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Subject: [DNA] Is the CRS H2b or H2a2? And other haplogroup name changes
Date: Tue, 2 Jan 2007 11:56:32 EST


Last year (a couple of weeks ago, actually) I posted a message about a change
in nomenclature for haplogroup H2, where the CRS resides.

http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2006-12/1166732993

The CRS was formerly labeled H2b, but that label was changed with the
publication of a recent paper:

Mol Biol Evol. 2006 Nov 10; [Epub ahead of print]

Origin and Expansion of Haplogroup H, the Dominant Human Mitochondrial DNA
Lineage in West Eurasia: the Near Eastern and Caucasian Perspective.

Roostalu U, Kutuev I, Loogvali EL, Metspalu E, Tambets K, Reidla M,
Khusnutdinova EK, Usanga E, Kivisild T, Villems R.

I forwarded my GENEALOGY-DNA message to the corresponding author Eva-Liis
Loogvali and asked for her feedback. Her reply explains the background and makes
a practical suggestion on how to handle nomenclature changes. I'd suggest
reading my old message in the archives first, then the response from her:

===== begin e-mail from Dr. Loogvali

Dear Ann Turner,
Of course you have got it right. Its like that with every nomenclature when
people are trying to classify natural objects. Evolution and lack of
recombination makes the mtDNA and Y chromosome haplogroups "real", but our limited data
allows to reveal only a fragmentary picture. As this picture is ever
improving, things have to be renamed once in a while, to follow the cladistic
nomenclature rules.

You are also right about the notion that better represented clades usually
get lower numbers-letters. For people who are trying to locate their position in
a DNA tree, it is best to use the Y chromosome researchers strategy: remember
the larger haplogroup name you belong to and the last defining mutation(s) of
a subhaplogroup. The particular case would come out as H2-750 or more
specifically H2-750-3388A (I believe its a transversion C to A, and not a transition
as the mtDNA mutations usually are).

Best Regards, Eva-Liis

===== end e-mail from Dr. Loogvali

Now that full sequence results are coming in from FTDNA, I've been writing
custom reports for a number of people who have a change in their haplogroup
assignment based on coding region mutations. When I dig into the background, I can
usually see why there is a difference, and I believe the coding-region
assignment should take precedence.

However, that leaves a dilemma for matching strategies at MitoSearch, where
people can search by haplogroup. Dr. Loogvali's suggestion of referring to
H2-750 would be the most stable in the long run, but there are thousands of
previous and future MitoSearch entries that will be based solely on HVR results and
labels like H2b (or T5 renamed T2, or U5a1a bumped up to U5a1).

I sort of cringe when I make this suggestion, but I have been advising people
to make dual entries at MitoSearch, with a detailed explanation in the notes
section. It seems like the best option at the moment for a hybrid database,
based primarily on HVR data for the present and foreseeable future. Any other
suggestions?

Ann Turner




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