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Y-SNPs first reported by Wilder et al. (2004)
Topic Started: Oct 30 2010, 05:52:30 PM (499 Views)
black man
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Re. Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males by Wilder et al. 2004 including their supplemental materials. (Do note that Hammer belonged to that team.

They refer to 43 Y-SNPs described in supplementary table 1 and 40 "haplotypes" in supplementary figure 1.

There are 46 Mongolian (according to pubmed apparently Khalkh) samples (don't trust in me, I don't know how to use pubmed functions).

No mutation was detected in 33 of them. Among them are probably those within hg C.

5 have the a G>A transition in common with 10/43 Sri Lankans, 26/47 Dutch and 23/48 Italians as for Alu element 486. So the latter mutation seems to have happened within hg P. However, Karafet only mentions two markers downstream within hg R which were reported by Wilder et al. So this one could be an already well-known mutation.

4 of them have a C>T transition in common with one Papuan as for Alu element DFFRY30, one the Mongolians having a G>C downstream mutation as for Alu element UTY62. According to Karafet et al. 2008, they all could share P93 within hg O3. if so, the one downstream probably eithe has the marker P101 or the marker P103. (Both are mentioned by Karafet et al. as having been reported first by Wilder et al.)

2 of them have a G>A transition as for Alu element 16e4.

2 of them have a G>A transition as for Alu element UTY87, one of the being downstream to the other having an additional G>T mutation as for Alu element DFFRY30.




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Edited by black man, Oct 31 2010, 04:13:52 PM.
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ren
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black man
Oct 30 2010, 05:52:30 PM
if so, the one downstream probably eithe has the marker P101
How can that be? P101 is defined by the G to A mutation at SMCY. If you look at Wilder's chart, no Mongolians have the G-A transition at SMCY.

http://www.nature.com/ng/journal/v36/n10/extref/ng1428-S2.pdf
Edited by ren, Oct 30 2010, 07:05:33 PM.
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black man
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ren
Oct 30 2010, 06:58:14 PM
black man
Oct 30 2010, 05:52:30 PM
if so, the one downstream probably eithe has the marker P101
How can that be? P101 is defined by the G to A mutation at SMCY. If you look at Wilder's chart, no Mongolians have the G-A transition at SMCY.

http://www.nature.com/ng/journal/v36/n10/extref/ng1428-S2.pdf


Where is SMCY mentioned as the location of P101? I'll rewrite or delete my post above if necessary.

As a gene region, "SMCY" occurs twice in table 1 of Wilder's paper, once with intron number 14/Alu family Y alpha 5, once with intron number 5/Alu family Y. No matter what that means, Wilder et al. consider these differences to be valid enough to refer to 43 different SNPs on p. 1123, the distribution of which among the samples is in supplementary table 1.
Edited by black man, Oct 31 2010, 11:29:06 AM.
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ren
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Quote:
 
Where is SMCY mentioned as the location of P101? I'll rewrite or delete my post above if necessary.

That's not in the paper, obviously, since it wasn't named P101 yet. In this link you will see that P101 is a a G-to-A transition at SMCY AluY2, position 20362006, which is in intron 5.

Quote:
 
As a gene region, "SMCY" occurs twice in table 1 of Wilder's paper, once with intron number 14/Alu family Y alpha 5, once with intron number 5/Alu family Y. No matter what that means, Wilder et al. consider these differences to be valid enough to refer to 43 different SNPs on p. 1123, the distribution of which among the samples is in supplementary table 1.


The P101 mutation is at SMCY2 in intron 5, but it doesn't matter.

No Mongolians have the G to A mutation at SMCY2, so it can't be P101. The ones with the mutation in the table are all Africans, so it's A3b1-P100, which has the same mutation at SMCY2 in intron 5.

Here, you see that P100 also has the G-to-A mutation at SMCY2, position 20362081, which is also in intron 5.




Did you delete one of your posts above or moved it somewhere else?
Edited by ren, Oct 31 2010, 03:49:25 PM.
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black man
The Right Hand
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ren
Oct 31 2010, 03:29:46 PM
Quote:
 
Where is SMCY mentioned as the location of P101? I'll rewrite or delete my post above if necessary.

