A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature

This article is for experienced genetic genealogists and requires an understanding of SNPs and haplogroups.

A very useful online resource for Y-chromosome researchers in the form of a simplified version of the Y-chromosome SNP tree has come online this week. The new pared-down version of the Y-tree is introduced in a paper by Mannis Van Oven, Anneleen Van Geystelen, Manfred Kayser, Ronny Decorte and Maarten H D Larmuseau entitled Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome. The paper has been accepted for publication in the scientific journal Human Mutation but has yet to go through the full editorial process. Mannis Van Oven's name is already well known to mitochondrial DNA researchers because he maintains the Phylotree website which hosts the definitive mtDNA tree. The simplified Y-tree is conveniently being maintained on the same website and can be found at www.phylotree.org/Y

The new Phylotree version of the Y-tree will serve as a complement to the full Y-SNP tree which is maintained by ISOGG (the International Society of Genetic Genealogy). The Y-tree is now a very complicated structure and is set to become even more detailed in the coming months with the flood of new Y-SNPs that are being discovered from academic projects and through commercial testing with Full Genomes Corp, the Genographic Project (Geno 2.0) and BritainsDNA/ScotlandsDNA (Chromo 2). There will always be a need to have the fine detail of the full high-resolution tree, especially when one is trying to drill right down to the low-hanging branches. However, sometimes it's useful to get an overview of the structure of the tree as a whole without the complication of all the addition sub-branches, twigs and twiglets, and this is something that the new Phylotree Y-tree does very nicely.

I'm very pleased to see that the paper acknowledges the contributions made by the many "independent researchers" within the genetic genealogy community. The resources that the authors used to compile their reference phylogeny included "a large number of websites maintained by independent researchers", all of whom are named in the acknowledgements.

An important innovation in this paper is a very welcome attempt to introduce a much-needed common standard for Y-SNP and Y-haplogroup nomenclature. As the authors explain "Due to multiple independent discovery events, a considerable number of Y-SNPs are known by multiple names". This diversity of names is a source of considerable confusion for both academic researchers and genetic genealogists. For example, haplogroup R1b1a2, the predominant European haplogroup, has two major branches. The markers that define these branches are known as P312 and U106 at the Genographic Project and Family Tree DNA but have the alternative names S116 and S21 at BritainsDNA/ScotlandsDNA. All four of these marker names appear in the scientific literature but the scientists often don't provide the alternative names. ISOGG provides a Y-SNP index which allows the researcher to check for other SNP names but not every researcher will know of this resource. The solution proposed by Van Oven et al is to decide on "one default name depending on which of the aliases is most frequently used in the literature", and these are the names which appear in the Phylotree Y-tree, though the alternative names are given in the accompanying spreadsheet.

It does of course remain to be seen if the scientists and testing companies will adopt the recommended nomenclature for the 417 SNPs included on the simplified Y-tree, but we can certainly hope that they will do so. Most of the names are already in use at Family Tree DNA and within the various FTDNA haplogroup projects. The one SNP name on the tree which will probably cause the most difficulties is R-M529, which is currently better known as L21 and sometimes S145. The name M529 seems to have been chosen because it was cited in an academic paper published in 2011 by Myres et al.¹ However, the name L21 is now so ingrained in the collective genetic genealogy consciousness that I suspect that the proposed new name will probably not catch on. BritainsDNA have always used their own proprietary S series naming system but I hope that they will at least consider adopting the new nomenclature for the core SNPs included on the Phylotree Y-tree so that we can all speak a common language.

In the coming months we can expect an explosion of new Y-SNPs now that the first results have started to come in for the Chromo 2 test from BritainsDNA/Scotlands DNA and from the full Y-chromosome sequencing tests at Full Genomes. However, the nomenclature will continue to be a big problem as each company tries to maintain a competitive advantage. Full Genomes have already indicated that they will be offering custom single SNPs for sale to compete with FTDNA. We can probably expect to see a flood of FG SNPs being made available in the next few months. The positions of the new FG SNPs on the tree are not yet known so no other companies will be able to offer these new SNPs. So far I've only seen one data file from the BritainsDNA Chromo 2 test. This file contains over 14,000 Y-SNPs, of which around 8000 or more are proprietary S series SNPs, only a tiny percentage of which are listed in the ISOGG Y-SNP index. It may be that many of the BritainsDNA SNPs will turn out to be equivalent to the SNPs that are already on the ISOGG tree or included on the Geno 2.0 chip, and these SNPs will almost certainly be included in the Full Genomes test. However, neither BritainsDNA nor the Genographic Project provide the genome reference positions for the SNPs on their chips so there is currently no way of knowing which S series SNPs are already known about and which ones are new.  Fortunately there are many pioneers with large pockets in the genetic genealogy community who can afford to have their DNA tested at Full Genomes, BritainsDNA and the Genographic Project. With data available for comparison from two or more companies it should then be possible for the volunteer haplogroup project administrators to compare the results and establish the positions of any newly discovered SNPs on the Y-tree.

