mtHaplogroup T

[fmoakes]

Quote:
Originally Posted by penguin
I know what you mean. When I first started 2.75 years ago, there were only 2 other T5s. Now there's 62.
I don't know what the growth function looks like since they began - would be fun to see that graph.


It is great that more Hg Ts have been tested in the HVR, resulting in more T5s. My wife is one of those 62, that you mention (mitoSearch 6QVCU). I, also, have her listed as 6KBQM (T2). She was initially listed as T5, by FTDNA based on her 16153A, as do the other 61 of you.
However, when her FGS (Full Genome Sequence) results came back, FTDNA changed her designation to T2. This is because the published papers for FGS Hg T results only separate Ts into T1 and T2. She matches the FGS T2 markers, 11812G and 14233G.
The fact that the definition for FGS T2 is entirely different than the definition for HVR1 T2 seems to not be very important at FTDNA. Only last week, I received another assurance that this issue is on the list to be addressed in a future revision to FTDNA's website. This has been going on since her FGS results came back in Dec 2006.
I would encourage all you mtHg Ts (especially T5s), that can afford the cost, to get the FGS test. You would be contributing to filling a real gap in the data of this new science that we all find so fascinating.
Floyd Oakes
Co-Administrator
OAK Family DNA Project

[fmoakes]

Quote:
Originally Posted by MMaddi
Well, since I have HVR1/HVR2 results and have been classified as T5, I'm waiting for an offer from FTDNA for a discount on the FGS to resolve that issue. Otherwise, it'll be awhile until I save up for the full price of the FGS.


Maybe we should request that FTDNA offer all T5s a special Coding region test for the T2 markers, 11812G and 14233G in lieu of the FGS. I have not looked closer, but maybe the T3s and T4s need the same test?
Floyd

[fmoakes]

Quote:
Originally Posted by Johnserrat
I'm all in favour of your plan Floyd! If FTDNA is willing sign me up.

John


John and other mtHg T5s,
Stay tuned. Something may happen.

In a message dated 11/28/07 7:08:19 PM, FMOAKES writes:

Bennett,
As you are aware, the subclade structure of mtHaplogroup T is in disarray.
My wife, Kit# 34796, was changed from HVR1 T5 to T2 when her FGS results were reported.
Eilleen reports that there are now 4 FTDNA Haplotypes that have been classified T2, following FGS testing, that have mutation 16153A, which is the basis for a T5 designation with an HVR only test.
I recently entered her HVR1&2 markers at the new GeneTree site, where they classified her as T2. They declined to disclose their mtHaplogroup sorting algorithm.
I understand and have no argument with FTDNA's process of classifying mtHg T subclades following the FGS test.
I would like to propose that FTDNA offer all HVR1 based T5 customers a special Coding Region test for the mutations, 11812G and 14233G, which I believe FTDNA uses to designate T2 with the FGS.
There has been some discussion on the FTDNA Forum that suggests there would be a good response to such an offer, to clarify their personal mtHt and assist in building the data base necessary to restructure the mtHg T subclade structure.
Thank you for your consideration,

Floyd Oakes
Co-Administrator
OAK Family DNA Project


In a message dated 11/28/07 10:23:23 PM, [email protected] writes:

Hi Floyd

As I understand it the leading mtDNA scientists have an agreed upon rule set that when just HVR-1 is used will define someone as T5 while hewn using the FGS (or perhaps just the HVR-2) would change that into T2, but clearly the FGS while expensive is the best scientifically

Let me speak to both of these guys and I’ll see if they feel this is do-able to test for these two markers locations to redefine folks as T2 versus T5

Best Regards

Bennett Greenspan
President
www.familytreedna.com

[fmoakes]

Quote:
Originally Posted by R2-D2
It sounds like 11812G and 14233G should define T2 instead of 16304C; and 16304C and 16153A should define subclades of T2.


I agree, based on what I've seen. A thorough study of the issue might uncover additional twists. I have not looked into the issue of T3 and T4. They seem to be standing out in the cold, since FGS Ts are only divided into T1 and T2.

[vraatyah]

Quote:
Originally Posted by R2-D2
It sounds like 11812G and 14233G should define T2 instead of 16304C; and 16304C and 16153A should define subclades of T2.

