July 22, 2013

Y chromosomes in Lingayat and Vokkaliga Dravidians from SW India

From the paper:
The virtual absence of Z283 subclades, namely Z280 and M458, and the total representation of R1a1a-derived samples by the Z93 marker in our dataset support an earlier observation that the M198 chromosome likely differentiated in the region between Eastern Europe and South Asia (Pamjav et al., 2012), and subsequently expanded in opposite directions. However, it will require additional R1a1a* samples from different populations across Eurasia to comprehensively evaluate the geographic origins, distribution and ethno-linguistic associations of the individual M198-derived lineages (Pamjav et al., 2012).
This study extends the results of Pamjav et al. 2012 which found only Z93 within R1a1 in mainland Indian populations. The authors estimate 12.8ky as the age of R-Z93 in the Lingayat, but since this uses the evolutionary mutation rate it should actually be divided by a factor of 3.6 which translates into ~1,500BC. So, it seems quite likely that R-Z93 moved from Central->South Asia during the Bronze Age, both on account of its age and the fact that it is a subset of Central Asian diversity. Haplogroup R2 with a nominal age of ~22ky in the Lingayat seems more like a Neolithic lineage.

Also of interest:
Another haplogroup that is associated with the spread of agriculture from the Fertile Crescent and Anatolia regions is J2-M172 (Cinnioğlu et al., 2004 and Semino et al., 2004). According to Sahoo et al. (2006), only J2 lineages, originating from West Asia rather than Central Asia, represent an external contribution to the Indian paternal gene pool. In particular, subclade J2a-M410 is believed to have entered through the northwestern corridor and subsequently diffused to the south and east (Sahoo et al., 2006 and Thangaraj et al., 2010). This haplogroup is present exclusively in the Lingayat (6.93%), except for one individual from Vokkaliga, suggesting gene flow from West Asia (Sahoo et al., 2006 and Thangaraj et al., 2010). Interestingly, four J2b2-M241 Lingayat males displayed a null allele at DYS458 and failed to produce the AMGY PCR amplicon while their X homolog (AMGX) amplified successfully. Comparison of Y-STR haplotypes of the affected males from the present study with those from the literature (Cadenas et al., 2006), demonstrated a high level of allele sharing, implying shared paternal lineages or a recent common ancestry for these groups of individuals.
According to the paper the Lingayat are a community that originally attracted members from across the caste system, while the Vokkaliga are involved in farming. An uneven distribution of haplogroup J2a has been previously observed, so I guess this paper adds to this evidence.

Gene Available online 7 May 2013

Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India

Shilpa Chennakrishnaiah et al.

Previous studies have shown that India's vast coastal rim played an important role in the dispersal of modern humans out of Africa but the Karnataka state, which is located on the southwest coast of India, remains poorly characterized genetically. In the present study, two Dravidian populations, namely Lingayat (N = 101) and Vokkaliga (N = 102), who represent the two major communities of the Karnataka state, were examined using high-resolution analyses of Y-chromosome single nucleotide polymorphisms (Y-SNPs) and seventeen short tandem repeat (Y-STR) loci. Our results revealed that the majority of the Lingayat and Vokkaliga paternal gene pools are composed of four Y-chromosomal haplogroups (H, L, F* and R2) that are frequent in the Indian subcontinent. The high level of L1-M76 chromosomes in the Vokkaligas suggests an agricultural expansion in the region, while the predominance of R1a1a1b2-Z93 and J2a-M410 lineages in the Lingayat indicates gene flow from neighboring south Indian populations and West Asia, respectively. Lingayat (0.9981) also exhibits a relatively high haplotype diversity compared to Vokkaliga (0.9901), supporting the historical record that the Lingayat originated from multiple source populations. In addition, we detected ancient lineages such as F*-M213, H*-M69 and C*-M216 that may be indicative of genetic signatures of the earliest settlers who reached India after their migration out of Africa.

Link

15 comments:

Dr Rob said...

Dienekes: "It seems quite likely that R-Z93 moved from Central->South Asia "

Of course, this is a logical deduction, but I see no explicit data, *at present*, that has shown this empirically, apart from Pamjav's earlier study which noted the presence of M458 & Z 280 in Mongolians and Uzbeks. However, tiny sample (5 & 9, resp, with 3 and 1 non-Z93 samples) and cannot rule it this was caused by *later gene flow* ie colonizing modern Russians.

have I missed something ?

mm said...

12,8 kY definitely looks more right then 1500 BC if Indoeuropean R1a1a1..spread out from Kurdistan from around 10500-9500 BC.

My Y haplogroup also starts with R1a1a1b2a1 If I remember correctly.

Why they would change this number by applying some coefficient?

Can one say that in general R group appeared from Kurdistan or is it not true and it existed in indigenous populations before that?



mm said...

I was wrong in previous comment - my haplogroup is R1a1a1b1a2b from Genographic 2.0. kit.

I run analysis with all DIY program calculators and they looked OK but what to do next?

This is outside topic, but is Genographic 2.0. code considered containing not all SNPs? Or less then other tests?

Nirjhar007 said...

These are indirect results, we need aDNA which will be provided by Farmana(2500b.c.) Skeletons.
Good day.

