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.

AncestryDNA updates

I wrote previously of my experiences with the AncestryDNA autosomal DNA test. I covered the consent forms and the admixture analyses in my first article. In a second article I looked at the matching process. One of the big criticisms that I and many others had with regard to the AncestryDNA test was the fact that the company, unlike 23andMe and Family Tree DNA, did not allow customers access to their raw genetic data. I am now pleased to advise that Ancestry have listened to the feedback and have finally made the raw data accessible.

The data can be accessed by logging into your AncestryDNA account and clicking on "Manage Test Settings". Before downloading the data it is necessary to re-enter your password. There are notices to advise that the downloaded data is subject to the AncestryDNA Terms and Conditions and the AncestryDNA Privacy Statement. The Terms and Conditions were revised on 20th March 2013 and now include what appears to be a new section laying out the Rules of Conduct. These state among other things that "You must also agree that you will provide valid and complete contact information, and that you will always have a valid email address on file with AncestryDNA." In addition the rules include the following somewhat puzzling condition: "You must not use the information from the AncestryDNA website or DNA tests (including any downloaded raw DNA data) in whole, in part and/or in combination with any other database for any discriminatory, breach of privacy or otherwise illegal activity (for example, to re-identify any anonymous donor or to make insurance or employment decisions)."

The Rules of Conduct conclude with the following paragraph: "These Rules of Conduct are not exclusive. If we believe, in our sole discretion, that you are in breach of this Agreement, are acting inconsistently with the letter or spirit of this Agreement or otherwise interfering with the efficient management or delivery of the AncestryDNA Website, Service or Content, we may limit, suspend or terminate your access to our AncestryDNA Website. In such a case, no portion of your subscription payment will be refunded. Should we decide to suspend or terminate your access for any reason other than your actions or omissions which we believe to be inconsistent with this Agreement we will refund to you any unused portion of your payment, which will be your sole and exclusive remedy upon such a suspension."

I am not at all clear how someone can use their own genetic data in any type of illegal activity and it seems to me that it is entirely my business what I do with my own genetic data and has nothing to do with AncestryDNA at all. The requirement to maintain a valid e-mail address is of some concern as this rather suggests that any account that does not have a valid e-mail address will be excluded from the AncestryDNA database. Inevitably subscriptions will lapse over time. People become ill and are no longer able to continue their family history research or they die and their account is not passed on to a relative. Does this mean that all these results will be removed from AncestryDNA because the accounts no longer comply with the Rules of Conduct?

The AncestryDNA Privacy Statement has been similarly updated with effect from 20th March 2013. Interestingly I note that Ancestry have now signed up to the Safe Harbor program which relates to the "collection, use and retention of personal data from European Union member countries and Switzerland". Does this mean that Ancestry are gearing up to make their test available in Europe? In section 3 "How does AncestryDNA use your personal information?" there is what appears to be a new addition and by testing with Ancestry you are now giving them permission to use "your personal information" to "research human genetic diversity". From what I can gather this permission applies even if you have, like me, not signed the separate AncestryDNA Consent Form.

Having gone through the instructions on the AncestryDNA website you are sent an e-mail to confirm the download. The e-mail is reproduced below.

Having confirmed the data download you are taken back to the AncestryDNA website and taken to a page where you can download the raw data. I have provided a screenshot below.

The data is downloaded as a zip file and when the file is unzipped it opens up in Notepad. The many citizen scientists in the genetic genealogy world are currently trying to examine and make sense of the raw data. It is likely that third party websites such as Gedmatch will provide a facility to upload AncestryDNA data. Support will no doubt also be provided for the other third-party tools which are listed on the autosomal DNA tools page in the ISOGG Wiki.

Interestingly, although Ancestry do not provide information on the X-chromosome and Y-chromosome SNPs on their chip or use these results for matching purposes, the raw data is included in the download file so by downloading the data it will be possible to get more value out of the test. It is not yet known which Y-SNPs are included on the chip but this information could potentially be of great value for anyone who has taken a Y-STR test and who wishes to learn more about their deep ancestry by participating in a Y-DNA haplogroup project.

Another big announcement about the AncestryDNA testing service was made today at Roostech by Tim Sullivan, Ancestry's President and Chief Executive Officer. He advised that the the Ancestry DNA is now available at the new low price of $99 to both subscribers and non-subscribers. The test was originally offered at $99 in the beta-testing period. The price was subsequently raised to $199 for non-subscribers and $129 for subscribers. The latest reduction means that the AncestryDNA test is now the same price as the 23andMe test. However, the 23andMe test provides many additional features, including health and trait information, which are not available from Ancestry.  Tim Sullivan also announced that Ancestry have over 120,000 autosomal results in their database. He promised that improved ethnicity results and improved cousin matches are on the way but no specifics were given.

Note that the AncestryDNA test is only available to US residents. Although I live in the UK, for some reason I was able to order the AncestryDNA test during the beta-testing phase, but I am one of only a tiny handful of non-US people in their database at present. It is not yet known when or if Ancestry will make their test available in other countries. For those of us who do not live in the US there is a straightforward choice between 23andMe and FTDNA's Family Finder test. Currently the most cost-effective way to get your results in both databases is to test with 23andMe and then transfer your results to FTDNA.

