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Jdean
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« on: August 10, 2010, 07:17:46 PM »

A question was raised on DNA Forum of the possibility of extending the R-L21 haplotype, I thought I would be a little presumptuous and have a poke at it.

Looking through the various R1b1b2 results over 67 on Ysearch it occurred to me that there may have been a split in P312

DYS522 = 10

appears to be ancestral to U106 and P312, but in P312 it looks likely there was an early mutation at that loci to 11.

Roughly 1/2 of P312 have 10 which was passed down to U152 and SRY2627, but L21 looks to have descended from the 11 side.
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« Reply #1 on: August 11, 2010, 01:00:33 PM »

A question was raised on DNA Forum of the possibility of extending the R-L21 haplotype, I thought I would be a little presumptuous and have a poke at it.

Looking through the various R1b1b2 results over 67 on Ysearch it occurred to me that there may have been a split in P312

DYS522 = 10

appears to be ancestral to U106 and P312, but in P312 it looks likely there was an early mutation at that loci to 11.

Roughly 1/2 of P312 have 10 which was passed down to U152 and SRY2627, but L21 looks to have descended from the 11 side.

What's the estimated mutation rate for DYS522?
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Jdean
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« Reply #2 on: August 11, 2010, 02:25:28 PM »

What's the estimated mutation rate for DYS522?

Unfortunately there are no published mutation rates for the advanced loci over 67 due to lack of information.

I'm doing a little more checking on my original data, and may have to tone down the level of excitement I initially felt about this.

Looking at the results it seems that about 25% of U106 also has 11 at this loci, and this appears to hold true for P310 though the level of data there is so limited that it would be foolhardy to draw firm conclusions.

That seems to suggest DYS522 is at least a medium speed mutater, however there is far fewer L21 people with 10 at this loci and you would think if it was medium speed that more would have mutated back to 10.

I've had to take two people out of my P312 data, one because he was R-L21+ (but hadn’t updated Ysearch) and the other because he hadn't tested L21 (and being of Welsh decent I wouldn't fancy betting money on him being L21 neg), however that still leaves 40% of that group with 11 &12 (which there’s one of) at DYS522. Of course if I were to loose a few more it would make the data a bit sick.

On the face of it I suspect DYS522 will prove to have a reasonably lowish mutation rate, this is based on the variance which is quite low

in L21 we have

10    7%
11    60%
12    32%

with no examples outside of that range

DYS390 and 391 seem about the closest to this sort of patter, so with nothing else to go on I would suggest that rates of between 0.27 to 0.31 per generation doesn’t sound to bad (though not exactly a scientific way of coming up with a rate)

Anyway at the moment we still have an unusually high level of 10 in P312 and a dominants in L21, as long as I don't have to take out anymore undeclared L21 results from my P312 data I still think this could be interesting. However with 25% of U106 also having that value I'm not entirely sure what can be done with it. I had initially thought that encouraging P312* people of European decent may add a new layer of information to the P312 distribution map, but presumably there are going to be later mutations to 11 after the birth of L21 and of course L21 may have mutated to 11 itself and not inherited that value.
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GoldenHind
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« Reply #3 on: August 11, 2010, 08:19:13 PM »

I am unable to find DYS522 in the list of FTDNA 67 markers. Am I missing something?
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Jdean
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« Reply #4 on: August 11, 2010, 08:50:34 PM »

I am unable to find DYS522 in the list of FTDNA 67 markers. Am I missing something?

It's one of the advanced markers which unfortunately doesn’t show up on FTDNA project pages.

This search ought to elicit most R1b1b2 people who have tested at least some of these and posted them on Ysearch


http://www.ysearch.org/search_results.asp?uid=C7BED&min_markers=70&mismatches_max=0&mismatch_type=sliding&mismatches_sliding_starting_marker=30
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Jdean
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« Reply #5 on: August 13, 2010, 07:08:11 AM »

Of course if I were to loose a few more it would make the data a bit sick.


I lost another two P312 people from my data last night, one L21+ the other L21?, so the data is 'looking a bit sick'.

At the moment using all downstream groups for U106 we have almost exactly 25% who are DYS522 = 11 or higher (only one and I'm not entirely convinced this person entered all his values correctly).

P312* (definitely no hidden L21 results left) is 6/18 which is a bit higher than 25% but with a data set this small not something you would want to bet the house on.

Interestingly there are no examples of SRY2627 who aren't 10 (only four examples though), and only 1 U152 person has DYS522 = 11 out of 12 people, all the rest are 10.


