Why would two full sisters have slightly different haplogroups reported with testing? [closed]

+10 votes
I received test results from a full sequence MtDna test at Ftdna in Jan, 2017: H3aj.  Subsequent autosomal testing at 23andme and LivingDna included assignment of haplogroup H.

Recently my full sister tested at 23andme and was assigned haplogroup H3af. (not on WikiTree)

Is there an explanation for this variation?  Which should be used in tracing our maternal line?


WikiTree profile: Jo McCaleb
closed with the note: answered
asked in The Tree House by Jo McCaleb G2G6 (9.4k points)
closed by Jo McCaleb
23andme tests out and reports the full sequence. Family Tree DNA only reports the full sequence if you pay for Full sequence mtDNA testing.

It appears that you only tested HRV1 and HRV2.

I tested first with FTDNA but did not pay for the full sequence test and my mtDNA is, per them, haplotype "J".

I subsequently tested at 23andme and they report my mtDNA haplogroup as J2b1a3.

I suspect that if you upgrade to a full sequence mtDNA test at FTDNA then you will get the same results as your sister.

By the way you appear to mistyped your sisters results. H3a is a valid haplogroup, H2af is not. It should read something like H2a1 or H2a2


8 Answers

+12 votes
Best answer
You and your sister are probably on different versions at 23andMe. Each version has a somewhat different SNP selection. I'm a bit surprised that you didn't get at least H3 from 23andMe and LivingDNA. Maybe you had a "private" mutation near the marker for H3 (6776), which interfered with the probe.

The full mitochondrial sequence will be more accurate (barring rare events such as parallel or reverse mutations).  I would suggest downloading the raw data from 23andMe and running it through James Lick's tool. He will highlight the mutations used to define the haplogroup according to the most recent phylogenetic tree. Do this also with your FTDNA results. I believe LivingDNA just gives you a short list of differences from the CRS, so Lick's utility won't work on that.
answered by Ann Turner G2G6 (6.1k points)
selected by Jo McCaleb

I'm pretty sure that when 23andme derives an mtDNA haplogroup/subclade from an autosomal DNA test, it's only an approximation. Expecting a completely correct mtDNA typing from an auDNA test is like measuring your cycling fitness based on how fast you run a mile.

No, 23andMe directly tests a subset of mtDNA SNPs, selected to be informative about haplogroups. There's no correlation whatsoever between autosomal DNA and mtDNA or Y haplogroups.
Okay, thanks for the info. But I'm guessing testing a subset means it's roughly akin to FTDNA's "mtDNA Plus" testing, and not their "mtDNA Full Sequence"?
It's sort of in between. FTDNA HVR+ gives you only the "backbone" haplogroup in most cases (a single letter like H or J). 23andMe tests a few thousand locations in the coding region, often (but not always) sufficient to reach the same subclade level as FTDNA, e.g. U5a1a1. The full mitochondrial sequence may sometimes reach a deeper subclade level, and it also reveals any "extra" mutations (ones not used to define a subclade).
+6 votes
Probably because you both inherited slightly different sets of DNA from your parents.

Both of you inherited 50% of your mums dna and 50% of your dads. Your sister may have inherited a largish amount of DNA from your parents, from the half that you didnt get. That will probably affect their ethnicity results (in that it will NOT be identical to yours) and thus also the haplogroup.
answered by Robynne Lozier G2G6 Pilot (498k points)
My question concerns Mitochondrial dna.  That is only inherited through our mothers.  Its what makes it useful for tracing maternal lines.  According to usual description, we don't expect a variation, even our fifth grandmother, etc. should be in the same group.
+8 votes
Well, one thing to consider is that your sister ( or your mother) might have had a genetic change which led to the change in haplogroup.  Another possibility is that 23and me might have read the two of you slightly differently.  You might want to repeat one or both your tests.
answered by Dave Dardinger G2G6 Pilot (368k points)
+6 votes
Howdy, not that I know much about mtDNA study, but if I read your message correctly, it seems that you and your sister each got your primary mtDNA tests at different companies.  I gather that different companies have different methods, algorithms or something like that for reading autosomal DNA and can generate different readings or results. Could not the difference between you and your sister simply be the results of the MtDNA being tested at two different companies?

Just an observation from someone with a beginners understanding of DNA study.
answered by Art Black G2G6 Mach 1 (17.6k points)
+8 votes
If both were tested at the same lab and at the same level then it is very likely their haplogroup would be reported the same.

It is best to use comparisons of RSRS or rCRS differences and not comparisons of reported haplogroups from different labs.
answered by Peter Roberts G2G6 Pilot (447k points)
+9 votes
Having the same mother you would necessarily belong to the same haplogroup. Probably 23andme updated their test to include more mtDNA markers or to their haplotree analysis between when it assigned you to H and your sister to H3aj. If you retested I expect it would assign you to the same haplogroup as her. But 23andme only partially tests mrDNA and only their high-level haplogroup assignment is reliable. Your full sequence results are definitive. It is an expensive test so there is probably no reason to have your sister do it too, she can just use your results. It is possible but unlikely that she has an additional mtDNA mutation that you do not, but any assignment to a different haplogroup would be spurious. The youngest of these two haplogroups is well over a thousand years old.
answered by Nathan Kennedy G2G6 Mach 1 (18.4k points)
+6 votes
I've run into this too and I assume that it's just an artefact of testing. My Mom and I are both on 23andMe. I tested earlier and got I2a. Then she tested and got I2.
answered by Orin Hargraves G2G2 (2.7k points)
+4 votes
Thank you to each of you for replying to my question. You've provided some different viewpoints.--Jo
answered by Jo McCaleb G2G6 (9.4k points)

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