Big Y DNA Results Divide and Unite Haplogroup Q Native Americans

featherOne of my long standing goals has been to resurrect the lost heritage of the Native American people.  By this I mean, primarily, for genealogists who search for and can’t find  their Native ancestors.  My blog,, is one of the ways that I contribute towards that end.  Many times, records are buried, don’t exist at all, or don’t reflect anything about Native heritage.  While documents can be somewhat evasive and frustratingly vague, the Y DNA of the male descendants is not.  It’s rock solid.

The Native communities became admixed beginning with the first visits of Europeans to what would become the Americas.  Native people accepted mixed race individuals as full tribal members, based on the ethnicity of the mother.  Adoption also played a key role.  If a female, the mother, was an adopted white child, the mother was considered to be fully Native, as was her child, regardless of the ethnicity of the father.

Therefore, some people who test their DNA expecting to find Native genetics do not – they instead find European or African – but that alone does not mean that their ancestors were not tribal members.  It means that these individuals have to rely on non-genetic records to prove their ancestors Native heritage – or they need to test a different line – like the descendants of the mother, through all females, for example, for mitochondrial DNA.

On the other hand, some people are quite surprised when their DNA results come back as Native.  Many have heard a vague story, but often, they don’t have a clue as to which genealogical line, if any, the Native ancestry originated.  Native ancestry was often hidden because the laws that prevailed at the time sanctioned discrimination of many kinds against people “of color,” and if you weren’t entirely of European origin, you were “of color.”  Many admixed people, as soon as they could, “became” white socially and never looked back. Not until recently, the late 20th century, when discrimination had for the most part become a thing of the past and one could embrace their Native or African heritage without fear of legal or social reprisal.

Back in December of 2010, we found the defining SNP that divided haplogroup Q between Europeans and Native Americans.  At the time, this was a huge step forward, a collaboration between testing participants, haplogroup administrators, citizen scientists and Family Tree DNA.

This allowed us to determine who was, and was not included in Native American haplogroups, but it was also the tip of the iceberg.  You can see below just how much the tree has expanded and its branches have been shuffled.  This is a big part of the reason for the change from haplogroup names like Q1a3 to Q-M346.  For example, at one time or another the SNP M3 was associated with haplogroup names Q1a3a, Q1a3a1 and Q1a3a1a.  On the ISOGG tree below, today M3 is associated with Q1a2a1a1.

isogg q tree

The new Family Tree DNA 2014 tree is shown below for one of the Big Y participants whose terminal SNP is L568, found beneath SNP CTS1780 which is found beneath L4, which is beneath L213 which is beneath L474 which is beneath MEH2 which is beneath L232 which is, finally, beneath M242.

ftdna 2014 q tree

The introduction of the Big Y product from Family Tree DNA, which sequences a large portion of the Y chromosome, provided us with the opportunity to make huge strides in unraveling and deciphering the haplogroup Q (and C, the other male Native haplogroup in the Americas) tree.  I am hopeful that in time, and with enough people taking the Big Y test, that we will one day be able to at least sort participants into language and perhaps migration groups.

In November, 2013, we asked for the public and testers to support our call for funds to be able to order several Big Y tests.  The project administrators intentionally did not order tests in family groups, but attempted to scatter the tests to the far corners, so to speak, and to include at least one person from each disparate group we have in the haplogroup Q project, based on STR matches, or lack thereof, and previous SNP testing.

Thanks to the generosity of contributors, we were able to order several tests.  In addition, some participants were able to order their own tests, and did.  Thank you one and all.

The tests are back now, and with the new Big Y SNP matching, recently introduced by Family Tree DNA, comparisons are a LOT easier.

So, of course, I had to see what I could find by comparing the SNP results of the several gentlemen who tested.

To protect the privacy of everyone involved, I have reduced their names to initials.  I have included their terminal SNP as identified at Family Tree DNA as well as any tribal, ethnic or location information we have available for their most distant paternal ancestor.

There are two individuals who believe their ancestors are from Europe, and there is a very large group of European haplogroup Q members, but I’m not convinced that the actual biological ancestors of these two gentlemen are from Europe.  I have included both of these individuals as well. Let’s just say the jury is still out. As a control, I have also included a gentleman who actually lives in Poland.

native match clusters

Of the individuals above, SD, CT and CM are SNP matches.

CD, WJS and WBS are SNP matches with each other.

BG and ETW are also SNP matches to each other.

None of the rest of these individuals have SNP matches.  (Note, you can click to enlarge the chart.)

native snp matches

In the table above, the Non-Matching Known SNPs are shown with the number of Shared Novel Variants.  For example, SD and CT have 4 non-matching SNPS and share 161 Novel Variants and are noted as 4/161.

