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From: "Ken Nordtvedt" <>
Subject: Re: [DNA] "Missing Data" in the SMGF Y-chromosome database.
Date: Thu, 13 Oct 2005 13:56:35 -0600
References: <20051012123429.58969.qmail@web50113.mail.yahoo.com> <001201c5cf66$cc04af00$676860cb@Marsh> <001f01c5cfc3$ed9ba4e0$1b6860cb@Marsh>


I wonder what's going on here? I checked a past tabulation of "Irish" R1b
from Sorenson --- with 25/11/14 at DYS390,391,392 plus 4 other fixed markers
to define the variety, and I found the DYS463 count only 1 haplotype short
of the full count of 152 haplotypes. This seems to further isolate this
"missing data" effect to a specific haplotype motif.

Ken


----- Original Message -----
From: "Alister John Marsh" <>
To: <>
Sent: Thursday, October 13, 2005 1:00 AM
Subject: Re: [DNA] "Missing Data" in the SMGF Y-chromosome database.


>I have spend a little time looking further at cases of missing DYS463. I
> have only considered cases where there were 1 or less missing marker from
> a
> 36 marker haplotype, and checked up to 150 haplotype near matches for each
> case. (Often to matches out to about 26/36) These are the percentages
> found for matches to the following haplotypes...
>
> [including DYS390/391/449/452/463- Sorenson calibration]
>
> A) R1b: 16.9% [24/11/28/29/25]
> B) R1b: 15.6% [24/10/30/29/25]
> C) R1b: 10.3% [24/10/28/29/25]
> D) R1a: 10.3% (small sample)
> E) R1b: 8.2% [23/11/30/30/24]
> F) I1c: 6.6%
> G) R1b: 3.4% [23/12/32/30/24]
> H) R1b: 1.3% [23/11/30/30/24] (Fresian type?)
> I) I1a: 0.9%
> J) E3b: 0.0% (small sample)
>
> A is my haplotype, and B & C were haplotypes about 10 or 12 mutations off,
> which however had something suggesting to me possibility of a very deep
> ancestry link.
>
> In the R1bs, most of the missing data I have found seems to trace to
> England
> or Ireland.
>
> In searching, it seems that there may be clusters of haplotypes which have
> similarities, associated with no data for DYS463. Similar seems to apply
> to
> DYS452. They occur in more than one haplogroup.
>
> The no data for DYS463 (and DYS452) seems to occur in different
> haplogroups
> at rates higher than other markers.
>
> If it is a separate events causing the 6.6% in I1c, or 10.3% in R1a, from
> the R1bs, I wonder if it could be a slow mutating STR in the neighbourhood
> of DYS463, rather than a SNP? Is that possible?
>
> There must be more than one cause of the no data events in DYS452 &
> DYS463,
> as it effects different haplogroups, but as some haplotype groupings
> have
> more missing data, there would seem a possibility that SNP type events
> near
> DYS463 may in some cases be a cause.
>
> John.
>
>
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