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mtDNA: Using Raw Data to Fill Out Your Subtree

October 11th, 2012 · by Cyndi · 6 Comments

I’ve been heavily into genealogy for the last year, fleshing out both my and my husband’s family trees.  Recently, I decided to delve into DNA.  I chose 23andme and have been thrilled with the results (this link gives me a small referral fee, thanks if you use it).

One of the things they tested me for was my mitochondrial DNA (mtDNA).  This is special DNA (not within the chromosomes) that everyone has but you only get it from your mother (it’s in egg cells but not sperm cells).  In theory, I have the same mtDNA as my mother, her mother, her mother, and so on back to the beginning of human history.  In practice, DNA copying isn’t perfect.  Mutations (think of them as typos) sneak in.  We can use the mutations to track maternal history across the generations, by when (and where) the splits happened.  Each set of mutations is labeled with what is called a Haplogroup.

My mtDNA Haplogroup, as calculated by 23andme, is U6a7.  About 45,000 years ago, a group of humans left Africa for Europe.  According to the mutation history, those who stayed in Europe had the Haplogroup U5 and those who turned back into northern Africa were U6.  About 35,000 years ago, U6a spread around northern Africa.  FamilyTreeDNA puts U6 at 36,200 years ago and U6a at 26,900 years ago.  But close enough.

23andme tells me my subclave is a7 but only gives information about U6 when saying this means my maternal line is from “North Africa, the Near East, Iberian Peninsula, Canary Islands” and that the population I best match are the Berbers.  Is my maternal line Muslim?  Or Sephardic Jewish?  I don’t know.  All I know is that I’m Ashkenazi Jewish on all sides and my maternal grandmother and her mother are from Kosice, Slovakia. I haven’t been able to go any further back.

The FamilyTreeDNA page on U6 gives far more subgroups: U6a7a, U6a7a1, U6a7a1a, U6a7a1b, U6a7a1c, U6a7a2, and U6a7b. Which one am I?  I wrote 23andme for help and they did take a lot of time to explain things, but none of it got me that far.  If you have a 23andme account, log in and go to Ancestry Labs, then choose Haplogroup Tree Mutation Mapper and submit your Haplogroup.  You’ll see a long list that looks like this:

U6a7 defining mutations
variant call rCRS anc
rs28357684 A 15043 G
i3001344 15043 G
i5049907 15043 G

 

The variant is the SNP, the piece of the gene where the mutation in question is.  The rCRS (also called position) is a number more commonly used but specific to a gene or, in this case, the mtDNA.  Anc means the ancestral, regular, non-mutation form and the call is the result, or the genotype, of the person tested.  This mutation defines U6a7 (and has three variants).  Since my call (A) is different from the ancestry (G), I have the mutation and therefore am U6a7.

Unfortunately, there’s nothing that goes beyond U6a7.  23andme doesn’t have a system to pay extra for a more detailed test.  But maybe the answer was already there.  I didn’t want to pay FamilyTreeDNA or another company for a test if I didn’t have to.  23andme also told me it was possible I simply didn’t have markers to identify subgroups, so another test might not give me a better answer.

So on to the raw data.  What could it tell me?

The Mutation Mapper page at 23andme shows you a circle with a lot of the raw data, but it is incomplete.  The better option is to to click on “Account” on the top of the page then choose “Browse Raw Data” and click on “MT.”  It’s faster if you download it all into a text file, but you can also look online.  (Of course, you can use raw data from any company.)

The data will look like this online:

Gene Position SNP Versions My Genotype
intergenic 3 i4001200 C or T T
intergenic 7 i4001110 A or G A
intergenic 9 i4001358 A or G G
intergenic 26 i4000553 C or T C

 

The downloaded version (the text file) looks a bit different:

rsid chromosome position genotype
i4001200 MT 3 T
i4001110 MT 7 A
i4001358 MT 9 G
i4000553 MT 26 C

 

The name of the gene (mtDNA has 37) and the SNP (or rsid) isn’t useful here, just look at the position (the rCRS).  This is how you’ll match up results with known mutations.  The versions are what’s possible and then it gives the test results, my genotype.  Note that it doesn’t say which result is a mutation and which is ancestral.  Nor do I know which positions have relevant mutations.  Time for more research.

The FamilyTreeDNA page on U6 does list all the mutations for each subgroup but not what the genotype is supposed to be.  I needed to keep looking.

I found this amazing resource:

http://www.phylotree.org/tree/subtree_U.htm
(they have other trees here: http://www.phylotree.org/tree/main.htm )

I paged down to U6a7 and saw that there were mutation lists for three variants: U6a7a, U6a7b, and U6a7c

Each mutation is in the form: letter-number-letter (plus some optional markers).  For example: T1193C.  This means rCRS 1193 has two genotypes, T and C.  The first letter is the “normal” or ancestral expression of that SNP.  The second letter is the mutation.

Another example: U6a7 is defined by: G15043A.  If this position is an A for you, then you have the mutation and are U6a7 (perhaps with some other precursors established).  If you have a G instead, then you do not have the mutation and are not U6a7.

Using Phylotree, this is what I did next:

  • U6a7a has 8 defining mutations.  I was tested for 4 of them.  3 were positive for the mutation and one was not.
  • U6a7b has 7 defining mutations.  I was tested for 4 of them, all negative.
  • U6a7c has 2 defining mutations.  I was tested for both and one was positive, the other negative.