We can easily tell which of the known SNPs are nonmatching, because they are shown on the participants match page.

snp matches page

What we don’t know, and can’t tell, is how many Novel Variants these people share with each other, and how many they might share with the individuals that aren’t shown as matches.

Keep in mind that there may be individuals here that are not shown as matches to due no-calls.  Only people with up to and including 4 non-matching Known SNPs are counted as matches.  If you have the wrong combination of no-calls, or, aren’t in the same terminal haplogroup, you may not be shown as a match when you otherwise would be.

The other reason for my intense interest in the Novel Variants is to see if they are actually Novel, as in found only in a few people, or if they are more widespread.

I downloaded each person’s Novel Variants through the Export Utility (blue button to the right at the top of your personal page,) and combined the Novel Variants into a single spreadsheet.  I colorized each person’s result rows so that they would be easy to track.  I have redacted their names. The white row, below, is the individual who lives in Poland.

novel variant 1

There are a total of 3506 Novel Variants between these men.  When sorting, many clustered as you would expect.  There is the Algonguian group and what I’ve taken to calling the Borderlands group.  This group has someone whose ancestor was born in VA and two in SC.  I have documentation for the Virginia family having descendants in SC, so that makes sense.  The third group is an unusual combination of the gentleman who believes his ancestors are from Germany and the gentleman whose ancestors are found in a New Mexico Pueblo tribe, but whose ancestor was, likely, based on church records, a detribalized Plains Indian who had been kidnapped and sold.

Clusters that I felt needed some scrutiny, for one reason or another, I highlighted in yellow in the Terminal SNP column.  Obviously the Polish/Pueblo matching needs some attention.

Another very interesting type of match are several where either all or nearly all of the individuals share a Novel Variant – 15 or 16 of 16 total participants.  I don’t think these will remain Novel Variants very long.  They clearly need to be classified as SNPs.  I’m not sure about the process that Family Tree DNA will use to do this, but I’ll be finding out shortly.

Here’s an example where everyone shares this Novel Variant at location 7688075,except the gentleman who lives in Poland, the man who believes his ancestor is from Germany, and the Creek descendant.

novel variant 2

I was very surprised at how many Novel Variants appear in all 16 results of the participants, including the gentleman who lives in Poland – represented by the white row below.

novel variant 3

So, how were the Novel Variants distributed?

Category # of Variants Comments
Algonquian Group 140 This is to be expected since it’s within a specific group.  Any matches that include people outside the 3 Algonquian individuals are counted in a separate category.  These matches give us the ability to classify anyone who tests with these marker results as provisionally Algonquian.
Borderlands 83 This confirms that these three individuals are indeed a “group” of some sort.  This also gives us the ability to classify future participants using these mutations.
All or Nearly All – 15 or 16 Participants 80 These are clearly candidates for SNPs, and, given that they are found in the Native and the European groups, they appear to predate the division of haplogroup Q.
Several Native and European, Combined 45 This may or may not include the person who lives in Poland.  This group needs additional scrutiny to determine if it actually does exist in Europe, but given that there are more than 3 individuals with each of these Novel Variants, they need to be considered for SNPhood.
Pueblo/NC 1
Poland/Borderlands 2
Mexico/Algonquian 2
German/Pueblo 9 I wonder if this person is actually German.
Poland/Mexico 20 I wonder if this person’s ancestors are actually from Poland.
Algonquian, NC, Creek 1
Borderland, Mexico, Creek 1
Algonquian/Cherokee 1
All Native, no Euro 2
Algonquian, Borderlands, Mexico, NC 1
Algonquian, Mexico, Borderlands 1
Borderlands, Pueblo 1
Borderlands, Creek, NC 1
Algonquian, Cherokee, Mexico 3
Algonquian, Pueblo, Creek, Borderlands 1
Cherokee, NC 2
Algonquian, Borderlands 2
Borderlands, NC 1
Algonquian, NC 1
Polish/NC 10

Some of this distribution makes me question if these SNP mutations truly are a “once in the history of mankind” kind of thing.  For example, how did the same SNP appear in the Polish person and the NC person, or the Pueblo person, and not in the rest of the Native people?

New SNPs?

So, are you sitting down?

Based on these numbers, it looks like we have at least 125 new SNP candidates for  haplogroup Q.  If we count the Algonquian and the Borderlands groups of matches, that number rises to about 250.  This is very exciting.  Far, far more than I ever expected.  of these SNPS, about half will identify Native people, even Native groupings of people.  This is a huge step forward, a red letter day for Native American ancestry!

SNPs and STRs

Lastly, I wanted to see how the SNP matching compared to STR matching, or if it did at all, for these men.

