George van Driem

The Koṅkaṇ region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity, yet its maternal genetic landscape remains largely unresolved. The present study captures the genetic affinities of the Koṅkaṇī population, residing along the Koṅkaṇ Malabar coast by analysing complete mitochondrial genomes (n = 85) and control region hypervariable sequences (n = 210). Our results reveal divergent maternal histories between the Sārasvata and the non-Sārasvata groups. Comparative analysis against over 5000 mitochondrial genomes from Eurasia demonstrates that the Koṅkaṇī maternal gene pool is shaped by both deep-rooted South Asian (macro-haplogroup M) and West Eurasian lineages. Demographic modelling identifies a pre-Last Glacial Maximum (LGM) expansion and a post-LGM recovery, with macro-haplogroup N lineages serving as the primary drivers of internal genetic structuring. At the subpopulation level, occupational groups such as the Khārvi and Kuḍubi exhibit genetic signatures that are consistent with historic founder events followed by increased genetic drift relative to Gauḍa Sārasvata Brahmins and Roman Catholics, where populations display higher haplotype diversity. Social practices, including endogamy, may contribute to the differences observed between these populations. While the non-Sārasvata group clusters with autochthonous tribes, the Sārasvata groups share genetic affinities with West Eurasian and Steppe-linked lineages, suggesting that the Bronze Age migrations into South Asia were not exclusively male-mediated. Overall, this study highlights the Koṅkaṇ coast as a genetic confluence, where Late Pleistocene migrations, LGM refugia, and Holocene admixture collectively shaped its maternal ancestry. It also illustrates how climate and social shifts moulded the extant genetic diversity along western India.

The Lhokpu people are a language community indigenous to the hills of southwestern Bhutan. Historically, the Lhokpu homeland extended further into the mountains of western Bhutan as well as out into the jungles on the plains of the Western Duars, where their ancestors used to hunt wild hnar ‘elephants’ and hnaisa ‘bear’. The Lhokpu language represents a distinct linguistic subgroup unto itself within the Trans-Himalayan language family, world’s second most populous language family in terms of numbers of speakers. Some grammatical features of the language have given rise to two hypotheses about the phylogenetic propinquity of the language within the language family. Salient cultural traits of the language community include the matrilocal and matriarchal structure of Lhokpu society as well as Lhokpu rites, rituals and burial practices.

Research has shown that the present-day population on the Indian subcontinent derives its ancestry from at least three components identified with pre-Indo-Iranian agriculturalists once inhabiting the Iranian plateau, pastoralists originating from the Pontic-Caspian steppe and ancient hunter-gatherer related to the Andamanese Islanders. The present-day Indian gene pool represents a gradient of mixtures from these three sources. However, with more sequences of ancient and modern genomes and fine structure analyses, we can expect a more complex picture of ancestry to emerge. Focusing on Dravidian linguistic groups, this study proposes a fourth putative source potentially branching from the basal Middle Eastern component that contributed to the Iranian plateau farmer related ancestry. The Elamo-Dravidian theory and the linguistic phylogeny of the Dravidian family tree provide chronological fits for the genetic findings presented here. Our findings show a correlation between the linguistic and genetic lineages in language communities speaking Dravidian languages when they are modelled together. We suggest that this source we identified in the Koraga tribe, which we shall call ‘Proto-Dravidian’ ancestry, emerged around the dawn of the Indus Valley civilisation. This ancestry is distinct from all other sources described so far, and its plausible origin not later than 4400 years ago on the region between the Iranian plateau and the Indus valley supports a Dravidian heartland before the arrival of Indo-European languages on the Indian subcontinent. Admixture analysis shows that this Proto-Dravidian ancestry is still carried by most modern inhabitants of the Indian subcontinent other than the tribal populations.

Brahui and Oraon: Tracing the Northern Dravidian genetic link back to Balochistan

The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics.

