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Saturday, 31 March 2018

Harvard's ''Genomic Formation of South and Central Asia ''

So here we have an aDNA paper from Narasimhan et al , published at bioRxiv today. It is a big paper, containing more than 350 ancient samples, from important ancient sites of Central Asia ,Iran and also S Asia. The apparent impression from the first read is that, they have found ''evidence'' of migration from Steppe to S Asia. They don't have Mature Harappan samples, which is a shame.The S Asian samples are from Swat/Pakistan dating from only around 1200 bce to historical period. In those samples they have found no R1a except a singleton R1a from Saidu_Sharif_IA I6891 (500-300 BCE) .The archaeological  studies from the past have shown that Swat culture had largely female centered characteristics rather than the expected opposite , see here for example.The importance of feminine  is also reflected in modern culture of Kalash also, like freedom of women, and goddess cult, see here.
Interestingly, they have ruled out BMAC as potential source population of S Asians, this goes against the traditional AIT model . I am suspecting for example, the West Siberian HG ancestry they have discovered is actually Central Asian HG component ,which included N India.In the BMAC main cluster they measure this ancestry at 13%, but in Sarazm EN , it had around 25% presence(just as in the samples from Pakistan!, suggesting dilution by West Asian migration rather than what they imply.) , in their qpAdm based analysis(p.22 main paper) we only see the green Siberian HG ancestry appearing in ancient S Asians, while EHG related one is absent. From main paper p.9:
Third, between 3100-2200 BCE we observe an outlier at the BMAC site of Gonur, as well as two outliers from the eastern Iranian site of Shahr-i-Sokhta, all with an ancestry profile similar to 41 ancient individuals from northern Pakistan who lived approximately a millennium later in the isolated Swat region of the northern Indus Valley (1200-800 BCE). These individuals had between 14-42% of their ancestry related to the AASI and the rest related to early Iranian agriculturalists and West_Siberian_HG.
There cannot be any doubt that this West_Siberian_HG-related ancestry was in  N India since at least 3000 BCE, but probably much earlier. Also finding ancestry related to ''S Asian HG''s may imply, that it was  also well present in N India prior to 2000 bce , but was it uniformly present? only aDNA from India will clarify.Their argument is mainly based on the samples like  Gonur2_BA migrant being representative of the whole SSVC population!. But in near future, if we get samples from SSVC proper and they show  strong relation to the SPGT samples, the whole argument falls.They also didn't find the S Asia specific R1a-L657, in any of their ancient samples ...

The Genomic Formation of South and Central Asia
            Vagheesh  M Narasimhan et al.
doi: https://doi.org/10.1101/292581
Abstract
The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

Yog

29 comments:

tim drake said...

Haplogroups A,BT and CT in turkmenistan ! Lots of R2a in Iran !! Quite interesting ,mal'ta is assigned the wrong haplogroup

Nirjhar007 said...

R1a from Saidu_Sharif_IA I6891 (500-300 BCE) is R1a-Z645 , that is ancestral to R1a-Z93 and R1a-283 Which is European.

tim drake said...
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Nirjhar007 said...

You have to take into account the dates of those three ''Indus_Periphery'' samples, which are from ~2700-2000 BC :).

Shiva Krishna said...
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Nirjhar007 said...

https://public.tableau.com/profile/vagheesh#!/vizhome/TheGenomicFormationofSouthandCentralAsia/Fig_1

tim drake said...

Why do I see AASI (assuming it's the yellow one) in west Siberian sample ?

Nirjhar007 said...

That admixture graph is hard to interpret , they will apparently publish updated version of the pre-print , I hope that will make things clear on that too.

tim drake said...

In figure 2 there are 7 ancestry components while admixture seems to have been run on K=6. I hope they run it for larger Ks.

Sanuj said...

Hi Nirjhar, there hv been claims made by someone identifying himself as Nick Patterson(don't know if it's an imposter) on eurogenes, that they couldn't retrieve aDNA from IVC samples despite efforts? Do we still expect a separate Rakhigarhi paper now? Is there you can check this with the Indian scientists involved?

tim drake said...
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tim drake said...

The paper lists bhumihars as custodians of Vedic texts , weren't they simply landlords ? The word "bhumi" itself means land lol

Nirjhar007 said...

qpAdm didn't pick any EHG as you notice in fig. 2C in those ancient S Asians . I am certain that even if it exists it will be around ~10% at best and most likely around ~5% , the local''WSHG ancestry'' is creating an elevated ''pseudo-steppe'' like effect combined with Iran neo in moderns . They are releasing genotype data today or tomorrow , so we will see soon how things are exactly standing.

The case of Bhumihars is not clear, some say they were elevated to Brahman status very recently.

But even in Suppl.info p.189 we find this (bold mine):



"On the Indian Cline, 5 of the 11 groups with Z>2.5 are of traditionally priestly status, even though only 17 of the 140 groups are of priestly status overall (Data S4).

(Groups of traditionally priestly status in the south show no enrichment of Steppe-related ancestry beyond the expectation from our model according to our analyses.)