The other unknown is whether or not Family Tree DNA will be responding to the competition from Full Genomes and BritainsDNA. Their group administrators' conference is taking place this weekend in Houston, Texas, and the conference schedule has now been made available online. Miguel Vilar from the Genographic Project will be providing a Geno 2.0 update and talking about the Y-2014 tree, and Michael Hammer will be talking about the "implications of the 2014 Y-tree". FTDNA usually make a big announcement at the conference and the speculation is that they will perhaps be announcing the launch of a new Geno chip and/or the introduction of a full Y-chromosome test. Spencer Wells has already indicated that a new Geno chip might be on the way as early as 2014.²

Unfortunately, all three currently available Y-SNP tests are very expensive and well beyond the means of the average genetic genealogist. I'm rather hoping that at some point one of the companies will introduce a cheaper Y-SNP test that will allow a customer to have a refined haplogroup designation sufficient to rule out false positive matches but without breaking the bank.

For the moment I would advise anyone considering ordering a Y-SNP test to wait and see what the results are from the tests taken by the early adopters. If you want to join the pioneers and experiment with one of the new SNP tests then you can see a chart comparing the services offered by the main testing companies in the ISOGG Wiki.

With so many exciting new developments I wonder what the Y-chromosome tree will look like in 2014. The ISOGG SNP Index lists all the SNPs that are either on the Y-tree or which are under investigation, but these SNPs represent less than 10% of the known Y-SNPs. David Reynolds maintains the ISOGG Y-SNP Compendium Spreadsheet which currently contains almost 40,000 additional Y-SNPs, and has indicated that he still has over 12,000 SNPs to add, time permitting. The SNPs in this spreadsheet have not all been validated and many are not available for testing at any commercial company. It may well be that the tree will increase in size ten-fold or more in the next twelve months which will represent a significant challenge for the volunteer ISOGG Y-SNP team who maintain the tree in their own free time.

Chris Tyler-Smith cautioned us in February at a special ISOGG presentation at the Sanger Institute in Cambridge that the Y-tree nomenclature system was set to break down in 2013, and indeed that already seems to be the case. He raised the possibility of using an ancestral reference sequence for the Y-chromosome along the lines of the RSRS (Reconstructed Sapiens Reference Sequence) introduced for mitochondrial DNA in 2012.³ I wonder if that is something that we will see implemented in 2014.

Whatever the future has in store it is certainly a very exciting time for Y-chromosome researchers and, as Chris Tyler-Smith commented in February, there will be "more opportunities than ever for computer-literate citizen scientists".

References
1. Myres NM, Rootsi S, Lin AA et al. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European Journal of Human Genetics 2011; 19 (1); 95-101.
2. Petrone J. National Geographic considering move to new SNP chip for Genographic Project. GenomeWeb, 13 August 2013.
3. Behar DM, Van Oven M, Rosset S et al. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics 2012; 90 (5): 936. 

Resources
- The ISOGG Y-DNA SNP testing comparison chart
- A list of Y-DNA haplogroup projects
- BritainsDNA haplogroup nicknames

See also
- A confusion of SNPs

© 2013 Debbie Kennett

My presentations at Genetic Genealogy Ireland 2013

Both of my presentations from the recent Genetic Genealogy Ireland conference held in Dublin from 18th to 20th October can now be found on the Genetic Genealogy Ireland YouTube channel. You can watch the recordings on YouTube or click on the links below.

 DNA for Beginners: The Three Tests


Chromosomes, Conquerors and Castles: DNA and the Cruise/Cruwys/Cruse One-Name Study 


The handout for my talks can be downloaded from my Dropbox account.

