Ethnic India: a genomic view, with special reference to peopling and structure

Abstract

We report a comprehensive statistical analysis of data on 58 DNA markers (mitochondrial [mt], Y-chromosomal, and autosomal) and sequence data of the mtHVS1 from a large number of ethnically diverse populations of India. Our results provide genomic evidence that (1) there is an underlying unity of female lineages in India, indicating that the initial number of female settlers may have been small; (2) the tribal and the caste populations are highly differentiated; (3) the Austro-Asiatic tribals are the earliest settlers in India, providing support to one anthropological hypothesis while refuting some others; (4) a major wave of humans entered India through the northeast; (5) the Tibeto-Burman tribals share considerable genetic commonalities with the Austro-Asiatic tribals, supporting the hypothesis that they may have shared a common habitat in southern China, but the two groups of tribals can be differentiated on the basis of Y-chromosomal haplotypes; (6) the Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads, but retreated to southern India to avoid dominance; (7) formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations; (8) the upper castes show closer genetic affinities with Central Asian populations, although those of southern India are more distant than those of northern India; (9) historical gene flow into India has contributed to a considerable obliteration of genetic histories of contemporary populations so that there is at present no clear congruence of genetic and geographical or sociocultural affinities.

Figure 1

Frequencies (%) of mitochondrial haplogroups M (hatched) and U (solid black) in 44 ethnic populations, and among sociocultural groups of populations (insets).

Figure 2

Frequencies (%) of subhaplogroups of (A) M and (B) U among tribal and ranked caste populations.

Figure 3

Frequencies (%) of Y-chromosomal haplogroups among ethnic populations. (Population codes are given in Table 1.)

Figure 4

Phylogenetic network of mtHVS1 sequences belonging to subhaplogroup M^*, with frequency distributions of motifs in populations.

Figure 5

Frequency distributions of Y-chromosomal STR haplotypes that best discriminate between the Austro-Asiatic (AA) and Tibeto-Burman (TB) population groups.

Figure 6

Neighbor-joining tree depicting genetic affinities among Indian ethnic populations based on (A) mitochondrial RSP haplotype frequencies, (B) Y-haplogroup frequencies, (C) Y-STRP frequencies, and (D) autosomal markers. The social [(UC) upper caste, (MC) middle caste, (LC) lower caste, (TR) tribal] and linguistic [(AA) Austro-Asiatic, (DR) Dravidian, (TB) Tibeto-Burman, (IE) Indo-European] background of each population is color-coded; the key to the color codes is given on the top right-hand corner.

Figure 7

Neighbor-joining tree depicting genetic affinities among categories of populations cross-classified by social rank [(UC) upper caste, (MC) middle caste, (LC) lower caste, (TR) tribal] and linguistic group [(AA) Austro-Asiatic, (DR) Dravidian, (TB) Tibeto-Burman, (IE) Indo-European] based on (A) mitochondrial RSP haplotype frequencies, (B) Y-haplogroup frequencies, (C) Y-STRP frequencies, and (D) autosomal markers.

Figure 8

Frequency distributions of mtHVS1 sequences shared between groups of populations—Austro-Asiatic (AA), Dravidian (DR), Tibeto-Burman (TB), and Indo-European (IE). (A) Number of sequences shared and (B) number of individuals sharing sequences.

Figure 9

Results of STRUCTURE analysis: Proportional contributions of five hypothetical ancestral populations to Austro-Asiatic (AA), Dravidian (DR), Tibeto-Burman (TB), and Indo-European (IE) groups.