This is in stark contrast to L21 where only 3/45 people are DYS522 = 10, and M222 who don't have a single example in 14 people.


I don't know if anybody thinks this may be worth investigating further but either way I'm off too France for a fortnight next week and away this weekend, so won't be in a position to do much with it.

« Last Edit: August 13, 2010, 07:24:05 AM by Jdean » Logged

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« Reply #6 on: August 13, 2010, 08:04:02 AM »

At the moment using all downstream groups for U106 we have almost exactly 25% who are DYS522 = 11 or higher (only one and I'm not entirely convinced this person entered all his values correctly).

My half maternal brother (Ysearch R6JX4) is  U106* with L69+ and is DYS522=10.
« Last Edit: August 13, 2010, 08:15:08 AM by mjost » Logged

148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Jdean
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« Reply #7 on: August 13, 2010, 09:16:29 AM »

My half maternal brother (Ysearch R6JX4) is  U106* with L69+ and is DYS522=10.


Thanks for that, my Ysearch didn't pick him up since it was aimed at FTDNA markers. I shall have to have a fiddle to see if I can come up with a better way of finding none FTDNA people.

As it happens there are three Genebase people hiding out under R1b1b2a1a2

GRH3M, 2NA5R and PXRQ3

They are likely P312 positive and ended up there over some confusion with FTDNA's haplogroup names.

They have an Irish descended chap for company

U3C6U

who has definitely tested positive for P312.

They are all 11 @ DYS522
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Jdean
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« Reply #8 on: August 16, 2010, 06:00:55 AM »

What's the estimated mutation rate for DYS522?

Unfortunately there are no published mutation rates for the advanced loci over 67 due to lack of information.

On the face of it I suspect DYS522 will prove to have a reasonably lowish mutation rate, this is based on the variance which is quite low

in L21 we have

10    7%
11    60%
12    32%

with no examples outside of that range

DYS390 and 391 seem about the closest to this sort of patter, so with nothing else to go on I would suggest that rates of between 0.27 to 0.31 per generation doesn’t sound to bad (though not exactly a scientific way of coming up with a rate)



I probably should have made it clear I was using percentages for the mutation rates for DYS390 & 391

So my horribly unscientific method of coming up with a mutation rate suggested to me a figure between

2.65E-03 - 3.11E-03


As I said there is very little data on these advanced loci, but today having a little mooch I came across this paper

http://sites.google.com/site/navascuesresearch/publications-conferences/journalpublications/burgarellanavascues2010

that was published in the 'European Journal of Human Genetics'

They used father son data and pupation studies to come up with there figures. The later being not far of my own method, but hopefully a tad more reliably than my 'um, I think it looks a bit like this'.

Anyway the rate they came up with for DYS522 was 2.77E-03

Which is in-between the Chandler rates for DYS390 & 391 as I suggested, I think I win a piece of cheese :)



Overall I'm beginning to wonder if there isn't more to this loci than meets the eye. In Ysearch you can only enter values between 9-13, and I could only find one example of 9 and about 2% at 13 over all hapogroups. Normally this sort of behaviour is reserved for the very slowest mutating loci.


Anyway I'm off on my hols tomorrow morning, back in a couple of weeks.
« Last Edit: August 16, 2010, 06:03:04 AM by Jdean » Logged

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« Reply #9 on: August 16, 2010, 10:22:09 AM »

What's the estimated mutation rate for DYS522?

Unfortunately there are no published mutation rates for the advanced loci over 67 due to lack of information.

On the face of it I suspect DYS522 will prove to have a reasonably lowish mutation rate, this is based on the variance which is quite low

in L21 we have

10    7%
11    60%
12    32%

with no examples outside of that range

DYS390 and 391 seem about the closest to this sort of patter, so with nothing else to go on I would suggest that rates of between 0.27 to 0.31 per generation doesn’t sound to bad (though not exactly a scientific way of coming up with a rate)



I probably should have made it clear I was using percentages for the mutation rates for DYS390 & 391

So my horribly unscientific method of coming up with a mutation rate suggested to me a figure between

