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Author Topic: Approx. hg: R-L21: L459  (Read 4725 times)
Jdean
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« on: February 05, 2011, 02:19:11 PM »

L459 was recently found in a L21 WTY participant.

This was posted on the DNA mailing list yesterday

"I just saw that L459 recently showed up on ymap.ftdna.com with
position information. Based on an analysis of 14 L21+ individuals in
1000 Genomes Project sequence data, I suspect this SNP is either very
shortly downstream of L21 or perhaps even upstream of L21...all 10 of
the L21+ individuals considered with coverage at this position seem to
be L459+."


So this could big a big one for L21 or P312*  !!!!!
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GoldenHind
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« Reply #1 on: February 05, 2011, 05:23:13 PM »

Very exciting. Maybe in a year or two FTDNA will get around to offering it.
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Jdean
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« Reply #2 on: February 06, 2011, 08:19:39 AM »

Very exciting. Maybe in a year or two FTDNA will get around to offering it.

Oh you cynic, how long did it take you to convince them to offer L238?

Looking through the posts regarding this it would appear U106 is confirmed negative, and the only other WTY participant tested for this region (R1a1a1) is also negative.

It would be handy to know the haplogroup for the reference sequence, I don’t know why they don’t provide that information as a matter of course.

As it happens we hopefully shouldn't have to wait too long for a P312 test for this SNP as there is a new P312* WTY participant, his kit hasn't been returned yet though.
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« Reply #3 on: February 07, 2011, 10:46:43 AM »

... Looking through the posts regarding this it would appear U106 is confirmed negative, and the only other WTY participant tested for this region (R1a1a1) is also negative. ...
As it happens we hopefully shouldn't have to wait too long for a P312 test for this SNP as there is a new P312* WTY participant, his kit hasn't been returned yet though.
This could be a critical SNP for P312* testing.  L21 may have found a brother.
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Jdean
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« Reply #4 on: February 07, 2011, 03:54:22 PM »

This could be a critical SNP for P312* testing.  L21 may have found a brother.

So far only L21+ people have been found with this SNP, 15 todate I think. This is leading to the suggestion that this SNP may end up being equivalent to L21, but I think that is the least likely outcome.

P312 and its subclades went of like a bomb across Europe and I find it hard to believe that the missing links for this SNP withered out whilst all the others charged off into the sunset.

At the moment P312* people look to be the most likely place to discover L549+ but assuming none of those turn up positive in the interim I shall be ordering this when it comes to market.
« Last Edit: February 07, 2011, 03:56:14 PM by Jdean » Logged

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« Reply #5 on: February 11, 2011, 11:30:40 PM »

This could be a critical SNP for P312* testing.  L21 may have found a brother.

Craig Venter (U106) genome is L459-, as is the HuGO reference sequence (P312+, L21-) and U152. The first Irishman to have his whole genome sequenced is L21+ M222- L459+. A Walk the Y member with the South Irish genotype is also L459+. The previous WTY participant with South irish genotype was not tested for L459. I understand that another 10 L21+ males are estimated to be L459+ but understand that these are not confirmed results.  Their genotypes were not disclosed, so the only firm ground so far seems to be that South Irish genotype males are the most likely to be L459+
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Jdean
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« Reply #6 on: February 12, 2011, 07:41:21 AM »

Craig Venter (U106) genome is L459-, as is the HuGO reference sequence (P312+, L21-) and U152. The first Irishman to have his whole genome sequenced is L21+ M222- L459+. A Walk the Y member with the South Irish genotype is also L459+. The previous WTY participant with South irish genotype was not tested for L459. I understand that another 10 L21+ males are estimated to be L459+ but understand that these are not confirmed results.  Their genotypes were not disclosed, so the only firm ground so far seems to be that South Irish genotype males are the most likely to be L459+

I don't know the haplogroup of the reference sequence used in the WTY (or indeed if they only use one), but it's definitely not exclusively HuGO. The sequence used to compare my U152 test was also U152 neg as was the one used for L21, the reference for P312 was positive though.

