Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India

Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers

BACKGROUND

The demographic history of South and Southeast Asia (S&SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&SEA at different time periods, to infer about the demographic history of this region.

RESULTS

We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between "language and genetics" or "geography and genetics" can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period.

CONCLUSION

Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&SEA. We postulate that pre-Neolithic ancestors of today's AAs were widespread in S&SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups.

Hemoglobin E in Northeast India: A review on its origin, distribution, migration and health implication

A systematic review of the studies on hemoglobin E in Northeast India has been carried out to understand the magnitude of research undertaken on this aspect during the last seven decades. Owing to the high prevalence of hemoglobin E in this part of India different authors have studied this hemoglobin from different perspectives and found conflicting results. However a systematic review of such studies is lacking from a holistic point of view. Most of the epidemiological, in vitro as well as in vivo studies show signatures of selection with this hemoglobin locus. However, how this polymorphism is maintained at different rates at different geographical region is still a matter of contention. This review will fill the gap from all perspectives starting from the frequency distribution of hemoglobin E and its spread in different parts of Northeast India, its relationship with malaria hypothesis, the population migration, population affinity and most importantly the health implication arising out of it. A probable origin of hemoglobin E among an Austroasiatic population of Northeast India has been postulated with the help of advance molecular anthropological knowledge like the deep rooted markers of mt DNA and Y-chromosome haplotypes.

Root canal configuration of permanent maxillary first molar in Khasi population of Meghalaya: An in vitro study

AIMS AND OBJECTIVE

To investigate the root canal configuration of permanent maxillary first molar in Khasi population of Meghalaya.

MATERIAL AND METHODS

Sixty (60) permanent maxillary first molars collected from patients of Khasi population of Meghalaya were studied using canal staining and clearing technique. Observations of the number of roots, root canal configuration, lateral canal, apical delta, and presence of the additional type of canals were made.

RESULTS

Based on Vertucci's classification the different types of canal identified are: Mesiobuccal root, Type I (28.3%), Type II (28.3%), Type IV (30.0%), Type V (5.0%), Type VI (6.7%), and an additional type of canal (2-1-2-1-2; 1.7%) were observed. The distobuccal root displayed Type I (95%), Type II (1.7%), Type V (3.3%). The most prevalent canal configuration in the palatal roots is Type I (98.3%), Type II (1.7%).

CONCLUSION

In Khasi population of Meghalaya, the most prevalent root canal configuration in the mesiobuccal root is Type IV followed by Type I and Type II. MB2 canals are present in more than 65% cases. In palatal and distobuccal roots, Type I configuration is present in most cases. Racial divergence may be responsible for such variations.

Polymorphisms and expression of TLR4 and 9 in malaria in two ethnic groups of Assam, northeast India

Infectious diseases have been postulated to play an important role in exerting pressure and in selection of TLR polymorphisms. Single nucelotide polymorphisms (SNPs) of TLR4 have been reported to show unique distributions in populations from Africa, Asia and Europe, and malaria is suggested to influence these patterns. In this context, we examined association of TLR polymorphisms with the risk of malaria in two ethnic groups—the Austro-Asiatics and Tibeto-Burmans—from malaria endemic districts of Assam to understand the influence of malaria in selection of TLRs in these genetically-distinct populations. TLR9 (T-1237C) mutation was positively associated with complicated ( P = 0.001) and frequent ( P = 0.035) malaria in Austro-Asiatics (relative risk = 0.595 95% CI: 0.479–0.836), but not in Tibeto-Burmans. Nonetheless, these alleles were not in Hardy-Weinberg Equilibrium in Tibeto-Burmans ( P < 0.001). In contrast, the TLR9 1486T/C genotype was favourable where it was negatively associated with complicated malaria (Fishers exact P = 0.014). Sequencing data revealed that the two populations differed in nucleotide diversity of the TLR9 promoter region. Enhanced expression of TLR4 ( P = 0.05), but not of TLR9, was associated with complicated malaria. Austro-Asiatics appeared to have accumulated favourable genotypes of TLR9, perhaps because of their longer exposure to malaria.