Family Tree DNA's Family Finder test is now much more expensive at $289 than the comparative offerings from 23andMe and AncestryDNA. The US is the prime market for all three companies. It will, therefore, be interesting to see how FTDNA respond to the competition. At the very least, it would be very useful if FTDNA could follow Ancestry's example and allow their customers access to their raw Y-SNP data. In theory FTDNA should be able to add AncestryDNA to their third-party transfer program, but the transfer currently costs $89, which is only $10 short of the cost of the 23andMe and AncestryDNA tests. Will FTDNA reduce the cost of the transfer to encourage more people to transfer their results and to widen their database? Whatever happens the competition will be very beneficial for the genetic genealogy community and we can no doubt look forward to many exciting developments in the next few years.

*Update 23rd March 2013*
I've now transferred my raw data from AncestryDNA into a spreadsheet. The file header contains the following information:

AncestryDNA raw data download
This file was generated by AncestryDNA at: 03/22/2013 10:39:55 MDT
Data was collected using AncestryDNA array version: V1.0
Data is formatted using AncestryDNA converter version: V1.0
Below is a text version of your DNA file from Ancestry.com DNA, LLC.  THIS INFORMATION IS FOR YOUR PERSONAL USE AND IS INTENDED FOR GENEALOGICAL RESEARCH ONLY. IT IS NOT INTENDED FOR MEDICAL OR HEALTH PURPOSES. THE EXPORTED DATA IS SUBJECT TO THE AncestryDNA TERMS AND CONDITIONS, BUT PLEASE BE AWARE THAT THE DOWNLOADED DATA WILL NO LONGER BE PROTECTED BY OUR SECURITY MEASURES. 

Genetic data is provided below as five TAB delimited columns. Each line corresponds to a SNP. Column one provides the SNP identifier (rsID where possible). Columns two and three contain the chromosome and basepair position of the SNP using human reference build 37.1 coordinates. Columns four and five contain the two alleles observed at this SNP (genotype). The genotype is reported on the forward (+) strand with respect to the human reference.

My AncestryDNA raw date file contains information on 701,478 SNPs divided into 25 chromosomes. I have data for:

- 17604 SNPs on chromosome 23
- 885 SNPs on chromosome 24
- 440 SNPs on chromosome 25

We of course only have 23 pairs of chromosomes. Ann Turner has clarified on the Genealogy DNA list that chromosome 23 is the X chromosome, chromosome 24 is the Y-chromosome, and chromosome 25 "is for XY SNPs, where the SNP is also found on the pseudo-autosomal regions (PAR) at the tips of the Y". As a female I do not have a Y-chromosome and most of my results for the Y are no calls (zeros). However, I do have results reported for 93 Y-SNPs. Apparently this is something to be expected for reasons which are not yet clear to me.

CeCe Moore was one of a number of genetic genealogists who had a meeting with the AncestryDNA people at Rootstech and she has advised on the Genealogy DNA list that Ancestry are working on a search function filtered by surname or user name. She further advises that Family Tree DNA are hoping to accept AncestryDNA uploads from the beginning of May and that Gedmatch will be able to accept AncestryDNA uploads in a couple of weeks.

*Update 24th March*
AncestryDNA have now added a section on raw data downloads to their FAQs which can be read here. Ancestry seem to be overly concerned about their customers misusing their data in some unforeseen way and provide a number of cautionary warnings about using your data on third-party websites.

*Update 25th March*
For a detailed report on AncestryDNA's plans see CeCe Moore's blog post on "AncestryDNA, Raw Data and Rootstech".

© 2013 Debbie Kennett

Sense About Genealogical DNA Testing

I wrote last week about the new report from Sense About Science on the subject of Sense About Genetic Ancestry Testing. While I welcomed the publication of this report I was concerned at some of the inaccurate media coverage it generated which gave the false impression that all genetic ancestry testing is "meaningless". The report made it quite clear that DNA testing can be legitimately used for genealogical purposes, but this aspect was overlooked in some of the newspaper articles who quoted from the report out of context. I was very pleased, therefore, that Sense About Science invited me to write a guest blog post for them to help set the record straight. The post, entitled Sense About Genealogical DNA testing, is now live on the Sense About Science website. I am very grateful to all  the geneticists and genetic genealogists who provided useful feedback which resulted in a much better article than I would ever have written on my own.

Sense About Genetic Ancestry Testing

The UK press has been flooded in the last year or so with stories about a number of people, including a few celebrities, who who have had their DNA tested and who have been told extraordinary stories about their ancestry. The Guardian reported that the actor Tom Conti is directly related to Napoleon Bonaparte. The Scottish comedian Fred MacAulay was told on BBC Radio Scotland that his dad's Y-chromosome DNA "put him in south-west Ireland as part of the descent of Irish kings who were captured by Vikings and then sold in the slave market taking him up to the Hebrides". The Daily Mail revealed that a Scottish pensioner by the name of Ian Kinnaird learnt from his mitochondrial DNA test that he is "the grandfather of everyone in Britain". While the BBC and the national press have uncritically lapped up these stories and published them without question unfortunately they contain many errors and exaggerations.