That's not in the paper, obviously, since it wasn't named P101 yet. In this link you will see that P101 is a a G-to-A transition at SMCY AluY2, position 20362006, which is in intron 5.


Then what is the SNP of the two Mongolians in SMCY intron 14 (3rd column of supplementary table 1)? Can this be looked up?

Btw, I got to this address via google: http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/?name=P103 . How do I get to the according page for P101?

Quote:
 
Did you delete one of your posts above or moved it somewhere else?


My post was about a typo I corrected above. Since you removed your post (on that typo), I removed my reply to you, too.
Edited by black man, Oct 31 2010, 07:59:33 PM.
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ren
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The mutation for P103 is C to G at UTY AluY62, or UTY62 in the table.
http://ymap.ftdna.com/cgi-bin/gb2/gbrowse_details/hs_chrY?ref=ChrY;start=13987225;end=13987225;name=P103;class=Sequence;feature_id=41836;db_id=ymap%3Adatabase
Quote:
 
My post was about a typo I corrected above. Since you removed your post (on that typo), I removed my reply to you, too.

Yes, but did you delete it or move it somewhere else? I'm just curious because I'm thinking of how to adjust members' post count if posts are deleted.
Edited by ren, Oct 31 2010, 04:56:18 PM.
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black man
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ren
Oct 31 2010, 04:51:10 PM
The mutation for P103 is C to G at UTY AluY62, or UTY62 in the table.
http://ymap.ftdna.com/cgi-bin/gb2/gbrowse_details/hs_chrY?ref=ChrY;start=13987225;end=13987225;name=P103;class=Sequence;feature_id=41836;db_id=ymap%3Adatabase
Quote:
 
My post was about a typo I corrected above. Since you removed your post (on that typo), I removed my reply to you, too.

Yes, but did you delete it or move it somewhere else? I'm just curious because I'm thinking of how to adjust members' post count if posts are deleted.
I moved it into a separate thread at the bottom of the fossil vault ("hidden" because the new, empty posts should not distract from the written posts at the top of the page). But before that I actually deleted one post of mine because it was off-topic and I was in a hurry.
Edited by black man, Oct 31 2010, 05:18:48 PM.
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ren
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What's interesting is how Karafet cites Wilder 2004a as the source of P101 discovery, and yet none. This led me to another article by Wilder in the same year:

Genetic Evidence for Unequal Effective Population Sizes of Human Females and Males
http://mbe.oxfordjournals.org/content/21/11/2047.full

which led me to

Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation
http://www.genetics.org/cgi/content/full/164/4/1495?ijkey=bd86db0432a585a20c149e07778513e7af5fb8a3

which led me to

Population genetic implications from sequence variation in four Y chromosome genes
http://www.pnas.org/content/97/13/7354.full




Which seems to be showing a lack of discovery of a mutation later to be called P101, so P101's discovery may be after Wilder 2004.
Edited by ren, Nov 2 2010, 04:46:27 PM.
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black man
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addendum:

From table 2 in "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups" you can deduce that YCC#57 is an Urdu-speaking man living in the Pakistani part of Kashmir, who carries the M134+ and P101+ mutations according to Karafet et al. 2008. Interestingly, this marker is still rarely tested. Dulik et al. didn't detect it in any of their North Asian samples, among which there were one Altaian carrying the M134+, M117+, P101- combination, a second Altaian carrying the M134+, M117-, P101- combination and Kazaks carrying the latter combination. P101 is also absent from Trejaut's SE Asian samples which primarily include southern Han and Austronesians.

Sources:
papers by...
- Dulik et al. 2011
- Dulik et al. 2012
- Trejaut et al. 2014
- The Y Chromosome Consortium 2002




old post

I think that there are two possibilities: either citation error by Karafet et al. ("Wilder 2004a" instead of maybe "personal communication") or transcription error at ymap.ftdna.com since P101 could have been directly below P100 in a table from which the data could have been transcribed.
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