Genetic Genealogy Ireland 2013

Last week I spent four enjoyable days in Dublin participating in the first ever Genetic Genealogy Ireland conference which took place at the Back To Our Past show at the Royal Dublin Society (RDS) in Ballsbridge just outside the city centre. Back To Our Past, now in its third year, is the premier genealogy event in Ireland, and is the Irish equivalent of Who Do You Think You Are? Live. Back To Our Past is held alongside the Senior Times Over 50s show which takes place in the same building, and for the price of a single ticket people can attend both events. Around 20,000 people attended last year over the course of the three days, and I'm sure that just as many people if not more will have attended this year's show.

Genetic Genealogy Ireland was sponsored by Family Tree DNA and organised by ISOGG - the International Society of Genetic Genealogy. Family Tree DNA were exhibiting at the event for the first time this year. FTDNA's involvement at Back To Our Past was the initiative of volunteer project administrator and US ISOGG member Derrell Oakley Teat, who suggested the idea to FTDNA staff back in January this year. Another ISOGG member Maurice Gleeson, the administrator of the Spearin and Irish Caribbean DNA Projects, had attended Back To Our Past in 2012 where he gave a very successful and well received lecture on DNA testing. He became involved in the organisation at an early stage and assumed responsibility for arranging the genetic genealogy lecture programme.  He approached the task with considerable enthusiasm and energy, and put together a fantastic and varied programme of talks. Katherine Borges, the Director of ISOGG, and Cynthia Wells, the administrator of the Lay/Ley DNA Project and co-administrator of the Talley DNA Project and the Wells DNA Project, both flew over from the United States to give presentations and to help on the FTDNA stand (or "booth" as they call it in America!). Some speakers came over from England and other speakers travelled to Dublin from all over Ireland. The full lecture schedule can be found here. It says a lot for the dedication of our genetic genealogy community that all the speakers paid their own way to attend the conference.

   The entrance to the Back To Our Past show 
at the RDS in Dublin.

I was invited to present two lectures. My first talk on Friday 18th October was entitled "Chromosomes, conquerors and castles: DNA testing and the Cruise/Cruse/Cruwys one-name study". On Saturday 19th October I gave a talk on "DNA for beginners: the three tests". Both of my talks seem to have been very well received. There was apparently a sudden rush for the FTDNA stand after my DNA for Beginners talk on Saturday! I was only able to attend the first two days of the conference as I had already been booked to do a talk for the Abingdon branch of the Berkshire Family History Society on the following Monday so I had to fly home on Sunday and consequently I missed the last day of the show which I understand was really busy. In contrast to WDYTYA Live, where Sunday is traditionally the quietest of the three days, several people told us that Friday is the quietest day at BTOP and Saturday and Sunday are always the busiest days.

During the first two days of the show I was helping out Derrell, Katherine and Cynthia on the FTDNA stand in between presenting my talks. John Blair and Geoff Swinfield also joined us later in the day. We had a non-stop stream of people visiting the stand to ask questions and to take DNA tests from the minute the show opened until late in the afternoon. It was difficult to find any free time to get away just to buy a drink or to get something to eat. Some people knew nothing about DNA testing and were coming up to the stand to find out how the process worked. We had a large quantity of leaflets from FTDNA and such was the interest that they had all run out before the end of show on Sunday. A lot of people wanted to know if their surname was represented in a project before deciding to test. We couldn't access the FTDNA database at the show so we sent them home with instructions to look up their names on the website. I suggested to several people that if they weren't able to test at BTOP they should wait until December to order a kit in the sale. I'm sure there will be an upsurge in orders from Ireland in the coming months. Other people, and especially those who had attended some of the talks, were happy to take a test there and then, and they will be able to look forward to receiving their results in the next six weeks or so. I spoke to a number of people who were interested in setting up DNA projects for their family history societies or their surname. A representative from the North of Ireland Family History Society came to speak to me after my talk and his society seem to be very keen to get involved in DNA testing. He insisted on taking a photo of me for their Facebook page! I was particularly pleased to meet up with one of the members of my Cruise DNA project who lives in Ireland and had come along to the show especially to meet me. He's very kindly offered to take me on a trip to Cruisetown (now known as Cruicetown), the former stronghold of one of the Irish branches of the Cruise family, the next time I visit Ireland.

