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Archiver > GENEALOGY-DNA > 2004-07 > 1089237069


From: "Ken Nordtvedt" <>
Subject: Re: [DNA] I1a and Distribution of DYS Values
Date: Wed, 7 Jul 2004 15:51:09 -0600
References: <5.1.0.14.2.20040707115344.022f78d8@mail.psu.edu>


Gordon, I will have to look at the Sorenson database. What you showed is
very valuable. I1a is decisively bi-modal at a number of new markers beyond
the YHRD markers. The dominant bimodality is the Garvey Universal haplotype
(which is the "Anglo-Saxon") versus the "Norse" which has 22 changed to 23
at DYS390 and 13,14 changed to 14,14 at DYS385a,b. I wonder why you pretty
much dropped discussion of 385a,b after your first distribution analysis?
It seems an important marker for the sub-clade structure in I1a, and I have
found it an important tag to keep my eye on. It mutates fairly often.
DYS385a,b = 14, 15 is another form found very often in Scandinavia, Very
often in Iceland, and hardly at all in Anglo-Saxony.

This Anglo-Saxon versus Norse split of the I1a population looks to be
roughly equal in the present databases. I'm not saying that about the real
world population; only the databases I have seen which are created and
contributed to by parties with specific interests. So what is so valuable
about what you have done is found some additional markers which are also
strongly bi-modal. Now it just has to be sorted out which binary choice of
each new marker (beyond the YHRD markers) goes with another and goes with
each already known (YHRD markers) modal haplotype's choices, most
importantly with the 22 versus 23 choice at DYS 390, but also with the 14
versus 15 choise at DYS19, then 12, 28 versus 12, 29 at 389i,ii and 13, 14
versus 14, 14 and 14, 15 at 385a,b. I have found some important (not
because I am 15 at DYS19, but because I think they are the oldest
sub-clades) modal haplotypes of I1a with DYS19 = 15; albeit they are low
population modal forms.

I know from the correlation studies I have done with YHRD that when you have
two strongly bi-modal haplotypes, they are correlated with each other in
almost all cases, and one choice at one marker preferentially goes with one
choice at the other. Its the sum of all these correlations between bi-modal
haplotypes that will allow us to construct very specific and diagnostic
extended haplotype structures for the various sub-clades. Then the
geographical differences among the sub-clades becomes interesting to more
people.

I find your information great, and I believe it opens up an avenue for
really pin-pointing the structure of the several modal haplotypes of I1a.

Ken


----- Original Message -----
From: "Gordon Hamilton" <>
To: <>
Sent: Wednesday, July 07, 2004 1:06 PM
Subject: [DNA] I1a and Distribution of DYS Values


