4. Mitochondrial Diversity: Haplogroups Second approach to study mitochondrial DNA data is based on analyses of haplogroups. While phylogenetics of haplogroups in itself is an important part of this approach, here we report mtDNA haplogroups with a view to answer the questions about population affinities, demic or cultural diffusion of language and agricultural technology and antiquity and unity of Indian populations. This chapter thus presents haplogroup frequencies and haplogroup sharing among the tribal populations of Maharashtra followed by haplogroup descriptions focussing on its estimated time to most recent common ancestor (TMRCA), sharing of haplogroups among populations and lastly, West Eurasian haplogroups which are important markers to shed light on demic or cultural diffusion of language and agricultural technology and populations movements to the subcontinent around Holocene. The chapter also presents the results of assessment of population affinities based on haplogroup frequencies and comments on the utility of mtDNA data vis-a vis genome wide autosomal data to understand population histories. Principal component analysis of Genome wide SNP analysis undertaken to understand the population structure among South Asian populations along with tribal and caste populations of Maharashtra, has been published (Jonnalagadda et al., 2019) as part of a larger analysis. Haplogroups and their clades observed in the study populations One of the objectives of the present research was to characterise the mtDNA haplogroups among the selected tribes of Maharashtra, viz. Bhil, Pawara, Kokana and Warli. As described earlier in the methodology chapter, sequenced control region of mtDNA (nucleotide positions 16024-576) were used to characterise the haplogroups. 95 Following the steps described in methodology chapter, it was possible to characterise almost all the mtDNA sequences from the four tribal populations under study into haplogroups without ambiguity (Figure 20, Table 24, Table 25, Table 26, Table 27). In total, 40 haplogroups were observed among the tribal populations of West Maharashtra (Figure 20). South Asian specific haplogroups and its clades observed are: M2a, M2b, M3, M30, M33, M35, M37, M*, M38, M53, M39, M4, M57, M5, M6, M64, M65, N5, R5, R6, R8, R30, U2a, U2b, U2c’d, Haplogroups shared with Western Eurasia are: X2d, J, T, HV14, H2, H3, H6, H13, U1, U5, K2a, U4a, U7 Haplogroups shared with Eastern Eurasia are: G2, M73, A1 A large proportion of haplogroups among the tribal populations belongs to South Asia specific branches of M, N, R and U (333 sequences, 89.037 %). All of the South Asia specific haplogroups exhibit a deep coalescence emphasizing the autochthonous nature of the Tribal populations of Maharashtra. A minor fraction (30 sequences, 8.021 %) of the total sequences belongs to west Eurasian haplogroups shared with South Asia. These haplogroups are crucial for understanding the putative agriculture and/or language related admixture and migrations from West Eurasia. Therefore, in the context of research questions of present study asking whether tribal populations of Maharashtra show any signs of agriculture or language related admixture, only the west Eurasian haplogroups are further discussed in relevant sections. 