The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations T. Kivisild, S. Rootsi, M. Metspalu, S. Mastana, K.

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The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations T. Kivisild, S. Rootsi, M. Metspalu, S. Mastana, K. Kaldma, J. Parik, E. Metspalu, M. Adojaan, H.-V. Tolk, V. Stepanov, M. Gölge, E. Usanga, S.S. Papiha, C. Cinnioğlu, R. King, L. Cavalli-Sforza, P.A. Underhill, R. Villems The American Journal of Human Genetics Volume 72, Issue 2, Pages 313-332 (February 2003) DOI: 10.1086/346068 Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 1 A network relating Chenchu and Koya mtDNA haplotypes. Node areas are proportional to haplotypes frequencies. Variant bases are numbered (Anderson et al. 1981) and shown along links between haplotypes. Character change is specified only for transversions. Insertions and deletions are indicated by “+” and “del,” respectively. Variation at hypervariable positions 16183 and 16517 is not shown. The American Journal of Human Genetics 2003 72, 313-332DOI: (10.1086/346068) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 2 A network of haplogroup M2 haplotypes. Circle areas are proportional to haplotypes frequencies. Variant bases are numbered as in figure 1. Bold circles represent haplotypes for which indicated coding region markers were determined. Recurrent mutations are underlined. Haplotypes restricted to South India, including Andhra Pradesh, Kerala, Karnataka, and Sri Lanka are shaded. Hv = Havik, Kd = Kadar, Mu = Mukri (Mountain et al. 1995); Bo = Boksa, Lm = Lambadi, Lo = Lobana, Up = Uttar Pradesh (Kivisild et al. 1999a); Te = Telugu (Bamshad et al. 2001); Cb = Konkanastha Brahmin, Ch= Chenchu, Gu = Gujarat, Ko = Koya, Kw = Kuwait, Mo = Moor, Pa = Parsi, Pu = Punjab, Si = Sinhalese, wB = west Bengal (present study). The coalescence times of the clusters are shown below cluster labels. The American Journal of Human Genetics 2003 72, 313-332DOI: (10.1086/346068) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 3 Y-chromosomal SNP tree and haplogroup frequencies in 8 Indian populations. Haplogroup defining markers (and their background average variances of 6 STR loci) are shown along the branches of the tree. The American Journal of Human Genetics 2003 72, 313-332DOI: (10.1086/346068) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 4 Multidimensional scaling plot of eight Indian and seven western Eurasian populations, using Fst distances calculated for 16 Y-chromosomal SNP haplogroups. From India: I-Ch = Chenchus, I-Ko = Koyas, I-Gu = Gujaratis, I-Be = Western Bengalis, I-Si = Singalese, I-Co = Konkanastha Brahmins, I-La = Lambadis. Western Eurasia: CA = Central Asia; Pk = Pakistanis (Underhill et al. 2000); WE = western Europe, including Dutch, French, and German samples; EE = eastern Europe, including Poles, Czechs, and Ukrainians; SE = southern Europe, including Greeks and Macedonians; Ge = Georgians; ME = Middle East, including Turks, Lebanese, and Syrians from Semino et al. (2000). The American Journal of Human Genetics 2003 72, 313-332DOI: (10.1086/346068) Copyright © 2003 The American Society of Human Genetics Terms and Conditions