Koṅkaṇ region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity. The genetic landscape of this region remains understudied. The present study features Koṅkaṇī population residing along the Koṅkaṇ Malabar coast. We have sequenced complete mitogenomes of 85 and the hypervariable region of 210 Koṅkaṇī individuals to understand the maternal gene pool of this region. Comparative analysis of the over 5000 mitogenomes revealed that the Koṅkaṇī population clustered at a convergence point on the PCA plot, presumably due to a diverse maternal gene pool with both autochthonous and West Eurasian components. A distinct clustering pattern was observed within the subgroups of Sārasvata and non-Sārasvata Koṅkaṇī groups, indicating unique ancestral maternal lineages in them. This distinction is majorly due to the N macrohaplogroup lineages found in this population. We observe low haplotype and nucleotide diversity in Citrapur Sārasvata Brahmins (CSB), Rājāpur Sārasvata Brahmins (RSB), Khārvi and Kuḍubi compared to Gauḍa Sārasvata Brahmins (GSB) and Roman Catholics. The assimilation of both pre and post Last Glacial Maximum (LGM) haplogroups like M57, M36, M37, M3, M30, R8 and U2 in the Koṅkaṇī population suggests active movement and settlement along the Koṅkaṇ region on the west coast of India since the Late Pleistocene through the Holocene.

Summary: Earlier models of grouping Indian populations were based on language families, social stratification and geographical location. Such grouping system has often resulted in oversimplification of ancestry inferences. Moreover, we do not find many studies focused on studying the variation within these groups and the role of past demographic events in shaping them. We analysed the Y-chromosome Short Tandem Repeats haplotypes from 8153 males from India and Eurasia to explore the impact of Holocene migration on the Indian gene pool. We used haplotype variation and date estimates to understand the characteristics of each haplogroup with respect to the different grouping models. Our findings show that the Neolithic agricultural expansion has had a strong influence in shaping the male gene pool of the Indian subcontinent. Haplogroups F, L and R1a contribute greatly towards stratifying Indian populations as hunter-gatherer related, farming-related and priestly groups respectively. Although the caste system enforced endogamy, a traditional occupation based admixture existed since the Neolithic times. Dispersal of haplogroup L from the Near East played a major role in the formation of an agriculturist population that formed an intermediary between the primitive tribes and the R1a-rich priestly group. This study shows that the frequency of R1a in the hunter-gatherer tribes (1.5%) is much lower than previously reported based on other models of population clustering.

Research has shown that the present-day population on the Indian subcontinent derives its ancestry from at least three components identified with pre-Indo-Iranian agriculturalists once inhabiting the Iranian plateau, pastoralists originating from the Pontic-Caspian steppe and ancient hunter-gatherer related to the Andamanese Islanders. The present-day Indian gene pool represents a gradient of mixtures from these three sources. However, with more sequences of ancient and modern genomes and fine structure analyses, we can expect a more complex picture of ancestry to emerge. In this study, we focus on Dravidian linguistic groups to propose a fourth putative source which may have branched out from the basal Middle Eastern component that gave rise to the Iranian plateau farmer related ancestry. The Elamo-Dravidian theory and the linguistic phylogeny of the Dravidian family tree provide chronological fits for the genetic findings presented here. Our findings show a correlation between the linguistic and genetic lineages in language communities speaking Dravidian languages when they are modelled together. We suggest that this source, which we shall call ‘Proto-Dravidian’ ancestry, emerged around the dawn of the Indus Valley civilisation. This ancestry is distinct from all other sources described so far, and its plausible origin not later than 4,400 years ago on the region between the Iranian plateau and the Indus valley supports a Dravidian heartland before the arrival of Indo-European languages on the Indian subcontinent. Admixture analysis shows that this Proto-Dravidian ancestry is still carried by most modern inhabitants of the Indian subcontinent other than the tribal populations. This momentous finding underscores the importance of population-specific fine structure studies. We also recommend informed sampling strategies for biobanks and to avoid oversimplification of ancestral reconstruction. Achieving this requires interdisciplinary collaboration.

[This corrects the article DOI: 10.3389/fgene.2023.1303628.].