Native American Y Haplogroup C-P39 Sprouts 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.



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28 thoughts on “Native American Y Haplogroup C-P39 Sprouts Branches!

  1. Thank you Roberta and Marie and all those who worked so hard on this project. My brother was one of the participants and we were very excited to get the news. In our wildest dreams we never expected to see a new branch on the tree that represented our Acadian family.

  2. Roberta, I am just a newbie in the Genetic Genealogy world. I really appreciate your blog. You do a great job sharing different areas of DNA research. I still don’t understand a bunch of it, but I am inspired by your posts. Thank you!

  3. In addition to thanking you, Roberta, and David, for all of your critical reviews of the initial project assessments and helpful suggestions to push the project forward, Janine Cloud and her team for helping us with our Big Y orders and project management, and Heather Kines for forwarding on our submission (to think it was only last week!) and Family Tree DNA’s Michael Sager for his extremely rapid response in integrating our new SNPs on the Y tree and for publishing all of the new subclade branches and labeling the kits as quickly as he did, I would like to thank the participants (the men who stepped up to the plate and had the test) and also the family members who help manage the kits and all those who believed in and worked with the C-P39 Y DNA project from the start. I’d give thanks to the “DNA angels” all across Canada and the United States who helped us find Y DNA test candidates — and then convinced them to “swab” — without whom we would not have so many great people participating in our study. I hope that all reading her blog take Roberta’s advice and contribute to our C-P39 Y DNA project — and help us fund more of the Big Y tests especially. Looking across the project, I wonder where other Big Y test results will fit within the new C-P39 tree — or will our project grow another branch?

  4. What do you know about the Y-DNA Q-M242 haplogroup? I read that Native Americans, Jews, and Scandinavians share this male haplogroup, quite a diverse group!

  5. Hello, I joined the project. I had my Dad’s DNA tested, FTNDA 37, we believe his mom has Am. Indian blood, but it is not showing up in his test. His test number is 549146. My husband works for Estes Brothers Construction, Inc from Jonesville, Lee County, VA, is Roberta any kin to them?

  6. I admin my Dad’s kit, could I join one of these groups? My Dad won’t himself and I would very much like to see what it’s about. Thank you

    • If your father is haplogroup C-P39 you are welcome to join the haplogroup C-P39 project. If your father is not haplogroup C, but is Native or thinks he’s Native on another line, he is welcome to join the American Indian project. If you manage his kit for him, you can certainly join him to any project you deem relevant.

  7. Roberta, are genetic scientists absolutely sure that only those two haplogroups you mentioned are Native American? Have a sufficient number of individuals been tested from every known tribe in the US to be absolutely certain of that?

    • So far, yes. There are many burials now, some in the US and some in Canada and South America. No haplogroups other than Q and C have been found in burials. There is some question about haplogroup O, but that is as yet unresolved. No other haplogroups, meaning European or African, have been found in burials pre-Columbian contact. If they are, that would be a very big game-changer.

      • Thanks very much. Is the haplogroup of the Lapps/Sami known? I’m guessing it would be similar to Inuit. I’m still trying to figure out where the 33% Scandinavian my Father’s sister tested with, and the 18% for my mom, came from when we not only don’t have any known Scandinavian lineage, but there are not even any rumors of that in our family legends. Plus they don’t seem to match anyone with a Scandinavian last name that I’ve found so far.

        • anonmouse…Please understand that the ethnicity calculations are FAR from perfect, and only general guidelines. Siblings can even vary widely, depending on which DNA they each inherited from their parents. As well, there are some specific disclaimers that the big testing sites (FT DNA, Ancestry, etc) should have up at all times.

          Scandinavian ancestry shows up for virtually EVERYONE that tests, IF they have English/British background, and sometimes German. Every single member of my family with English ancestry has tested for some significant percentage of Scandinavian, but we know that is false. Don’t worry yourself that there is some kind of hidden Swedish ancestor, etc that doesn’t show up on your paper tree. When these testing companies do comparative analysis for different ethnic groups, they simply look for matches in population genetics databases. If you have an understanding of British and northern European history, you’ll know that many Germanic/northern populations (Angles, Jutes, Saxons, for example) migrated throughout the area, including England and Denmark/Scandinavia in the last 1500 years. Genetically, that is NOT long enough for any of these populations to mutate specific markers for there local population. So “German” DNA looks similar or the same as “English” DNA and also Scandinavian DNA (simplified here, as obviously these populations have multiple DNA sources). In reality, you are seeing misleading reporting based on very small databases and an unwillingness of these companies to educate their patrons about how the ethnic %s work. It’s makes for great commercials…but that’s NOT how it actually works.

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  9. Thanks Roberta , on one of my mothers Native American segments only one match has a NA haplogroup , it is Y -dna C on 23andme , and this segment is his only one . Is there any to compare him on gedmatch to those you have tested ? Thank You . Rick

      • I will suggest that the next time I message him . I hope to have enough info on the segment to put a Tribal label on it soon , so I will message him , and all matches on the segment . I can’t tie it to any family line yet but a tribe is a good start .

        • If he tests and joins the C-P39 project at FTDNA, we may be able to link him to a surname through his best matches on the Y – as well as a region. Depending on his surname, and who he matches, we may be able to link him to an ancestor.

  10. This should be Southern Tuscarora , or Coree in nature . I have surffed his gedmatch using one on many , looking for other matches that relate to his C Y-dna . I am Eastern Creek and as such have other Eastern Creek matches , one has a D1 mt dna that we suspect the D1 ancestor was not Creek , is on his one to many . Most Eastern Creek are related , or related to someone who is , and we descend from more than one tribe or group from the East as well as Creek , so we have a good idea which ancestor,s are Creek related and those that are not .The C match is not Eastern Creek , and I suspect his people went to Utah very early , so I am assuming he , and my D1 match connect ancestry wise in the Carolina,s given her known ancestry . It wood be nice to get answers without much work , I will contact him in the next few days .

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