Additional file 2.

Phylogenetic tree based on 80 complete mtDNA sequences from haplogroup Z. Mutations relative to the RSRS [35] are indicated on the branches. Capital letters are used for transitions and lowercase letters for transversions. Heteroplasmies are labeled using the IUPAC code and capital letters (e.g., 73R). Recurrent mutations are underlined. Reversal mutations are suffixed with ā€œ!ā€. Insertions are indicated by a dot followed by the position number and type of inserted nucleotide(s). Deletions are indicated by a ā€œdā€ after the deleted nucleotide position. The control-region sequence is not reported for the sample As30. For phylogeny construction, the highly variable site 16519 and the length variation in the poly-C stretches at nps 303-315 and 16184-16194 were not used. A-C transversions at nps 16182 and 16183 were excluded because of their dependence on the presence of the C-T transition at np 16189. The box containing the sample ID is color coded according to the geographic origin of the sample, and the accession number and/or the publication from which it was retrieved is denoted below the ID. Coalescence time estimates expressed in kilo years ago are shown next to clade labels and were calculated based on the rho statistic and standard deviation as in [59,90]. The calculator provided by [91] was used to convert the rho statistics and its error ranges to age estimates with 95% confidence intervals. Sample As30 was excluded from the calculations, as its control region is not reported.

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Fedorova et al. BMC Evolutionary Biology 2013 13:127   doi:10.1186/1471-2148-13-127