I concluded that I was U6a7a.  (Why I didn’t get perfect matches, I don’t know.  This data was pretty clear, but I don’t know how to interpret it when it’s not.)

That is as far as I could go at Phylotree, so I headed back to
http://www.familytreedna.com/public/U6mtdna/default.aspx?section=results

Next, there is U6a7a1 and U6a7a2.  Within U6a7a1 there is U6a7a1a, U6a7a1b, and U6a7a1c.  I suspected I was U6a7a1b because it’s the Sephardic cluster and also in the general area my maternal line is from.  That one is defined by the mutation 150.  But this site doesn’t tell you which letter is the mutation.  I had to look elsewhere for that.  I did some more research and discovered that the mutation will be T.  I found that here (I’m not Dominican but that didn’t make the page less useful to me): http://www.familytreedna.com/public/dominicansephardim/default.aspx?section=results

What am I?  I’m a 150T.  So I concluded that my mtDNA is U6a7a1b.

I also joined the FamilyTreeDNA U6 project.  The leader asked for my raw data and I gave it to him.  He agrees.  I’m U6a7a1b.  He says “You have an extra mutation 16295T” (not one of the positions I had looked at).  So far there are only 12 people in the U6a7a1b section of the project, and I’m the only one with the extra mutation.

What does this mean?  It means I can now trace my maternal line to a mutation split that happened about 1,500 years ago, a “Sephardic cluster from Spain, Italy, Germany, Poland and Ukraine.”  With the extra mutation, I might even be able to narrow it down further.

Who are my ancestors?  Let’s go back to the Dominican page:

Haplogroup U6 can be considered to be the mt-DNA equivalent of Y-DNA haplogroup E1B1B in that it is of North African origins and its distribution matches the Afro Asiatic linguistic expansion. The U6 research project has discovered what it believes to be a Sephardic Cluster in haplogroup U6A7A1B characterized by mutation 150T. U6 can be found in small percentages among Sephardic Jews and even Ashkenazic Jews. Similar to haplogroup E1B1B, U6′s presence among Jews may date back to ancient times when the founding members of the Israelite tribes performed conversions on local Canaanite women, to allow them marry tribal members prior to their descent to Egypt. Another possibility is that this lineage joined the ancient Israelites along with the “mixed multitude” that came out of Egypt with the Israelites, as described in the Bible. It is also possible that Berber conversions to Judaism during the Muslim occupation of Spain introduced this lineage to the Sephardic gene pool. This haplogroup has been found in the Sephardic Jewish communities of the former Ottoman Empire. A member of this project with a tradition of Jewish ancestry on his/her maternal line, and is a member of this haplogroup, can be considered to be likely of Jewish descent.

So wow.  23andme gives me “northern Africa” but a bit of sleuthing gives me evidence that my maternal line (the one that counts here) is Jewish possibly all the way back to the Exodus (perhaps further).  With Sephardic ancestry to boot.  Amazing.

Categories: Genealogy
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6 responses so far ↓

  • 1 S Lofton // Apr 6, 2013 at 5:44 pm

    Wow.You know more of how to decipher mtdna in laymans terms better for regular folks to comprehend. Your end conclusion is the same as it is for me. Using autosomal & mtdna results point my genetic ancestry as Jewish – Saphardi.
    U6a3b:
    CRS VALUES:
    EXTRA MUTATIONS
    291.1A 309.1C 315.1C
    C960D T1809C C5554a
    G6182A A111272G A15380G
    A16183c C16519T

    MISSING MUTATION C146T

  • 2 Cyndi // Apr 6, 2013 at 7:07 pm

    Thanks! Are you part of the U6 project at FTDNA? Really good folks there. Interesting that your U6 branch is also Sephardic. Because not all U6 are even Jewish. I didn’t realize there were U6a3′s who were too. Very cool.

    Cyndi

  • 3 David // May 7, 2013 at 10:12 am

    Wow, that’s amazing! I got my 23andme results some weeks ago and, to be honest, I’m a bit lost!! I’ve been shocked and investigating the paternal line but, it’s time to go for the maternal one also, which is like yours U6a7
    I was trying to go farther with genealogy (but it has been a bit desperating). I’m trying to understand what you did to obtain the subgroup…
    By the way, to be a part of the FamilyTreeDNA U6 project it’s ok if you are not FT tested?

  • 4 Cyndi // May 7, 2013 at 10:59 am

    Hi David. Please go to 23andme and initiate a share request with me. I’m under Cyndi Norwitz. Chances are we aren’t closely related, despite sharing the mtDNA, but I’d like to see anyway. I do have a 23andme transfer to FTDNA but not an mtDNA test there. The gentleman who runs the U6 project was fine with me joining and I emailed him my raw data to confirm the halpogroup. But I don’t know if you can join if you don’t have an FTDNA account at all. His contact info is on the FTDNA page for U6, so I’d just ask him.

    Cyndi

  • 5 Amy // May 30, 2013 at 11:42 pm

    This is absolutely great info for me. I am adopted and have no idea what my genealogy or bio relatives are. I received the first part of my info from 23andme yesterday evening. My health risks and maternal haplogroup. I am U6a7 and until reading this I had no clue want it really meant. Thanks. I will be uploading my raw data to other databases as soon as I receive it.

  • 6 Cyndi // May 31, 2013 at 7:36 am

    Thanks Amy. I don’t match autosomally with most other U6a7s, but please feel free to initiate a genome share with me on 23andme. If your recent ancestry is Jewish, we’ll likely match somewhere :-)

    Cyndi

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