Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: dispersal of modern human in South Asian corridor

Abstract

To construct maternal phylogeny and prehistoric dispersals of modern human being in the Indian sub continent, a diverse subset of 641 complete mitochondrial DNA (mtDNA) genomes belonging to macrohaplogroup M was chosen from a total collection of 2,783 control-region sequences, sampled from 26 selected tribal populations of India. On the basis of complete mtDNA sequencing, we identified 12 new haplogroups--M53 to M64; redefined/ascertained and characterized haplogroups M2, M3, M4, M5, M6, M8'C'Z, M9, M10, M11, M12-G, D, M18, M30, M33, M35, M37, M38, M39, M40, M41, M43, M45 and M49, which were previously described by control and/or coding-region polymorphisms. Our results indicate that the mtDNA lineages reported in the present study (except East Asian lineages M8'C'Z, M9, M10, M11, M12-G, D) are restricted to Indian region.The deep rooted lineages of macrohaplogroup 'M' suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups of India. Hierarchical analysis of molecular variation (AMOVA) shows substantial subdivisions among the tribes of India (Fst = 0.16164). The current Indian mtDNA gene pool was shaped by the initial settlers and was galvanized by minor events of gene flow from the east and west to the restricted zones. Northeast Indian mtDNA pool harbors region specific lineages, other Indian lineages and East Asian lineages. We also suggest the establishment of an East Asian gene in North East India through admixture rather than replacement.

Figure 1. Geographical locations of the Indian tribal populations in the present study.

Figure 2. Phylogenetic tree based on complete mtDNA sequences for haplogroup M in India.

Suffixes A, C, G, and T indicate transversions, “d” indicates a deletion, and a plus sign (+) indicates an insertion; 9bpins means 9-bp insertion (CCCCCTCTA) in the COII/tRNA^Lys intergenic region. The A/C stretch length polymorphism in regions 16180–16193 and 303–315 and mutation 16519, all known to be hyper variable, were disregarded for tree reconstruction; recurrent mutations are underlined and the @ indicates back mutation. Haplogroup names indicated in Blue are defined in the earlier works, pink are redefined and red are newly identified in the present study.