CRS Extended Haplogroup

This posting will assuredly come under the category of “things you never really wanted to know.”  The only time this will really come in useful is if Trivial Pursuit adds a genetic genealogy category, which, by the way, I think would be a wonderful idea!

Did you ever wonder about the person who took the original mitochondrial DNA test and became the Cambridge Reference Sequence?  That was in 1981, so that person may well still be alive today.  The Cambridge Reference Sequence, or CRS, is the standard to which the rest of us are compared.  Our results for mitochondrial DNA testing are the differences between us and that mystery person, so while we probably don’t realize it, the CRS and that person are important to all of us.

Simply by the luck of the draw, given that haplogroup H comprises about 50% of the population of Europe, they are likely to be from haplogroup H.  But are they?

Does anyone know?  Ok, Rebekah Canada can’t play, because, well, I know that she knows.  She helped me unravel this.  That should tell you something right there if you’re familiar with some of the genetic genealogy players.  Rebekah is one of the admins for the massive haplogroup H project and the sole admin for many of the subgroups.  So like Bill Hurst is Mr. MtDNA and Jim Logan is Mr. Hap J, Rebekah is Ms. H.  So that should confirm for you right there that indeed the CRS is haplogroup H.  And it is, but which subgroup?

Every haplogroup has a defining list of mutations that must be present (or back mutated) in order to assign that haplogroup level.  This week, I had a client who had a long list of those haplogroup mutations attributed to their haplogroup by definition, but none of the haplogroup defining mutations were listed on their CRS mutation list.  Confused?  There’s a reason for that.  Keep reading.

Care to guess why their list of haplogroup defining mutations was not on their personal page list of mutations?  Someone out there is pretty sharp….indeed….you’re right….it’s because they matched the CRS at all of those haplogroup defining levels.  This means that this person IS the same haplogroup as the CRS.

Does anyone know what haplogroup the CRS falls into at the full sequence level?

Drum roll…….

H2a2a.

Here are the required mutations for the different subclades of H that lead us to H2a2a.  This is the list of mutations that this client “should have” on their personal page.

Haplogroup Required Mutations
H 2706A,   7028C
H2 14384A
H2a 4769A
H2a2 750A
H2a2a 263A, 8860A, 15326A

However, someone who falls into haplogroup H2a2a won’t show any of these mutations on their list of mutations on their personal page that differs from the CRS, because the CRS is defined as “normal” and everything else is a mutation.

These results, shown above, with the exception of two mutations in the HVR2 region, are equivalent to the Cambridge Reference Sequence.  That means that whatever mutations that anonymous CRS individual had when they were sequenced in 1981 became “the norm” and everyone else is compared against them.  So if they HAVE a mutation, it’s not listed as such because it’s now “normal.”  Does this seem somehow backwards?  It is.  But it’s because that’s all we had in the beginning and we had to start with what we had and where we were in 1981.

This backwardness is particularly evident at location 16519.  You’ll notice that this person doesn’t show a difference at this location.  Most of the people in Europe show this location as a mutation.  What this really means is that the CRS has a mutation at that location, but since it’s considered the norm, the rest of the people, well over 50%, show this as a mutation.

But since these haplogroup defining mutations are the “norm” and since they define the CRS, they don’t show up on the list of mutations that differ from the CRS.  The only two mutations that this person has that differs from the CRS are the insertions at locations 309 and 315, shown above.  So in reality, this means that this person has all of those mutations in the haplogroup defining chart above, which are for comparison purposes, “normal,” plus the two below that differ from the CRS.

I realize this is a bit confusing.  Instead of comparing mitochondrial DNA to someone buried on a branch of haplogroup H who was alive in 1981, we should really be comparing everyone to Mitochondrial Eve.  That is exactly why the scientific world is moving to the RSRS model, the Reconstructed Sapiens Reference Sequence.  The RSRS mutations for this person are shown below, as compared to mitochondrial Eve, and you’ll notice all of the mutations shown in the chart above that define haplogroup H2a2a are present, plus the two at location 309 and 315.

And so, this concludes todays lesson in useless trivia and things you never really wanted to know….

13 thoughts on “CRS Extended Haplogroup

  1. That was great! I really enjoyed reading it but one had to suspect something a long those lines. Thank you for that information. Can’t help but laugh about it. Really is funny!

    Georgia Mathis Cummons H5b–0 matches

  2. Roberta, when you wrote about this the first time, I joined the mtDNA Community and found abt 11 matches. Since then, no one has been added to the group. Would it be helpful if more people would add their information to the Community?? Maybe you need to explain how again.
    BTW, I’m a T1a1 now.

      • Consider yourself lucky! I have not found any matches. My mtDNA Haplogroup is L3b1a7. I have found one match at HVR1 and HVR2, and 4 with matching haplotypes for HVR2. However, no luck for FMS. Good luck to you!

        Sent from my iPhone

  3. Roberta, maybe you meant “Mr. mtDNA K” or just “Mr. K,” not “Mr. mtDNA.”

    I’m not sure about “the scientific world is moving to the RSRS model, the Reconstructed Sapiens Reference Sequence.” Several decades ago the USA started moving to the metric system. Highway signs all had KM above miles. Now they don’t. PhyloTree Build 14, which came out with the RSRS paper, was in RSRS format. Soon after that an rCRS version was published. See this page for a comment with Build 15: http://www.phylotree.org/rCRS-oriented_version.htm

    Sorry for the delay in responding; I had to drive across western KS and eastern CO yesterday and stay awake!

    Bill Hurst

    • I think Roberta said scientific world rather than the world of Mannis van Oven. I think science is ready to move on from the rCRS. Roberta gives a great example of how misleading the lack-of-mutations is for those very close to the rCRS. It is a hindrance to understanding all the way back to the L3 split though.

  4. Thank you for an excellent explanation. I’m H2a2a and your blog post helped me understand the CRS. I guessing I must be related to the original CRS person from 1981.

    • A back mutation is when a mutations happens, like from A to C, and then the reverse happens, a mutation from C to A. It initially looks like no mutation happened, unless you are aware of the intermediate step and that two mutations actually happened.

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