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Sunday, March 20, 2016

Rakhigarhi ancient DNA paper probably a while away


Back in December The Guardian published an article saying that ancient DNA results from the Harappan site of Rakhigarhi, northern India, "may come within weeks" (see here).

I'm guessing now that it was just a slow news day feature, because we've seen nothing since, and the Korean team entrusted with doing the paleogenomics work has just come back from another dig at Rakhigarhi (see here). Best case scenario, it'll take them months to process the remains, analyze the DNA, and get something published.

On a more positive note, National Geographic is now backing the effort, I'm guessing with funds and/or equipment, which might mean more sophisticated outcomes, like hopefully a few full genomes.

My lab performed excavation in Rakhigarhi/India for Feb 19 to Mar 8 (Hong JH); Mar 4 to Mar 13 (Shin DH), 2016. The excavation is supported by National Geographic Foundation.

...

As regards our plans for the relevant human remains, they will be collected via a procedure specifically designed to minimize contamination by modern DNA. They will then be moved to and maintained at Deccan College. Subsequent anthropological analyses will proceed as follows: 1) gross anthropological study (determination of sex and age, identification of any pathological signs in bones, forensic investigation for race determination, etc.); 2) paleoparasitological study (analysis of soil sediments on hipbones, determination of any presence of parasite eggs, drawing of tentative conclusions on parasitic infection of Harappan people); 3) aDNA mitochondrial, Y-chromosomal, autosomal and stable-isotope analyses (obtainment of information on maternal and paternal lineages); 4) first-ever facial reconstruction of approximately 4,500-year-old Harappan person, a member of one of the greatest civilizations in human history (based on DNA and forensic data obtained in this study). It is anticipated that by the proposed research and the various advanced techniques entailed, a full and very detailed biological and anthropological picture of the Harappan people will be obtained.

Source: Excavation in Rakhigarhi on March

Update 25/03/2016: However, this talk will be presented later this year at the WAC-8 conference in Kyoto, which suggests that a paper with ancient DNA results from some of the Rakhigarhi remains is basically ready.

Harappan Burial Sites in India: Recent Research Trends

Astha Dibyopama1, Vasant Shinde1, Dong Hoon Shin2, Chang Seok Oh2 and Nilesh P. Jadhav1

1Department of Archaeology, Deccan College Post Graduate and Research Institute, India 2Institute of Forensic Science, Seoul National University, Korea

Harappan civilization flourished mainly in northwestern province of Indian subcontinent, roughly between 4000 to 1500 BCE. There are about more than fifty burial sites of the Harappa Civilization discovered so far. Of them, Lothal, Kalibangan, Rupar, Rakhigarhi, Farmana, Tarkhanwala Dera, Sanauli, Bedwa, Puthi Seman, Bhorgarh etc. are major sites yielding the remains of Harappan burial. Until the early 1980’s, the study of human skeletons was primarily focused to answer specific questions pertaining to establishing the ethnic or racial identity of the concerned population and was used primarily to complement archaeological hypotheses of cultural migration or diffusion. Recently, however, more efforts are also made to study diet, health and genetics of Harappan population. The aim of present paper is to show how these scientific methods that are recently applied to Harappan burial studies are useful for the complete reconstruction of Harappan civilization and its people.

Source: Papers presented in WAC8, Kyoto

47 comments:

Rob said...

Worth the wait im sure

Hector said...

Korea is a technologically advanced nation and I have highest respect for their general intelligence, especially their kids, who perform superbly in things like International Mathematical Olympiad but...

You should not expect too much details in their work as they are very behind in this field. And I am quite sure that this is not a full genome sequencing or anything close to it. I suspect it will be quite crude.

But I am glad it is Shin, not Lee(Central University) who is considered to be a loon. Lee had worked on Mongolian remains 2-3000 BP and wasted a lot of valuable material; I hate him for that. Shin is considered to be more legitimate a scholar.

I hope it is not STR matrices he is getting for Y-DNA. His previous works are all like that with only a few SNP markers.

Nirjhar007 said...

Interesting probably they publish more samples results than we are thinking .

There is no doubt the results will be monumental...

Hector said...

On the other hand, Shin complied with requests from Korean amateurs to test for certain SNPs and was able to refine "Southern Branch" of C3(M217) before anyone else, so he is aware of the recent develoment in this field...

