Maternal variation in Huichol and Mixtec populations from Mexico

noncoding sequences between the genes (Anderson et al., 1981). The only noncoding region
is the displacement loop (D-loop), or control region. It is a 1,121 bp sequence that is involved
in mtDNA replication and transcription. D-loop is the most polymorphic segment of mtDNA
(Aquadro and Greenberg, 1983; Stoneking et al., 1991). All polymorphisms in D-loop are
concentrated in 3 hypervariable regions (HVS) (Vigilant et al., 1989): HVS- I (nps 16024-
6365), HVS- II (nps 73-340) and HVS- III (nps 438-576). recent common ancestor (MRCA),
or “mitochondrial Eve”. Secondly, the high copy number of mtDNA per cell (Alberts et al.,
1989; Bogenhagen and Clayton, 1974) makes easy to use it in laboratory research, and also
recover it from ancient biological material in sufficient quantities. Finally, mtDNA is
characterized by rapid evolution rate due to the lack of protective proteins, ineffective DNA
reparation system, as well as the high concentration of oxidative radicals in the mitochondrion
(Clayton, 1982; Richter et al., 1988). In comparison with nuclear DNA, mtDNA nucleotide
substitution rate is 5 to 10 times higher and it is estimated 2-4% per site per million years
(Brown et al., 1979; Wilson et al., 1985). And it is even higher (to 10 times) in the control
region hence the presence of HVS sequences (Parsons et al., 1997). This entirely makes
mtDNA an effective marker for evolutionary studies at recent levels of divergence (Avise et
al., 1987).
1.2 Mitochondrial molecular clock
The molecular dating technique is an additional tool that can define the timeline of human
evolution if the archaeological or fossil records cannot provide thus. The basis for molecular
clock hypothesis is that mutations tend to accumulate in DNA sequence at relatively constant
rate. Estimates of the average rate at which human mtDNA mutates are very variable and
depend on the data and methods used for estimation. There are two main methods used: the
pedigree and the phylogenetic methods. The pedigree method is based on the comparing of
parent/offspring pairs or analyzing mtDNA sequences of individuals from a deep-rooted
genealogy (Heyer et al., 2001). The phylogenetic method is based on the reconstruction of the
haplotype of the MRCA from a sample with minimum two genetic lineages. For estimation of
human mutation rate usually the ancestral haplotype of the human-chimpanzee common
ancestor is reconstructed (Henn et al., 2009). The pedigree-based rates are much higher (to 10
times) than those obtained by using phylogenies (Forster et al., 1996; Howell et al., 2003).
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