+
GRC000511	14346	G-	T-
GRC007030	21869	G-	T-
GRC025666	30225	G-	T-
GRC017251	137133	G-	T-
GRC014326	E5945	G-*	T-*

Note that the forward segment for GRC014326 (Bernard's sample) is not available on Finch2, and L69 & L159 are difficult to read (slight heterozygous signal) on the reverse segment, which appears to be the majority case for all of the reverse segments.  (Actually some gave a phantom L159+ or L69+ that wasn't supported on the much clearer forward segment).  Frankly I'm a bit at a loss as to why Thomas called Bernard's L69 as T+ --- not that I want to stir up a hornet's nest here...

[secherbernard]

I looked at the raw sequences for L69 and L159 for the L21* guys that have their WTY data on Finch2 so far:

GRC#	Kit#	L69	L159
GRC011196	14738	G-	G+
GRC000511	14346	G-	T-
GRC007030	21869	G-	T-
GRC025666	30225	G-	T-
GRC017251	137133	G-	T-
GRC014326	E5945	G-*	T-*

Note that the forward segment for GRC014326 (Bernard's sample) is not available on Finch2, and L69 & L159 are difficult to read (slight heterozygous signal) on the reverse segment, which appears to be the majority case for all of the reverse segments.  (Actually some gave a phantom L159+ or L69+ that wasn't supported on the much clearer forward segment).  Frankly I'm a bit at a loss as to why Thomas called Bernard's L69 as T+ --- not that I want to stir up a hornet's nest here...

Vince,

Thomas Krahn told me that my forward sequences have been
accidentally deleted. My WTY has been re-run, and would be available next week.

Bernard

[Mikewww]

I hope Kristen S doesn't mind, but she did a nice summary of L159 results on the Beatty_Byrnes_DNA forum.  Here it is:

Summary of L159 results

We received a LOT of L159 test results this week, and we only have one more
pending. That one is for a Byrne, and since we already have 2 L159+ results
for Byrne men, I think we can guess what his result will be.

Here is a summary of L159 results relating to the project.

There are 26 L159+ results for men in the BeatyByrneMcLaughlin (Leinster
cluster) subgroup of the project. Here is a list of the surnames of the most
distant known ancestors of those men with kit numbers:

Adams N47848
Baldwin 66478
Beatty variants 3032 3055 82065 (& 42452 EDIT: MW per P.Beattie)
Brock 148922
Byrne 31911 45482
Cienfuegos-Jewett 96196
Dillon 74201
Dooley 159523
Doty 33100
Ferguson 89387
Fitzpatrick 151633
Flynn 138193
Foley N17860
Gaston N38274
Jorda n 9002
Kavanagh 92117 96585
Mackgahye (Megehee) 51942
McDonald 85603
McInvale 30554
McLaughlin 84037
Owen 85858
Robinson 95057

There is also one L159+ result for a man who was in the BeatyByrneMcLaughlin
cccg + ccgc cousins? subgroup:
Quilliam 88224
I have regrouped this Quilliam descendant.

We also have 5 L159- results for members of the BeatyByrneMcLaughlin
subgroup:
Long 112787
Long 94614
Mann 94217
Martin 100935
McConnell 141428

There is another L159- result for a man who is in the Results Pending group
as he waits for his DYS464X results. I predict that he will test 2c2g based
on the similarities between his haplotype and the haplotypes of the last 4
men listed above:
Mullins 125258

I would predict that other members of the McConnell/McDonald family of
141428 would also test negative for the L159 SNP. Those that I would predict
L159- results for are McConnell/49867, McDonald/72239, and McConnell/112904.

I have regrouped the above L159- tested and predicted men, too. Nearly all
of them have GATAH4=10 and most of the distinct surnames have DYS464c=16. They also have DYS448=19 and all but one have DYS442=12. I mention these marker values because they are not typical for the cluster as a whole.

We do have two L159- results for men who aren't in the BeatyByrneMcLaughlin
subgroup:
Ross 77904, who I moved to a new subgroup for his Ros/Mascy cluster earlier
today
Hamon 84034, the unclustered L21+ ccgg man whose results seem most similar to the BeatyByrneMcLaughlin modal haplotype

I am aware of 3 other men with L159+ results:
Downing 92891, listed in the R-L159 project
Manning 145899, listed in the R-L159 project
O'Connor N12712, listed in the R-L21 pro ject

Downing is clearly a member of the cluster, and the Manning haplotype does
show some similarity to Leinster cluster haplotypes, but the O'Connor
haplotype is very different.