Since I am almost certain that he did not do a full sequencing here, I am only interested to know whether he did get a proper advice for the choice of SNPs.

Balaji said...

I hope and expect that the Reich lab will also be involved.

Hector said...

I checked their credentials and Hong JH is a junior partner of Shin. Shin is a forensic medical doctor from Seoul National University, not a specialized population geneticist.

By profession he has been inclined to emphasize STR for Y-DNA and most of his previous works are such. Will National Geographic push him toward testing more SNPs? I don't know. He appears to plan to use the equipments at the Indian university(Dekaan or something) so...

I hope that the Korean team is just a part of joint effort, not the leading researchers.

Nirjhar007 said...

Keep patience, have trust....

Davidski said...

By the time this paper comes out a whole lot of other papers will probably be released, very likely including ancient genomes from Iran and Central Asia. So we'll know what to expect.

Nirjhar007 said...

No, I don't think it will be that easy, but we are slowly moving towards a more clearer picture. Its still early days to conclude anything btw...

Krefter said...

First R1a-M417 from Yamnaya. rozenfag found the article.

http://xn--c1acc6aafa1c.xn--p1ai/?page_id=7492&cpage=1#comment-2830

Coldmountains said...

It seems that R1a was found in Yamnaya but it is not confirmed yet. Thanks to rozenfeld on Anthrogenica for sharing the link http://генофонд.рф/?page_id=7492&cpage=1#comment-2830

"Nadezhdinka is a grave 1 of kurgan 1. It is the main grave. The boy lie in a deep pit, Y-hapl: R1a1a1d2a. He was laying on the back, feet bent, arms not survived. The head was covered by dark red ocher, next to the left shoulder there were round-bottom vessel and conch shell. Both grave and inventory - typical for Volga Yamnaya. Kurgan was on a bank of Bolshoy Irgiz river(left tributary of a Volga) — N 52 12', Е 48 39 '.
I have to note that East Yamnaya(Volga-Ural) is dated 3400 — 2900 ВС. West Yamnaya - 3100-2400 ВС.

And later he wrote: The result was sent by professor Reich, is not yet published."

Krefter said...

Translation. The haplogroup nomenclatur looks like R1a-Z94, and the burial is from Volga, so probably another ancestor of the Bronze age Z93-brothers, like the Poltvaka outlier was.
Nadezhdinka - a burial mound 1c 1. It is basic. In a deep pit lying teen - boy: Y-hapl. R1a1a1d2a. Lying on his back, legs tucked, hands are not preserved. The head was sprinkled with dark red ocher, he stood at the left plechal round bottom flask, lay shells fold. And rite and inventory - typical pit Volga culture. Barrow was standing on the bank of the river. B.Irgiz (left tributary of the Volga.) - N 52 degrees 12 minutes E 48 degrees 39 minutes.
I must say that the East Wing Yamnik (Volga-Urals) covers the period 3400 - 2900 BC. West Wing 3100-2400 BC.
Alexander, and where you met about haplogroups Eneolithic hvalyntsev?

Karl_K said...

I agree with Krefter. He seems to be making the most sense here.

Nirjhar007 said...

Very interesting thanks for bringing the update!.
We wait and see if it is a dead branch or not...

Nirjhar007 said...

Its coming David tick-tock- tick-tock tick-tock tick-tock- tick-tock tick-tock 3:D....

Davidski said...

You must realize by now that Harappa can't be ancestral to any European or steppe group, and none of the samples will be Z93.

Nirjhar007 said...

LOL,

Sledging will not work ;D..

udaya udaya ranasinghe seneviratne said...

Rakhigarhi DNA is already with Deccan College.We can go on with various surmises till they are published

Amal said...

Do you know if the DNA results from Rakhigarhi skeletons have been published in the WAC-8 conference in Kyoto. The conference just got over (Aug 28 to Sep 2, 2016). Eagerly waiting for the results.

Davidski said...

The results haven't been published yet. The poster from the presentation on Rakhigarhi at WAC8 is available here, but it doesn't give any details about the DNA results from Harappan remains.

http://shinpaleopathology.blogspot.com.au/2016/05/new-presentation-harappan-burial-sites.html

kapila said...

is there any updates about the dna results? suspense is killing!

Davidski said...

Nothing yet.