It was reported on DNA-Forum that Greg Magoon has found 13 L21+ L459+ individuals in the 1000 Genomes Project. So far no L21- L459+ or L21+ L459- have been found but of course the no. of people tested for this region are very small todate.
« Last Edit: February 12, 2011, 07:48:00 AM by Jdean » Logged

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rms2
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« Reply #7 on: February 12, 2011, 02:57:18 PM »

It would be cool if someone could be found who is either L459+ and L21- or L21+ and L459-.
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Jdean
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« Reply #8 on: February 12, 2011, 03:25:56 PM »

It would be cool if someone could be found who is either L459+ and L21- or L21+ and L459-.

This SNP is about as new as you can get but I'm itching for FTDNA to offer it up to Joe Public, hopefully they won’t keep us on tenter hooks for too long.
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cmblandford
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« Reply #9 on: February 13, 2011, 02:00:50 AM »

Quote
It would be cool if someone could be found who is either L459+ and L21- or L21+ and L459-.

For those of us L21+ who have not found a SNP or even a close haplogroup, L459- could be seriously interesting.  BTW, within L21+ has any pattern developed for those who have tested L459+?
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Jdean
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« Reply #10 on: February 13, 2011, 10:34:58 AM »

For those of us L21+ who have not found a SNP or even a close haplogroup, L459- could be seriously interesting.  BTW, within L21+ has any pattern developed for those who have tested L459+?

Unfortunately I don't know much about the 1000 Genomes Project but I would be surprised if all 13 of the L21+ people in it fell into an identifiable cluster. It would be nice to get the data for the P312+ people in this project, does anybody know who they are?, the entire project is huge and I don’t have anything big enough to store it on !! plus my service provider would charge me a hefty fee for the pleasure of downloading it.

L459 is probably going to be just upstream or downstream of L21. It may be so close that we never find the split but I would be surprised if that were the case.

 P312 and his offspring were born during a time of massive expansion not that long ago which is why it is so difficult to differentiate between the various haplogroups, even when STR tested to the absolute limits (my closest matches at 96 loci are U152??).

It would seem odd to me if L459+ L21-/ L459- L21+ didn’t manage to leave its own branch during this period. However if that is true then it would suggest L459 occurred almost simultaneously with L21, which raises the hopes of many more relevant SNPs being found under P312 splitting everybody down into smaller and smaller groups in the not too distant future.
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« Reply #11 on: February 13, 2011, 04:45:01 PM »

For those of us L21+ who have not found a SNP or even a close haplogroup, L459- could be seriously interesting.  BTW, within L21+ has any pattern developed for those who have tested L459+?

Unfortunately I don't know much about the 1000 Genomes Project but I would be surprised if all 13 of the L21+ people in it fell into an identifiable cluster. It would be nice to get the data for the P312+ people in this project, does anybody know who they are?, the entire project is huge and I don’t have anything big enough to store it on !! plus my service provider would charge me a hefty fee for the pleasure of downloading it.

L459 is probably going to be just upstream or downstream of L21. It may be so close that we never find the split but I would be surprised if that were the case.

 P312 and his offspring were born during a time of massive expansion not that long ago which is why it is so difficult to differentiate between the various haplogroups, even when STR tested to the absolute limits (my closest matches at 96 loci are U152??).

It would seem odd to me if L459+ L21-/ L459- L21+ didn’t manage to leave its own branch during this period. However if that is true then it would suggest L459 occurred almost simultaneously with L21, which raises the hopes of many more relevant SNPs being found under P312 splitting everybody down into smaller and smaller groups in the not too distant future.

Well let's hope you're right about the last part. I don't feel too sorry for those of you who are stuck at L21* though.

As to the first part, it sounds to me like a project for mikewww.
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Jdean
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« Reply #12 on: February 13, 2011, 07:51:44 PM »

Well let's hope you're right about the last part. I don't feel too sorry for those of you who are stuck at L21* though.

At the end of the day I don't really know if there is that much difference in being P312* or L21*, the age is about the same, the distribution is almost identical, even the modal haplotype is the same :) but thanks to L21 p312* is a lot smaller now. If another SNP were discovered that split P312*  the way that L21 did then both positive and negative people would benefit.

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rms2
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« Reply #13 on: February 14, 2011, 08:30:44 AM »



. . . I don't feel too sorry for those of you who are stuck at L21* though.

. . .

I agree with your sentiment there. I think anyone who has gotten as far SNP-wise as we have has been blessed.

