Classification tree of M9a'b rooted in haplogroup M9. (a) The tree includes 120 complete sequences and illustrates sub-haplogroup affiliations (see Additional file 4). Sequences 1, 5 to 12, 16 to 25, 42 to 43, 54, 60 to 64, 77 to 78, 81 to 88, 93, 97 to 117 were newly collected and indicated as circles, while the others from published sources were represented as squares. The nucleotide positions in the sequences were scored relative to the revised Cambridge Reference Sequence (rCRS) . Transitions are shown on the branches and transversions are further annotated by adding suffixes. The deletions and insertions are demonstrated by ''d'' and ''+'', respectively. Amino acid replacements are in red and marked by a single-letter code, whereas synonymous replacements are in blue. Changes in transfer RNA and ribosomal RNA genes are denoted by "t" and "r", respectively. The prefix @ designates back mutation and recurrent variants are underlined. "R" and "Y" specify the heteroplasmic status of A/G and C/T at a certain site, respectively. All heteroplasmic variants and the potential pathogenic transition 11778  are not considered in the ages estimates and are marked in italics. The insertion of C at site 5899 seemed to be missing in sequences 88 to 91, which is tentatively noted as "@5899+C?". (b) The geographic origin of samples is shown by different colors corresponding to their respective different locations in the map.
Peng et al. BMC Biology 2011 9:2 doi:10.1186/1741-7007-9-2