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Background  Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.     Results  The phylogenetic tree constructed from sequencing information of twenty four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the formulation of a new lineage M30, distinguished by the presence of 12007 transition, and comprises of the recently defined M18 and a potential new sub-lineage possessing substitution at 16223 and 16300. M30 further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage M* with HVSI sequence 16223,16325. No new substitutions were found in M25 and the M3 mt DNA genome could only be tentatively rooted by 16126 mutation. M4 and M*(16251, 16267) lineages could not be resolved distinctly.     Conclusions  This study describes seven new basal mutations and fourteen lineages that substantially contribute to the present understanding of superhaplogroup M. The phylogenetic tree supported by median-joining network helps in distinctly identifying the genetic relation between different M lineages that could not be achieved solely by control region sequence information. Although high control region diversity has been reported in the different M lineages distributed in India, complete sequencing of M* and defined lineages suggests that these mt DNA genomes emerged from a limited number of branches arising from the M trunk.

Phylogeny of the M superhaplogroup inferred from complete mitochondrial genome sequence of Indian specific lineages