The Austroasiatic Munda population from India and Its enigmatic origin: a HLA diversity study

The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article ( Nunes et al. 2011 ), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families. We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

Indian subcontinent harbours both the human mtDNA macrohaplogroups M and N, of which M is the most prevalent. In this study, we discuss the overall distribution of the various haplogroups and sub-haplogroups of M among the different castes and tribes to understand their diverse pattern with respect to geographical location and linguistic affiliation of the populations. An overview of about 170 studied populations, belonging to four distinct linguistic families and inhabiting different geographic zones, revealed wide diversity of about 22 major haplogroups of M. The tribal populations belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro-Asiatic speakers) exhibited differences in their haplogroup diversity. The northern and southern region castes showed greater diversity than the castes of other regions.

Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands

The population genetics of the Indian subcontinent is central to understanding early human prehistory due to its strategic location on the proposed corridor of human movement from Africa to Australia during the late Pleistocene. Previous genetic research using mtDNA has emphasized the relative isolation of the late Pleistocene colonizers, and the physically isolated Andaman Island populations of Island South-East Asia remain the source of claims supporting an early split between the populations that formed the patchy settlement pattern along the coast of the Indian Ocean. Using whole-genome sequencing, combined with multiplexed SNP typing, this study investigates the deep structure of mtDNA haplogroups M31 and M32 in India and the Andaman Islands. The identification of a so far unnoticed rare polymorphism shared between these two lineages suggests that they are actually sister groups within a single haplogroup, M31'32. The enhanced resolution of M31 allows for the inference of a more recent colonization of the Andaman Islands than previously suggested, but cannot reject the very early peopling scenario. We further demonstrate a widespread overlap of mtDNA and cultural markers between the two major language groups of the Andaman archipelago. Given the "completeness" of the genealogy based on whole genome sequences, and the multiple scenarios for the peopling of the Andaman Islands sustained by this inferred genealogy, our study hints that further mtDNA based phylogeographic studies are unlikely to unequivocally support any one of these possibilities.

Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations

Background

The Austro-Asiatic linguistic family, which is considered to be the oldest of all the families in India, has a substantial presence in Southeast Asia. However, the possibility of any genetic link among the linguistic sub-families of the Indian Austro-Asiatics on the one hand and between the Indian and the Southeast Asian Austro-Asiatics on the other has not been explored till now. Therefore, to trace the origin and historic expansion of Austro-Asiatic groups of India, we analysed Y-chromosome SNP and STR data of the 1222 individuals from 25 Indian populations, covering all the three branches of Austro-Asiatic tribes, viz. Mundari, Khasi-Khmuic and Mon-Khmer, along with the previously published data on 214 relevant populations from Asia and Oceania.

Results

Our results suggest a strong paternal genetic link, not only among the subgroups of Indian Austro-Asiatic populations but also with those of Southeast Asia. However, maternal link based on mtDNA is not evident. The results also indicate that the haplogroup O-M95 had originated in the Indian Austro-Asiatic populations ~65,000 yrs BP (95% C.I. 25,442 – 132,230) and their ancestors carried it further to Southeast Asia via the Northeast Indian corridor. Subsequently, in the process of expansion, the Mon-Khmer populations from Southeast Asia seem to have migrated and colonized Andaman and Nicobar Islands at a much later point of time.

Conclusion

Our findings are consistent with the linguistic evidence, which suggests that the linguistic ancestors of the Austro-Asiatic populations have originated in India and then migrated to Southeast Asia.

Peopling of South Asia: investigating the caste-tribe continuum in India

In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA

BACKGROUND

India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations.

RESULTS

No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes.

CONCLUSION

The present study suggests that the vast majority (> 98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.