Davidski said...

They should have included the new 1000 Genomes samples in this study. These samples provide a very useful overview of the character of R1a-Z93 in India, and how its SNP diversity decreases from near the Khyber Pass in Pakistan to Sri Lanka in the south.

See here...

http://eurogenes.blogspot.com.au/2013/05/south-asian-r1a-in-1000-genomes-project_15.html

terryt said...

"Can one say that in general R group appeared from Kurdistan or is it not true and it existed in indigenous populations before that?"

R itself probably first formed from P in India even though R's relation' Q looks to have first formed somewhere northwest of India/Pakistan. R2 is found in INdia although it could be an immigrant from the north. However P is part of MNOPS which also includes K1, K2 and K3. That places the origin of the whole of that haplogroup branch somewhere close to SE Asia.

Nirjhar007 said...

@Davidski
Mate, just wait for the aDNA its gonna rock your world!! same for Dienekes as well.
Good day.
p.s. Davidski, why do you think Australia is so poor in cricket now?
N.

Dr Rob said...

@Nirhajir ". Davidski, why do you think Australia is so poor in cricket now?"

Its surely because R1a originated in India ??

mm said...

@terryt

"R itself probably first formed from P in India even though R's relation' Q looks to have first formed somewhere northwest of India/Pakistan. R2 is found in INdia although it could be an immigrant from the north. However P is part of MNOPS which also includes K1, K2 and K3. That places the origin of the whole of that haplogroup branch somewhere close to SE Asia."

Thank you very much. So it is the origins of P which might be interesting as Q arises in the same NW direction from India as is Kurdistan. I suspect they are pretty close to Kurdistan, to the south in general. Have to look up MNOPS and K's.

Dr Rob said...

TerryT

"R itself probably first formed from P in India even though R's relation' Q looks to have first formed somewhere northwest of India/Pakistan. R2 is found in INdia although it could be an immigrant from the north. However P is part of MNOPS which also includes K1, K2 and K3. That places the origin of the whole of that haplogroup branch somewhere close to SE Asia."

As always, you make logical comments, though I'm not sure why the 'supergroup' must necessarily be placed more close to SE Asia than at the central - south Asian corridor. Remember that population fluctuations in the prehistory of northern India might have obliterated vestiges of the groups found in SE Asia and not more western areas.

Davidski said...

Gee, I don't know, maybe Z93 is a favorable mutation for fast spin bowling?

terryt said...

"As always, you make logical comments, though I'm not sure why the 'supergroup' must necessarily be placed more close to SE Asia than at the central - south Asian corridor. Remember that population fluctuations in the prehistory of northern India might have obliterated vestiges of the groups found in SE Asia and not more western areas".

Thank you. It is possible that population fluctuations have obliterated some haplogroups in South Asia but I suspect that is unlikely. A reasonable vatiety survive there. Obliteration is more likely in Central Eurasia during ice ages. The reason I plump for SE Asia is that the vast majority of MNOPS* haplogroups are found there. M and S in New Guinea/Melanesia, K1-P60 in Australia/New Guinea, K2-P79 in Melanesia, K3-P261 in Bali, and K* in the Timor/Flores region. O is not too far away, probably having diverged from N in Northern China. That leaves just P as the great migrator.

"Davidski, why do you think Australia is so poor in cricket now?'

Just good luck for everybody else, I guess. However they can still beat New Zealand. But that doesn't really count.

Nathan Paul said...

Surprising Aryan Invasion Theorists did not jump on this. May be the data is disappointing.

The genetic ratio is along similar lines across Indian Sub continent including may be Afghanistan.
( Again I am not sure Afghanistan is still being classified as part of Indian Sub continent. At least it used to be)


Eastern India will have less L and more K* and R2

North West ( Pak+Afghans) will have less H as Roma sent packing to Europe.

North will have higher R1a ratio and South will have bulk of R2.

Cricket:
People like Border and Wagh should motivate youngsters(with a fist) instead of being on the sidelines.

Nirjhar007 said...

@Dr Rob
''@Nirhajir. Davidski, why do you think Australia is so poor in cricket now?"

Its surely because R1a originated in India ??''
No! and of course are you blind? can't you read a name correctly?.
@Davidski
''Gee, I don't know, maybe Z93 is a favorable mutation for fast spin bowling?''
No that is absurd! it is the money which is spinning in their heads now and making them play like school boys, though it is expectable from them.
good day.

Nirjhar007 said...

@Nathan Paul
''Surprising Aryan Invasion Theorists did not jump on this. May be the data is disappointing.''
All the data i have researched in favor of ''Aryan Invasion'' from every article to research paper is disappointing;-).

''The genetic ratio is along similar lines across Indian Sub continent including may be Afghanistan.
( Again I am not sure Afghanistan is still being classified as part of Indian Sub continent. At least it used to be)''
Yes Afghanistan can be considered as a part of South Asia-
http://en.wikipedia.org/wiki/South_Asia#Geography
''Cricket:
People like Border and Wagh should motivate youngsters(with a fist) instead of being on the sidelines.''
Its hard but i don't see much Australian cricketers these days whom really feel proud of wearing the Baggy Green as they did 6-7 years back.
Good day.