16304 defines T2b; as to the ancestral T2, the closest candidate site within the CR is 16296 which usually predicts being in T2.

On the other hand, if some T5 testees want to to be places into T2, why those with 16292 who were once placed into T3 don't want a coding region check to fall into T2c? Actually it's a sort of the same thing as happened to T5.

[fmoakes]

16304 defines T2b; as to the ancestral T2, the closest candidate site within the CR is 16296 which usually predicts being in T2.

On the other hand, if some T5 testees want to to be places into T2, why those with 16292 who were once placed into T3 don't want a coding region check to fall into T2c? Actually it's a sort of the same thing as happened to T5.

I am curious about your comment that "16304 defines T2b".
I believe the mutations used by FTDNA to make T subclade designations are those in:
Journal of Genetic Genealogy 2:1–11, 2006

Phylogenetic Networks for the Human mtDNA Haplogroup T
David A. Pike

Subgroup Associated HVR1 Mutations
T1 16163–16186–16189
T2 16304
T3 16292
T4 16324
T5 16153
Table 1: Mutation Positions and Subgroups

In Ian Logan’ site
www.ianlogan.co.uk 'mtDNA'
the T2 tree shows T2 qualifying mutations as “11812 and 14233, 16296 varies, 16304 varies”.
16292 (Pike’s T3) is a subordinate branch as is 16153 (Pikes’s T5) on another branch. However I was unable to locate 16324 (Pike’s T4) in any part of Logan’s mtHg T tree.

I agree, more than just the current T5s need at least the Coding Region test for mutations 11812 and 14233.
Floyd Oakes

[vraatyah]

I am curious about your comment that "16304 defines T2b".
I believe the mutations used by FTDNA to make T subclade designations are those in:
Journal of Genetic Genealogy 2:1–11, 2006

Phylogenetic Networks for the Human mtDNA Haplogroup T
David A. Pike

Subgroup Associated HVR1 Mutations
T1 16163–16186–16189
T2 16304
T3 16292
T4 16324
T5 16153

before the complete sequencing was introduced

In Ian Logan’ site
www.ianlogan.co.uk 'mtDNA'
the T2 tree shows T2 qualifying mutations as “11812 and 14233, 16296 varies, 16304 varies”.

16296 varies, 16304 does not (with few exceptions). Actually, "16304 varies” is likely because Ian prefers phylogenetic methods other than parsimony.

However I was unable to locate 16324 (Pike’s T4) in any part of Logan’s mtHg T tree.

There are no completely sequenced T4 molecules.

[fmoakes]

vraatyah,
I am still curious about your comment that "16304 defines T2b".
Do you have a ref. document for that designation?
Floyd

[vraatyah]

vraatyah,
I am still curious about your comment that "16304 defines T2b".
Do you have a ref. document for that designation?
Floyd

what kind of paper do you mean? an official sealed certificate? I don't. Instead, you may go to the Genbank database, download all the complete sequences available, run your phylogenetical programs (all you rely on) and make your own conclusions. Instead you may read some papers with sufficient RFLP data published last years, and correspond to their authors, if they have any idea on this topic (how 16304 is related to coding-region markers). Do you prefer a simple answer, like a table in Pyke's paper? OK. "Usualy T+16304 = T+5147".

[swbtmis]

16458T and T2

does anyone know what the 16458T indicates in a T2?

seems rather rare.

I have it in HVR2 and only found 16 other T2's out of hundreds with it.\

could it indicate an area?

[c_thompson_68]

Any updates on mtHaplogroup T3? I am an adoptee with no matches or ancestral origins listed from the ftDNA database. I believe my birth-mother's surname is of French Norman origin.

What is the geographic location T3, is it Scandinavian, or Celtic? I have heard there are T3's in Iceland, and the Vikings frequently took Celtic wives, and Iceland has a high percentage of people of Celtic ancestry. Other T3s have appeared in areas briefly colonized in the past by the Normans: Italy, Malta, etc.

Since I have not yet meet my birth-mother, I cannot provide more information on family history. I was hoping someone else could provide an update on mtDNA Haplogroup T3.

Haplogroup - T3
HVR1 differences from CRS
16126C,16183C,16189C,16292T,16294T,16296T,16380T,1 6519C

HVR2 differences from CRS
73G,146C,263G,309.1C,309.2C,315.1C,522-,523-