Genetic Ancestry of Nepalis

Genetic Ancestry of Nepalis

One evening, few years back, my grandpa passed down a legacy to me and my cousins – the story of our ancestors. I belong to a Newar community which is one among the indigenous people of Kathmandu Valley. Newars have been living in Kathmandu valley from the prehistoric times. As per my grandpa, our ancestors were Tibetan merchants mostly dealing with the Royals in and around Kathmandu valley. After the unification of Nepal by the Great King Prithvi Narayan Shah, our major family link with Tibet was broken and those who survived fled within Kathmandu Valley. Introducing another twist to the story, I’m officially a Buddhist but culturally we are a hybrid of Buddhist and Hindu. This allowed me to ponder a bit – were we initially Buddhist (Tibetan) and adopted Hinduism more recently or is the other way around? Evidence also comes from our language – Nepal Bhasa and associated Ranjana script which has combination of both Tibetan as well as Sanskrit (Indian) flavors and still used in many parts of Tibet, Nepal and India. Being a student of genetics, this triggered a curiosity within me for years, where did the early ancestors in Nepal came from?

Nepal, geographically, is between Tibet (China) and India. These neighbors represent two distinct ethnicity – the Mongols from Tibet and the Aryans from India. It is natural to think and of course an intelligent guess would be that Nepalese are mostly the hybrids of Mongols and Aryans. Earlier works by Gayden et al. found that parental group of Newar people consists mainly of Central Asia and India.  Also Y chromosome haplotypes of R, O and H among others is present among Newars (Gayden et al., 2007). But still the question remains, who came to Nepal first – the Mongols or the Aryans?

At present, scientific community has widely accepted the recent African origin of modern humans 200,000 years ago better known as “Out of Africa” theory. However, controversies still exist whether the early human originated in Africa (single-origin hypothesis) or were originated at several locations including Africa (multiple-origin hypothesis) (Harpending and Eswaran, 2005; Lui et al., 2006). It is believed that the modern human left Africa 125,000 years ago and reached the present day Middle-East Asia from where they dispersed into three different directions (at different time-scales) – one lineage to the Europe, second lineage towards China and the third lineage into South Asia (India).


A map of early human migrations


The northeast Indian passageway connecting the Indian subcontinent to East/Southeast Asia is thought to have been a major corridor for human migrations. Indeed, abundant East Eurasian mitochondrial DNA (mtDNA) lineages have already been detected in the northeast Indian populations raising the possibility that the East Eurasian influence could trace its origin back to the dispersal of Tibeto-Burman people who arrived at Nepal via northeast India (Cordaux et al., 2004; Reddy et al., 2007). Recently, by comparing the Y-chromosome lineages between the Nepalese and the Tibetan populations, Gayden et al. have proposed that the East Eurasian genetic components had been introduced into Nepal from Tibet directly (Gayden et al., 2007; Gayden et al., 2009). But still this raised a major question – did Tibetan cross the great Himalayas to enter Nepal?

A recent study by Wang et al. entitled “Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes”, published in March 2012, finally came up with an answer.  For this, mtDNA was collected from 246 unrelated individuals from Kathmandu and Eastern Terai. Other data from both mtDNA as well as Y-chromosome was obtained from various published studies as detailed in Table-1 in the paper.

Sampling locations of the populations analyzed in this study. The Nepalese populations collected in this study are highlighted with solid pentacles, and the black dots represent the populations retrieved from the literature.

Different loci of mtDNA and Y-chromosome are used as genetic markers to trace the great human migration and ancestry. The mtDNA traces the maternal lineage (as mitochondria of a zygote is always contributed by the mother) and Y-chromosome of course traces the paternal lineage (as only the father contributes Y-chromosome to a zygote destined to become a male). Often Mitochondrial Eve and Y-chromosomal Adam are referred to as the ancestors of every human being living on earth today. They are certainly not the first female and male on the earth as the Bible interprets, there were many humans in addition to Mitochondrial Eve and Y-chromosomal Adam, but they are the only surviving genetic markers/lineage till date that has been passed on to the existing human population. (For more information on the topic)

The study revealed that genetic components of East Eurasian (36.59%) and South Asian (51.63%) ancestry have comprised the vast majority of the Nepalese gene pool. Majority of the samples belonged to the already defined haplogroups, such as, M3, M5, M18, M30, M35, M43, D4, R8 and M60. (Haplogroup represents the group of individuals having similar alleles or SNP profile). Furthermore the study revealed a novel haplogroup characterized by variations 9266 and 11827, which was named as M81.

