I knew the mitochondrial DNA update at Family Tree DNA was coming, I just didn’t know when. The “when” was earlier this week.
Take a look at your mitochondrial DNA haplogroup – it maybe different!
Today, this announcement arrived from Family Tree DNA.
We’re excited to announce the release of mtDNA Build 17, the most up-to-date scientific understanding of the human genome, haplogroups and branches of the mitochondrial DNA haplotree.
As a result of these updates and enhancements—the most advanced available for tracing your direct maternal lineage—some customers may see a change to their existing mtDNA haplogroup. This simply means that in applying the latest research, we are able to further refine your mtDNA haplogroup designation, giving you even more anthropological insight into your maternal genetic ancestry.
With the world’s largest mtDNA database, your mitochondrial DNA is of great value in expanding the overall knowledge of each maternal branch’s history and origins. So take your maternal genetic ancestry a step further—sign in to your account now and discover what’s new in your mtDNA!
This is great news. It means that your haplogroup designation is the most up to date according to Phylotree.
I’d like to take this opportunity to answer a few questions that you might have.
What is Phylotree?
Phylotree is, in essence, the mitochondrial tree of humanity. It tracks the mutations that formed the various mutations from “Mitochondrial Eve,” the original ancestor of all females living today, forward in time…to you.
You can view the Phylotree here.
For example, if your haplogroup is J1c2f, for example, on Phylotree, you would click on haplogroup JT, which includes J. You would then scroll down through all the subgroups to find J1c2f. But that’s after your haplgroup is already determined. Phylotree is the reference source that testing companies use to identify the mutations that define haplogroups in order to assign your haplogroup to you.
It’s All About Mutations
For example, J1c2f has the following mutations at each level, meaning that each mutation(s) further defines a subgroup of haplogroup J.
As you can see, each mutation(s) further refines the haplogroup from J through J1c2f. In other words, if the person didn’t have the mutation G9055A, they would not be J1c2f, but would only be J1c2. If new clusters are discovered in future versions of Phylotree, then someday this person might be J1c2f3z.
Family Tree DNA provides an easy reference mutations chart here.
What is Build 17?
Research in mitochondrial DNA is ongoing. As additional people test, it becomes clear that new subgroups need to be identified, and in some cases, entire groups are moved to different branches of the tree. For example, if you were previously haplogroup A4a, you are now A1, and if you were previously A4a1 you are now A1a.
Build 17 was released in February of 2016. The previous version, Build 16, was released in February 2014 and Build 15 in September of 2012. Prior to that, there were often multiple releases per year, beginning in 2008.
Vendors and Haplogroups
Unfortunately, because some haplogroups are split, meaning they were previously a single haplogroup that now has multiple branches, a haplogroup update is not simply changing the name of the haplogroup. Some people that were previously all one haplogroup are now members of three different descendant haplogroups. I’m using haplogroup Z6 as an example, because it doesn’t exist, and I don’t want to confuse anyone.
Obviously, the vendors can’t just change Z6 to Z6a, because people that were previously Z6 might still be Z6 or might be Z6a, Z6b or Z6c.
Each vendor that provides haplogroups to clients has to rerun their entire data base, so a mitochondrial DNA haplogroup update is not a trivial undertaking and requires a lot of planning.
For those of you who also work with Y DNA, this is exactly why the Y haplotree went from haplogroup names like R1b1c to R-M269, where the terminal SNP, or mutation furthest down the tree (that the participant has tested for) is what defines the haplogroup.
If that same approach were applied to mitochondrial DNA, then J1c2f would be known as J-G9055A or maybe J-9055.
Why Version Matters
When comparing haplogroups between people who tested at various vendors, it’s important to understand that they may not be the same. For example, 23andMe, who reports a haplogroup prediction based not on full sequence testing, but on a group of probes, is still using Phylotree Build 12 from 2011.
Probe based vendors can update their client’s haplogroup to some extent, based on the probes they use which test only specific locations, but they cannot fully refine a haplogroup based on new locations, because their probes never tested those locations. They weren’t known to be haplogroup defining at the time their probes were designed. Even if they redefine their probes, they would have to rerun the actual tests of all of their clients on the new test platform with the new probes.
Full sequence testing at Family Tree DNA eliminates that problem, because they test the entire mitochondria at every location.