As genetic genealogists we normally use DNA as a tool to help with our genealogical research. However, DNA testing can also provide some insight into one's deep ancestry. A man can take a Y-chromosome DNA test to explore his ancestry on the direct paternal line. Both men and women can take a mitochondrial DNA test to explore their ancestry on the direct maternal line. When you receive your Y-DNA or mtDNA results you are given a haplogroup assignment. The haplogroup represents your branch on the human Y-DNA or mtDNA family tree. Haplogroups are defined by markers known as SNPs (single-nucleotide polymorphisms) - small changes in the letters of the DNA alphabet. The Y-DNA tree is maintained by ISOGG - the International Society of Genetic Genealogy - and can be found here. The mitochondrial DNA tree is maintained by Mannis van Oven from the University Medical Center in Rotterdam in the Netherlands and can be found on the Phylotree website.

Haplogroups do tend to cluster in specific geographical regions and attempts can be made to explore the origins of these haplogroups by looking at their distribution and diversity in present-day populations, but there are inherent biases in the available databases, nowhere enough samples have been obtained and sometimes the conclusions drawn are highly speculative. Nevertheless many scientific papers have been published in peer-reviewed scientific journals on the origins of the different haplogroups, but with the discovery of more new markers on an almost daily basis these studies can often become out of date as soon as they are published. It can, of course, be fun to see who else shares your haplogroup. There is a page on Wikipedia which provides a list of the haplogroups of historical and famous figures, and there is also a famous DNA page on the ISOGG website. However, the markers that define these haplogroups often arose many thousands of years ago so it is therefore somewhat meaningless to declare, for example, that Tom Conti is directly related to Napoleon when they only share a common ancestor from several thousand years ago on their direct paternal line and they share that ancestor in common with thousands of other men in the same haplogroup. A DNA test cannot tell you that you are descended from a slave who was captured by the Vikings, and it is quite preposterous to tell someone that he is the ''grandfather of everyone in Britain" for many reasons not the least of which is that this ridiculous claim was based on a mitochondrial DNA test and males cannot pass on mtDNA to their children!

To counter some of these outlandish claims and to help the public to understand the issues involved the charity Sense About Science has produced a very useful new booklet entitled Sense About Genetic Ancestry Testing which can be downloaded from their website. The booklet has been written by a number of distinguished geneticists and explains very clearly the problems of assigning ancestry from a DNA test. Unfortunately some of the reports in the newspapers and online have commented on the publication of this booklet and given the story a somewhat misleading slant. The Telegraph has, for example, declared that "DNA tests [are] branded 'meaningless'" while the BBC more cautiously warns that "Some DNA ancestry services [are] akin to 'genetic astrology'".  It is important to note that these headlines apply only to certain deep ancestry tests and not to the tests that we use for our genealogical research. As the Sense About Science authors note in their report:

"There are credible ways to use the genetic data from mtDNA or Y chromosomes in individual ancestry testing, such as to supplement independent, historical studies of genealogy. If, for example, two men have identified – through historical research, possibly involving surnames – a common maleline ancestor in the sixteenth century, it would be reasonable to use their Y chromosome data to test this. There are some ancestry testing companies that offer this service."

I hope that lessons will have been learnt as a result of the Sense About Science publication and that the hyperbole of recent months will not be repeated. It is perhaps too much to hope that the press will take a more responsible attitude and will only publish stories based on scientific research published in peer-reviewed scientific journals rather than rehashing sensational stories from press releases submitted by PR companies as publicity stunts. In the meantime I would urge everyone to heed the words of Professor David Balding on the Sense About Science website: "Be wary of news items about genetic history - that someone famous is related to the Queen of Sheba or a Roman soldier.  Often these come from PR material provided by genetic testing companies and can be trivial, exaggerated or just plain wrong."

If you wish to get your DNA tested either for genealogical purposes or to explore your deep ancestry there are a range of companies to choose from. The ISOGG Wiki has many valuable resources including a number of charts comparing the offerings of the various testing companies. Whatever your reason for taking a DNA test you will get the best value for your money if you choose a company which provides a genealogical matching database where you can contact your matches and get involved in projects. The two companies that I recommend are Family Tree DNA and 23andMe. Family Tree DNA host all of my DNA projects. They offer the widest range of tests and have by far the largest genetic genealogy database. They have over 7300 surname projects, a large number of geographical projects as well as projects for all the Y-DNA and mtDNA haplogroups. The 23andMe test is essentially a health and traits test but it also provides haplogroup assignments and it includes a cousin-matching service, known as Relative Finder, based on autosomal DNA. If you are interested in the 23andMe test you can read my reviews here.

© 2013 Debbie Kennett