2.65E-03 - 3.11E-03


As I said there is very little data on these advanced loci, but today having a little mooch I came across this paper

http://sites.google.com/site/navascuesresearch/publications-conferences/journalpublications/burgarellanavascues2010
that was published in the 'European Journal of Human Genetics'
They used father son data and pupation studies to come up with there figures. The later being not far of my own method, but hopefully a tad more reliably than my 'um, I think it looks a bit like this'.
Anyway the rate they came up with for DYS522 was 2.77E-03
Which is in-between the Chandler rates for DYS390 & 391 as I suggested, I think I win a piece of cheese :)
Overall I'm beginning to wonder if there isn't more to this loci than meets the eye. In Ysearch you can only enter values between 9-13, and I could only find one example of 9 and about 2% at 13 over all hapogroups. Normally this sort of behaviour is reserved for the very slowest mutating loci.
My opinion is that no single STR should be considered stand-alone... at least generally speaking.   Any one can have a mutation to any STR and no matter how slow it is, it could happened in the last generation.  The power of STR's is finding a pattern that seems to show up across multiple people.... an STR signature.  Of course, STR signatures should only be considered within the same deep clade.
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Jdean
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« Reply #10 on: August 16, 2010, 10:53:57 AM »

My opinion is that no single STR should be considered stand-alone... at least generally speaking.   Any one can have a mutation to any STR and no matter how slow it is, it could happened in the last generation.  The power of STR's is finding a pattern that seems to show up across multiple people.... an STR signature.  Of course, STR signatures should only be considered within the same deep clade.

Generally I agree with you, you often see people mussing over a particular value that they have and what it could me. Of course the answer almost inevitably is 'by itself very little'.

However what interests me about this loci is it appears to be the only one where there is a marked difference between L21 and P312. If L21 inherited this difference from it's P312 forefather then there may be the possibility of discovering something further about P312 and the origins of L21, but that would depend on there being a meaningful distribution pattern to DYS522 = 10 in P312.

Of course it is also possible that L21 had an early mutation to this value, in which case this probably won't offer anything new to our knowledge beyond 11 is modal for L21 at this loci which by itself wouldn't be very exciting.
« Last Edit: September 18, 2010, 07:55:56 AM by Jdean » Logged

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GoldenHind
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« Reply #11 on: August 16, 2010, 08:01:05 PM »







My opinion is that no single STR should be considered stand-alone... at least generally speaking.   Any one can have a mutation to any STR and no matter how slow it is, it could happened in the last generation.  The power of STR's is finding a pattern that seems to show up across multiple people.... an STR signature.  Of course, STR signatures should only be considered within the same deep clade.

Yes, but there is always the possibility of finding another single marker which is very indicative, like DYS492.
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Jdean
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« Reply #12 on: August 16, 2010, 08:05:45 PM »







My opinion is that no single STR should be considered stand-alone... at least generally speaking.   Any one can have a mutation to any STR and no matter how slow it is, it could happened in the last generation.  The power of STR's is finding a pattern that seems to show up across multiple people.... an STR signature.  Of course, STR signatures should only be considered within the same deep clade.

Yes, but there is always the possibility of finding another single marker which is very indicative, like DYS492.

With a bit of luck
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Jdean
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« Reply #13 on: September 18, 2010, 05:56:36 AM »

My half maternal brother (Ysearch R6JX4) is  U106* with L69+ and is DYS522=10.


As it happens there are three Genebase people hiding out under R1b1b2a1a2

GRH3M, 2NA5R and PXRQ3

They are likely P312 positive and ended up there over some confusion with FTDNA's haplogroup names.

They have an Irish descended chap for company

U3C6U

who has definitely tested positive for P312.

They are all 11 @ DYS522


Having let this lie a bit I've been going back over my data and trying to add more to it.

GRH3M who is one of the R1b1b2a1a2 people in Ysearch posted on the Yahoo L21 project the other day advertising his extended STR results, so presumably he is L21 and not U106 as I suspected.
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« Reply #14 on: September 20, 2010, 09:41:46 AM »

I am unable to find DYS522 in the list of FTDNA 67 markers. Am I missing something?
It's one of the advanced markers which unfortunately doesn’t show up on FTDNA project pages.
This search ought to elicit most R1b1b2 people who have tested at least some of these and posted them on Ysearch
http://www.ysearch.org/search_results.asp?uid=C7BED&min_markers=70&mismatches_max=0&mismatch_type=sliding&mismatches_sliding_starting_marker=30
David Wilson maintains C7BED, the R1b1b2 extended modal Ysearch ID.  He lists 522=11 as the mode (most common value.)

I recently pulled from Ysearch all of the confirmed R-L21* people that had tested for at least 67 markers.  I found
522=10  5
522=11  25
522=12  13

11 is clearly the mode but 11 vs 10 vs 12 this is not a solid indicator of L21+ versus L21-.  I don't have any info on U106 or other subcladess.

I'll post the L21 extended results on the R-L21* Yahoo Groups "Files" link when I get everything formatted.

