Genomic diversities and affinities among four endogamous groups of Punjab (India) based on autosomal and mitochondrial DNA polymorphisms

Human Biology, Dec 2002 by Kaur, Inderjeet, Roy, Sangita, Chakrabarti, Subhabrata, Sarhadi, Virinder Kaur, Et al

Abstract Nineteen insertion/deletion and restriction site polymorphisms on autosomal and mitochondrial genomes and mitochondrial DNA hyper-variable segment 1 sequences were used to study genetic diversities and affinities among four endogamous groups of Punjab, India. High values of heterozygosity were noted in all four groups, both in the autosomal and mitochondrial genomes. The coefficient of gene differentiation among the groups, however, was found to be low. Genetic distance and phylogenetic analyses based on these data indicated that inferences on affinities among the populations were different when the two sets of loci (autosomal and mitochondrial) were considered separately. We have interpreted these results on the basis of some known historical data on migrations into this region. The results of this study when compared with the findings of some previous studies indicate that there are regional differences in the patterns of correlation between genomic and sociocultural affinities within India.

The study of evolution and genetic relationships among contemporary human populations has shed light on the origin of modern humans and also on the nature, extent, and causes of genetic differentiation. India represents one of the most interesting global regions in human evolution, primarily because some of the most ancient out-of-Africa waves of human migration appear to have passed through India (Cann 2001). Further, northern India has been a virtual melting pot of humans who have entered India in historic times (Thapar 1966). As groups of humans entered India, there must have been differential admixture of genes brought in by these immigrants with those of preexisting local ethnic groups, who were already socially structured in a hierarchical manner. Therefore, population groups of northern India are of great interest from the standpoint of the peopling of India. In the present study, we have included four endogamous groups resident in the north Indian State of Punjab, with a view to understanding the extent of genetic diversities and affinities among them. This study has been conducted using two sets of DNA markers, autosomal and mitochondrial. The autosomal set includes eight insertion/deletion (InDel) polymorphisms. The mitochondrial set includes 11 markers (10 restriction site polymorphisms [RSPs] and 1 InDel) and hyper-variable segment-1 (HVS1) sequences.

Alu elements are a family of short interspersed elements (SINEs) with about 500,000 members distributed throughout the primate genome (Batzer and Deininger 1991; Deininger and Batzer 1993). The human-specific Alu InDels are highly polymorphic in most human populations, and since their ancestral states are known, these InDels are particularly useful in tracing the ancestry through phylogenetic trees more effectively (Perna et al. 1992; Batzer et al. 1994, 1995, 1996). Alu insertions do not occur multiple times at the same chromosomal location; therefore, the sharing of Alu elements is necessarily because of common ancestry. This fact makes the Alu elements useful markers for various population genetic studies (Batzer et al. 1994; Stoneking et al. 1997). Only a single major study using Alu InDel polymorphisms has been conducted in India (Majumder et al. 1999). This study on 14 ethnic groups of India, however, did not include populations from Punjab. Lack of data on north Indian populations on these InDel polymorphisms, especially from Punjab, motivated us to undertake this study. Further, although some earlier mitochondrial DNA (mtDNA) studies (Kivisild et al. 1999) on Indian populations have been based on HVS1 sequence data from individuals drawn from Punjab, these samples were included without regard to their endogamous group identity. It was also of interest to cross-validate the findings of Bamshad et al. (2001) on the origin of Indian castes. Bamshad et al. (2001) found that caste groups in the uppermost rung of the social hierarchy were the closest to Europeans, and that this affinity declined as one descended the social ladder of the caste groups.

In the present study, eight human-specific InDel loci were examined on 192 individuals, 48 each from four ethnic groups, namely, Brahmins, Khatris, Jat Sikhs, and Scheduled Castes of Punjab, India. Of these eight loci, six were Alu insertion loci; the seventh locus (CD4) was a deletion locus. Further, we have also included an eighth locus, which is an mtDNA segment insertion in the human nuclear genome (Zischler et al. 1995). Ten mtDNA RSPs and one mtDNA InDel have been screened. In addition, we have sequenced the HVS1 segment (nt [nucleotide] 16024-16380) of the mtDNA in a subset of 57 individuals (about 15 individuals drawn randomly from each of the four populations).

Materials and Methods

Populations Studied. Four endogamous groups of Punjab consisting of Brahmins, Khatris, Jat Sikhs, and Scheduled Castes were studied for eight InDel loci. The Brahmins are geographically distributed over the entire State of Punjab. They are traditionally priests and torch-bearers of Aryan rituals, but now they participate in various, primarily white-collar, occupations. The Khatris occupy the central region of Punjab. Their main occupation is trade. There are some subgroups of this caste. Consanguinity is practiced within the subgroups, but the level of inbreeding is low. Jat Sikhs are predominantly agriculturists and inhabit all regions of the state. They may have entered Punjab after the Brahmins and Khatris (Ibbetson 1916a, b). The Scheduled Castes are primarily menial workers and occupy the lowest rung in the social hierarchy. They also inhabit all regions of the state. According to the Hindu caste system in Punjab, Brahmins are at the top of the social ladder and the Scheduled Castes are at the lowermost rung. The position of Jat Sikhs and Khatris is controversial. According to one view Jat Sikhs are at the top since they are the most predominant caste group ([approximate]60%) among the Sikhs (followers of Sikhism). The social ranking of the Khatris, or the Kshatriyas of the original Manu's classification of castes, is below the Brahmins and just above the Scheduled Castes. The origin of Jat Sikhs is also disputed. While one view is that they are one of the Rajput tribes, another is that the Rajputs belong to the original Aryan stock that entered India, and the Jats belong to a later wave of immigrants of Indo-Scythian stock (Ibbetson 1916a,b). A total of 192 blood samples of unrelated individuals, 48 from each endogamous group belonging to different social strata, were collected randomly from different geographical locations of Punjab, India.