Native Male Y DNA Haplogroup C-P39 Branches

I am extremely pleased to provide an update on the Haplogroup C-P39 Native American Y DNA project. Marie Rundquist and I as co-administrators have exciting discoveries to share.

As it so happens, this announcement comes almost exactly on the 4th anniversary of the founding of this project at Family Tree DNA. We couldn’t celebrate in a better way!

Native American Y DNA Haplogroups

Haplogroup C is one of two core Native American male haplogroups. Of the two, haplogroup Q is much more prevalent, while haplogroup C is rare. Only some branches of both haplogroup Q and haplogroup C are Native American, with other branches of both haplogroups being Asian and European.

C-P39 is the Native American branch of haplogroup C, and because of its rarity, until now, very little was known. There were no known branches.

In February 2016, Marie Rundquist created a focused project testing plan to upgrade at least one man from each family line to the full 111 markers along with a Big Y test in order to determine if further differentiation could be achieved in the C-P39 haplogroup lineage.

Haplogroup C-P39 Sprouts Branches

In November 2016, Marie presented preliminary research findings at the International Genetic Genealogy Conference in Houston, Texas, with a final evaluation being completed and submitted to Family Tree DNA for review in March 2017. As a result, Marie provides the following press release:

April 29, 2017: Based on a recent “Big Y” DNA novel variant submission from the C-P39 Y DNA project, the Y Tree has been updated by Family Tree DNA scientists. With this latest update, in addition to the C-P39 SNP that distinguishes this haplogroup, there are now new, long-awaited, downstream SNPs and subclades, as reflected in the Y Tree that offer new avenues for research by members of this rare, Native American haplogroup. A summary of new C-P39 Y DNA project subclades follows:

  • North American Appalachian Region: C-P39+ C-BY1360+
  • North American Canada – Multiple Surnames: C-P39+ C-Z30765+
  • North American Canada – Multiple Surnames: C-P39+ C-Z30750+
  • North American Canada: Acadia (Nova Scotia): C-P39+ C-Z30750+
  • North American Canada: Acadia (Nova Scotia): C-P39+ C-Z30754+
  • North American Southwest Region: CP39+ C-Z30747+

The following SNP (BY18405+) was found to have been shared only by two C-P39 project members in the entire Big Y system, as reported here:

  • North American Canada Newfoundland: C-P39+ C-BY18405+
  • North American Canada: Gaspe, QC: C-P39+ C-BY18405+

The ancestors of two families represented in the study, one in the Pacific Northwest and another in the North American Southwest did not experience any mutations in the New World and Big Y results are within the current genetic boundaries of the C-P39 SNP haplogroup as noted.

The Family Tree DNA C-P39 Y DNA Project is managed by Roberta Estes, Administrator, Marie Rundquist, Co-Administrator, and Dr. David Pike, Project Advisor. The “Big Y” DNA test is a product of Family Tree DNA.


The New Tree

The new C-P39 tree at Family Tree DNA is shown, below, including all the new SNPs below P39, a grand total of eight new branches on the C-P39 tree.

It’s just so beautiful to see this in black and white – well, green, black and white. It’s really an amazing accomplishment for citizen scientists to be contributing at this level to the field of genetics.

Beneath C-P39, several sub-branches develop.

  • BY1360 which is represented by a gentleman from Appalachia.
  • BY736 which is represented by two downstream SNPs that include the surnames of both King and Brooms from Canada.
  • Z30747 which is represented by a Garcia from the southwest US, following by downstream subgroup Z30750 represented by a Canadian gentleman, and SNP Z30754 represented by the Acadian Doucette family from Nova Scotia.

This haplotree suggests that the SNP carried by the gentleman from Appalachia is the oldest, with the other sub-branches descending from their common ancient lineage. As you might guess, this isn’t exactly what we had anticipated, but therein lies the thrill of discovery and the promise of science.

The Next Step

Just like with traditional genealogy, this discovery begets more questions. Now, testing needs to be done on additional individuals to see if we can further tease apart relationships and perhaps identify patterns to suggest a migration path. This testing will come, in part, from STR marker testing along with Big Y testing for some lines not yet tested at that level.

We’re also hopeful, of course, that anyone who carries haplogroup C-P39 or any downstream branch will join the C-P39 project. Collaboration is key to discovery.


If you would like to donate to the C-P39 project general fund to play a critical role in the next steps of discovery, we would be eternally grateful. At this point, we need to fund at least 4 additional Big Y tests, plus several 111 marker upgrades, totaling about $3000. You can contribute to the project general fund at this link:

Thank you in advance – every little bit helps!