Only two men match each other on any STR markers.  CD and WJS matched on 12 markers, but not on higher panels.  The TIP calculator estimated their common ancestor at the 50th percentile to be 17 generations, or between 425 and 510 years ago.  We all know how unrealistic it is to depend on the TIP calculator, but it’s the only tool we have in situations like this.

Given that these are the only two men who do match on STR markers, albeit distantly, in a genealogical timeframe, let’s see what the estimates using the 150 years per SNP mutation comes up with.  This estimate is just that, devised by the haplogroup R-U106 project administrators, and others, based on their project findings.  150 years is actually the high end of the estimate, 98 being the lower end.  Of course, different haplogroups may vary and these results are very early.  Just saying.

CD has 207 high quality Novel Variants.  He shares 188 of those with WJS, leaving 19 unshared Novel Variants.  Utilizing this number, and multiplying by 150, this suggests that, if the 150 years per SNP is anyplace close to accurate, their common ancestor lived about 2850 years ago.  If you presume that both men are incurring mutations at the same rate in their independent lines, then you would divide the number of years in half, so the common ancestor would be more likely 1425 years ago.  If you use 100 years instead of 150, the higher number of years is 1900 and the half number is about 950 years.

It’s fun to speculate a bit, but until a lot more study has occurred, we won’t be able to reasonably estimate SNP age or age to common ancestor from this information.   Having said all of that, it’s not a long stretch from 710 years to 950 years.

It looks like STR markers are still the way to go for genealogical matching and that SNPS may help to pull together the deeper ancestry, migration patterns and perhaps define family lines.  I hope the day comes soon that I can order the Big Y for lots more project members.  Most of these men do have STR marker matches, and to men with both the same and different surnames.  I’d love to see the Big Y results for those individuals who match more closely in time.

This is still the tip of the iceberg.  There is a lot left to discover!  If you or a family member have haplogroup Q results, please consider ordering the Big Y.  It would make a wonderful gift and a great way to honor your ancestors!

You can also contribute to the American Indian project at this link:

In order to donate to the haplogroup C-P39 project which also includes Native Americans, please click this link:



I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

50 thoughts on “Big Y DNA Results Divide and Unite Haplogroup Q Native Americans

  1. Roberta, I am Q-CTS1780 … concerning the Q-CTS1780’s in Poland and Germany, my cousin told me I have a male cousin in Japan tracing from the Korean War. I did have male relatives who went to Europe during World War 1 and World War 2. ?????
    Lenny Trujillo

  2. My cousin is in the Q-M3 Project, not the overall Q project. He did not do BigY, but did test M3+, M19-, M194-, M199-. He triangulates back on the Y-STR tests with two others to an ancestor who lived 1765-1843 in SE Georgia (who is my 4th great-grandfather, not on my Y). Does this indicate a likely origin from a Southeastern tribe? Since the surname’s origin is possibly Hispanic, I have wondered if it could have been Caribbean in origin. But there are no Taino or other Caribbean tribes in your list. Thanks.

  3. When is a mutation a SNP and when is it a Novel Variant? I’m looking forward to the answer to this, and understand it may take considerable time to be resolved. I think it premature to mark the difference at how many men share Novel Variants, as relatively few have tested Big Y, even within projects for subclades of R1b. Two men sharing a set of Novel Variants does not a family make. My situation is an example: My terminal SNP is, according to FTDNA, L176.2, a subclade of R1b, and I share with only one other person who tested Big Y, 31 Novel Variants, yet at the STR level we have a genetic distance of 15 of 67 STRs. Our MRCA is before the Norman invasion, which makes sense given his surname is of Norman origin and my putative birth father was French Canadian. But that is still a very distant relation! Clearly as more men test, more will share some or all of those Novel Variants. I believe it important for the genetic genealogy community that Novel Variants not be given less attention than SNPs ; they are, IMO, potentially the most informative of genetic markers, and may all in fact be SNPs. The haplotree will grow exponentially with more men testing positive for these Novel Variants.

    • It’s a Novel Variant until “someone” decides that there are enough occurrences of the mutation for it to be considered a SNP. Then it will be named and placed on the tree. the Native comparisons I did were extremely interesting for exactly the same reasons you mentioned about your SNP vs STR matches. These two tools will dovetail very nicely I think in trying to sort out both short and longer term relatedness.

  4. My grandmother knew her grandmother and called her “Indian.” I have a picture of her that makes her look NA. DNA shows European.

  5. My earliest known ancestor was born in Magdeburg, Prussia (present day Germany) c1784 and came to England via France around 1800. He was thought to be of African descent on the basis of his dark skin corroborated by photograph of his son taken 1870.

    I am Q-Z780-CTS1780!

    Perhaps my ancestor was Native American and taken into slavery by the invading Europeans?
    My surname may therefore be that of the slave owner.


