WTY and new SNPs in the A haplogroup


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PostPosted: Tue Apr 03, 2012 5:16 pm
4 WTYs - pending:
N64496 - on the tree side A0
229035 (A-M114) - on the tree side A1
229033 (A-P114)
229037 (A-P28)

Then again there will be interesting results - for the entire tree Y-DNA! :)
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PostPosted: Wed Apr 11, 2012 12:18 am
I have some good news! These four WTYs are now underway. The first step, PCR, has already been completed on the P114, M114, and P28 samples, and it is now in progress on the Perry sample, which is 215865 rather than N64496.

Both samples 229033, which is P114+, and 215865, are on the A0 side of the tree. It will be very valuable and important to be able to compare these two WTY sequences!

The P114 sample was donated to science by one of the Bakola Pygmies. It will be virtually the same as the sample used by Cruciani to represent A1b. We will no doubt discover new SNPs in it, and both these SNPs and the V-SNPs from Cruciani will be ones we'll want to test in our A0a project member, Boon, kit N71150 (and hopefully a new kit soon), and in similar ones like kit 224786, and certainly in the Simms family when we can get a good sample for this.

And of course we'll be comparing the 229033 WTY results to Perry's. Whichever SNPs are positive in both, will be the earliest part of the A0 trunk. It would be amazing if they didn't share any SNPs. We'll see if there are just a few, or many.

The other two samples, 229035 and 229037, are in the former A2, now A1b1a. They represent the subclades A1b1a1a1a and A1b1a1a1b, respectively. They'll help us to clarify A1b1a, in which we have new SNPs and branches from previous WTYs.

Thomas told me that although the PCR for Perry was slightly delayed, it will be the first one to be scored. :-) So we can look forward to seeing results hopefully within this week!

Bonnie

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PostPosted: Wed Apr 11, 2012 7:31 am
Certainly, it is necessary to be pleased with these tests. :)
But all at the same time and to sadden, because the entire week I must without the dream, be on guard at the computer, waiting for this news. :(

However I have a question:
Whether some comparing will be from 482 SNPs, already found by Roche 454 in the J1 haplogroup?
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PostPosted: Thu Apr 12, 2012 5:45 pm
Dear Stan,

Here is some news for you! Thomas says:

Of course we don't have primers for all Y SNP candidates up to YSC888 because they were sequenced from a genomic DNA library.
However when YSCs fall on a PCR amplicon used in WTY, then we'll report them of course.

While I'm writing this Astrid just discovered that Perry has DYF399X 21t-23t-26t, this means NO C-type allele!
So this is already the first SNP found in this sample if you want...


I think Ted Kandell will be very interested in the DYF399X results.

Bonnie
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PostPosted: Fri Apr 13, 2012 5:29 pm
All right, today there are some new SNPs, but not yet from Perry! It looks like the A0a-P114+ sample went first, actually. That way, we can compare Perry against ALL the branches of A0 and not be confused about any new SNPs we find in him -- we'll know whether or not each SNP is shared with the already-known A0 branches.

Thomas found 14 new SNPs in the P114+ sample, L1070-L1084. There aren't so many as in the other hg. A WTYs, since this sample is almost identical to the one Cruciani had used for his A1b. These SNPs are already on Ymap, but not yet on the Ytree (at the time I'm writing). Figuring out the right phylogeny can wait until we have more results and can thoroughly check where they should go on the tree.

The most likely reason Perry doesn't have a C allele at DYF399, according to Thomas, is that the mutation giving the C allele, normally found in all other Y lineages, hadn't happened yet when his lineage branched off from the tree!

Bonnie

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PostPosted: Fri Apr 13, 2012 8:08 pm
Rootsy wrote:All right, today there are some new SNPs, but not yet from Perry! It looks like the A0a-P114+ sample went first, actually. That way, we can compare Perry against ALL the branches of A0 and not be confused about any new SNPs we find in him -- we'll know whether or not each SNP is shared with the already-known A0 branches.

