July 05, 2009

Y chromosomes and mtDNA of Tharus from Nepal

From the paper:
J-M410, which was associated with the first farmer dispersal in Europe [13, 82, 83, 84], shows variance values of 0.346 in the Tharus and 0.339 in Indian groups [15]. These values are lower than those (0.467 and 0.479) observed in Anatolia [13, 82] and (0.410) in Southeast Europe [83, 84] and therefore are compatible with a dispersal of this lineage from somewhere in the Middle East/Asia Minor.
Y chromosome frequencies:

Estimates of Western Eurasian/East Asian/Indian area components is below. Note that some haplogroups such as R1a (considered here to be "Indian area") have contested origins, and were widely distributed in Western Eurasia even prehistorically. Thus, it is unclear what proportion of them represents a Western Eurasian vs. an Indian area origin.

The latest Y-STR diversity estimates (incl. this paper for Tharus from Eastern Terai and Indians) do suggest a substantially greater antiquity of R1a1 in the Indian subcontinent than in most of West Eurasia, but, as of yet, there is no sign that the R1a1 monolith will be broken by phylogeographically interesting downstream markers which would allow us to make a better sense of it.

UPDATE (July 6)

A reader points me to a fairly nuanced description of R1a1 in the paper.
Actually, the high frequency of the R1-M17 haplogroup found in the Central Eurasian territory, together with its gradient of diffusion that was associated with the Indo-European expansion [74, 75, 76], would leave some uncertainty about its geographic origin. However, the high microsatellite variation supports an ancient presence, dated in our samples over 14 ky [see Additional file 3] of the M17 marker in the Indian subcontinent, as suggested by Kivisild et al. [11], and sustained by Sengupta et al. [15] and Thanseem et al. [71], who consider the Indo-European M17 only a contribution to a local Early Holocene pre-existing Indian M17.
This is also what I consider the most likely scenario (although I disagree on the date of 14ky, which was calculated with the "evolutionary mutation rate"): that the exogenous Indo-Aryans included R-M17 Y-chromosomes, but the totality of South Asian R-M17 Y-chromosomes cannot be ascribed to them.

The Tharus themselves are actually speakers of an Indo-Aryan language, and the presence in them of the J-M172/R-M17 combination as the major West Eurasian element in their gene pool is noteworthy. In my opinion it is precisely this combination that dominated early Indo-Aryans, although it may have met in India earlier J/R variants.

(Paper by Thanseem et al. referenced in the above quote; interestingly, according to that paper, J2 and R-related lineages occur at twice the frequency in upper than in lower castes, which seems consistent with my hypothesis, and other evidence.)

BMC Evolutionary Biology doi:10.1186/1471-2148-9-154

Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation

Simona Fornarino et al.

Abstract (provisional)


Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.


High-resolution analyses of mitochondrial-DNA (including 34 complete sequences) and Y-chromosome (67 SNPs and 12 STRs) variations carried out in 173 Tharus (two groups from Central and one from Eastern Terai), and 104 Indians (Hindus from Terai and New Delhi and tribals from Andhra Pradesh) allowed the identification of three principal components: East Asian, West Eurasian and Indian, the last including both local and inter-regional sub-components, at least for the Y chromosome.


Although remarkable quantitative and qualitative differences appear among the various population groups and also between sexes within the same group, many mitochondrial-DNA and Y-chromosome lineages are shared or derived from ancient Indian haplogroups, thus revealing a deep shared ancestry between Tharus and Indians. Interestingly, the local Y-chromosome Indian component observed in the Andhra-Pradesh tribals is present in all Tharu groups, whereas the inter-regional component strongly prevails in the two Hindu samples and other Nepalese populations. The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population.



Gioiello said...

It has be noted that they use the mutation rate of 0,00069 you usually define "infamous" and re R1a1 they say that probably it is very ancient in India from Central Asia but probably an Indo-European R1a1 has entered India in the times and the modalities we know. And I think this very likely.

Dienekes said...

The mutation rate they use is not what's interesting, but the fact that the STR variance is greater here than in eastern Europe. It does not seem at present at all that South Asian R1a1 variation is a subset of eastern Europe.

eurologist said...

The latest Y-STR diversity estimates (incl. this paper for Tharus from Eastern Terai and Indians) do suggest a substantially greater antiquity of R1a1 in the Indian subcontinent than in most of West Eurasia...

Some of us have argued that and a generally very old dispersal of major Y-DNA groups from northern India/ Pakistan/ adjacent regions into Europe for a while. Which also means a very old age of these, of around or more than 40,000 years.

I believe mutation rates once I see a number of them derived from very clear, known migrations, timings, and fitted to reasonable population models. Australia comes to mind, as do the Americas. Until then, I trust archeology and the "simplest" migration models better than anything else.

Anatole Klyosov said...

>The mutation rate they use is not what's interesting, but the fact that the STR variance is greater here than in eastern Europe."

What do you call "fact" here? The authors cited that the "variation" of R1a1 among 114 individuals in India equals to 0.291, and among 8 Andra Pradesh individuals to 0.988. No comparison to Europe. A huge deviation of "37.7+/-21.5 KY in the last case. In India it is 14+/-3.1 KY, which after dividing by 3 (from the Zhivotovsky coefficient) gives its normal 4600+/-1000 ybp.In fact, using 25- and 37-marker haplotypes, it is 4300+/-560 ybp in India. No haplotypes are provided, hence, impossible to verify the data in the paper. Regarding 49a,f/TaqI Ht11 ONLY in India, with a refernce to a 2001 article which did not show it, it cannot be serious. How R1a1 got to Europe then, presumably from India?