I was very surprised at the number of visitors from America, all of whom were particularly interested in the Genetic Genealogy Ireland conference. There was one American visitor in the audience for one of my talks who introduced himself to me afterwards and said that he'd read both of my books! We tested quite a few Americans on the FTDNA stand. Two FTDNA project admins from America, Jim O'Halloran and Mike Carragher, had been thinking about a trip to Ireland and when they heard about BTOP they decided to plan their trips around the show. They were both hoping to travel around Ireland afterwards to test more people for their projects. All my American friends commented on how welcoming the Irish people were to Americans - they welcomed them back as long lost cousins. We all loved the Irish sense of humour and their relaxed attitude to life.

The long queue waiting for the doors to open

 for the Over 50s Show at the RDS.

A number of project administrators offered to sponsor DNA tests for people with their surnames. The free DNA tests are already a well-established tradition at Who Do You Think You Are? Live, and they went down very well in Ireland too. It's always pot luck as to whether or not someone with the right surname comes along to the show, but a number of projects were lucky to get new project members. We did free DNA tests for the surnames DOOLAN, HUDSON, KNOWLES, TAYLOR (2) and WATSON. I haven't seen the full list and other projects might have been successful too. There is a page on the Genetic Genealogy Ireland website which lists all the surnames for which sponsored tests were available. Even if you were not able to attend BTOP do check out the list and the comments section to see if your name is featured. I'm sure the project admins would be delighted to hear from you. There is also an additional listing of surname projects offering free DNA tests on this page in the ISOGG Wiki. Some of the names in the Wiki were not included in the Irish offer so do check out this page as well.

 A quiet time on the FTDNA stand
towards the end of the day on Saturday.

We had some enjoyable get-togethers in the evenings. It was a pleasure to meet Margaret Jordan who runs the large Ireland Y-DNA Project which now has over 5000 project members and is the third largest DNA project at FTDNA. Margaret told me that there is now a growing interest in DNA testing in Ireland. When she first took over the project the majority of project members were in the US but in recent years Irish people have begun to embrace DNA testing and Irish residents now comprise about 20% of her project members with the numbers increasing every week. I was also pleased to meet Elizabeth O'Donoghue/Ross, Nigel McCarthy and Finbar O'Mahony who run the Munster Irish DNA Project. I was also pleased to meet Gerard Corcoran who is ISOGG's representative in Ireland.There is a lot more DNA activity in Ireland than I had realised, and it is good to know that we have so many people living in the country who can help with the educational process.

Unfortunately I did not have time to attend any of the lectures as we were so busy on the FTDNA stand, though I did manage to catch the tail end of the L21 discussion panel on Friday. Maurice Gleeson worked hard co-ordinating all the lectures, introducing the speakers and making sure that all the equipment worked properly which was not an easy feat. He recorded all the lectures and, where the speakers have given permission, he has uploaded the recordings to the new Genetic Genealogy Ireland YouTube channel.  I gave two talks at the conference and both of my talks can now be seen on YouTube. On Saturday the subject of my presentation was "DNA for beginners: the three tests". On Friday I presented a lecture entitled "Chromosomes, conquerors and castles: DNA and the Cruise/Cruwys/Cruise one-name study". The handout for my talks can be downloaded from my Dropbox account.

Maurice Gleeson speaking to 
a packed audience at Back To Our Past.

All in all I think it was a very successful event. The DNA lectures seemed to be very well attended and were often more popular than the talks in the main lecture programme. We sold lots of FTDNA test kits on behalf of FTDNA, and I rather suspect we will all be back again next year.

Further links
- Genetic Genealogy Ireland 2013 website
- Genetic Genealogy Ireland on Facebook
- Genetic Genealogy Ireland YouTube channel
- ISOGG Wiki

© 2013 Debbie Kennett

My new position as Honorary Research Associate at UCL

I am very honoured to have been conferred the status of Honorary Research Associate in the the Department of Human Genetics, Evolution and Environment at University College London. The appointment took effect from 1st July and runs for five years ending on 30th June 2018. The letter confirming my status has only just arrived so I have not been able to announce the news before.

Professor Mark Thomas and Professor David Balding kindly nominated me for this position. I first met them at Who Do You Think You Are? Live in February this year and have worked closely with them since then to help counter some of the inaccurate and sensationalist genetics stories that have appeared in the press while at the same time clarifying the legitimate genealogical applications of DNA testing. My appointment will allow me to have access to the considerable library and e-library facilities at UCL to help with my research, and I will be able to participate in seminars and lab discussions. I very much look forward to the collaboration continuing.