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 GRANT FIVE DAYS OF FREE ACCESS TO ALL IRISH RECORDS IN CELEBRATION OF ST PATRICK’S DAY 2017

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.

Friday, 17 February 2017

Launch of The Journal of Genealogy and Family History

The Journal of Genealogy and Family History, a new open access peer-reviewed genealogy journal, published by the Register of Qualified Genealogists, is launching in April 2017 at Who Do You Think You Are? Live.


Here is the official press release I received:
Media release - The Journal of Genealogy and Family History 
Launching in April 2017, the new Journal of Genealogy and Family History (JGFH) will address the current need for a high quality, peer reviewed publication, covering broad scholarly research in genealogy and family history in a 21st century online format. The journal will be offered to readers and contributors for free, on an open-access, non-commercial basis, with content available under a Creative Commons Attribution License. The scope of the journal will include any field or academic discipline associated with genealogy or family history research such as heraldry, demography, education and record conservation.

Articles will offer the reader insights into current thinking and practice and provide an outlet for theoretical and speculative ideas within genealogy and family history. Topics will be wide ranging, and include for example:
  • Family histories which demonstrate new and innovative approaches and analytic techniques;
  • Locational studies
  • The use of new technologies
  • Software applications and databases
  • The use of DNA analyses to better understand kinship
  • Ancestry and populations Micro histories which may focus on personal, local, community and social histories.
  • Ethical and legal issues surrounding the practice of genealogy 
The journal will attract authors from around the world who wish to have their genealogical and family history work published in a credible form and made available to anyone who chooses to read it. All articles submitted for publication will undergo anonymous peer review, which will provide a rigorous and robust process of close scrutiny.

The Editor, Jessica Feinstein, says: "I am very excited to be part of the great team involved in this venture, and look forward to enabling authors in our field to publish academic articles that will advance genealogical research in many areas." 
The editorial board will include prominent individuals from within the field of genealogy and family history as well as associated disciplines. 
The Journal of Genealogy and Family History is registered at the British Library with ISSN 2399-2964. 
The journal was initiated and designed by the Register of Qualified Genealogists and will be published via their website at: http://www.qualifiedgenealogists.org/jgfh 
The Register of Qualified Genealogists will be at Who Do You Think You Are Live, Birmingham NEC from Thursday 6 – Saturday 8 April 2017 on table number 2. Come and find us for a chat and to see a preview of the first issue..............
http://www.whodoyouthinkyouarelive.com
The names of the Editorial Board were not included in the press release and were not available on the website. However, the Editor has kindly given me a list of the names:

Nick Barratt
Caroline Brown
John Cleary
Bruce Durie
Marjory Harper
Ian G Macdonald
Tahitia McCabe
Rebecca Probert
David Rencher
Michael Tobias
John Tunesi
The biographies of the editorial board members should be up on the website soon.

Comment
The Journal of Genealogy and Family History is published under the auspices of a relatively new organisation called the Register of Qualified Genealogists. The RQG is set up as a private company. To qualify for membership it is necessary to have completed one of a very limited range of postgraduate genealogical courses offered by UK institutions. The full list of qualifying courses can be seen here. Members are required to adhere to a professional code. There are a number of other organisations that professional genealogists can join. AGRA (the Association of Genealogical Researchers in Archives) is the premier organisation in England and Wales. Membership of AGRA is not contingent on the completion of a course but potential members are required to submit a research portfolio for scrutiny and have to attend an interview. In Scotland there is the Association of Scottish Genealogists and Researchers in Archives (ASGRA). Accredited Genealogists Ireland (AGI) is the equivalent organisation in Ireland. The Association of Professional Genealogists is a US-based organisation but accepts members from anywhere in the world. Members are required to abide by a code of conduct and must commit to a programme of continuing education. The APG operates as a not-for-profit business organisation. In addition there are a number of different professional organisations in other countries. For details see the AGRA FAQs and Cyndi's List for details. Given that so many other professional organisations already exist, there have been questions about the need for a new organisation.

While it is common practice in academia for writing and research to be subjected to the process of peer review it is rare in the world of genealogy. There are a number of genealogy journals that accommodate the publication of lengthy scholarly articles with citations. In the UK the Genealogists' Magazine has been published by the Society of Genealogists since 1925. There are a number of scholarly journals in the US such as the National Genealogical Society Quarterly, the New England Historical and Genealogical Society Register and The American Genealogist. For descriptions of the US journals see this article by Kimberly Powell on five genealogical journals you should be reading.

There is also the newly re-launched Journal of Genetic Genealogy (JOGG) which is published online and is open access. JOGG has an editorial board and all the articles go through a formal peer review process. The articles are indexed by Google Scholar, and as a result some of these articles have been cited in academic journals.

The big limitation with all these scholarly genealogy journals, with the exception of JOGG, is that they are essentially a closed shop. They are not picked up by indexing services such as Google Scholar, so unless you are a member of the society in question you are likely to be unaware of any interesting articles on your subject of interest. The Society of Genealogists have commendably made back issues of the Genealogists' Magazine available on CD. It is now also possible to search for articles in PERSI (the Periodical Source Index), which provides a subject index to over 11,000 historical and genealogical journals. This index is freely available courtesy of Findmypast. A growing number of images is being added to the collection, but the images are only available to Findmypast subscribers. There is an excellent guide to using PERSI in the FamilySearch Wiki. If you find an article of interest that is not included in the image collection it might be possible to order a copy for a small fee from your local library or to purchase a copy using the British Library's On Demand Service or an equivalent service in other countries, provided that copies of the journal have been sent to one of the legal deposit libraries.

The whole point of publishing is so that others can build on our research, and we are not constantly re-inventing the wheel. If our work is not easily accessible then other researchers are less likely to find it. I therefore welcome the launch of this new open access peer-reviewed genealogy journal which has the potential to bring scholarly genealogical articles to a wider audience. However, the journal will live or die on the quality of the articles published. It will be interesting to see how the journal develops in the months and years to come.

This article was updated on 18th February 2017 to include information about additional professional genealogy organisations, and to correct the details about the RQG in the light of comments received below.