Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

Abstract

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.

GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

“…3), clearly demonstrates the findings of allele frequency patterns from South Asian Afghanistan - V, Caucasian - VI and South Indian Andhra Pradesh - VII as an “Other than Africa” split among 45 GAHPs for GST M1-T1 null genotypes with respect to their geographical distribution. This observation of other than Africa split in this study has been reported here in agreement to the concepts of later migration of the populations in regions other than Africa [60, 64]. In conclusion, the data of seven patterns for GST M1-T1 null allele frequency from Xhosa tribe (I), Zimbabwe (II), Ethiopia (III), Egypt (IV), Afghanistan (V), Caucasian (VI) and South Indian Andhra Pradesh (VII) reported in this study compare constructively with the earlier studies that suggested the PAs of relatively recent origin show comparatively small genetic differences and high genetic affinity among them [11, 46, 52, 58].…”

“…2 and 3) has been reported as pattern - V for GST M1-T1 null genotypes in accordance to the reports of various authors [60, 62, 64]. Further, population in Pakistan (South Asia) has been reported with Afghanistan (South Asia) pattern for GST M1-T1 null allele frequency (Table 3) in this study, though it was found with genetic affinity to PAs from Mongolia (East Asia), Europe (South, East and West) and Andhra Pradesh (South India) in corroborate to the earlier reports of Templeton (2002), who stated the findings of considerable overlap among East Asians, Europeans and South Indian populations [64].…”

“…2 and 3) among the 45 GAHPs in this study. These observations of South East Asian and South American PAs with the null allele frequency pattern from South Indian Andhra Pradesh PA are in agreement to the reports of agro-pastoral system in South India that acted as agricultural center and source of dispersion to lineages from different preexisting populations [60]. Furthermore, the reported East Africa patterns from Zimbabwe (II), Ethiopia (III) among India, Iran (South Asia) and South Asian pattern from South Indian Andhra Pradesh (VII) among Vietnam (South East Asia) populations in this study for GST M1-T1 null allele frequency are in concordance to the reports of migration pattern of Homo sapiens from East Africa with the demographic expansions by Field and Lahr (2006), who investigated the geographic information systems during oxygen isotope stage 4 [62].…”

West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system

“…However, this claim should not be considered exclusively to establish the fact that Dravidian populations of India originated in west Asia and then migrated to south India (Sengupta et al 2006). The co-presence of these west Eurasian mtDNA and Y-chromosome haplogroups in Dravidianspeaking tribal and caste groups in South India suggest that their spread is not associated with the Indo-Aryan migration (Arunkumar et al 2012). A large proportion of the west Eurasian mtDNA haplogroups observed among the higher-ranked caste groups, their phylogenetic affinity and age estimate indicate recent Indo-Aryan migration to India from west Asia.…”

Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese

“…A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal 2004; Metspalu et al 2004;Sahoo et al 2006;Thanseem et al 2006;Sengupta et al 2006;ArunKumar et al 2012), and autosomes (Reich et al 2009;Metspalu et al 2011;Moorjani et al 2013;Juyal et al 2014;Basu et al 2015). Till recently, the Y-chromosome analysis mostly relied on calculating frequencies of pre-defined haplogroups, and the time and place of origin have been estimated for some of these.…”