Mitogenomes show continuity of Neolithic populations in Southern India

New paper (behind paywall) Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India, by Sylvester et al. Genetica (2018).

This paper used a complete mtDNA genome study of 113 unrelated individuals from the Melakudiya tribal population, a Dravidian speaking tribe from the Kodagu district of Karnataka, Southern India.

Some interesting excerpts (emphasis mine):

Autosomal genetic evidence indicates that most of the ethnolinguistic groups in India have descended from a mixture of two divergent ancestral populations: Ancestral North Indians (ANI) related to People of West Eurasia, the Caucasus, Central Asia and the Middle East, and Ancestral South Indians (ASI) distantly related to indigenous Andaman Islanders (Reich et al. 2009). It is presumed that proto-Dravidian language, most likely originated in Elam province of South Western Iran, and later spread eastwards with the movement of people to the Indus Valley and later the subcontinent India (McAlpin et al. 1975; Cavalli-Sforza et al. 1988; Renfrew 1996; Derenko et al. 2013). West Eurasian haplogroups are found across India and harbor many deep-branching lineages of Indian mtDNA pool, and most of the mtDNA lineages of Western Eurasian ancestry must have a recent entry date less than 10 Kya (Kivisild et al. 1999a). The frequency of these lineages is specifically found among the higher caste groups of India (Bamshad et al. 1998, 2001; Basu et al. 2003) and many caste groups are direct descendants of Indo-Aryan immigrants (Cordaux et al. 2004). These waves of various invasions and subsequent migrations resulted in major demographic expansions in the region, which added new languages and cultures to the already colonized populations of India. Although previous genetic studies of the maternal gene pools of Indians had revealed a genetic connection between Iranian populations and the Arabian Peninsula, likely the result of both ancient and recent gene flow (Metspalu et al. 2004; Terreros et al. 2011).

mtdna-dravidian-south

Haplogroup HV14

mtDNA haplogroup HV14 has prominence in North/Western Europe, West Eurasia, Iran, and South Caucasus to Central Asia (Malyarchuk et al. 2008; Schonberg et al. 2011; Derenko et al. 2013; De Fanti et al. 2015). Although Palanichamy identified haplogroup HV14a1 in three Indian samples (Palanichamy et al. 2015), it is restricted to limited unknown distribution. In the present study, by the addition of considerable sequences from the Melakudiya population, a unique novel subclade designated as HV14a1b was found with a high frequency (43%) allowed us to reveal the earliest diverging sequences in the HV14 tree prior to the emergence of HV14a1b in Melakudiya. (…) The coalescence age for haplogroup HV14 in this study is dated ~ 16.1 ± 4.2 kya and the founder age of haplogroup HV14 in Melakudiya tribe, which is represented by a novel clade HV14a1b is ~ 8.5 ± 5.6 kya

hv14-mtdna-haplogroup
Maximum Parsimonious tree of complete mitogenomes constructed using 38 sequences from Melakudiya tribe and 11 previously published sequences belonging to haplogroup HV14 [Supplementary file Table S2] Suffixes @ indicate back mutation, a plus sign (+) an insertion. Control region mutations are underlined, and synonymous transitions are shown in normal font and non-synonymous mutations are shown in bold font. Coalescence ages (Kya) for complete coding region are shown in normal font and synonymous transitions are shown in Italics

Haplogroup U7a3a1a2

The coalescence age of haplogroup U7a3a1a2 dates to ~ 13.3 ± 4.0 kya. (…)

Although, haplogroup U7 has its origin from the Near East and is widespread from Europe to India, the phylogeny of Melakudiya tribe with subclade U7a3a1a2 clusters with populations of India (caste and tribe) and neighboring populations (Irwin et al. 2010; Ranaweera et al. 2014; Sahakyan et al. 2017), hint about the in-situ origin of the subclade in India from Indo-Aryan immigrants.

I am not a native English speaker, but this paper looks like it needs a revision by one.

Also – without comparison with ancient DNA – it is not enough to show coalescence age to prove an origin of haplogroup expansion in the Neolithic instead of later bottlenecks. However, since we are talking about mtDNA, it is likely that their analysis is mostly right.

Finally, one thing is to prove that the origin of the Indus Valley Civilization lies (in part) in peoples from the Iranian plateau, and to show with ASI ancestry that they are probably the origin of Proto-Dravidian expansion, and another completely different thing is to prove an Elamo-Dravidian connection.

Since that group is not really accepted in linguistics, it is like talking about proving – through that Iran Neolithic ancestry – a Sumero-Dravidian, or a Hurro-Dravidian connection…

Related

Mitogenomes show ancient human migrations to and through North-East India not of males exclusively

middle-bronze-age-asia

New open article Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively, by Sharma et al., Scientific Reports 8, N. 851 (2018)

Abstract:

Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.

Conclusion:

To conclude, the extent of presence of variants defining novel HGs or personal variants indicate high diversity in maternal genetic component of the population of J&K. Statistical analyses indicate that maternal population in J&K have undergone expansion, along with other regions of Indian sub-continent9. However, signatures of maternal gene pool expansion in the region past LGM and early Holocene era are also seen, and this is a unique observation for the present study. These distinct signatures and maternal lineages, never reported before in India, apparently suggest that this region might have served as a corridor, yet also as a reservoir for many unreported lineages.

The overall diversity seen in the maternal gene pool of J&K suggests that the migrations to and through this region were not exclusively of males. This data has refined the existing phylogenetic tree and added to the information further diversity of mtDNA in Indian populations. Further, this preliminary study highlights the importance of the region and emphasizes that the populations of this region should be studied extensively to understand the gene pool of Indian populations. Along with the Y chromosomal and mtDNA markers, a study of autosomal markers is also warranted in these population groups. It is anticipated to help in finding some of the missing links in the evolution of modern humans and their migratory history to and from the mainland India and the Indian subcontinent, a future perspective of our study. Further, we would like to emphasize that the endogamous populations should be studied with respect to their individual evolutionary and migration histories, rather than pooling these together as one group, an underlying drawback that has plagued many of the Indian population based studies in the past, diluting individual signatures and masking stories their DNA has to tell.

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