Geographical locations of the Indian tribal populations in the present study. doi:10.1371/journal.pone.0007447.g001 

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... polymorphisms reveal a population’s genetic structure, migration and admixture in the past, susceptibility to illness and genetic causes of diseases. A phylogenetic approach is strongly recommended to avoid spurious positive associations between mtDNA mutations and diseases [1]. The pathogenic role of the mitochondrial genome requires more extensive surveys of the mtDNA sequences in different populations and patient groups. Technological improvements in DNA sequencing has made it possible to sequence complete mtDNA genome faster. Attempts have been made to reconstruct the phylogenies and prehistoric dispersal of modern humans in Europe, Africa, Oceania, East Asia, Southeast Asia and South Asia [2,3–24] with complete mtDNA sequence information. The out-of-Africa scenario [25] has hitherto provided little evidence of the precise route by which modern humans might have left Africa. Two major routes of dispersal have been hypothesized: one is through North Africa into the Levant [26], and another is through Ethiopia along South Asia [27–28]. The proposed northern route of initial dispersal of modem humans from Africa could not be sustained by complete and in-depth analysis of mtDNA in recent times [29]. The mitochondrial haplogroup M which was first regarded as an ancient marker of East-Asian origin [30–31], had been found at high frequency in India [32] and Ethiopia [33], thus raising the question of its origin. The presence of M haplogroup in Ethiopia, named M1, led to the proposal that haplogroup M originated in eastern Africa, approximately 60,000 years ago, and was carried towards Asia [34]. Contrary to the above, in 2006, Olivieri [35] reported that about 40,000 to 45,000 years ago, predominant North African clades M1 and U6 arose in southwestern Asia and moved together to Africa. Their arrival temporally overlapped the event(s) that led to the peopling of Europe by modern humans and most likely the result of the same change in the climatic conditions that allowed humans to enter in to the Levant, opening the way to the colonization of both Europe and North Africa. In the light of above, the origins of Asian M lineage in Eastern Africa became ambivalent. Macrohaplogroup M is ubiquitous in India and covers more than 70 per cent of the Indian mtDNA lineages [28,36–38]. Recent studies on complete mtDNA sequences ( , 187) tried to resolve the phylogeny of Indian macrohaplogroup M. As a result, M2, M3, M4, M5, M6 [28,36,39–40], M18, M25 [38], M30, [41], M31 [42,24] M33, M34, M35, M36, M37, M38, M39, M40 [22], M41, M42 [43], M43 [23,44], M45 [45], M48, M49, and M50 [46] haplogroups of M that was identified in India helped to a certain extent in understanding M genealogy in diversified Indian populations. In the above background, extensive sequencing of complete mtDNA of South Asia, particularly India, is essential for better understanding of the peopling of the non-African continents, and pathogenesis of diseases in various ethnic groups with different matrilineal backgrounds. The frequency distribution of M haplogroups has been shown in Table 1. In the present study, 12 novel haplogroups M53 to M64 (Table 2) have been identified, and the phylogenetic status of previously identified haplogroups based on control region and/or coding region information have been ascertained or redefined from 26 tribal population based dataset (Fig. 1). The novel haplogroups are named according to the nomenclature system published elsewhere [47]. Phylogeny tree based on 737 (641 from our study and 96 from earlier studies) complete mtDNA sequences, for haplogroup M in India is shown in Fig. 2. The phylogeny trees of haplogroups M53 to M62 have been shown in Fig. S1. Haplogroup M53 encompasses ten samples from Kamar, 6 samples from Nihal, 4 samples from Pauri Bhuiya of the present study and R188 of [22]. Haplogroup M53 has diversified in the central India. Haplogroup M54 is the most frequent in Jenu Kuruba of southern India and insignificant in Hill Kolam of central India. Haplogroup M55 has been identified in one Katkari and eight Mathakur samples from