Additional file 2.
– Phylogenetic tree based on 105 M1 full sequences. All positions are scored against the RSRS  and are transitions, unless followed by a capital letter that marks the resulting transversion. Indels are scored with i or d, heteroplasmies follow the IUB code and reversal to ancestral state by an exclamation mark (!), double back mutations by two exclamation marks (!!). The positions are colour coded according to their status: purple – non-coding; blue – non-synonymous; and black – synonymous. Variations in the C tracts were mostly ignored (i.e., 16182C, 16193C, 309+2C, etc.) unless stated on the tree. The box containing the sample ID is colour coded according to the publications from which they were retrieved (See the main text for the full reference), and below it their geographic origin is colour coded (See Additional file 7 for the specifics). Sequences available only for the coding region, or for which some parts are missing, are flagged with a yellow mark under the geographic origin. The order for the root mutation(s) for M1a1g, M1a1h, M1a7 and M1b2c were deduced from additional partial sequencing (See Additional file 3).
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Pennarun et al. BMC Evolutionary Biology 2012 12:234 doi:10.1186/1471-2148-12-234