Phylogeography of mitochondrial DNA and Y-Chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India

Abstract

Polymorphisms in mitochondrial (mt) DNA and Y-chromosomes of seven socially and linguistically diverse castes and tribes of Eastern India were examined to determine their genetic relationships, their origin, and the influence of demographic factors on population structure. Samples from the Orissa Brahmin, Karan, Khandayat, Gope, Juang, Saora, and Paroja were analyzed for mtDNA hypervariable sequence (HVS) I and II, eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnostic for Indian- and Eurasian-specific haplogroups. Our results reveal that haplotype diversity and mean pairwise differences (MPD) was higher in caste groups of the region (>0.998, for both systems) compared to tribes (0.917-0.996 for Y-STRs, and 0.958-0.988 for mtDNA haplotypes). The majority of paternal lineages belong to the R1a1, O2a, and H haplogroups (62.7%), while 73.2% of maternal lineages comprise the Indian-specific M*, M5, M30, and R* mtDNA haplogroups, with a sporadic occurrence of West Eurasian lineages. Our study reveals that Orissa Brahmins (a higher caste population) have a genetic affinity with Indo-European speakers of Eastern Europe, although the Y-chromosome data show that the genetic distances of populations are not correlated to their position in the caste hierarchy. The high frequency of the O2a haplogroup and absence of East Asian-specific mtDNA lineages in the Juang and Saora suggest that a migration of Austro-Asiatic tribes to mainland India was exclusively male-mediated which occurred during the demographic expansion of Neolithic farmers in southern China. The phylogeographic analysis of mtDNA and Y-chromosomes revealed varied ancestral sources for the diverse genetic components of the populations of Eastern India.

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

“…The sub-haplogroup also exhibited its presence in Reddy and Thogataveera populations of Andhra Pradesh ). M2a has also been reported in Karan and Gope populations of Orissa (Sahoo and Kashyap 2006) and in two individuals of Maratha population from Western India (Gaikwad and Kashyap 2005). Another sub-haplogroup of M2, M2b, defined by the presence of T16357C mutation in addition to the M2 defining basal mutations, was reported in an individual from Kuruva population of Karnataka (Rajkumar et al 2005).…”

“…M3a was concentrated in northwestern India (22% among Parsees of Mumbai) suggesting that the region may have been the ancestral source. High frequencies of M3a were also reported among the Rajputs of Rajasthan (14%), Brahmins of Uttar Pradesh (16%) (Metspalu et al 2004), and in Karan and Juang populations of Orissa (Sahoo and Kashyap 2006). The coalescence times of M3 and M3a was calculated to be 27,100 ± 10,200 and 16, 400 ± 6100 yr, respectively .…”

“…It was also the most frequent haplogroup (17%) among the three tribal populations (Pardhan, Naikpod and Andh) ). Gaikwad and Kashyap (2005) observed M3 in Maratha population of western India, and Sahoo and Kashyap (2006) reported the presence of M3 among the Khandayats of eastern India. M3 was observed even among Paniya from Kerala .…”

“…Bihar 5 Rajkumar et al 2005Thangaraj et al 2005bThangaraj et al , 2006 53-57 Orissa 15 Roychoudhury et al 2000Roychoudhury et al , 200158-72 Basu et al 2003;Cordaux et al 2003;Rajkumar et al 2005;Kumar et al 2006;Sahoo and Kashyap 2006;Thangaraj et al 2006. Jharkhand 7 Thangaraj et al 2005b73-79 Rajkumar et al 2005;Kumar et al 2006; West Gujarat 3 Metspalu et al 2004;Thangaraj et al 2006.…”

Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians

“…Moreover, H-M69 lineages more concentrated into clade H1-M52 in Indians, yet were rare and even absent in other populations. 32,40,[58][59][60] We only distinguished four Y chromosomes harboring M69 from the Uygur population. The restricted and occasional distribution of G-M201, H-M69 and I-M170 under trunk F-M89 among northwestern populations of China and Central Asians may result from gene flows mediated by 'Silk Road' from West Eurasia and South Asia.…”