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From: "O. W. Odom" <>
Subject: [DNA] More on mt Haplogroup "U5a2"
Date: Mon, 17 Dec 2007 00:08:36 -0600


I have done more study of the subclade of mitochondrial Haplogroup U5a
defined by coding mutations A13827G and G13928C ( a transversion), and
usually accompanied by HVR1 mutations C16114A (a transversion), C16192T,
C16294T, and G16526A. I am now calling this subclade "U5a2" for simplicity,
realizing that this may not be its eventual name.There are now about 15
complete sequences in GenBank (thanks to Ron Scott for the summary) with
the above defining coding mutations: 1 from Portugal submitted by Pereira
et al., 3 from the U. S. submitted by FT-DNA (including my own sequence), 1
from eastern Siberia ( a Koryak) submitted by Ingmann, and 10 from Finland
submitted by Moilanen, Finnila, et al. All 15 of these sequences also show
all of the above HVR1 mutations except for one case in which 16192T has
apparently back mutated to the original C. But perhaps the most interesting
thing, in agreement with results reported by Ann Turner and Anne
Nelson, is that all of these sequences show some additional mutations
defining further subclades. These additional mutations range from a single
back mutation (at 16256, one of the original defining mutations for U5a)
for the Portugal sample, to 3 additional mutations for my sequence and 4
for one of the other FT-DNA submissions. Some of these additional mutations
are in HVR1 itself, but more are in the coding region. So I fully concur
with Ann and Anne that there is a wealth of new information to be obtained
from the mt full genome sequence.

I have also looked at U5a HVR1 data at the Haplogroup U5 project and at
Mitosearch to see if the temporal order of occurrence of the "U5a2"
-associated HVR1 mutations can be determined. Using the maximum parsimony
principle, it looks as if the order of occurrence of these 4 mutations was
first 16526A, then 16192T, then 16294T, and finally 16114A. This
conclusion is based on the finding of 9 U5a sequences having 16526A but not
the other 3, 25 sequences having 16526A and 16192T but not the other 2, 2
sequences having 16526A, 16192T, and 16294T, but not 16114A, and 27
sequences having all 4 mutations. Four sequences have 16526A, 16294T, and
16114A, but not 16192T, which I attribute to a back mutation in the latter.
The most uncertain part of this timeline seems to be the order of
appearance of 16294T, since only 2 sequences support its appearance before
16114A. When the coding region mutations 13827G and 13928C appeared
relative to the HVR1 mutations is not known since most of this analysis was
done with HVR1-only data, but there is one U5a Finnish complete sequence
with just 16526A, and it does not show 13827G and 13928C, which suggests
these coding region mutations appeared after 16526A.

By the way, I also looked at Ingmann's mtDB to see how common the defining
mutations for "U5a2" are in other branches of the mitoTree. Individually,
all of these mutations occur in other branches. C16294T is even one of the
defining mutations for mt Haplogroup T. However, the combination of 13827G
and 13928C seems to be specific for "U5a2" as is the combination of 16526A
and 16114A, or 16294T and 16114A.

Obed






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