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Comparative Study
, 75 (6), 966-78

Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia

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Comparative Study

Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia

Malliya Gounder Palanichamy et al. Am J Hum Genet.

Abstract

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of >800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.

Figures

Figure  1
Figure 1
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. ; Maca-Meyer et al. ; Taylor et al. ; Derbeneva et al. ; Herrnstadt et al. , ; Ingman and Gyllensten ; Mishmar et al. ; 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.
Figure  1
Figure 1
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. ; Maca-Meyer et al. ; Taylor et al. ; Derbeneva et al. ; Herrnstadt et al. , ; Ingman and Gyllensten ; Mishmar et al. ; 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.
Figure  1
Figure 1
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. ; Maca-Meyer et al. ; Taylor et al. ; Derbeneva et al. ; Herrnstadt et al. , ; Ingman and Gyllensten ; Mishmar et al. ; 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.
Figure  1
Figure 1
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. ; Maca-Meyer et al. ; Taylor et al. ; Derbeneva et al. ; Herrnstadt et al. , ; Ingman and Gyllensten ; Mishmar et al. ; 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.
Figure  2
Figure 2
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.

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