Dienekes said...

No, variance in the Indians studied in this paper is 0.45, and in Tharus from Eastern Terai it is 0.5 (albeit a very small sample). These are similar to 0.505 for South India or 0.475 for Southern Pakistan and 0.426 for West India in the paper by Mirabal et al. I linked to. These are much higher than Poland, Ukraine or any Russian location.

Y-STR variance, for what it's worth, shows no support for an origin of all South Asian R1a1 Y-chromosomes from Eastern Europe.

Gioiello said...

Probably India has had the same destiny of Western Europe: an ancient presence of R1a1 in India and of R1b1b2 in Western Europe and a late migration from South Russia of Indo-European speaking peoples who have little influenced the Genetics. This is said in the paper and this I think is probably the truth.

Anatole Klyosov said...

Yes, indeed, var = 0.291 (N=114, years 14000+/-3100 bp) is from Sengupta (Indians pooled), cited by the authors. In the paper:

Tharus, N=14, var = 0.399, 16600+/-3900 bp, which is within margins of error with the Sengupta data (see above), which in turns gives 4600 ybp for the Indians (after conversion of the "Zhivotovsky coefficient".

The high variance is for two small groups,
A.Pradesh, N=8, var = 0.988, 37700+/-21500 ybp, and
Tharus E, N=5, var = 0.500, 20300+/-9100 ybp.

The small groups leave some doubts on the data obtained, paricularly when the margin of error brings them back to the Sengupta estimates and then again to 4,000+ ybp for R1a1 in India. By the way, Chenchu R1a1 gives 3000 and 325 ybp (the last is a series of practically indentical, hence, very "young" haplotypes, from the 17th century).

Nevertheless, I can accept that there are two sets of R1a1 haplotypes in India: one is of >7-10,000 ybp, another was brought by the Aryans, of about 4200+/-500 ybp. The Russian-Ukrainian (and Central Asian) R1a1 are of 4850+/-500 ybp (a common ancestor). This is a way to explain the apparent contradiction between the two sets. However, both sets were brought from outside from India. I have data supporting this concept (to be published).

pconroy said...


...from outside TO India?

Gioiello said...

Yes, Conroy. We aren't "British". Sometime we do some mistake.

Anatole Klyosov said...

Yes pconroy, they are FROM outside, far FROM India, brought TO India.

The thing is that the European (east and west) R1a1 haplotypes are very similar (practically indentical) with the "Indo-European" Indian R1a1, in all 12-, 25, 37- and 67-marker haplotypes. Indian R1a1 25-, 37- and 67-marker haplotypes taken from YSeach and from the "Indian project" present a quite uniform haplotype tree pointing at a common ancestor who lived a few centuries later than that of the Russian-Ukrainian-Polish-German-Scandinavian-"nameit"-Central Asian R1a1 common ancestor (though, technically speaking, within the margin of error). That ancestral haplotype was, undoubtedly, brought to India by the R1a1 tribe which was called (then or later) the Aryans, and which had closed the loop (made a bridge) between Europe and India (and Iran) with the Indo-European languages. In fact, the Aryan languages. The age of the common ancestor in Russia-Ukraine and in India I have listed above.

The ancient South-Indian R1a1 haplotypes are quite different from the Indo-European ones. Their (ancient) base (ancestral) haplotype has DYS19 = 17 (not 15-16), DYS391 = 9 (not 10-11), DYS389-1 = 14 (not 13), DYS389-2 = 18-19 (not 17, as typically in Europe and IE-Indian haplotypes). They are different, period. And they have nothing to do with the IE R1a1 haplotypes, except of belonging to the same haplogroup.

Therefore, all attemplt to reject the "IE pathway" using those ancient Indian haplotypes are fruitless. They are kind of apples and oranges.

Furthermore, those ancient Indian R1a1 haplotype do not have an Indian origin. Wait for the paper I had referred to.

pconroy said...


Thanks for the succinct reply!

This is very interesting. So where do you suppose the IE R1a1 homeland was, is it the Balkans or Central Asia??

AP said...

"These are similar to 0.505 for South India or 0.475 for Southern Pakistan and 0.426 for West India in the paper by Mirabal et al. I linked to."

Indicating an origin in the plateau rather than northern India.
This is consistent with the mtDna data (at least for U*).

"Regarding 49a,f/TaqI Ht11 ONLY in India, with a refernce to a 2001 article which did not show it, it cannot be serious."

Very true. It appears to be a misstatement since "high incidence of 49a,fHt11 seemed to be typical of the East European populations ... Actually, in East Europe, all the derivatives of the 49a,f Ht 11 were observed (9 vs 6 in the “Balkans,” 4 in the “Middle East,” 1 in India, and 2 in West Europe).

"How R1a1 got to Europe then, presumably from India?"

As we get more data, the locus seems to shift east & south, and my guess is that is where the population withdrew in the last ice age, ie, even northern India was relatively empty.

Sakyasingh said...

Being a Tharu from eastern Nepal and social anthropologist trying to understand my own selfless self. Thanks guys for explaining my genomic codes.