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

Citizen science discovery rewrites human Y-DNA tree

The following press release was received from Family Tree DNA and relates to the news announced at Who Do You Think You Are? Live in February 2013 of the citizen science discovery of the new ancient root of the human Y-chromosome tree. Family Tree DNA have announced to project administrators that the 12-marker Y-DNA test will be sold at the new permanent low price of $49 (£32) with effect from 1st April 2013. The 12-marker test is currently on sale at a special low price of $39 (£26).  FTDNA already have the world's largest Y-chromosome database with almost 250,000 samples from around the world. However, with a world population of over seven billion people there is still much to be learnt about our genetic heritage and we can expect many more exciting discoveries in the months and years to come as more people get their DNA tested.

Family Tree DNA's Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

-- By Offering Low Cost DNA Test, Family Tree DNA Aims to Expand Reach of DNA Testing to Encourage Further Exciting Discoveries About Human Origins --

HOUSTON, March 26, 2013 /PRNewswire/ -- Gene By Gene, Ltd., the Houston-based genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic's Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years. This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree" in The American Journal of Human Genetics earlier this month. The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of the University of Arizona, who currently serves on Gene By Gene's advisory board, and two of the company's staff scientists, Drs. Thomas and Astrid-Maria Krahn.
The DNA sample had originally been submitted to National Geographic's Genographic Project, the world's largest "citizen science" genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA's database for genealogical research. Once in Family Tree DNA's database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

"This whole discovery began, really, with a citizen scientist – someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products," said Gene By Gene President Bennett Greenspan. "While reviewing samples in our database, she recognized that this specific sample was unique and brought it to the attention of our scientists to do further testing. The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution."

The discovery took place at Family Tree DNA's Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project. Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company's Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations. Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

"Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago," said Dr. Michael Hammer. "Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade. This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise."

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%. By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research. They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity. Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago. Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests. DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide. Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

WDYTYA Live Day 3 Part 2: The new ancient root of the Y-tree

Sunday is always the quietest day at WDYTYA and in a lull at the end of the day I took the opportunity to listen to a fascinating talk by Dr Michael Hammer from the University of Arizona on "DNA and our ancestral origins". The talk began with an explanation of the two different models of human evolution - the Out of Africa replacement model and the multiregional model. Hammer discussed the important work of Svaante Pääbo from the Max Planck Institute who has sequenced the Neanderthal and Denisovan genomes. All non-Africans carry traces of Neanderthal DNA. Small percentages of Denisovan DNA are found today only in populations in Melanesia. I have been surprised to see that most of the people who have taken the new Geno 2.0 test from the Genographic Project have reported receiving small percentages of Denisovan DNA, despite having ancestors who lived in Europe and not Melanesia. These figures can be seen in this thread on the Genealogy DNA mailing list. I asked Michael Hammer why this should be the case, and he suggested that these results must surely be in error. It is very difficult to detect introgression and the DNA that is being assigned as Denisovan is probably ancient DNA indicative of ancient shared ancestry between humans, Denisovans and Neanderthals rather than genuine Denisovan DNA. The X-chromosome provides further insight into our ancient origins and intriguingly a haplotree constructed from part of the X-chromosome shows that the most recent common ancestor on our X-chromosome line traces back not to Africa but to Asia, and the TMRCA (time to the most recent common ancestor) is around two million years ago.

However, for genetic genealogists by far the most exciting part of Michael Hammer's talk was the story of the discovery of the new ancient root of the human Y-chromosome tree, which had first been announced to a select audience at the Family Tree DNA group administrators' conference in November 2012. The most extraordinary part of the story is that it was a citizen science discovery. An African American gentleman in South Carolina submitted a sample of his DNA to National Geographic's Genographic Project. He subsequently transferred his Y-DNA results to Family Tree DNA where he joined the haplogroup A project. Bonnie Schrack, the very astute administrator of the haplogroup A project, noticed that FTDNA had not been able to assign a haplogroup to the sample. She decided to take matters into her own hands and raised some money so that the Y-chromosome could be sequenced as part of the Walk through the Y programme run by Thomas Krahn, FTDNA's chief Y-chromosome scientist. It proved impossible to place the sequence on the Y-tree as all the SNP markers were ancestral, but there were also many new SNPs found in the sample. The challenge was then to determine precisely where the sample belonged on the tree as it fell outside the range of all known Y-chromosome lineages. Additional sequencing was done on chimps and gorillas for comparison purposes, and it was eventually determined that the sequence defined a new root of the Y-tree dating back around 338,000 years before present. The new root was given the name of haplogroup A00 leaving room for the possibility that additional divergent lineages might one day be discovered and it would then be a simple matter of adding additional zeros.

The research was published on 28th February in the American Journal of Human Genetics in an article entitled An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. The official press release from the University of Arizona can be read here. CeCe Moore, who attended the FTDNA conference, provides further details on her blog. The paper concludes with the following sentence: "Finally, the discovery of the A00 lineage demonstrates the power of public participation in the scientific process — a venture that is likely to continue in the current era of personal genomics." We have only captured a tiny fraction of the genetic diversity of the world at present. I wonder how many more exciting discoveries are waiting to be made as more people start to get their DNA tested and as more samples are tested from around the world and particularly in Africa. We can also expect many of these discoveries to be made by citizen scientists working as volunteer project administrators at commercial genetic genealogy testing companies.

There was so much going on at WDYTYA that unfortunately I did not have time to visit all the stands. I had wanted to ask Ancestry if they had any plans to launch their autosomal DNA test outside the US. Luckily David Hollister, a fellow member of the Guild of One-Name Studies, was able to have a word with them. He reported that they are not yet ready to launch their test outside the US for the following reasons:

- Complicated EEC Regulations.
- Probably not enough profit in it.
- Labs are too busy

David subsequently made further enquiries with Ancestry and was told by Karen Richardson, their Senior Manager for Community Marketing, that there is no definitive answer on the launch of the DNA test in the UK though  "there is the hope that it might be in 2014, but we can't guarantee that".

The day ended at 4.30 pm, and it was then time to pack up the stands and head home. Max Blankfeld, FTDNA's Vice President of Marketing, had two enormous bags full of DNA swabs to take back with him to Houston, Texas. The company sold a record number of kits at WDYTYA this year. These samples are now starting to be processed. I have already had two new people join my Devon DNA Project who tested at WDYTYA, and I shall look forward to receiving their results in the next couple of months.

See also
- Who Do You Think You Are? Live 2013 Days 1 and 2
- Who Do You Think You Are? Live Day 3: Alistair Moffat on how DNA is rewriting British history

© 2013 Debbie Kennett