Mitochondrial genome data:
For the analysis of the mtDNA polymorphisms, we downloaded a total of 86 sequences from the mtDB website maintained by Max Ingman. The sequences downloaded were all 53 sequences from Ingman et al. (2000) and all 33 sequences from Maca-Meyer et al. (2001). The sequences were downloaded in interleaved format and are contained in the file mtDNAsequences.int (n.b., size: 1.8 Mb).
The sequences were then processed by a python script interleave2MDB.py that identified the bi-allelic segregating sites and output the respective data for such sites to a file in the MDBlocks format. To control whether the script processes the complete sequence with or without the D-loop, the value of a flag variable DloopExcluded is changed at beginning of the script (non-zero values of DloopExcluded will cause the scrip to exclude the D-loop). The resulting files were: mtDBwDloop.dat and mtDBnoDloop.dat. The analysis conducted in our paper is based on these two files.References:
Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708-713 (2000).
Maca-Meyer, N., Gonzalez, A. M., Larruga, J. M., Flores, C. & Cabrera, V. M. Major genomic mitochondrial lineages delineate early human expansions. BMC Genet 2, 13 (2001).