We have a lot of information to chew on these days. :)

I'll add that the 3 members of the 11-13 Combo group that we know have tested L159 are all L159-
Bussey 93174
Massey 137133
Ross 77904

[Mikewww]

Is it fair to assume that the odds, are very high, like 99%, that if a person is predicted R1b1b2 AND is L159.2+ we should consider them as default L21+  ?

[R1B1]

I am the O'Connor that tested possitive to R-L159.2

My kit # should read N12172

Y-search #MPZR9
My first 25
12 24 14 10 11 14 12 12 12 13 13 29 18 9 10 11 11 25 15 19 29 15c 15c 16c 16g
 I have 67+ str's

I have a reasonable match with a Lawrence Conner / Dublin 1850
12 24 14 10 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 18 18 37 38 12 12
12 24 14 11 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12
12 24 14 11 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12

The Leinster Murphy Group have a likeness to me.
Murphy Leinster Haplotype:
12 24 14 11 11 14 12 12 12 13 13 29 19 09 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12

My 391=10 is found in both Lawrence Conner and a few in the Murphy Leinster Group.
The Group in Green http://www.pricegen.com/murphy.html

I have a 36/37 Murphy Match at FTDNA.

 

[Mikewww]

Thanks for the correction.  Are you 464x=2c2g like most of the Beatty-Byrnes Group, or are you 3c1g?

I am the O'Connor that tested possitive to R-L159.2

My kit # should read N12172

Y-search #MPZR9
My first 25
12 24 14 10 11 14 12 12 12 13 13 29 18 9 10 11 11 25 15 19 29 15c 15c 16c 16g
 I have 67+ str's

I have a reasonable match with a Lawrence Conner / Dublin 1850
12 24 14 10 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 18 18 37 38 12 12
12 24 14 11 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12
12 24 14 11 11 14 12 12 12 13 13 26 18 09 09 11 11 25 15 19 29 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12

The Leinster Murphy Group have a likeness to me.
Murphy Leinster Haplotype:
12 24 14 11 11 14 12 12 12 13 13 29 19 09 10 11 11 25 15 19 30 15 15 16 16 11 11 19 23 16 15 19 18 37 38 12 12

My 391=10 is found in both Lawrence Conner and a few in the Murphy Leinster Group.
The Group in Green http://www.pricegen.com/murphy.html

I have a 36/37 Murphy Match at FTDNA.

 

[R1B1]

I am 15c 15c 16c 16g

[vtilroe]

This has probably been noted elsewhere months ago, but Durall (U3SVK) is L21+  L69+ from his 23andMe probe, but L69 was dismissed at the time for being too "flippy", having also occurred in R1a, R-M269* and R-U152*.

[NealtheRed]

So there are now two confirmed L69+, but now you're saying the SNP is too unstable? Durall sounds French.

[vtilroe]

Durall's L69 was discovered late 2008 / early 2009 - I don't remember when exactly.  I only came across it again after scanning Adriano's 23andMe data earlier today.

L69 -- and by extension L159 -- always have been unstable, as far as using them for deep-ancestral phylogeny.  However what we are realizing is that they could be useful for bridging the gap between STR haplotypes and the more stable SNPs - which is exactly what you're discovering in the case of L159.2 and the Leinster group.

If L69.4 has a high correlation with a French cluster - well, then!

I guess the thing to do is to compare U3SVK with UE9BU, and see how well they match up.  Survey says: 47/67 match.

According to McGee's utility, the MRCA could be in the neighbourhood of 50-75 generations ago.

[secherbernard]

This has probably been noted elsewhere months ago, but Durall (U3SVK) is L21+  L69+ from his 23andMe probe, but L69 was dismissed at the time for being too "flippy", having also occurred in R1a, R-M269* and R-U152*.

That's a good news for me!! I am not, now, the only one L21+ L69+. I have written an email to Chris Durall and ask him about his paternal origine.

Bernard

[secherbernard]

This has probably been noted elsewhere months ago, but Durall (U3SVK) is L21+  L69+ from his 23andMe probe, but L69 was dismissed at the time for being too "flippy", having also occurred in R1a, R-M269* and R-U152*.

Vince,

Have you heard any thing about the DYS464X of Durall ?

I have a cccc DYS464 configuration with a 14.3 micro allele. It can be interesting to know if Durall has the same DYS464X configuration.

Bernard

[secherbernard]

If L69.4 has a high correlation with a French cluster - well, then!

I guess the thing to do is to compare U3SVK with UE9BU, and see how well they match up.  Survey says: 47/67 match.

According to McGee's utility, the MRCA could be in the neighbourhood of 50-75 generations ago.

Well, so the MRCA lived about during Roman times. It is very interesting!

Bernard