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Comparative Study
. 2003 Feb;72(2):313-32.
doi: 10.1086/346068. Epub 2003 Jan 20.

The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations

Free PMC article
Comparative Study

The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations

T Kivisild et al. Am J Hum Genet. .
Free PMC article


Two tribal groups from southern India--the Chenchus and Koyas--were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.


Figure  1
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.
Figure  2
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.
Figure  3
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.
Figure  4
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).

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