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.

Monday, 20 March 2017

AncestryDNA updates and the forthcoming new Genetic Communities feature

It was announced at Rootstech back in February that AncestryDNA are planning to launch a new Genetic Communities feature. See this blog post from the Ancestry Insider for details. I received a St Patrick's Day e-mail from AncestryDNA and it seems that the Communities feature is due to be launched at the end of March. The launch is conveniently timed to coincide with Who Do You Think You Are? Live which takes place in early April. Not all Ancestry customers have received the marketing e-mail and it seems to have been aimed at people in the UK and Ireland. According to the e-mail the "new Genetic Communities feature will map where your family may have lived across 19 different Irish areas, from Derry to Cork. But you're probably not 100% Irish - so we'll also identify the communities that you belong to around Britain and the rest of the world."  The e-mail includes a link to this landing page  which has a few additional details. .

I've been included in the beta-testing program for the new Communities feature but the version I currently I have on my account is not necessarily the finished product so I will report on this feature after the official launch. At present I'm in one community for Southern England but I suspect that there will be further refinements in due course.

In the meantime you can get a glimpse of some of the Irish Genetic Communities on Mike Mulligan's Ancestry Special, a special edition of the Irish TV programme The Late Late Show. The four guests, Maura Derrane, Eamon Dunphy, Jason Byrne and Michael Healy-Rae, were given their DNA results live on air by Mike Mulligan from AncestryDNA. The programme is available on the RTE Player until Sunday 17th April.

AncestryDNA have now published a Genetic Communities White Paper explaining the science behind the new feature, which is well worth a read. The AncestryDNA team have done a superb job explaining some quite complicated concepts in an easily understandable way.

If you want to learn more about the underlying research which led to the development of the Genetic Communities you can read the scientific paper Clustering of 770,000 genomes reveals post-colonial population structure of North America Nature Communications published in Nature Communications in February. The paper includes a 126-page Supplementary Discussion document which is an interesting read in its own right and includes lots of maps and some fascinating background information on migration patterns. If a lengthy scientific paper is not to your liking, Leah Larkin has written a handy blog post providing a useful summary of the paper.

It's interesting to note that AncestryDNA have filed a series of patents to protect their rights in this research.

AncestryDNA now also seem to be encouraging their customers to participate in research. This banner has just appeared on my Ancestry account.

When I click through I am taken to this page which encourages me to increase my level of participation in Ancestry research.

There is a new Informed Consent form for the Ancestry Human Diversity Project which was updated on 8th February 2017.

There is also what appears to be a new page on the Ancestry Privacy Principles, which serves as a gateway to all the privacy-related topics on the website. I was particularly interested to see this new page on AncestryDNA Research and Collaboration.

It is an individual decision whether or not to participate in research but whatever you decide make sure you read through all the forms in their entirety before making your decision.

See also the blog post from Judy Russell Update in AncestryDNA research consent.

Monday, 13 March 2017

Free access to Irish records on Findmypast for the next five days in celebration of St Patrick's Day

The following press release has been received from Findmypast.


Findmypast makes entire collection of more than 116 million Irish records free for five days
All 116 records free from the 13th  to the 17th March 2017

Leading family history website, Findmypast, has just announced that they will be making their entire collection of Irish records free for five days to help budding genealogists uncover their Irish heritage ahead of St Patrick’s Day 2017.

From today, Monday 13th March, until 11.59pm (GMT) Friday 17th March, all 116 million records within Findmypast’s Irish collection will be completely free to search and explore, providing family historians from around the globe with the opportunity to learn more about the lives of their Irish ancestors.

This includes free access to:
  • Over 10 million Irish Catholic Parish Registers 
  • Over 15 million Census, Land & Substitute records including the 1901 and 1911 censuses 
  • Over 30 million detailed Court & Prison Records 
  • Over 33 million Irish newspaper articles spanning the years 1708 to 1956 
  • Over 7.3 million Dog Licences 
  • Over 24 million Irish Passenger Lists 
  • Over 2.4 million workhouse & poor law records 
  • Over 1.4 million Irish Quaker records 
  • Over 350,000 records from World War 1, the Easter Rising & more 
  • Landed Estates Court records featuring details of over 500,000 tenants residing on estates all over Ireland 
  • The complete Griffith's Valuation 
  • Over 2.3 million Social History & Directory Records, including the most comprehensive online collection of national directories, dating back to 1814 
  • Indexes to Irish wills dating from 1270 – 1858
Free Live Webinar
On Thursday March 16th at 4pm GMT, Findmypast will be hosting a free St Patrick’s Day Webinar presented by Fiona Fitzsimons, the founder and research director of Eneclann, a Trinity College Campus Company. Fiona manages teams of expert researchers to provide Irish and British family history as well as running a successful probate genealogy service. Her talk, entitled, “Secrets to Successful Irish Family Research”, will cover strategies for online research, Irish customs & traditions and collateral records to help “bridge the gaps”.

New Records Available To Search
Thousands of additional records will be added to Findmypast’s extensive Irish collection on Friday 17th March. This will include substantial updates to their collection of Irish Society of Friends (Quaker) records, new directories, administrations, family histories, memorial inscriptions and more. Visit the dedicated Findmypast Friday page to keep up to date with the latest additions.