In fact, the mad desire to go further and further downstream is a virus that has passed me by pretty much. I haven't been able to work up much excitement about any of the latest SNPs discovered south of L21.

Just recall the bad old days when so many of us were stuck at M269 and had to endure being regaled with the glories of the "master subclades".

What I am most enthusiastic for is a new SNP or two that will break up R-P312*. That would be something worth getting worked up about.
« Last Edit: February 14, 2011, 08:32:11 AM by rms2 » Logged

alan trowel hands.
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« Reply #14 on: February 14, 2011, 01:04:53 PM »



. . . I don't feel too sorry for those of you who are stuck at L21* though.

. . .

I agree with your sentiment there. I think anyone who has gotten as far SNP-wise as we have has been blessed.

In fact, the mad desire to go further and further downstream is a virus that has passed me by pretty much. I haven't been able to work up much excitement about any of the latest SNPs discovered south of L21.

Just recall the bad old days when so many of us were stuck at M269 and had to endure being regaled with the glories of the "master subclades".

What I am most enthusiastic for is a new SNP or two that will break up R-P312*. That would be something worth getting worked up about.

I think the lack of understanding of S116* is  a major missing link.  There seems to be geographical patterning in clades both upstream of S116 and upstream of L11 but S116* and L11* lack an easily understandable geography. 

I would guess that is because they are are paragroups.  I suppose the more we break them down the closer we can get to identifying the most 'ancestral' element of them in SNP terms.  Perhaps once that presumably small group (given the rapid succession of SNPs from L11 onwards) is identified maybe its geography will be interesting.  In simple theory you would think that L11^ and S116* when shrunk down and refined by new SNPs should have some geographical pattern placing them in sequence between L51 on the one hand and U152/L21/U106 etc on the other.  However, we should also maybe expect the unexpected. 
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« Reply #15 on: February 14, 2011, 06:56:14 PM »

Well let's hope you're right about the last part. I don't feel too sorry for those of you who are stuck at L21* though.

At the end of the day I don't really know if there is that much difference in being P312* or L21*, the age is about the same, the distribution is almost identical, even the modal haplotype is the same :) but thanks to L21 p312* is a lot smaller now. If another SNP were discovered that split P312*  the way that L21 did then both positive and negative people would benefit.



The last time I looked at the P312* and L21 maps rms maintains, the area in which P312 has been found is much wider than that for L21. Also they appear to me to have a differing distribution in Britain. I would agree though that they aren't radically different. I think we will start to find significant differences as further subclades are discovered.
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alan trowel hands.
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« Reply #16 on: February 14, 2011, 09:04:04 PM »

Well let's hope you're right about the last part. I don't feel too sorry for those of you who are stuck at L21* though.

At the end of the day I don't really know if there is that much difference in being P312* or L21*, the age is about the same, the distribution is almost identical, even the modal haplotype is the same :) but thanks to L21 p312* is a lot smaller now. If another SNP were discovered that split P312*  the way that L21 did then both positive and negative people would benefit.



The last time I looked at the P312* and L21 maps rms maintains, the area in which P312 has been found is much wider than that for L21. Also they appear to me to have a differing distribution in Britain. I would agree though that they aren't radically different. I think we will start to find significant differences as further subclades are discovered.

My guess is that when its split up by new SNPs and only a small amount of the S116* remains 'ancestral' in downstream SNP terms, the latter will be located somewhere in eastern France of SW Germany or adjacent while much of the current Iberian S116* hotspot will transpire to simply be currently unknown sibling clades to the other S116 clades etc. It has always been hard to see how S116 could really have originated in the current S116* hotspot of Iberia when the general phylogenic trend of R1b1b2 in Europe seems to be SE/E to W/NW and also variance seems to show that S116 clades are younger in Iberia.  I suppose if that happens we shouldnt be too surprised.  Frequency is no guide to origin point.   
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Jdean
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« Reply #17 on: March 06, 2011, 07:36:42 PM »

L459 is now available from FTDNA.
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« Reply #18 on: March 07, 2011, 03:23:25 AM »

My guess is that when its split up by new SNPs and only a small amount of the S116* remains 'ancestral' in downstream SNP terms, the latter will be located somewhere in eastern France of SW Germany or adjacent while much of the current Iberian S116* hotspot will transpire to simply be currently unknown sibling clades to the other S116 clades etc. It has always been hard to see how S116 could really have originated in the current S116* hotspot of Iberia when the general phylogenic trend of R1b1b2 in Europe seems to be SE/E to W/NW and also variance seems to show that S116 clades are younger in Iberia.  I suppose if that happens we shouldnt be too surprised.  Frequency is no guide to origin point.   
I agree. R-P312* is hard to deal with in terms of "hot spots" and variance. A couple of new SNP's could change our outlook. 