Therefore, it’s important to be familiar with your haplogroup, because you might match someone it doesn’t appear that you match. For example, our haplogroup A4a=A1 example. At 23andMe the person would still be A4a but at Family Tree DNA they would be A1.
If you utilize MitoSearch or if you are looking at mtDNA haplogroups recorded in GedMatch, for example, be aware of the source of the information. If you are utilizing other vendors who provide haplogroup estimates, ask which Phylotree build they are using so you know what to expect and how to compare.
Knowing the history of your haplogroup’s naming will allow you to better evaluate haplogroups found outside of Family Tree DNA matchs.
You can view the Phylotree Update History at this link, but Built 17 information is not yet available. However, since Family Tree DNA went from Built 14 to Build 17, and other vendors are further behind, the information here is still quite relevant.
If you’re wondering how much the tree grew, Build 14 defined 3550 haplogroups and Built 17 identified 5437. Build 14 utilized and analyzed 8,216 modern mitochondrial sequences, reflected in the 2012 Copernicus paper by Behar et al. Build 17 utilized 24,275 mitochondrial sequences. I certainly hope that the authors will update the Copernicus paper to reflect Build 17. Individuals utilizing the Copernicus paper for haplogroup aging today will have to be cognizant of the difference in haplogroup names.
If your haplogroup changed, or the haplogroup of any of your matches, your matches may change. Family Tree DNA utilizes something called SmartMatching which means that they will not show you as a match to someone who has taken the full sequence test and is not a member of your exact haplogroup. In other words, they will not show a haplogroup J1c2 as a match to a J1c2f, because their common ancestors are separated by thousands of years.
However, if someone has only tested at the HVR1 or HVR1+HVR2 (current mtDNA Plus test) levels and is predicted to be haplogroup J or J1, and they match you exactly on the locations in the regions where you both tested, then you will be shown as a match. If they upgrade and are discovered to be a different haplogroup, then you will no longer be shown as a match at any level.
The differences can be caused by the level of testing done, which phase of the Genographic project that you tested, and when.
- Geno 1 tested all of HVR1.
- Geno 2 tested a selection of SNPs across the mitochondrial genome to give a more refined haplogroup using Build 14.
- Geno 2+ used an updated selection of SNPs across the mitochondrial genome using Build 16.
If you have HVR1 either transferred from the Genographic Project or from the FTDNA product mtDNA, you will have a basic, upper-level haplogroup.
If you tested mtDNA Plus with FTDNA, which is HVR1 + HVR2, you will have a basic, upper-level haplogroup.
If you tested the Full Mitochondrial Sequence with Family Tree DNA, your haplogroup will reflect the full Build 17 haplogroup, which may be different from either the Geno 2 or Geno 2+ haplogroup because of the number and selection of SNPs tested in the Genographic Project, or because of the build difference between Geno 2+ and FTDNA.
I want to say a special thank you to Family Tree DNA.
I know that there is a lot of chatter about the cost of mitochondrial DNA testing as compared to autosomal, which is probe testing. It’s difficult for a vendor to maintain a higher quality, more refined product when competing against a lower cost competitor that appears, at first glance, to give the same thing for less money. The key of course is that it’s not really the same thing.
The higher cost is reflective of the fact that the full sequence mitochondrial test uses different technology to test all of the 16,569 mitochondrial DNA locations individually to determine whether the expected reference value is found, a mutation, a deletion or an insertion of other DNA.
Because Family Tree DNA tests every location individually, when new haplogroups are defined, your mitochondrial DNA haplogroup can be updated to reflect any new haplogroup definition, based on any of those 16,569 locations, or combinations of locations. Probe testing in conjunction with autosomal DNA testing can’t do this because the nature of probe testing is to test only specific locations for a value, meaning that probe tests test only known haplogroup defining locations at the time the probe test was designed.
So, thank you, Family Tree DNA, for continuing to test the full mitochondrial sequence, thank you for the updated Build 17 for refined haplogroups, and thank you for answering additional questions about the update.
If you haven’t yet tested your mitochondrial DNA at the full sequence level, now’s a great time!
If you have tested at the HVR1 or the HVR1+HVR2 levels, you can upgrade to the full sequence test directly from your account. For the next week, upgrades are only $99.
There are two mtDNA tests available today, the mtPlus which only tests through the HVR1+HVR2 level, or about 7% of your mitochondrial DNA locations, or the mtFull Sequence that tests your entire mitochondria, all 16,569 locations.
Click here to order or upgrade.