  6. Pingback: Haplogroup Projects | DNAeXplained – Genetic Genealogy

  7. I had my uncle tested at family tree dna to a 12-marker, and his Haplogroup is Q-M242. Through genealogy when can trace his male line to his great-great-grandfather to Mexico. So is it fair to say his paternal line is Native American?

      • Which ones do you recommend? Also my uncle wants to use his dna to help Native American projects which ones are good ones to go to?

        • Depending on what you want to do and how many matches he has, you might want to upgrade his markers from 12. That won’t help with his haplogroup. Right now, the best value for the money is the Geno 2 test through National Geographic, then transfer your results to Family Tree DNA. that will tell you the downstream SNPs for him and will confirm Native or not. My preference would be the Big Y test but it costs more than twice as much – but it reads the entire Y chromosome for SNPs and discovers if he carries SNPs never before found.

          Also, please join the American Indian project, which I manage, and let me know in an e-mail when you do. When you join, an e-mail is automatically sent with some questions.

  8. Roberta….I believe Todd was talking about our family here in southeast Georgia. Our last know ancestor was John Rewis 1765-1843. I don’t think i know Todd. Maybe he is related to a Rewis in south Georgia who matched mom’s brother Daniel? All Rewis males have tested Q-M3 and the Jarriels match the Rewis family also. My mom is Rewis and Jarriel. I do not believe that we have any Hispanic or Caribbean connection. My grandfather Rufus Rewis told me we came from native people from North Carolina. I believe it is possible that we have a Lumbee connection but not sure. Our family has always claimed Cherokee maybe for political reasons. Would you advise us to take the Big Y. We are members of the American Indian Q1a3a1: the Q-M3 Haplogroup Project …

  9. Pingback: Haplogroups and The Three Brothers | DNAeXplained – Genetic Genealogy

  10. Pingback: New Haplogroup C Native American Subgroups | DNAeXplained – Genetic Genealogy

  11. Pingback: Finding Your American Indian Tribe Using DNA | DNAeXplained – Genetic Genealogy

  12. Pingback: Finding Your American Indian Tribe Using DNA | Native Heritage Project

  13. So is there any way for me to know which tribe my cousin belongs to, his haplogroup is Q1a3a* per

    I was hoping there was a list online but I saw something indicating that it was the South American Indians

  14. Pingback: DNAeXplain Archives – Intermediate DNA Articles | DNAeXplained – Genetic Genealogy

  15. I am in the Y-DNA .. Indigenous Q Group … My second cousin told me about 3 years ago … “you probably don’t know that you have a Japanese cousin” as his father (Q Indigenous Y-DNA) was stationed in Japan during the Korean War and fathered a son. Therefore, if this male Japanese performs a Y-DNA test he will register at a Q Indigenous Y-DNA . DNA does indeed travel far.
    Lenny Trujillo

    • This is an interesting quandary. I only show three people in the American Indian project with this SNP. One is you. The other two have ancestors from New Mexico. I would say there is something here yet to be learned.

      • My father is Q-Z780. He was adopted and never knew his biological parents which is why we did the DNA test (we used Living DNA). I am trying to learn more about haplogroup q and the subclade Q-Z780. Is there a way for him or I to enter this study?

        • Yes, you would probably want to order the Big Y-700 which includes both the STR markers for matching the most resolution possible for the haplogroup itself. Then, based on the surname, you may want to join a surname project as well as other projects, such as the American Indian project. I would also suggest the Family Finder test so that you can see who you match. You can expect many matches at FTDNA. Here’s the link again.

          • Thank you for your prompt and thorough response! This is very exciting for my family, specifically my father. I really appreciate your website and the help!

          • Yes, the surnames are to whoever he matches, regardless of whether that surname matches yours or not.

          • Hi Roberta, We ordered the Big Y-700 for my father as suggested. Though I am not sure how to read his results. Panel 1-5 have been provided though we are still waiting on 6 and 7.

            His previous test from LivingDNA resulted with him being Q-Z780 the test results from Family Tree DNA state his Hapalogroup is Q-M242 what does this mean? And how do we read the results?

          • I’m writing a series about just that. There are several articles if you search by key word too.

  16. hello, I’m Q-m346 – Q-y4800 and I’m from the US, as far as I know me and My been here as long as ever, I’m consider to be african american according to what the US says lol but I don’t believe that history tell another story lol, but does anyone know what population Q-Y4800 is most common in.

    • You can still be ethnically African American with 1 male American Indian ancestor 400 years ago. There is no conspiracy to hide history from you. Unless you are implying that African Americans are aboriginal, and history is one big conspiracy. Then you would have to explain where the millions of Native Americans came from and why don’t African Americans live on isolated reservations, and why they all don’t have Native DNA?

Leave a Reply to robertajestesCancel reply