The Principal Component Analysis (PCA) of 43 populations under study revealed 3 among 5 of the Nepalese population clustered with Tibetan population. This means that 3 of the Nepalese population are very similar to the clustered Tibetan population.

[PCA is a very popular statistical technique to analyze High-Dimensional Dataset. Simply putting it, whenever there are multiple variables/factors describing a population then the dimension of data (or degree of freedom) is proportional to the number of variables which makes it very difficult to analyze as well as visualize the data. PCA reduces all these n-variables to 2 Components (or sometimes 3 if needed) so that it will make us easy to find correlation among the different variables. (For more information on the topic)]

Principle component analysis (PCA) of the populations under study.

The pairwise-distance data reveals that the Nepalese population is closely related to the Tibetan population. Following is a UPGMA tree constructed from the distance data in Table-2.

UPGMA tree constructed from the distance data in Table-2

The results of the admixture estimation analysis revealed that the Tibetans made major contribution to virtually all Nepalese populations (except for the eastern Tharu population)

Admixture analysis of the Nepalese by comparing with its potential parental populations (Tharu_E : Eastern Tharu) (Note: the error bars have not been plotted for the sake of simplicity)

On the basis of the constructed median networks, several features could be observed:

  1. the Nepalese share some basal or internal haplotypes with the Tibetans;
  2. the Nepalese harbor a number of unique haplotypes at the terminal level, most of which branched off directly from the nodes occupied almost exclusively by the Tibetan lineages and
  3. only a few haplotypes are shared sporadically between the Nepalese and the northern Indians.

Taken together, the Nepalese lineages of East Eurasian ancestry generally show much closer affinity with the ones from Tibet, albeit a few mtDNA haplotypes, likely resulted from recent gene flow, were shared between the Nepalese and northern (including northeast) Indians.

[Note: Median Network is more or less similar to a phylogenetic tree but based on graph theory. These median networks are more informative than regular phylogenetic tree as the former considers the different evolutionary rate prevalent at different nodes of the network. Computationally it is termed as “Speedy Construction and Greedy Reduction” !!]

Time estimation results revealed that haplogroups G2a2 and M9a1a2a have very similar ages ~6 kya (6,000 years ago). The previous work has suggested that the maternal genetic components from the northern East Eurasian was introduced into Tibet around 8.2 kya (Zhao et al., 2009) and time estimation resulted from this study fit the dating frame very well. Now it is convincing that the East Eurasian had entered Nepal across the Himalayas around 6 kya, a scenario in good agreement with the previous findings from linguistics and archeology. Yes, the Tibetans (Mongols) did cross the great Himalayas to enter Nepal even before the Aryans arrived.


Wang HW, Li YC, Sun F, Zhao M, Mitra B, Chaudhuri TK, Regmi P, Wu SF, Kong QP, Zhang YP. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes. J Hum Genet. 2012 Apr;57(4):228-34 (Download Full Text Article)

Related Papers:

  1. Gayden et al. The Himalayas as a directional barrier to gene flow. Am. J. Hum. Genet. 80, 884–894 (2007).
  2. Fornarino et al. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol. Biol. 9, 154 (2009).
  3. Su et al. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107, 582–590 (2000).
  4. Cordaux et al. The Northeast Indian passageway: a barrier or corridor for human migrations? Mol. Biol. Evol. 21, 1525–1533 (2004).

About the Contributor: Raunak Shrestha

Raunak completed his B. Tech. in Biotechnology from Kathmandu University in 2009. Currently he is a Bioinformatics PhD student under CIHR/MSFHR Bioinformatics Training Program at University of British Columbia, Vancouver, Canada. He has been working in Laboratory for Advanced Genome Analysis (LAGA) at Vancouver Prostate Center (VPC) and his research works revolves around Prostate Cancer Genomics & Bioinformatics.

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  1. suvash awal05-15-12

    Great to know about the ancestral trail of our origin.