Reconstructing the demographic history of the Himalayan and adjoining populations

Ethno-geographic distribution and histopathological classification of nasopharyngeal carcinoma in a single center in Nepal

INTRODUCTION

Nasopharyngeal carcinoma (NPC) shows geographic and ethnic variation with specific etiopathogenesis. This study characterized the distribution of NPC patients stratified by ethnicity, geography, and histology in a tertiary-level cancer center in Nepal.

METHODS

A descriptive retrospective study was designed to analyze NPC cases from different regions among patients visiting the hospital from 2016 to 2021. Demographic and clinical information was obtained from medical records. Ethical approval was granted by the Nepal Health Research Council (NHRC). Data analyses and visualization were carried out with R software.

RESULTS

During the six-year period, a total of 65 individuals were diagnosed with NPC, comprising 42 males and 23 females. Patient median age was 43 years (range 11-85 years). A bimodal age distribution of cases was observed with peaks in patients aged 30-39 years and 50-59 years. Of the NPC patients studied, 29 were from Koshi Province, with 7 cases from Ilam district and 6 cases from Morang district. There were 18 patients in Bagmati Province, and Kathmandu district had the highest number of cases within this region, with 8 patients. The highest proportion of cases were observed among patients of Janajati ethnicity (60%), including Rai, Limbu, and Sherpa people. Histologically, undifferentiated non-keratinizing NPC was the most commonly observed subtype, accounting for 43.1% of cases, followed by 20% differentiated non-keratinizing NPC and 4.6% keratinizing NPC across the entire sample population. The majority of patients (75.3%) were diagnosed at an advanced stage (stage III or IV) with none diagnosed at stage I.

CONCLUSIONS

In our study, most cases of NPC occurred in patients from provinces in eastern Nepal (Koshi province), and of the Janajati ethnic community. The most common histological subtype was undifferentiated non-keratinizing carcinoma. Further epidemiological studies could address differences in prevalence and the challenge of late presentation of NPC patients in Nepal.

The maternal genetic origin and diversity of the extant populations of the Ladakh region in India

Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the "Land of high passes" one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.

The matrilineal ancestry of Nepali populations

The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.

Signatures of high altitude adaptation in Tibeto-Burman tribes of the Darjeeling Hill Region

OBJECTIVES

The long-term isolation, endogamy practices, and environmental adaptations have shaped the enormous human diversity in India. The genetic and morphological variations in mainland Indians are well studied. However, the data on the Indian Himalayan populations are scattered. Thus, the present study attempts to understand variations in the selected parameter among four Tibeto-Burman speaking ethnic tribal populations from the Darjeeling Hill Region (DHR) in the Eastern Himalaya Biodiversity Hotspot region of India.

METHODS

A total of 178 healthy male individuals (Lepcha 98, Sherpa 31, Bhutia 27, and Tibetans 22) living at an altitudinal range of 1467-2258 m above the sea level were studied for the 10 parameters namely, weight (kg), height (cm), body mass index (BMI) (kg/m² ) systolic and diastolic pressure (mm of Hg), pulse rate (per minute), saturation of peripheral oxygen (SPO₂ ) (%), hemoglobin (g/dl), hematocrit (HCT) (%), and blood glucose (mg/dl). The data was statistically analyzed using analysis of variance and multiple linear regression methods.

RESULTS

Our analysis revealed comparatively lower hemoglobin and HCT levels, and higher systolic and diastolic blood pressure in the Sherpas followed by the Tibetans. This may be reflecting the persistence of high-altitude adaptation signatures even in lowlands. Interestingly, the Tibetans differed significantly from other populations in terms of their higher body weight, height, and BMI.

CONCLUSION

Thus, our study showed the persistence of high altitude signatures in Tibetans and Sherpa inhabited the DHR. Additionally, we also observed significant differences in the anthropometric and physiological parameters among the Tibeto-Burman populations of the DHR.

An initial investigation of dental morphology variation among three southern Naga ethnic groups of Northeast India

OBJECTIVES

This study examines dental morphology trait prevalence among three southern Naga groups and compares them to 10 ethnic groups from other regions of South Asia to accomplish two objectives: assess the biological relationship of these Tibeto-Burman-speakers to speakers of non-Tibeto-Burman languages in other South Asian regions, and determine which traits distinguish northeast Indians from other South Asians.

METHODS

Dental morphology traits were scored with the Arizona State University Dental Anthropology System. Tooth-trait combinations were evaluated for significant inter-trait correlation and intra-trait correspondence within dental fields. Comparisons were based on simple trait prevalence and with Smith's MMD. Affinities based on the former were accomplished with correspondence analysis and principal components analysis. Affinities based on the latter were undertaken with neighbor-joining cluster analysis and multidimensional scaling.

RESULTS

After elimination due to inter-trait correlations and uniform prevalence, biodistances based on the remaining 17 tooth-trait combinations identify significant differences between northeast Indians and other South Asian ethnic groups due to high frequencies of shoveling on the maxillary incisors and Cusp 6 on the mandibular molars coupled with low frequencies of Carabelli's trait and Cusp 5 on UM1 and UM2, respectively.

CONCLUSIONS

Patterns of biodistances obtained from dental morphology are consilient with those obtained from DNA indicating statistically significant differences between northeast Indians from members of ethnic groups of other regions of South Asia. Researchers should explore the sex-specific patterns. Biodistances should not be limited to "key" teeth within dental fields, for in almost every case traits present on mesial and distal teeth yield non-redundant information.