C7BED doesn't have a result for DYS589.  Does anyone know what is modal for 589 for R1b?
« Last Edit: September 20, 2010, 10:00:34 AM by Mikewww » Logged

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Jdean
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« Reply #15 on: September 20, 2010, 01:46:37 PM »

David Wilson maintains C7BED, the R1b1b2 extended modal Ysearch ID.  He lists 522=11 as the mode (most common value.)
 

As you said 11 is modal at 522 for R-L21, however 10 is modal for U106, P312, U152, SRY2627 and as far as I can tell the R1b1 groups above U106 & P312.

This begs the question as to what the R1b1b2 extended modal represents, presumably it was conceived before P312 and L21 were discovered and also at a time when extended results were even more thin on the ground (we’re hardly tripping over them now)

There are other values that also don’t sound right by my calculations.

DYS494 is 9 for U106, P312, U152 and L21 as apposed to 10 in C7BED.  Likewise C7BED has DYS636 @ 11, where as my calculations put the modal at 12 for all of the aforesaid haplotypes.

The other value that may also be interesting is DYS714. C7BED has this @ 26 which is the value I’ve calculated for U106, P312 and U152, however L21 appears to be 25. I haven’t looked closely at this yet but by eye it looks to have quite a high variance especially in P312, so some of these may change with more data.


WRT DYS589, all of the above mentioned haplogroups are reasonably strongly 12 so far at this loci.


I originally started this thread hopeful that there may be something interesting about L21 having a modal value of 11, unfortunately the more I look at it the less likely I think it could be used to prove anything much. However I would suggest that a value of 12 could be used to suggest L21+, it appears to be a rare result for other R1b1b2 groups (I’ve only found 1 so far) but is reasonably common for L21. Probably not terribly useful though :)

« Last Edit: September 20, 2010, 01:48:09 PM by Jdean » Logged

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« Reply #16 on: September 21, 2010, 12:17:59 PM »

David Wilson maintains C7BED, the R1b1b2 extended modal Ysearch ID.  He lists 522=11 as the mode (most common value.)
 

As you said 11 is modal at 522 for R-L21, however 10 is modal for U106, P312, U152, SRY2627 and as far as I can tell the R1b1 groups above U106 & P312.

This begs the question as to what the R1b1b2 extended modal represents, presumably it was conceived before P312 and L21 were discovered and also at a time when extended results were even more thin on the ground (we’re hardly tripping over them now)

There are other values that also don’t sound right by my calculations.
....
Do you feel like you have enough extended haplotypes to have an accurate mode for each of these subclades?  The people that have these plugged into Ysearch are a bit limited.  I've found Ysearch can have errors also, because people typically manually put in their data.

I recommend obtaining a more accurate picture of the modes for 522 from Ethnoancestry.  I think they were the first to offer it.
Quote from: ISOGG
Ethnoancestry YSTR18 test offers 12 markers not commercially available at other companies.  The following markers are ones that have only been previously used for academic genetic studies: DYS522....
http://www.isogg.org/ydnachart1.htm

Are you sure there are no conversion factors for putting 522 into Ysearch?
« Last Edit: September 21, 2010, 12:18:55 PM by Mikewww » Logged

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Jdean
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« Reply #17 on: September 21, 2010, 03:05:18 PM »

Mike

The data I have is small but quite persuasive, it could definitely do with more samples though, unfortunately there don't appear to be that many extended results on Ysearch past the SMGF loci.

I completely agree with you regarding treating Y-search data with a touch of caution. There is room for human error, and I'm sure some data is assumed or calculated by the people entering it. Also unfortunately it is very hard to find out if people marked as P312 have tested for L21, or indeed are L21 but haven't changed there haplogroup status in Y-Search.

This is the data I have on the STRs I mentioned, but leaving P312 out for now.

DYS494

                    8              9              10


U106            1              18             4

U152            0               8             0

L21              0             38             6



DYS522

                   10             11            12           13


U106           18               6             0             1

U152            8                0             0             0

L21              3                27          13            0


DYS636

                   11                12           13


U106            3                  18            1

U152            0                  8             0

L21               5                 33            1   


As I said the nos. are on the small side, but the distributions are quite clear.

Do you know if it's possible to see Ethnoancestry or Genebase results anywhere?

I'm at least reasonably sure that there is no conversion necessary for DYS522, leastways there is no mention of it on Ysearch.


All the best


Dave
« Last Edit: September 21, 2010, 06:10:30 PM by Jdean » Logged

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