GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2004-07 > 1089242437


From: "Whit Athey" <>
Subject: RE: [DNA] I1a and Distribution of DYS Values
Date: Wed, 7 Jul 2004 19:20:37 -0400
In-Reply-To: <5.1.0.14.2.20040707115344.022f78d8@mail.psu.edu>


Hi Gordon. The information on allele frequencies matches exactly with the
modal values I have found from DYS-455=8 haplotypes in Y-Base, except for
DYS-390, which you noted showed bimodal values. In my data, the 23 value
runs slightly ahead, whereas you found the 22 value to be slightly more
prevalent.

Whit


-----Original Message-----
From: Gordon Hamilton [mailto:]
Sent: Wednesday, July 07, 2004 3:06 PM
To:
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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