> Recently there has been some interest and discussion regarding the
> distribution of various DYS values for the I1a haplogroup. An estimate of
> these distributions can be obtained using the SMGF database and methods
> similar to those previously reported for the distribution of YCAIIa,b for
> this haplotype (see
> http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2004-06/1086169717).
> These results are reported here.
>
> As in the previous analysis, the SMGF database
> (http://smgf.org:8081/pubgen/site28.jsp) was searched using information on
> the more common I1a haplotypes given by Dennis Garvey
> (http://freepages.genealogy.rootsweb.com/~dgarvey/DNA/RelGen/YSTR.htm)
that
> he obtained from the YSTR.org database
(http://www.ystr.org/index_gr.html).
>
> Of the top 30 most common haplotypes listed by Garvey, 5 are considered to
> be I1a. It will be noted that at 6 markers the values are identical for
all
> 5 of these common haplotypes. The 6 loci (DYS#) and the repeat values at
> each (given in parentheses) are as follows: 19 (14), 389i (12), 389ii
(28),
> 391 (10), 392 (11), 393 (13). Since it appears that virtually all I1a
> haplotypes have a repeat value of 8 at DYS 455, an initial search of the
> SMGF database was performed using these 7 loci and repeat values (this 7
> loci haplotype is referred to as the Garvey Universal I1a [or GU I1a]
> haplotype). The GU I1a haplotype has 475 exact matches (7/7) in the SMGF
> database that contains a total of 8,735 genotypes (as of 24 June 2004).
>
> A search was then conducted plugging in various repeat values for each of
> the various other DYS loci in addition to the above and looking for 8/8
> matches. In each of the following the number of repeats for each DYS locus
> is given followed by the frequency of an exact match in parentheses. In a
> few cases the frequencies do not add up to exactly 475 presumably because
> of some outliers.
>
> DYS 385a,b: 12,15 (1); 12,14 (16); 13,13 (26); 13,14 (190); 14,14 (113);
> 13,15 (32); 14,15 (62); 15,15 (14); 13,16 (13); 13,17 (2); 15,16 (3);
15,17
> (1).
>
> DYS 388: 12 (2); 13 (6); 14 (434); 15 (17); 16 (16).
>
> DYS 390: 21 (4); 22 (262); 23 (192); 24 (17)
>
> DYS 426: 9 (0); 10 (2); 11 (469); 12 (3); 13 (0).
>
> DYS 437: 15 (22); 16 (436); 17 (17).
>
> DYS 438: 7 (0); 8 (3); 9 (7); 10 (460); 11 (4); 12 (0).
>
> DYS 439: 9 (1); 10 (18); 11 (358); 12 (74); 13 (23); 14 (1).
>
> DYS 447: 20 (0); 21 (10); 22 (108); 23 (291); 24 (57); 25 (4); 26 (0).
>
> DYS 448: 18 (4); 19 (29); 20 (409); 21 (31); 22 (2).
>
> DYS 449: 24 (0); 25 (6); 26 (31); 27 (41); 28 (191); 29 (133); 30 (55); 31
> (16); 32 (1); 33 (1).
>
> DYS 454: 10 (4); 11 (460); 12 (11).
>
> DYS 458: 12 (2); 13 (2); 14 (58); 15 (306); 16 (90); 17 (16); 18 (1).
>
> DYS 459a,b: 7,8 (1); 7,9 (17); 8,8 (16); 8,9 (417); 8,10 (9); 9,9 (14);
> 9,10 (1).
>
> DYS 460: 9 (10); 10 (355); 11 (107); 12 (3).
>
> DYS 461: 10 (71); 11 (362); 12 (40); 13 (2).
>
> DYS 462: 9 (1); 11 (4); 12 (322); 13 (142); 14 (6).
>
> GGAAT1B07: 9 (1); 10 (10); 11 (453); 12 (11).
>
> YCAIIa,b: 17,21 (1); 19,19 (9); 18,21 (6); 19,20 (6); 19,21 (424); 19,22
> (13); 20,21 (4); 21,21 (9); 19,23 (1); 18.22 (0).
>
> Y-GATA-A10: 11 (4); 12 (55); 13 (337); 14 (55); 15 (24).
>
> Y-GATA-C4: 20 (5); 21 (174); 22 (199); 23 (71); 24 (20); 25 (6).
>
> Y-GATA-H4: 10 (62); 11 (389); 12 (23); 13 (1).
>
> As noted by others and as indicated above, virtually all (about 99%) of
> these I1a haplotypes have 11 repeats for locus DYS 426. In order to obtain
> an estimate of the distribution of those DYS loci present in the GU I1a
> haplotype, further searches were performed using in each case 11 for DYS
> 426 and the GU I1a haplotype but allowing in turn one of the DYS loci in
> the GU I1a haplotype to vary. In each case 8/8 exact matches were
recorded.
>
> DYS 19/394: 12 (0); 13 (6); 14 (469); 15 (101); 16 (16); 17 (4); 18 (0).
>
> DYS 391: 8 (0); 9 (5); 10 (469); 11 (42); 12 (1).
>
> DYS 392: 10 (0); 11 (469); 12 (10); 13 (5); 14 (0).
>
> DYS 393: 11 (1); 12 (13); 13 (469); 14 (47); 15 (8); 16 (0).
>
> DYS 455: 8 (469); 9 (1); 10 (0); 11 (2).
>
> DYS 389i,ii: 12,26 (1); 11,29 (2); 11,27 (2); 12,27 (12); 12,28 (469);
> 12,29 (82); 13,29 (36); 13,30 (14); 12,30 (8); 14,30 (3).
>
> These latter results confirm that there is very little, if any,
> distribution in the repeat value of 8 for DYS 455 in these I1a haplotypes.
> They also indicate that for I1a haplotypes there is very little
> distribution in the repeat value of 11 for DYS 392 as well. However, there
> is enough variance in repeats for the other loci (19/394, 391, 393,
> 389i,ii) that there are clearly considerably more I1a individuals in the
> SMGF database than the 475 found using the GU I1a haplotype.
>
> The repeat patterns for several of the DYS loci indicate a bimodal
> distribution suggesting that the I1a haplotypes being sampled are derived
> from at least 2 different subclades. However, for other DYS loci it
appears
> that all of the I1a haplotypes sampled started from a single repeat value.
> Those more statistically sophisticated than I am could therefore
presumably
> calculate at least relative values for the mutation rates at these DYS
> loci. Or assuming a specific time when the SNP mutation leading to the I1a
> haplogroup occurred, estimates of the actual mutation rates at these DYS
> loci could presumably be made.
>
> Gordon Hamilton
>
>
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