Pinpointing the Geographic Origin of 165-Year-Old Human Skeletal Remains Found in Punjab, India: Evidence From Mitochondrial DNA and Stable Isotope Analysis

In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ¹⁸O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ¹⁸O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers.

COVID-19: Impact on linguistic and genetic isolates of India

The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.

The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations

With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.

Heterogeneity in Hematological Parameters of High and Low Altitude Tibetan Populations

Introduction

High altitude hypoxia is believed to be experienced at elevations of more than 2500 meters above sea level. Several studies have shed light on the biochemical aspects of high altitude acclimatization, where participants were sojourners to the high altitude from low altitude areas. However, information regarding the difference between the high altitude adapted Tibetans living at high altitude and their counterparts who reside at low altitude are lacking. To understand this, we have measured various hematological parameters in the Tibetan populations, who are residing in both high and low altitudes in India.

Methods

A total of 168 individuals (79 from high altitude (≥4500 meters) and 89 from low altitude (~850 meters) were recruited for this study. Hematological parameters such as red blood cells (RBC) count, hematocrit (HCT), hemoglobin concentration (Hb), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration (MCHC) were measured from the individuals from high and low altitudes. Serum erythropoietin (EPO) was measured by ELISA. Statistical analyses were performed to compare data from both of the altitudes. Gender-wise comparison of data was reported. Correlation analysis was performed within relevant parameters.

Results

Highly significant differences (p <0.0001) between high and low altitude Tibetans were detected in RBC count, HCT, Hb, MCHC in both males and females and in MCV in females. In the case of MCHC, however, age and BMI were potential confounders. Nominally significant differences (p <0.05) were detected in MCV and MCH within males. No significant difference in serum EPO level was found between altitude groups, in any gender. No significant correlation was found between serum EPO with Hb as well as serum EPO with HCT.

Discussion

Our study explores significantly lower RBC count, HCT, Hb, MCH, MCHC and higher MCV in long-term Tibetan residents living at low altitude compared to their high altitude counterparts, which is likely due to the outcome of hematological adaptation to a relatively hyperoxic environment in low altitude areas.

Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

As a result of the expansion of old Tibet on the Qinghai-Tibet Plateau, Tibetans diverged into three main branches, Ü-Tsang, Amdo, and Kham Tibetan. Ü-Tsang Tibetans are geographically distributed across the wide central and western portions of the Qinghai-Tibet Plateau while Lhasa is the central gathering place for Tibetan culture. The AGCU Y30, a 6-dye fluorescence kit including 30 slowly and moderately mutated Y-STR loci, has been validated for its stability and sensitivity in different biomaterials and diverse Chinese populations (Han and other minorities), and widely used in the practical work of forensic science. However, the 30 Y-STR profiling of Tibetan, especially for Ü-Tsang Tibetan, were insufficient. We utilized the AGCU Y30 to genotype 577 Ü-Tsang Tibetan unrelated males from Lhasa in the Tibet Autonomous Region of China to fill up the full and accurate Y-STR profiles. A total of 552 haplotypes were observed, 536 (97.10%) of which were unique. One hundred and ninety-four alleles were observed at 26 single copy loci and the allelic frequencies ranged from 0.0017 to 0.8180. For the two multi-copy loci DYS385a/b and DYS527a/b, 64 and 36 allelic combinations were observed, respectively. The gene diversity (GD) values ranged from 0.3079 at DYS391 to 0.9142 at DYS385a/b and the overall haplotype diversity (HD) was 0.9998, and its discrimination capacity (DC) was 0.9567. The population genetic analyses demonstrated that Lhasa Ü-Tsang Tibetan had close relationships with other Tibetan populations from Tibet and Qinghai, especially with Ü-Tsang Tibetan. From the perspective of Y haplogroups, the admixture of the southward Qiang people with dominant haplogroup O-M122 and the northward migrations of the initial settlers of East Asia with haplogroup D-M175 hinted the Sino-Tibetan homologous, thus, we could not ignore the gene flows with other Sino-Tibetan populations, especially for Han Chinese, to characterize the forensic genetic landscape of Tibetan.

Genetic and linguistic non-correspondence suggests evidence for collective social climbing in the Kol tribe of South Asia

Both classical and recent genetic studies have unanimously concluded that the genetic landscape of South Asia is unique. At long distances the ‘isolation-by-distance’ model appears to correspond well with the genetic data, whereas at short distances several other factors, including the caste, have been shown to be strong determinant factors. In addition with these, tribal populations speaking various languages add yet another layer of genetic complexity. The Kol are the third most populous tribal population in India, comprising communities speaking Austroasiatic languages of the Northern Munda branch. Yet, the Kol have not hitherto undergone in-depth genetic analysis. In the present study, we have analysed two Kol groups of central and western India for hundreds thousands of autosomal and several mitochondrial DNA makers to infer their fine genetic structure and affinities to other Eurasian populations. In contrast, with their known linguistic affinity, the Kol share their more recent common ancestry with the Indo-European and Dravidian speaking populations. The geographic-genetic neighbour tests at both the temporal and spatial levels have suggested some degree of excess allele sharing of Kol1 with Kol2, thereby indicating their common stock. Our extensive analysis on the Kol ethnic group shows South Asia to be a living genetics lab, where real-time tests can be performed on existing hypotheses.

The peopling of Lakshadweep Archipelago

The archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia.

The genetic makings of South Asia

South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.