Maternal variation in Huichol and Mixtec populations from Mexico

the defining transition at nps 1243. The Huichol haplotype has a reversion at position 1243,
but according to the nps at 15629 and 16241, it is positioned to belong to C4c1a subclade of
C4a1 subhaplogroup. It also has unique SNP at 9938 position and a transversion at nps 11861.
The coalescent age estimates for C4c and C4c1 haplogroups were calculated by Rho (ρ)
statistics. The calculations were performed on all substitutions excluding the 16182C,
16183C, 16194C and 16519 mutations. Mutational distances were converted into years using
the corrected molecular clock proposed by Soares et al., (2009).
The average distance (ρ) of the haplotypes from the root of C4c haplogroup was 5,059 with
the standard error (σ) of 1,1. This corresponds to a divergence time of 13,500 ± 5,900 years
according to Soares et al., 2009. The estimated time for C4c1, with ρ=3,84 and σ=0,8,
corresponds to a divergence time of 10,200 ± 4,300 years.
The determination of a founder micro-haplogroup C4c in the Central American population
can lead to several conclusions. The distribution pattern of two minor-haplogroups X2a and
C4c is very similar (especially in comparison with D4h3), except the presence of two
Columbian C4c and one newly determined Mexican C4c samples south from United States.
The coalescence ages of both X2a and C4c founders are also similar, which supports the idea
that these two lineages arrived together from the Beringia through ice-free corridor after LGM
(Hooshiar Kashani et al., 2011; Perego et al., 2009). The frequencies of C4c and X2a
nowadays are very low. Because the C4c frequency in an ancient Oneota site in Western
Illinois could have reached ~8,3% (Stone and Stoneking, 1998), it is possible that the
frequencies of X2a and C4c might be higher, and their geographic distribution could have
been wider than today (Hooshiar Kashani et al., 2011). Because of the mtDNA sensibility to
genetic drift, it is possible that X2a lineages were more widely spread, but have gone through
extinction and X2a is not present and C4c is extremely rare in modern populations from south
of the USA. However, X2a and C4a could also have gone through, at least partly, separate
demographic events.
The newly sequenced Huichol belongs to C4c1a subclade (defining mutations 15629 and
16241) together with three Cherokee from North Carolina and Oklahoma (Figure 10). This
shows that Huichol is more closely connected with the North America than with the South
America, as it is previously described for Mexican Native Americans (Sandoval et al., 2009).
However, Huichol sample differs from them by its unique mutations: 1243 reversion, SNP at
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