New citizen science project to collect DNA samples from Cameroon

I wrote back in November last year of the citizen science discovery of haplogroup A00 the oldest and most deep-rooted branch of the human Y-chromosome tree which dates back around 338,000 years. The scientific paper resulting from this discovery "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree" was published in February of this year in the American Journal of Human Genetics.

Bonnie Schrack, the administrator of the Haplogroup A Project at Family Tree DNA who was instrumental in the discovery of haplogroup A00, is now launching an ambitious new citizen project. She is working in collaboration with Matthew Fomine Forka Leypey, a Cameroonian doctoral candidate at the University of Yaounde, on a project to collect many new DNA samples from Matthew’s own Mbo people, and others across Cameroon, in order to greatly expand our knowledge of A00.

I’m copying below with Bonnie’s permission the letter she submitted to our ISOGG Project Administrators’ mailing list as Bonnie can explain the project far more eloquently than I can:

Dear friends and fellow enthusiasts 

I have an exciting announcement to share with you. Until now, we as genetic genealogists and researchers of deep ancestry have always been dependent on the field research carried out by professional, academic population geneticists, whose priorities and interests have been different from ours. They were the only ones with access to the grant funding necessary to finance such projects. 

It's a new day now - the times they are a-changin'. "Crowdfunding" is one of the hottest new developments in the online world, and with good reason. Now, we the people can launch all kinds of projects, and we can decide what we want to support with our own funds. 

Today we go live with our crowdfunding page for the first grassroots, citizen science organized project to collect DNA samples in the field, in Cameroon! We're using the Microryza website, which is devoted to crowdfunding science research. Here's the link: 

http://microryza.com/projects/y-dna-a00-and-the-peoples-of-cameroon-in-search-of-the-homeland

OR  

http://bit.ly/13Z3et8 

Many of you heard about our discovery of the A00 haplogroup, the world's earliest-branching Y-chromosome lineage. It was found in a WTY of the Perrys, an African-American family with an extremely unusual and unique haplotype, and then we found a few haplotypes matching them from members of two African ethnic groups, the Mbo and the Bangwa, who are neighbors in Southwest Cameroon. A few tiny bits of Mbo DNA were shared with Dr. Michael Hammer, and sequenced by his lab and Thomas Krahn at FTDNA. The SNPs confirmed that they belonged to the same haplogroup as the Perry family. 

Calculations by Dr. Fernando Mendez, and others in our community, have placed the branching age of this lineage at anywhere from 200,000 to 338,000 years ago - at the dawn of modern humans' emergence, or before. And so little is known about it!  How far does it extend from those few Mbo and Bangwa families, and can it be found in other peoples? Is A00 a remnant of the earliest, indigenous hunting and gathering peoples of Africa, and if so, when and where were they assimilated into other peoples, who are now settled farmers (though they still hunt)? 

For the first time since A00 has been known to exist, a young Cameroonian scholar, Matthew Fomine Forka Leypey, a member of the Mbo ethnic group, will visit the villages known to harbor significant numbers of A00 members, sample there, and collect information on the families. How do we know which villages have A00?  Because Matthew collected the original Mbo samples, and over 2000 other DNA samples from all over Cameroon, as part of his dissertation research! His data indicate that the Mbo and Bangwa are only two of a number of peoples who have A00 among them. About a dozen other ethnic groups include A00 members, including some Pygmies! Those samples, though, are no longer available to us. 

Now it's time to gather our own samples. We have a series of five field trips planned, to gather samples of diverse peoples in Western, Southern and Eastern Cameroon. Our analysis will include some special areas of knowledge from Matthew's studies, such as how different peoples support themselves within forest and grasslands ecologies, and the effects of polygamy vs. monogamy in patterns of populations' Y-chromosome DNA. 

In the past, it has always been thought necessary to make DNA donors anonymous when they participate in scientific studies. In this project, however, we'll be asking for the donors' names, for several reasons:
1. We want to give them the possibility of receiving their test results, if they are interested
2. We want there to be a future possibility of families who match them, such as African Americans, to know their matches, if they opt in
3. We hope to gather a second sample (saliva) from one or more donors, in order to have a full Y genome sequence done
4. We hope to correlate the haplogroups and haplotypes we find with families of different known histories, such as royal lineages, traditional religious office-holders, and those that are known to have had ancestors held as slaves by local rulers. 

Of course, their names will not be made public except, should they decide to participate and future funding allows it, to their individual DNA matches. 

This is a kind of research, combining genealogy with population genetics, that academics rarely undertake, but which has been occasionally done in papers such as this one by one of the co-authors of our last paper, Dr. Krishna Veeramah: Sex-Specific Genetic Data Support One of Two Alternative Versions of the Foundation of the Ruling Dynasty of the Nso in Cameroon. 

We have four weeks to raise the $2500 needed to launch our first field trip in Cameroon. Our deadline is August 19th. Then Matthew will set out for the remote mountain villages where he was raised. We look forward to bringing you all along on this great adventure. 

In addition, apart from the appeal for fieldwork support per se, we're looking for a few generous individuals who'll help us obtain a decent (can be used) laptop and a digital camera for Matthew, who's a very low-income grad student. We're also looking for a trustworthy person flying to Cameroon who can take these along, saving us the exorbitant shipping fees. 

Please write to me if you have any leads.

In the near future, the next fundraising campaign will ask for your support for the DNA extraction and the screening of our first set of samples for A00. Stay tuned! Please visit and "like" our page on Facebook:  

https://www.facebook.com/A00.Cameroon.Project

Looking forward to seeing you, with gratitude for your support,  

Bonnie Schrack

I hope that some of you will be inspired to help this very worthwhile project. If you want to get in touch with Bonnie you can contact her via the Haplogroup A Project website. You can also find her on Twitter where she goes by the name of @Greenleafy.

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