This subgroup is characterized by having the P39 mutation within C2.

So far this mutation has been found only among Native Americans of Canada and the United States.  
C2 has been found among native men of the Venezuela-Colombia border area in South America, but 
all these men are negative for the P39 subgroup.

The most specific information on the distribution of C-P39 in a published study can be found in 
American Y Chromosomes into the Americas," by Stephen L. Zegura, Tatiana M. Karafet, Lev 
A. Zhivotovsky,. and Michael F. Hammer."  This was published in Molecular Biology and 
Evolution, vol 21(1), pp 164-75, published in 2004.  Figure 4 has the most specific information on P39. 

The authors found the following P39 men among the sampled men
Tanana of Alaska, 5 of 12
Cheyenne, 7 of 44
Sioux, 5 of 44
Apache, 14 of 96
Navajo, 1 of 78

But no C at all was found among Inuits, other Southwest Indians, Pima, Pueblo, Nixtec, Zapotec, 
Mixe, Maya, Ngobe, Kuna, Waunaan and Emberra or among the Wayu of South America.  Many 
of the samples were originally reported in a study by Karafet and others in the American Journal 
of Human Genetics in 1999, but a test for P39 was not then available.  Figure 1 in the Karafet study
 is helpful because it shows where the samples were taken.

In the Haplogroup C project, samples are available from men listing origins in areas of Canada, with 
the exception of one man with Virginia ancestry.  This is the first evidence of  P39 in Canada and 
Virginia.  The Native Americans of western Canada have not been sampled for this.

With (a) no P39 samples outside North America and (b) men in South America who are Cs but 
lack P39, this raises the possibility that P39 arose within an ancestor living in North America.  
Added to the complications, a comparison of our eastern Canadian marker values to those of 
the C2 not P39 in South America, a number of differences are noted, and this holds open the 
possibility they could be descendants of entirely different C2 ancestors in Asia and thus descended 
from two different C2 migrations to the Americas.   It should be noted also in the Zegura article 
that among haplogroup C men in the figure 4 phylogenetic diagram, the C3b men do not cluster 
with the South American C2 not P39 men.  But this was based only on 10 STR markers, and 
the diagram would not be as convincing as one with more markers.

Marker       E. Canadian    South American
                   C2               C2 not P39
DYS 19          15                  15
DYS389         13,29              12,27
DYS390         23                   24
DYS391           9                    9
DYS392         11                   11
DYS393         12                   12
DYS385         15,16              12,13
DYS438         10                   10
DYS439         11                   12
DYS437         14                   14
DYS448         21                   21
DYS456         16                   15
DYS458         18                   17
The South American data are from a study by Geppert and others using C2 (not P39 subgroups) 
samples from the Ecuadorian rain forest, and the Canadian data are from the Haplogroup C Project.

Subgroups under P39 are currently being validated and can be seen on the Composite C Tree under P39.

This explains some recent Native American origins research, but it is not clear how P39 men fit into this