The pattern suggests shows that priestly status in the traditional caste system, at least in northern India has a connection to Steppe ancestry. These results are intriguing in light of the fact that Sanskrit—the language of the ancient Vedic texts—is Indo-European. Priestly groups in India are traditionally custodians of texts written in Sanskrit, so these results point to a new line of evidence—beyond the evidence for a correlation of Indo-European languages to Steppe_EMBA admixture both in Europe and in South Asia (11)—for an origin of at least some aspects of Indo-European culture in South Asia in the Steppe."


.........................................................................................

Not too compromising, they try to be cautious, but still forcing the data to defend the steppe theory.

If we see the figure S4.3, the southern situation is actually the opposite, with most priestly groups on the negative side (and only two on the positive side, but <2). The northernmost group (Kashmiri pandits) is actually below zero(-0.5 in xls)!. It is true that Brahmin Tiwaris have the highest Z-score (4.3), but Chamars who have 4 are outcaste!,and Adiyans who have 3.5 are Dravidians of Kerala!... So, their model actually does not work with IEs and castes.So, the connection of Brahmans with presumed steppe people is not clear at all, and maybe it is due more to recent history and geographical position than to their origins.
We will need the aDNA from Haryana etc.
See also:https://en.wikipedia.org/wiki/Sakaldwipiya

tim drake said...

"maybe it is due more to recent history and geographical position than to their origins. " - Remember the how i talked about the Sakas :/ . The Z >=4 are found in UP/Bihar/Nepal region (the ganga-yamuna plains) - wasn't that the traditional stronghold of the Sakas (i might be completely wrong here) ? Aren't the kanya kubjas saka descendants ?
I am pretty sure they dropped the bengali priestly class because of tibeto-burman/east asian admixture :) . Regarding South, there is a legend how Parshurama came to the south along with the priests after drying up of river saraswati.

tim drake said...

shakdwipi = dwip means island/land right ? so,from the land of shaka :) ?

Nirjhar007 said...

shakdwipi = dwip means island/land right ? so,from the land of shaka :) ?

Possible :).

Samurai Jack said...

When can we expect the Rakhigarhi papers? What should we make out from the Dainik Jagaran Article regarding the same (apparently an interview with Dr. Rai)?

Nirjhar007 said...

Will definitely update after confirmation :).

Jagran article is genuine .

tim drake said...

THe yellow color in the admixture graph in the pre-print and in the tableau dashboard you linked seems to have two components - one V1(associated with West Siberian HG which caused me some confusion) and other V6(associated with South Asia),is there any way to request the authors to provide a separate color for the V6 component for the admixture graph in the tableau? I hope they run it for K=7 also, it would be much better

tim drake said...

"Will definitely update after confirmation :)" -- Any updates?

M Z said...

Can you explain where the authors of the paper see the increase in steppe ancestry in Late Iron Age Swat? It looks like almost complete continuity in the ADMIXTURE run and the PCA:

blob:https://imgur.com/cfeecec3-5d6b-49c9-901e-8ddd8668882b

I don't have an opinion on the prehistory of India, but unfortunately it looks like the authors forced their preferred model without exploring alternatives in this case.

M Z said...

Some of the stuff in their analyses just seem outright wrong. Tribals from Kerala have almost as much steppe ancestry as Brahmins from UP? What's going on there.

Nirjhar007 said...

For the Swat situation, refer to this nice comment by commentator Alberto :
https://eurogenes.blogspot.in/2018/04/bronze-age-central-asia-terra-incognita.html?showComment=1523628896344#c3814921351072060258

tim drake said...

"Some of the stuff in their analyses just seem outright wrong. Tribals from Kerala have almost as much steppe ancestry as Brahmins from UP? What's going on there" -- Hey MZ, in the supplementary xls sheet provided with the preprint, i see high Z scores (more steppe ancestry than expected) but don't see high Steppe ancestry (MAP estimates) in the kerala tribals.

Atri├░r said...

Hi Nirjhar,

As per your comment on eg, here I am. Do you see my email? I can submit in the 'follow by email' section.

Nirjhar007 said...

No I can't see ...just post your mail , I will not publish....

tim drake said...

Nirjhar, what are your thoughts on the milk thing :) ? If lactose tolerance only arrived with after 1700 BC wouldn't that mean the domestication of Bos taurus indicus (zebu) happened after that event ?

Nirjhar007 said...

Zebu domestication in S Asia must be older :).

tim drake said...

nirjhar, in the admixture plot listed at page 166 of the supplementary file , the ONGE have quite a decent % (~25% to my naked eye) of Iranian agriculturalist like component (represented by teal color). How is this even possible for a sea-locked,isolated,insular population like Andamanese Onge ? If what Dr gyaneshwar said in that video is true (i.e "dravidian" expansion towards north-west india) then that teal color representing the Iranian agriculturalists should be present without any yellow introgression in pre-Neolithic/Neolithic samples in the Punjab region. Thoughts ?