Maternal variation in Huichol and Mixtec populations from Mexico

* let dry at 37ºC for 5 min
*add 10 μl formamide
hold at room tºC
* suspend load on the sequencing plat
The reaction products were sequenced with an Applied Biosystems ABI 3730xl 96-capillary
DNA analyzer.
2.2.5 Statistical analysis
Mutations were scored relative to the revised Cambridge Reference Sequence (rCRS)
covering the nucleotide positions 16024- 680 (Andrews et al., 1999). For DNA sequence
assembly and analysis software Sequencer 4.10.1 was used. Each deviation was confirmed by
manual checking on electropherogrammes. For reconstructing phylogenetic networks
Network (version 4.6.1.0) and Network Publisher (version 1.1.0.7) software were used
(Bandelt et al., 1999).
Haplogroup frequencies for Middle American populations are based on HVS I data and are
combined from current study and literature. They are shown in Figure 4. The detailed
information for frequencies and references are in Supplementary materials (Suppl. Table1).
For network analysis in addition to present study 658 published sequences from USA
Southwest and Mexico populations were used (Table 1). The data was provided by Dr. Brian
M. Kemp and has been previously published (Kemp et al., 2010). We restricted our haplotype
analysis with this data to include samples where both, HVS 1 and 2, are available to increase
the resolution of analysis. The location of populations and their language families from Kemp
et al., 2010 are shown in Table1.
Median-joining haplotype networks were constructed separately for haplogroups A2, B2, C1
and D1. The X haplogroup data was removed from the analysis, because it did not occur in
my analysed samples. The positions nps 16519, 16188.1, 16193.1, 16193.2, 309.1, 309.2,
309.3, 315.1, 573.1, 573.2, 573.3, 573.4 were removed from the analysis because of their
recurrent nature.
19