96 Figure 20: mtDNA haplogroups observed in the present study 97 Table 24: Frequency and Percentages of Macrohaplogroup M lineages Branches Bhil Kokana Pawara Warli Total Haplogroups Freq. % Freq. % Freq. % Freq. % Freq. % M* 0 0 0 0 1 1.099 0 0 1 0.267 M* Total M* 0 0 0 0 1 1.099 0 0 1 0.267 M2a1 0 0 1 1.136 0 0 0 0 1 0.267 M2a1a 0 0 0 0 1 1.099 3 3.093 4 1.07 M2a1a+207 0 0 5 5.682 1 1.099 2 2.062 8 2.139 M2a M2a1a3 0 0 1 1.136 0 0 0 0 1 0.267 M2a1a3+16093 0 0 5 5.682 0 0 3 3.093 8 2.139 M2a1b 5 5.102 0 0 6 6.593 0 0 11 2.941 Total M2a 5 5.102 12 13.636 8 8.791 8 8.248 33 8.823 M2b 1 1.02 1 1.136 0 0 1 1.031 3 0.802 M2b M2b2 0 0 0 0 0 0 2 2.062 2 0.535 Total M2b 1 1.02 1 1.136 0 0 3 3.093 5 1.337 M3 0 0 0 0 4 4.396 0 0 4 1.07 M3a1+204 4 4.082 2 2.273 8 8.791 4 4.124 18 4.813 M3c1b 0 0 0 0 0 0 1 1.031 1 0.267 M3 M3c2 0 0 3 3.409 0 0 0 0 3 0.802 M3d 1 1.02 2 2.273 0 0 0 0 3 0.802 Total M3 5 5.102 7 7.955 12 13.187 5 5.155 29 7.754 M30 1 1.02 0 0 0 0 1 1.031 2 0.535 M30+16234 4 4.082 0 0 0 0 1 1.031 5 1.337 M30a 2 2.041 0 0 0 0 0 0 2 0.535 M30b 1 1.02 0 0 0 0 0 0 1 0.267 M30 M30c1 0 0 0 0 2 2.198 0 0 2 0.535 M30d 0 0 0 0 2 2.198 0 0 2 0.535 M30f 0 0 0 0 5 5.495 0 0 5 1.337 M30g 0 0 2 2.273 0 0 0 0 2 0.535 Total M30 8 8.163 2 2.273 9 9.89 2 2.062 21 5.615 M33a1b 1 1.02 1 1.136 0 0 0 0 2 0.535 M33a2a 1 1.02 0 0 1 1.099 0 0 2 0.535 M33 M33b+16362 0 0 1 1.136 0 0 0 0 1 0.267 Total M33 2 2.041 2 2.273 1 1.099 0 0 5 1.337 M35+199 0 0 0 0 1 1.099 0 0 1 0.267 M35b 0 0 0 0 0 0 1 1.031 1 0.267 M35b+16304 2 2.041 0 0 0 0 6 6.186 8 2.139 M35 M35b1 2 2.041 0 0 0 0 1 1.031 3 0.802 M35c 10 10.204 0 0 2 2.198 0 0 12 3.209 Total M35 14 14.286 0 0 3 3.297 8 8.247 25 6.684 M37 M37+152+151 2 2.041 0 0 0 0 14 14.433 16 4.278 98 Branches Bhil Kokana Pawara Warli Total Haplogroups M37e2 1 1.02 0 0 0 0 0 0 1 0.267 Total M37 3 3.061 0 0 0 0 14 14.433 17 4.545 M38c 0 0 0 0 0 0 1 1.031 1 0.267 M38 Total M38c 0 0 0 0 0 0 1 1.031 1 0.267 M39 0 0 0 0 1 1.099 0 0 1 0.267 M39b 0 0 1 1.136 0 0 0 0 1 0.267 M39 M39b1 3 3.061 0 0 3 3.297 0 0 6 1.604 Total M39 3 3.061 1 1.136 4 4.396 0 0 8 2.139 M4a 3 3.061 5 5.682 0 0 2 2.062 10 2.674 M4a Total M4a 3 3.061 5 5.682 0 0 2 2.062 10 2.674 M53 0 0 0 0 1 1.099 0 0 1 0.267 M53 Total M53 0 0 0 0 1 1.099 0 0 1 0.267 M57+152 3 3.061 0 0 1 1.099 0 0 4 1.07 M57a 1 1.02 0 0 6 6.593 0 0 7 1.872 M57 M57b 0 0 2 2.273 0 0 0 0 2 0.535 M57b1 5 5.102 0 0 8 8.791 0 0 13 3.476 Total M57 9 9.184 2 2.273 15 16.484 0 0 26 6.952 M5a2a1a2 0 0 2 2.273 0 0 0 0 2 0.535 M5a3b 0 0 0 0 1 1.099 0 0 1 0.267 M5a4 0 0 1 1.136 2 2.198 1 1.031 4 1.07 M5 M5a'd 5 5.102 8 9.091 2 2.198 4 4.124 19 5.08 M5b2a 0 0 0 0 2 2.198 1 1.031 3 0.802 Total M5 5 5.102 11 12.5 7 7.692 6 6.186 29 7.754 M6 0 0 0 0 0 0 7 7.216 7 1.872 M6 Total M6 0 0 0 0 0 0 7 7.216 7 1.872 M64 0 0 5 5.682 0 0 0 0 5 1.337 M64 Total M64 0 0 5 5.682 0 0 0 0 5 1.337 M65 0 0 1 1.136 0 0 0 0 1 0.267 M65a+@16311 1 1.02 0 0 0 0 0 0 1 0.267 M65 M65b 1 1.02 0 0 2 2.198 0 0 3 0.802 Total M65 2 2.041 1 1.136 2 2.198 0 0 5 1.337 M73a 2 2.041 0 0 0 0 0 0 2 0.535 M73 Total M73a 2 2.041 0 0 0 0 0 0 2 0.535 G2b1a1 1 1.02 0 0 2 2.198 0 0 3 0.802 G2b G2b2a 0 0 0 0 0 0 2 2.062 2 0.535 Total G2b 1 1.02 0 0 2 2.198 2 2.062 5 1.337 99 Table 25: Frequency and Percentages of Macrohaplogroup N (xR) lineages Branches Bhil Kokana Pawara Warli Total Haplogroups Freq.