Subcontinental ancestry of the most basal Eurasian/Oceanian branches of the mtDNA phylogeny. South Asian and western Eurasian haplogroups are defined as described in the present study; for East Asian haplogroups, see Kong et al. (2003); for haplogroup P, see Forster et al. (2001); O and S are newly defined here on the basis of the data from Ingman and Gyllensten (2003). Potential coalescences based only on a single highly variable site are disregarded.

Phylogenetic tree of 75 Indian complete mtDNA sequences. Parts A, B, C, and D of the figure are the phylogenies of the N, pre-HV and JT, U, and Indian autochthonous R haplogroups, respectively. Mutations are scored relative to the rCRS (Andrews et al. 1999). Indian populations: A = Bhargava, B = Chaturvedi, C = Brahmin, R = Reddy, S = Khasi, SW = Rajbhansi, T = Thogataveera. Twenty-five additional complete sequences were taken from the literature (Finnilä et al. 2001; Maca-Meyer et al. 2001; Taylor et al. 2001; Derbeneva et al. 2002a; Herrnstadt et al. 2002, 2003; Ingman and Gyllensten 2003; Mishmar et al. 2003; Coble et al. 2004), and we referred to particular samples from these articles by SF, NM, RT, OD, CH, IG, DM, and MC, respectively, followed by “#” and the original sample code. Suffixes A, C, G, and T indicate transversions; “d” denotes a deletion, and a plus sign (+) denotes an insertion; recurrent mutations are underlined; “h” indicates heteroplasmy; and italics highlight likely oversights. Mutations in the single reported haplogroup N1a lineage labeled by an asterisk (*) are our reconstruction. The linkage between coding- and control-region mutations in the new haplogroup U2d is tentative. Since the variation at 16519 is extremely hypervariable, only the most parsimonious solution is offered here. For haplogroups H and U5, see articles by Loogväli et al. (2004) and Tambets et al. (2004), respectively.