I want to personally congratulate Marie for her hard work and dedication over the past year to bring this monumental discovery and tree update to fruition. It’s truly an incredible accomplishment representing countless hours of behind the scenes work.

Marie and I would both like to thank all of our participants, individuals who contributed funds to the testing, Dr. David Pike as a project advisor and, of course, Family Tree DNA, without whom none of this would be possible.

DNA Testing for Native Heritage

If you are male and have not yet Y DNA tested, but believe that you have a Native ancestor on your direct paternal (surname) line, please order at least the 37 marker test at Family Tree DNA. Your results and who you match will tell that story!

People with Native heritage on any ancestral line are encouraged to join the American Indian Project at Family Tree DNA. If you have tested elsewhere, you can download your results to Family Tree DNA for free.

For additional information about DNA testing for Native American heritage, please read Proving Native American Ancestry Using DNA.

If you’d like to take a DNA test, click here.


About Roberta Estes

Scientist, author, genetic genealogist. Documenting Native Heritage through contemporaneous records and DNA.
This entry was posted in Acadian, Appalachia, Canada, DNA, Micmac and tagged . Bookmark the permalink.

15 Responses to Native Male Y DNA Haplogroup C-P39 Branches

  1. Pauline Barraza says:

    Found out through that there is 39% Native American ancestry, but was adopted in 1958. Unable to obtain adoption records identifying biological parents. How do we approach determining tribal relationships?

    • Silvia says:

      Oh my gosh. That is my exact story. Adopted is 75 with no records. Got my ancestry results less than a week ago. I am 45% American Indian but as with you i have no backround whatsoever. I have the same question as you. Have you had any luck with those two websites the person suggested?

      • Pauline Barraza says:

        Yes, I was provided with a couple of links on the topic. First, the point that was made most strongly is that the Native American nations aren’t really interested in increasing their numbers especially since that reduces their cut of cash from their now prosperous business ventures. Next, the actual genealogical records of your biological parents and relatives are the most reliable source and preferred over DNA, which really can’t be matched in their records, unless a blood relative who has also submitted their DNA to for example, and they notify you of those matches. So it’s really kind of a dead end as far as determining your specific lineage/tribe/nation. Having been adopted, raised an only child and with both adoptive parents now dead, we had hoped to learn more but it doesn’t seem possible. Finally, avoid those non-federally recognized tribes which are apparently very willing to take your money to be a member.

  2. April says:

    I have a second to fourth cousin match on ftdna with a person that is from the blue jacket line, and was part of a DNA project. I have not found the link yet and wanted to know if there is a good place for documents to find his link to me. I adopted but already know bio mom.

  3. Gilberto Abascal says:

    Hi Roberta! I fall under group C, but I can’t figure out specifically which sub group. Admittedly, I am having a hard time understanding it all. Where would I be able to find that under Family Tree?

  4. Anthony Garza says:

    Hello, I have tested my Arredondo family line to the early 18th century. I traced them back to San Miguel de Aguayo (Bustamante, Nuevo Leon, Mexico). They were (according to church records) Alazapa Indians, an indigenous tribe of Nuevo Leon, believed to be under the umbrella of Coahuiltecan Indians. My predicted haplogroup is C-M216. I only did a Y37 to start. I am hoping to either get a SNP pack or Big Y in the future to refine it. I have only one match to a C-M217, which is understandable. I wonder if the Coahuiltecans are related at all to other Indigenous groups in the US?

    • Related depends on timeframe. They are related in that they all descended from the group who crossed from Beringia. The question is when the various lines split. The Big Y is on sale now.

  5. Sherril Stewart says:

    Hi Roberta, I recently had a cousin DNA match at 23andMe with 21.5 % Native American, his haplogroup is C-Z30538 and his father is 1/2 Ho-Chunk Nation (Winnebago) and 1/2 French. My direct Native American maternal ancestor I believe was also Winnebago from the Wisconsin/Minnesota area. I am haplogroup B2. No matches except for my known close relatives. I sent him this website to get more information. I can send you his name via email if you would like it.
    Sherril Stewart

  6. John Provencio Ortega Harding says:

    These people are my people, I am Apache, Authapaskin. My Family is Garcia southwest, Doucete Canada Nova Scotia. I have lots of information on my people. Feel free to contact me. John Provencio Ortega Harding. Chihene Chiricahua Warmsprings Apache, Geronimo’s People. Viva Los Apaches !!!!

  7. Joshua Reome says:

    Hi I am trying to find out about Anne Marie mi’kmaq if you can help thank you

  8. Hello again Roberta,
    Can you please tell me if there has been a genetic code established for the ‘panis’ in Windsor (Sandwich) – Amherstburg region of Ontario?

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