western India. Haplogroups M56 and M57 have been sharing a nucleotide transition at np 16311. Haplogroup M56 has been identified among the Korku of central India. Haplogroup M57 is recognizable among three Dongri Bhill, two Katakari and a Kathakur sample drawn from western India. Haplogroup M58 encompasses 4 Munda samples, 1 Nihal, 1 Wanchoo and R58 of [22]. The earliest branch of this lineage has been represented by Wanchoo tribe in Northeast India, whereas the younger branches are present in central Indian tribes. Haplogroups M63 and M64 have been added to the superbranch, M4 9 30 nested in M. Six Madia sequences have been grouped into haplogroup M63 (Fig. S2). Haplogroup M64 has been identified in Nihal population of central India (Fig. S2). Haplogroup M59 encompasses 1 Pauri Bhuiya, 2 Sonowal Kachari, and 1 Malpaharia samples from East and Northeast India. Haplogroup M60 constitutes three samples from the Gallong, two samples from Sonowal Kachari and two samples from Toto, drawn from Northeast Indian tribal populations. The Dirang Monpa (1), Shertukpen (4) and Lachungpa (5) form a new haplogroup named as M61. Lineages DR53 and DR79 from Assam state share eleven specific coding region mutations and seven control region mutations to form a haplogroup, M62 (Fig. S1). A super-branch, M4 9 30 nested in macrohaplogroup M harbors haplogroups M4, M18, M30, M37, M38, M43, M45, M63 and M64 that shares the transition at np 12007 and encompasses 95 complete mtDNA sequences, represented by all tribal populations except Malpaharia, Sonowal Kachari, Betta Kuruba, Toto and Wanchoo (Fig. S2). From our large dataset, subhaplogroup M2a and M2b of M2 remain unchanged (Fig. S3). Under haplogroup M3, subhaplogroup M3a has been subdivided into M3a1 and M3a2 in the present study and it encompasses 10 Kamar, 4 Kathodi, 6 Jenu Kuruba, 1 Katkari and 1 Dongri Bill samples. The new sub branch M3b encompasses six Kamar sequences from central India. M3c encompasses one sample each from Madia and Andh. (Fig. S3). A new subhaplogroup, M4c of M4 has been identified in Shertukpen (ST36) and Dirang Monpa (DR77) of Northeast India (Fig. S2). The frequency and diversity of haplogroup M5 reveals that it might have originated in central India and spread out to the eastern and western regions of India. Presence of M5a1b in Slavonic populations [48] and western Indians show its recent migration into the Eurasia. Novel subhaplogroups M5a3 to M5a5 have been defined in the present study while single sequences reported by [22] T13 and A64, B26 have been assigned to M5b and M5c haplogroups respectively (Fig. S4). Haplogroup M6 has been redefined with 9 mutations, unlike in the earlier study [22] with 11 mutations. The haplogroup M6 has branched into M6a and M6b. M6a has further branched into M6a1 and M6a2 in the present study. The Lineages of Pauri Bhuiya, Munda, Hill Kolam and R56 of [22] have been classified under M6a1. Lineages R65 of [22] and P31 of [23], categorized under M6b earlier, have been assigned to M6a2 in the present study. Subhaplogroup M6b has been found in Korku (KK56) and Andh (AD27) of central India (Fig. S3). Haplogroups M30, M31, M33, M34, M35, M37, M39, M40, M41, M43, M45 and M49 have been well defined with additional data in the present study. Basal definition of M30 corroborates with earlier works [22]. Subhaplogroup M30e has been newly identified among Kathodi, Kathakur and Mathakur of western region of India (Fig. S2). One of the Andaman’s specific haplogroup M31 has been identified in 5 Pauri Bhuiya and 2 Munda samples from our database, and the results have been published [24]. In the present study under Haplogroup M33 from 25 samples of 7 tribes, sub-branches M33a [23], M33b [46] and M33c have been identified. M33a has been further subdivided into 3 new subhaplogroups i.e., M33a1, M33a2 and M33a3. Seven Lepcha (LP) samples have been grouped under M33a1a, whereas 7 samples of Dongri Bhill have been categorized under M33a1b along with T9 sample of [23]. Sample C182 of [22] has been assigned as M33a2 along with Nihal, Korku and Katkari samples. A lineage of Toto has been assigned as M33a3. The lineages of Madia (MA114) and Sonowal Kachari (SK53) have been grouped under M33b. Five samples of Malpaharia have been ...