Saturday, 25 March 2017

The updated mtDNA tree at Family Tree DNA and an upgrade sale

Family Tree DNA have finally updated the mitochondrial DNA haplogroup assignments for all their customers to Build 17, the latest version of the mtDNA tree. The mtDNA tree is documented by scientists on the Phylotree website. Build 17 of the mtDNA was introduced in February 2016, but until this week FTDNA were using Build 14, which dates back to April 2012, so this update is long overdue. Here is what FTDNA have said about the upgrade in an e-mail to group administrators:
You or your members may have received an email about the update of the mitochondrial DNA database from Build 14 to Build 17, which is the most recent phylogenetic build for mtDNA. This update has been in the works for several months while the scientific team tested and verified the programming and results. We were able to release it this week, so some of you may have seen a change to your mtDNA haplogroup. 
To give you an idea of the scope of this project, Build 14 was based on the analysis of 8,216 modern mitogenomes, while Build 17 was designed using 24,275 mtDNA sequences - almost three times as much information! Build 17 increased to 5437 nodes from 3550 in Build 14, an increase of 1887 haplogroups. Obviously, the update provides a much finer resolution in terms of haplogroup assignment. 
In a very few cases haplogroups may have reverted to a higher branch on the tree. Usually, this is because in Build 14, some of the branches of the tree were predicted, not confirmed. The additional sequences added between Build 14 and Build 17 did not provide supporting data to justify their existence, so these branches have been removed.
What this means in practice is that some people who have taken a full mitochondrial sequence (FMS) test with Family Tree DNA will now find that they have extra letters and numbers in their haplogroup name reflecting the latest discoveries in mtDNA research. For example if you were previously a U4a1a you might learn that you are now either a U4a1a1, a U4a1a2 or a U4a1a3. This is because, as more and more full sequences have become available, it is possible to identify new subclades or branches on the tree.

You can see an updated list of the mtDNA haplogroup-defining mutations on the FTDNA website. Not all subclades have been updated this time but it is always possible your subclade could be refined the next time the tree is updated.

To see where you belong on the mtDNA tree go to the Phylotree website and navigate to your branch of the tree. In the screenshot from Phylotree below you can see the three new daughter clades of U4a1a. Next to the subclade names there is a list of the mutations that define these subclades. The letter and number codes on the far right represent the GenBank IDs of the sequences that were used to define these new subclades.









For a sequence to be used to build the tree it has to be published in the GenBank database. Sequences appearing in scientific papers are uploaded to GenBank on publication. In addition, many Family Tree DNA customers have uploaded their sequences to GenBank so that they can contribute their results to science. If your sequence is used to identify a new subclade you might have the honour of having your sequence listed as one of the two references for that subclade. You might even find that your sequence gets used in a scientific paper! My own personal mtDNA sequence has already appeared in two scientific papers to date.

If you are interested in uploading your mtDNA sequence to GenBank you can find further information on the ISOGG Wiki page on GenBank

It's important to remember that you will share your mtDNA sequence with your siblings, your mother, and any cousins who descend in an all-female line from your matrilineal ancestors. There are 37 genes in the mtDNA molecule and in some cases people will have mutations that have medical significance so any mutation that potentially affects you will also affect your other matrilineal relatives. It's very rare to find such mutations but it's always a good idea to get your sequence checked out before sharing it publicly. If you are technically minded you can look up your own mutations on Mitomap. Alternatively you can order a custom mtDNA report from Dr Ann Turner for a small and very reasonable fee. I ordered a report for myself and I can highly recommend this service. 

If you want to find out more about your haplogroup have a look at Rebekah Canada's wonderful Encyclopedia of mtDNA Origins. If you type in the name of your subclade you can pull up a list of all the sequences in your subclade on GenBank and in the Genographic Project database together with a list of relevant publications from the scientific literature, and an estimate of the age of your subclade.

There are some cases where the haplogroup names have not yet been updated. We have a few examples in the mtDNA Haplogroup U4 Project. These have occurred where the subclade-defining mutation is an insertion or deletion. An example of an insertion is 965.2C. This means that, in comparison to the reference sequence, the person has two extra Cs at position 965. An example of a deletion is 301-  or T310d. The way the deletion is reported depends on which reference sequence is being used  – the revised Cambridge Reference Sequence or the Reconstructed Sapiens Reference Sequence. What this deletion means is that there is a letter T in the reference sequence but this letter T is not present in the person who has tested. The FTDNA algorithms currently seem to be unable to handle these insertions and deletions but hopefully this will be sorted out in due course.

In the meantime if you want to check your own haplogroup assignment you can use James Lick's mtHap tool, which is equipped to handle insertions and deletions. It's also a good idea to join the relevant mtDNA Haplogroup Project. Some of the volunteer haplogroup project admins will be able to check the haplogroup assignment for you.

FMS upgrade sale
To coincide with the update to the mtDNA tree FTDNA have announced an upgrade sale. For the next week only you can upgrade to the full sequence from HVR1 or HVR1+HVR2 for just $99. You will only get the detailed haplogroup assignment with the full sequence test. The FMS upgrade is particularly useful if you have a lot of matches at the lower testing levels. mtDNA can also be used at FTDNA in combination with autosomal DNA testing to rule matches in or out on the matriline. Remember too that FTDNA is the only company where you can use your mtDNA results for genealogical matching purposes.They have the world's largest database of full mitochondrial sequences. As of today's date there are 99,847 FMS records in their database. It's only a matter of time before the 100,000 milestone is reached.

6 comments:

Louis Kessler said...

Mine is in the queue. Maybe I'll be number 100,000. :-)

Debbie Kennett said...

That would be exciting!

Kalani said...

Thank you so much for this post! I didn't realize FTDNA had a section on their haplogroup defining mutations. But in my project, I already gathered those mutations. And figured out from Phylotree what those mutations would be and was discussing it in detail with my co-admin yesterday morning.

I'll see you at Jamboree! :)

Debbie Kennett said...

There are lots of treasures on the FTDNA website but many of them take some finding! I'm looking forward to meeting you at Jamboree. I'm fascinated by your Polynesian research.

thesunshines101 said...

I'm confused ..do I have to order new test to see if my haplogroup k (K1c1) changed? I tested ftdna a year ago April..but recently tested living DNA and my haplogroup k (K1c1) is the same..thanks for any input

Debbie Kennett said...

No you don't need to order a new test. Not all haplogroups have changed. Make sure you add your results to the Haplogroup K Project at Family Tree DNA:

https://www.familytreedna.com/groups/mt-dna-k/about/background

Bill Hurst, the volunteer project admin, will be happy to advise you on your results. Share with him your Living DNA results too if you've not done the full sequence test with FTDNA.