Friday, March 1, 2013

Citizen Science Helps to Rewrite the Y Chromosome Tree and Illuminate the Ancestral Roots of African American Project Members

The academic paper describing the discovery of a new root of the human Y chromosome tree, An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree, was finally released. This is important news for the entire scientific community, however it is possibly even more significant for our community of citizen scientists. Well-known genetic genealogist Bonnie Schrack is listed among the authors of this groundbreaking paper, which was published in the American Journal of Human Genetics on Thursday. She is the administrator of the Y-Haplogroup A Project at Family Tree DNA and was the one who first came upon the very unusual results from a project participant that ignited this entire discovery

Bonnie Schrack, Y Haplogroup A Project Admin and Citizen Scientist

At the Family Tree DNA Conference last November, we were treated to a sneak peek into this history-changing research. I chose not to cover it at that time out of deference to the academics' plans to publish. However, I am now free to discuss the presentation and the findings. I'm sure many blogs will cover the more technical aspects of this important paper and the A00 Haplogroup, but I would like to focus on what this discovery means for us as genealogists and citizen scientists.

At the FTDNA conference, Bonnie Schrack described how several of her project participants just didn't seem to fit into any of the known haplogroup subclades. She brought this to the attention of FTDNA's Dr. Thomas and Astrid Krahn who, after much investigation and several Walk Through the Y tests on these divergent Y chromosomes, alerted Dr. Michael Hammer to one especially unique Y-chromosome. And the rest, as they say, is history.

Bonnie explains in her speaking notes, "All the project administrators out there have probably had the experience of having a few project members who don’t fit into your main groups, who have no matches. They’re usually not very happy about it! But for a haplogroup project, these same samples can be gold...These rare haplotypes are just what we need to explore and clarify the phylogenetic tree. With SNP testing, we can identify new clades, new branches on the tree, and they can become the heroes!" (Bonnie's slides and speaking notes can be found on her Haplogroup-A site.) 

The AJHG paper thanks FTDNA customer, Jacqueline Johnson, and her male cousins for their contributions. It was one of these cousins, tested as part of Johnson's family history research, through whom this discovery was made. We do not know his name (and if he wants privacy, hopefully it will stay that way), but he is an African American man, descended from a former slave named Albert Perry (b.c. 1819-1827) who lived in York Co., South Carolina. Let's call him "Mr. A00 Perry". You can see his results, as well as those of one of his distant cousins descended from the same patrilineal ancestor, in the Haplogroup A Public Project Y here. They are listed at the very top, kits N64496 and 215865. (You can see some of the other interesting haplotypes just below these.)

One of the many very exciting aspects of this discovery for genealogists is that the scientists were able to compare the values of six of the Y-STRs commonly tested for genealogical DNA tests from "Mr. A00 Perry's" results to a database at an academic institution to determine that this haplotype is similar to 11 samples from Mbo individuals, a Bantu speaking population from western Cameroon.

The paper explains:  
We then genotyped a set of six Y chromosome short tandem repeats (Y-STRs) (DYS19, DYS388, DYS390, DYS391, DYS392, and DYS393) and found that the A00 chromosome carried the following alleles: 16-11-19-10-12-13. Upon searching a large pan-African database consisting of 5,648 samples from ten countries (Cameroon, Nigeria, Ghana, Senegal, Uganda, Tanzania, Malawi, Zimbabwe, Mozambique, and South Sudan), we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (~6.3%) Mbo individuals from western Cameroon.

Citizen scientist extraordinaire, Bonnie Schrack adds additional insight regarding her project members' probable direct paternal line origins on Dienekes blog:
Another thing I might mention is that our African American project members are a far closer match to the Bangwa people, whose haplotypes are found in the SMGF database...than to the Mbo who were sequenced. The Bangwa and Mbo are close neighbors, and rivals...when talking about who our project member's kinfolk in Africa might be, it's a far better chance they're Bangwa, from Fontem, Lebialem, than Mbo. We found two SNPs in our project members that were negative in the Mbo -- perhaps they'd be found positive if Bangwa were tested.

The Y-STR markers in question are all tested as part of the first panel for Y-DNA tests at Family Tree DNA. This means that a simple 12 marker Y-DNA test (currently only $39) would show if a man potentially matches this very unique haplotype or not. One of the Haplogroup A Project's stated goals is "to provide information on ancestral origins for African-American participants". This exciting discovery does just that and shows us the potential that is out there for African Americans searching for their African roots. 

The paper estimates that the most recent common ancestor between "Mr. A00 Perry" and the Mbo men could be as recent as about 500 years ago:
We also estimated the level of variation among nine A00 lineages (i.e., including one additional Mbo individual) by using a battery of 95 Y-STRs for which all individuals had no missing data. A median-joining network shows that the African American A00 lineage is 11 mutational steps from the nearest Mbo and that the maximum difference between any pair of Mbo is nine steps. On the basis of these levels of within- and between-group variation, we calculated a second divergence time estimate of 508–2,428 years.

This is certainly powerful and, potentially, meaningful information for "Mr. A00 Perry" and his family. Let's review what they have learned:
  1. It has been determined that the Y chromosomes most similar to his are currently found in the Southwest Region of Cameroon on the West Coast of Africa.
  2. This fits well with their known family history of descent from Albert Perry, a slave, and the transatlantic slave trade originating from this area to the Americas.
  3. The lower end of the estimated range for the common ancestor between "Mr. A00 Perry" and the Mbo men also fits well within the time frame of the slave trade. If it is true that the Bangwa men are more closely related to him than the Mbo men, this makes for an even stronger case.
Cameroon is on the West Coast of Africa

Transatlantic slave trade routes

These momentous discoveries were made thanks to tenacious and inquisitive citizen scientists, as well as willing participants within the framework of a commercial testing company. Not only were the noteworthy haplotypes originally recognized by genetic genealogist Bonnie Schrack, but the subsequent research was largely funded by the genetic genealogy community as well (notably Stan Pietrzak and Hamma Bachir Ahmed). Further, the private participants identified as potentially historically significant willingly underwent additional testing where necessary.

The paper concludes with this:
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.

I think we can all bet on that!

This just goes to show that we have much more to learn about our shared history. Now, get out there and test those family members! You never know what you might find...Maybe you will help to unearth the next big discovery.  Citizen science has come of age!


  1. I've read this twice, but I must confess not to understand it....and if it's monumental, I really want to understand it. Might you be able to explain it in genealogy-for-dummies language. I recently had my mdDNA tested as part of the National Geographic Genographic Project, so I've been trying hard to figure it all out. Thx, Ellen

  2. Major Kudos!!!, Bonnie.


  3. Thanks, Mr Perry. For your participation on Genographic Project and FTDNA, the Geneticist can learned more about Human Genealogy and get it then keep your high valuable / "Gold" Y Chromosome. The Genographic Project and FTDNA should give him a reward or somethink like that even though it is an "accidental" oportunity.

  4. Which are more accurate to determine Y Chromosome Haplogroup: STR's Testing (12 - 111 markers) or SNP Testing (Geno 2,0 NG and FTDNA a Big Y)?

    1. SNP testing is what determines your haplogroup subclade.

    2. What the difference about Geno 2,0 and Geno 2,0 NG and an FTDNA Big Y DNA Test? My Y Chromosome Hg O-M175 from Geno 1st Y DNA testing result and Y Hg O-CTS5492 from Geno 2,0 result.