Who knows? Maybe one new SNP breaking up Iberian R-P312* will be as old as P312 and found no where else but Iberia and Italy.  Maybe that would be the Jean M's "stelae" people who might ultimately be the first Bell Beakers..
http://www.buildinghistory.org/distantpast/bellbeaker.shtml

Maybe not, but that's why we need to whittle down R-P312*.  Along that line, did any R-P312* sign up for the WTY deal last week?  I'm not sure we need them all, but a number of L21 people did.  I will have to say I'm impressed with the passion of the L21 crowd, either that or their (our) craziness.
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Jdean
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« Reply #19 on: March 07, 2011, 05:15:13 AM »

Maybe not, but that's why we need to whittle down R-P312*.  Along that line, did any R-P312* sign up for the WTY deal last week?  I'm not sure we need them all, but a number of L21 people did.  I will have to say I'm impressed with the passion of the L21 crowd, either that or their (our) craziness.

One new kit no. has turned up on Finch since the offer, there is also another kit that was ordered in Jan but not yet returned.

Only one L21 kit has been added since the offer went out, I wonder how many applications were approved?
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« Reply #20 on: March 07, 2011, 04:28:22 PM »

My guess is that when its split up by new SNPs and only a small amount of the S116* remains 'ancestral' in downstream SNP terms, the latter will be located somewhere in eastern France of SW Germany or adjacent while much of the current Iberian S116* hotspot will transpire to simply be currently unknown sibling clades to the other S116 clades etc. It has always been hard to see how S116 could really have originated in the current S116* hotspot of Iberia when the general phylogenic trend of R1b1b2 in Europe seems to be SE/E to W/NW and also variance seems to show that S116 clades are younger in Iberia.  I suppose if that happens we shouldnt be too surprised.  Frequency is no guide to origin point.   
I agree. R-P312* is hard to deal with in terms of "hot spots" and variance. A couple of new SNP's could change our outlook. 

Who knows? Maybe one new SNP breaking up Iberian R-P312* will be as old as P312 and found no where else but Iberia and Italy.  Maybe that would be the Jean M's "stelae" people who might ultimately be the first Bell Beakers..
http://www.buildinghistory.org/distantpast/bellbeaker.shtml

Maybe not, but that's why we need to whittle down R-P312*.  Along that line, did any R-P312* sign up for the WTY deal last week?  I'm not sure we need them all, but a number of L21 people did.  I will have to say I'm impressed with the passion of the L21 crowd, either that or their (our) craziness.

'M. Faulconer', whose profile lists him as P312*, announced on the DNA forum (under a thread relating to R1a WTY) that his application for WTY had been approved by FTDNA.
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« Reply #21 on: March 14, 2011, 07:42:36 PM »

L459 is now available from FTDNA.

Who needs WTY, let's go for L459.  I am in ....... (-;


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Jdean
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« Reply #22 on: March 14, 2011, 08:30:41 PM »

L459 is now available from FTDNA.

Who needs WTY, let's go for L459.  I am in ....... (-;


A lot cheaper too plus you’re guaranteed a result, + or -, the more the merrier :)
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« Reply #23 on: March 17, 2011, 01:40:45 AM »

L459 is now available from FTDNA.

Who needs WTY, let's go for L459.  I am in ....... (-;


A lot cheaper too plus you’re guaranteed a result, + or -, the more the merrier :)

Due 5/2/11, batch 404, it will be interesting.
« Last Edit: March 17, 2011, 01:44:31 AM by cmblandford » Logged

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Jdean
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« Reply #24 on: March 17, 2011, 12:00:54 PM »


Due 5/2/11, batch 404, it will be interesting.

Mine's the week before but FTDNA are really dragging there heels at the moment.
« Last Edit: March 17, 2011, 12:44:19 PM by Jdean » Logged

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