This is my first post in a serious on updating the Y-DNA Q-M242 tree. Today, I write about updating the Native American Q branch, Q-M3. Q-M3 is the best known and highest frequency branch of Y-DNA haplogroup Q in native populations of the Americas. Members of the lineage reach from the Eskimo like peoples of far North Eastern Asia across the sea to Canada and throughout both North and South America. As such, it is a vital tool for understanding the histories and peoples of the Americas. Until the past few years though, little had been done to discover and investigate its branches.
As of today, project membership includes:
Big Y: 148
The first step in updating the Q-M3 tree is creating a potential single tree based on all current trees. That means combining the Family Tree DNA Tree (Y-Haplotree), the ISOGG Draft Tree curated by Ray Banks, and the YFull Tree based on NexGen sequenced samples. It also means reviewing published papers for branches that are not part of any of those trees.
The second step is verifying the number and type of sample used to define each branch. For example, was the Y-SNP the result of data mining published NexGen sequencing results or from Sanger direct sequencing? If the Y-SNP is comes from NexGen sequencing what is the coverage level? While tests like BIG Y have an average coverage of 60X, other results from research efforts like 1K Genomes may only have a coverage level of 4X. Higher coverage levels mean higher confidence in the results.
The next step is checking the origin and other available demographic information for each sample. Trees are rather dull without information about the ethnic background of those tested. Where available, we fill in the population information for each sample, the published sources, and identification numbers used at YFull and in publication.
Y-SNP Quality Checks
As I have mentioned in past posts, Y-SNPs are usually single events and are highly reliable. However, there are exceptions. Some parts of the Y-chromosome are too unstable to be reliably sequenced. Other parts are what is called psudo-autosomal. That means that at times they will recombine (mix) with the X-chromosome a male inherits from his mother and that mixed Y-chromosome will be passed on to a son. Regions considered unreliable (Adamov et al., 2015) are:
2,900,000 to 6,600,000
13,000,000 to 13,820,000
22,216,800 to 22,512,940
Y-SNPs in these regions or found to occur across many parts of the Y-Tree will usually be excluded from the final version of the tree.
Q-M3 Merged Tree V1
Vladimir and I have put together our first version of a merged tree. This brings together the three trees as the first step. We are working on the additional steps outlined above.
Thank you for being part of the project.
R.A. Canada and the Q-M242 Team
- Adamov, D., Guryanov, V., Karzhavin, S., Tagankin, V., & Urasin, V. (2015). Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data. The Russian Journal of Genetic Genealogy (Русская версия), 68-89.
- Jota, M.S., Lacerda, D.R., Sandoval, J.R., Vieira, P.P.R., Santos‐Lopes, S.S., Bisso‐Machado, R., Paixão‐Cortes, V.R., Revollo, S., Fujita, R., Salzano, F.M. and Bonatto, S.L., (2011). A new subhaplogroup of native American Y‐Chromosomes from the Andes. American journal of physical anthropology, 146(4), 553-559.
- Karmin, M., Saag, L., Vicente, M., Sayres, M.A.W., Järve, M., Talas, U.G., Rootsi, S., Ilumäe, A.M., Mägi, R., Mitt, M. and Pagani, L., (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome research, 25(4), 459-466.
- Malyarchuk, B., Derenko, M., Denisova, G., Maksimov, A., Wozniak, M., Grzybowski, T., Dambueva, I. and Zakharov, I., (2011). Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. Journal of human genetics, 56(8), 583-588.