Haplogroup C is one of two haplogroups, the other being Q, which are found as part of the Native American paternal population in the Americas.  Both C and Q were founded in Asia and subgroups of both are found today in Asia, Europe and the New World.  The subgroups found in the Americas are generally unique to that location.  I wrote about some of the early results of haplogroup Q being divided into subgroups through Big Y testing here.

In the Americas, haplogroup Q is much more prevalent in the Native population.  Haplogroup C is rarely found and originally, mostly in Canada.

This chart, compliments of Family Tree DNA, shows the frequency distribution in the Americas between haplogroups Q and C.

However, in the Zegura et al article in 2004, haplogroup C was found in very small percentages elsewhere.

The authors found the following P39 men among the samples:

Northern Athabaskan:

• Tanana of Alaska, 5 of 12

Southern Athabaskan:

• Apache, 14 of 96
• Navajo, 1 of 78

Algonquian (Plains):

• Cheyenne, 7 of 44

Siouan–Catawban (Plains):

• Sioux, 5 of 44

I was speaking with Spencer Wells (from the Genographic Project) about this at one point and he said to keep in mind that the Athabaskan migration to the Southwest was only about 600 years ago. That is why our one Southwestern C-P39 looks like he is related to all the other families about 600 years ago.

There are competing theories about whether the Athabaskan came down across the plains or along the western mountains/coast. I found a few recent studies that say both are likely true.  We don’t know if the C-P39 found on the Plains is residual from the migration event or from another source.

In the American Indian DNA Project and other relevant DNA projects, we find haplogroup C in New Mexico, Virginia, Illinois, Canada, New Brunswick, Ontario and Nova Scotia.

In 2012, Marie Rundquist, founder of the Amerindian Ancestry Out of Acadia DNA Project as well as co-founder the C-P39 DNA project wrote a paper titled “C3b Y Chromosome DNA Test Results Point to Native American Deep Ancestry, Relatedness, among United States and Canadian Study Participants.

At this that time, haplogroup C-P39 (formerly C3b) was the only identified Native American subgroup of haplogroup C.  Since that time, additional people have tested and the Big Y has been introduced.  Just recently, another subgroup of haplogroup C, C-M217, was proven to be Native and can be seen as the first line in the haplotree chart shown below.

The past 18 months or so with the advent of full genome sequencing of the Y chromosome with the Big Y test from Family Tree DNA and other similar tests have provided significant information about new haplotree branches in all haplogroups.

Ray Banks, one of the administrators of the Y DNA haplogroup C project and a haplogroup coordinator for the ISOGG tree has been focused on sorting the newly found SNPs and novel variants discovered during Big Y testing into their proper location on the Y haplogroup tree.

I asked Ray to write a summary of his findings relative to the Native American aspect of haplogroup C.  He kindly complied, as follows:

By way of a simplified explanation, a 2012 study by Dulik et al. reported that southern Altains (south central Russia) were the closest living relatives of Amerindian Haplogroup Q men they could identify.

Male haplogroup Q is the dominant finding within Amerindian populations of the Americas.

But male haplogroup C-P39 is also found in smaller percentages among Amerindians of North America.  A second type, of a different, poorly defined C, has been identified among rainforest Indians of northwestern South America.

The 2004 study by Zegura et al. reported that C-P39 was present in some quantities among some Plains and Southwest Indians of the United State, as well among Tananas of Alaska.  No one has done a comprehensive inventory of Amerindian Y-DNA haplogroups.  A high percentage of the Amerindian samples at Family Tree DNA that are P39, in contrast, report ancestry in central or eastern Canada.

It does not seem that anyone has yet definitively addressed whether C-P39 men have a different relationship pattern in relation to Asian groups than seen in haplogroup Q.  Another question is whether they might have been involved in a more recent migration from Asia than Q men who seem to have quickly migrated to all areas of South America as well.

Four men in the Haplogroup C Projects have made their Big Y results available for analysis.  All are from Canada, living in areas varying from central to maritime Canada.

These results show that the four men can be divided into two main groups.  The mutations Z30750 and Z30764 have been tentatively assigned to represent these subgroups.  The number of unique mutations for each man suggests these two subgroups each diverged from the overall P39 group about 3,500 years ago.  This is based on the 150 years per mutation figure that is being widely used.  There is no consensus for what number of years per mutation should be used.  Likewise, the total number of shared SNPs within P39, suggests 14,100 years as the divergence time from any other identified Y-DNA subgroup.  The Composite Y-DNA Tree by Ray Banks contains about 3,700 Y subgroups for comparison.

The nearest subgroup to P39 has been identified as the F1756 subgroup, last line in the chart above.  These both share as a common earlier subgroup, F4015.   This parallel F1756 subgroup has been identified in Geno 2.0 testing as well as Big Y as containing mostly men from Kazakhstan, Kyrgyzstan and Afghanistan.  Some apparently have a tradition of a migration from Siberia.

There is available a Big Y test from among this group, and more recently complete Y sequencing in the sample file GS27578 at the Estonian Genome Centre.

Each of these men potentially could have shared one or more of the P39 equivalents creating a new subgroup older than P39.  But this is not the case.  The Big Y results are not complete genome sequencing, and they perhaps miss 30% of useful SNPs, mostly due to inconclusive reads.

The man in the Estonian collection is of particular interest because he is described as an Altaian of Kaysyn in Siberia, Russia.  He is not from the same town as samples in the earlier Dulik study, and thus no direct comparisons can be made.

The Big Y F1756 sample is geographically atypical because the man is Polish but still shares the unusual DYS448=null feature seen in all the available F1756 men in the C Project.  The project P39 men have either 20 or 21 repeats at this marker, instead of a null value.

In conclusion, the age of the P39 group and the failure of others so far to share its many equivalent mutations suggest together that the C-P39 men could have been part of the earliest migration to the Americas.  Like the Q men, the nearest relatives to C-P39 men have central Asian or Siberian origins.

Despite some identification of P39 branching.  Much work needs to be done to understand the branching due to the lack of availability of samples.

So, what’s the bottom line?

1. C-P39 is being divided into subgroups as more Big Y and similar test results become available. If additional individuals who carry C-P39 were to take the Big Y test, especially from the more unusual locations, we might well find additional new, undiscovered, haplogroups or subgroups.  Eventually, we may be able to associate subgroups with tribes or at least languages or regions.
2. If you are a Y DNA haplogroup C individual, and in particular C-P39, and have taken the Big Y test, PLEASE join the haplogroup C and C-P39 projects. Without a basis for comparison, much of the benefit of these tests in terms of understanding haplogroup structure is lost entirely.

As always, the power of DNA testing is in sharing and comparing.

Thank you Ray Banks, Marie Rundquist and DNA testers who have contributed by testing and sharing.

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