Thomas found 14 new SNPs in the P114+ sample, L1070-L1084. There aren't so many as in the other hg. A WTYs, since this sample is almost identical to the one Cruciani had used for his A1b. These SNPs are already on Ymap, but not yet on the Ytree (at the time I'm writing). Figuring out the right phylogeny can wait until we have more results and can thoroughly check where they should go on the tree.
The most likely reason Perry doesn't have a C allele at DYF399, according to Thomas, is that the mutation giving the C allele, normally found in all other Y lineages, hadn't happened yet when his lineage branched off from the tree!
Bonnie

Already finish this testing, because I cannot neither sleep nor dream! :evil:
In Polish:
"sen", when somebody is sleeping
"sen", when somebody is dreaming
One without second in Poland cannot do without! :D

Postscript.
I don't understand the role of the C allele in DYF399 :?:
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PostPosted: Fri Apr 13, 2012 11:40 pm
Dear Stan,

I sympathize, I hardly slept much last night either! :shock:

Here is what Thomas said in explanation of DYF399:
You don't need to know much about DYF399 to understand that it's a SNP in the flanking region of one copy of the STR that defines the C-type.
This SNP wasn't present when Perry's line split off from the tree. The other A0 samples have a C-type allele.

Off course he may have lost the C-type by a recLOH, however I haven't seen that before at DYF399 (the third arm is quite different from the other two, so recombination is rare), so I believe it's more likely that his line never had a C-type allele ever.


If you don't understand the second part, don't worry about it - it isn't very important.

I'm dying to see the Perry results too!

On SMGF today, I found one match for him in Nigeria with only very slight differences from the Cameroon samples, which is interesting, giving more evidence suggesting that this type of Y-DNA could be from the area surrounding the Cross River Valley, on both East and West sides.

Veeramah has data from Nigeria with three samples from the Cross River area which are like Simms or Smith in our project, and one sample which is like Boon (but they have only 6 markers tested!). We aren't seeing these so much in the SMGF data -- just a matter of luck as to where samples were collected.

Bonnie

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PostPosted: Sat Apr 14, 2012 3:29 pm
Hi all,

This news has appeared in Finch: the Perry sequence was done on Thursday the 12th, Astrid is scoring it, and they have covered 407186 bases, excellent coverage, though not as high as they've gotten on a few other WTYs.

The big news for the moment, even though it doesn't yet reflect the Perry WTY, is in the new shape of the Ytree. A0 now splits into two groups, which we can call A0a and A0b. A0a now includes two branches, one with Jones and the other with the Bakola who's P114!

On the P114 branch, the ten new SNPs L1070, L1072, L1073, L1075, L1076, L1078, L1079, L1080, L1081, and L1082 now appear.

Meanwhile the seven SNPs L979, L980, L987, L996, L1011, L1015, and L1017, previously discovered in the Jones WTY, are now found to be shared by both of the branches of A0a. The Bakola would be A0a1 and Jones would be A0a2. Jones has the six SNPs L981, L983, L988, L994, L1007, and L1014 defining his branch.

What's in A0b? That's the Dorsey branch! He still has 23 SNPs, L92.2, L1035, L1036, L1037, L1038, L1039, L1040, L1041, L1042, L1043, L1044, L1045, L1046, L1047, L1048, L1049, L1050, L1051, L1052, L1054, L1056, L1057, and L1058, on his branch! He splits off above the seven A0a SNPs.

Above all of these, at the A0* node, shared by both A0a and A0b, are no less than 40 SNPs! This includes L896, formerly thought to define A0b.

The Perry WTY is going to almost certainly break up these 40 SNPs, since we already know that he's negative for two of them, V166 and L896.

Anyone else noticing interesting new developments, please share them!

Bonnie
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PostPosted: Sun Apr 15, 2012 10:27 am
Have seen moments ago "changes 1 day ago" in the root Y-Branches on ytree.ftdna.com and in an instant have looked here whats going on.

Looks like Rootsy, their A-HG friends and the FTDNA-Team (Thomas Krahn & Co) are doing fine work these days!!!
Congratulations!!!
The root of Y is has some more secrets to discover. Here the actual FTDNA-root-tree as screenshot to memorize this moment:
Image

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PostPosted: Sun Apr 15, 2012 8:25 pm
Alpeu wrote:Have seen moments ago "changes 1 day ago" in the root Y-Branches on ytree.ftdna.com and in an instant have looked here whats going on.

Looks like Rootsy, their A-HG friends and the FTDNA-Team (Thomas Krahn & Co) are doing fine work these days!!!
Congratulations!!!

Tomorrow there will be a change then again?
Stan
Last edited by Atim on Mon Apr 16, 2012 7:32 pm, edited 1 time in total.
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