B2d but 24 extra mutations and 1 missing

[mcornejo]

Hi, I submitted my wife's sample for FMS and FF, the mtDNA haplogroup according to FTDNA is B2d, there are no matches at all. The FMS results show 24 extra mutations and 1 missing mutation.

I downloaded the FASTA file and ran it through other tool/database available online, Human Mitochondrial Database, which predicted the haplogroup as R_16189 with a higher confidence than that one reported for B2d.

Since there are no matches and there are many extra mutations and 1 missing, I thought of asking through this forum if there is a probability of error and if yes, what steps (besides getting in touch with FTDNA) are recommended, in order to reduce uncertainty.

Thanks to all in advance.

[Ann Turner]

Have you tried James Lick's tool?

http://dna.jameslick.com/mthap/

[mcornejo]

Hello Ann,

Thanks for suggesting James Lick's tool. The results in that tool confirm B2d and extra mutations. Perhaps B2d is a haplogroup without a large amount of samples in FTDNA and hence the reason why there were no matches and so many mutations?

Results from JL's tool, which I am not 100% on how to interpret them, so I will keep doing some more research.


Best mtDNA Haplogroup Matches:

1) B2d

Defining Markers for haplogroup B2d:
HVR2: 73G 263G 498- 499A
CR: 750G 827G 1438G 2706G 3547G 4122G 4123G 4769G 4820A 4977C 6473T 7028T 8281- 8282- 8283- 8284- 8285- 8286- 8287- 8288- 8289- 8860G 8875C 9682C 9950C 11177T 11719A 13590A 14766T 15326G 15535T
HVR1: 16189C 16217C

Marker path from rCRS to haplogroup B2d (plus extra markers):
H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 16189C ⇨ R(T16189C) ⇨ 8281- 8282- 8283- 8284- 8285- 8286- 8287- 8288- 8289- ⇨ B ⇨ 16217C ⇨ B4 ⇨ 827G 15535T ⇨ B4b'd'e'j ⇨ 499A 4820A 13590A ⇨ B4b ⇨ 3547G 4977C 6473T 9950C 11177T ⇨ B2 ⇨ 498- 4122G 4123G 8875C 9682C ⇨ B2d ⇨ 152C (309.1C) (309.2C) (315.1C) 1719A 8485A 11914A 11986T 16111T (16182C) (16183C) 16324C (16519C)

Good Match! Your results also had extra markers for this haplogroup:
Matches(37): 73G 263G 498- 499A 750G 827G 1438G 2706G 3547G 4122G 4123G 4769G 4820A 4977C 6473T 7028T 8281- 8282- 8283- 8284- 8285- 8286- 8287- 8288- 8289- 8860G 8875C 9682C 9950C 11177T 11719A 13590A 14766T 15326G 15535T 16189C 16217C
Extras(7): 152C (309.1C) (309.2C) (315.1C) 1719A 8485A 11914A 11986T 16111T (16182C) (16183C) 16324C (16519C)


Kind regards.

[Ann Turner]

The total number of differences depends on how close you are to the reference sequence. For the RSRS (Reconstructed Sapiens Reference Sequence,an attempt to infer what the sequence for mitochondrial "Eve" looked like), everyone living today is equidistant from her and will have dozens of differences. For the CRS (Cambridge Reference Sequence), it depends on how close you are to the random sample used to perform the first sequence, which happened to be a European sample in haplogroup H. The RSRS is not in very wide use, and the James Lick tool uses the CRS.

"Extra" mutations generally refer to ones not used to define a haplogroup. Are you saying that your RSRS results show such a large number? And that they are different from what James Lick calls "extras"? Maybe a screen print would help. Oh, and the deletion 8181-8189 is actually just one mutational event. There's a repeat pattern of those 9 bases and the deletion (occasionally insertion)is a bit of a hot spot, showing up in a number of different haplogroups.

[mcornejo]

Hi Ann, thank you for your comment. Below I am commenting to each of your points.

- "Extra" mutations generally refer to ones not used to define a haplogroup. Are you saying that your RSRS results show such a large number?

*Yes, the count of extra mutations is 24 in RSRS results, hence the reason I was curious to understand if it is normal to see such a large number.

- And that they are different from what James Lick calls "extras"? Maybe a screen print would help.

* I am attaching screen shots of FTDNA's RSRS and CRS results.

Thanks for your help!

[Ann Turner]

OK, a lot of those "extras" can be discounted. I question whether the deletion of 9 bases 8281-8289 should even go in that section, as they are part of the definition for B2. Other mutations In James Lick's list of extras are in parentheses because they are "hot spots" -- very variable positions, which can differ even between siblings. 522.1A and 522.1C appear in many people's lists because of the way the RSRS was calculated. And so forth.

The more substantive extras are in Lick's list without parentheses. Those could eventually be part of a motif for a new subclade under B2d. In any event, the lack of a match for your wife's results would reflect the low representation of B2d in the FTDNA database, not a problem with the sequence analysis.

[Armando]

The way the deletion of 9 bases 8281-8289 is showing in the results as extras could be part of the reason there are no matches, although it is an uncommon subclade. I know of relatives of mine that have solid documentation back to the same ancestor and have only a difference of one mutation but don't show as matches because of how the "extras" show up. There are actually several situations like that. Gail of the H10 haplogroup project has mentioned a matching problem with other people also and has reported it to FTDNA. Here is one post where she mentions that problem - http://forums.familytreedna.com/show...85&postcount=4