Additional file 4.
– Phylogenetic tree based on 139 U6 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 (!). 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 which they are from (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 are flagged with a yellow mark under the geographic origin. The potential reticulation created by position 150 between sub-clades U6a3a and U6a3c was resolved on the more frequent occurrence of 150 in various different haplogroups’ backgrounds (See ). We refined here the phylogeny of the Canary-specific branch formerly known as U6b1 [27,29]. There is an array of 2 common mutations before the branch splits into the so-called Canary-specific branch and one apparently specific to Northwest Africa. We propose therefore to rename U6b1a as U6b1a1 to comply with the revised phylogeny. The mutations order of some clades (U6a1a1b, U6a1a2, U6a2b, U6a2b1, U6a3d, U6a3d1, U6a3d1a, U6a6a, U6b1b1) was deduced for additional partial typing (see Additional file 5).
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Pennarun et al. BMC Evolutionary Biology 2012 12:234 doi:10.1186/1471-2148-12-234