The DNA results are ready, but they're top secret for now. The researchers were going to have a meeting in July to see what to do with them. If they decided to put out a paper, then we might see it before the end of the year.

udaya udaya ranasinghe seneviratne said...

According to some clues I got from Dr Shinde DNA result would be similar to land owing as well as feudal ruling group of Sinhalese in Sri Lanka an Island located 1000 km from Lothal Dockyards.

udaya udaya ranasinghe seneviratne said...

Now the main teams may be from Cambridge and Harward as well as a university in Denmark.Theae are the places where original research in the world been done.

Davidski said...

You're rambling on a bit there. I don't really know what you're trying to communicate.

udaya udaya ranasinghe seneviratne said...

Results having only R1a type may be a reason for not publishing them as there are lot of people in India who are H in Y chromosome who lived on the strength of the very thought that they are the descendants of Indus civilization.Publication of the results will cause separatist agitations by this demoralized groups who live on the margins of Indian and Sri Lanka cultures

Davidski said...

If the results included R1a they would've been published already, because R1a in Harappan remains would mean that R1a didn't arrive in India during or after the Harappan collapse as per the classic Aryan Invasion Theory.

So the Y-haplogroups of the Harappans tested to date are something else than R1a, which is a bit of a problem.

My guess is that they're now trying to figure out what to do to minimize the damage. Maybe they'll try and find more samples, and hope for the "correct" results, or they'll just try to package the awkward results that they do have as something positive, in other words, as something that backs up Out of India, or at least muddies the water and attempts to refute the Aryan Invasion Theory.

udaya udaya ranasinghe seneviratne said...

It can also be R2 which is in 25% of Sinhalese and marker of eliteness in Sinhalese together with R1a1.It is more specific to Sri Lanka than R1a1 and for some reasons it did not spread beyond Saraswathi valley.May be its bearers were more traditional than R1a1 bearers

Davidski said...

It might well be R2, which wouldn't be surprising since R2 has already been found in Early Neolithic Iranian farmers, who show a very strong relationship to modern day South Asians, probably because they're in large part ancestral to them.

But R2 would still be a problem, because it's not possible that the Early Neolithic Iranian farmers were Proto-Indo-Iranian speakers, and the main Y-haplogroup marker in Kurgan samples classified as early Indo-Iranian speakers is R1a, and usually R1a-Z93, which is common in South Asia, especially among Indo-Iranian speakers from upper castes.

So if the Harappan results include just R2 and no R1a, that's very awkward for the Indian archaeologists in charge of the work.

misnomer said...

Interesting pre result analyses guys. Waiting for the results too. But the age of remains is too young to make a difference if r1a is found. Absence of r1a will be monumental. Going by previous studies estimating 15000 bp as z93 age in india and str based age determination error of 2.5x as david has stated earlier, r1a should most likely be present. Am i correct in this line of thinking?

Davidski said...

R1a in South Asia is essentially Z93, and Z93 is a sister clade of the Balto-Slavic-Norse Z282, which began expanding on the Eastern European steppes at the earliest 6,000 years ago.

This expansion is recorded in present-day South Asian Z93 Y-chromosomes, but that doesn't mean it had initially anything to do with South Asia.

Indeed, Harappa had nothing to do with the Eastern European steppes. It was a culture and population linked to present-day Iran and, to a lesser degree, Central Asia and the Arabian Peninsula.

So it's extremely unlikely that any Harappan remains will carry R1a, unless we're talking about some freak occurrence. But considering that the remains that are being tested come from typical mature Harrapan graves, then don't expect any surprises, in other words no R1a.

udaya udaya ranasinghe seneviratne said...

There is a report in times of India where an officer in department of archeology Haryana states on the condition of anonymity that present people in Rakhigarhi are descendants of people who lived there 7500 years ago and it is the continuously inhabited place in the world for the longest duration.

Davidski said...

Well I doubt that there was a complete population replacement in that part of India since the Bronze Age, so he's basically correct.

In fact, I'd say the same thing even without knowing the Harappan ancient DNA results.

udaya udaya ranasinghe seneviratne said...

Rakhigarhi is populated by Jats and Brahmans who are more than 90% R1a1 and it is surrounded by one of the 2 epicenters of R1a1 center where this Y haplogroup hovers around 80% .Other area is in Eastern Poland close to Lithuania.But Rakhiarhi or Saraswathi Drushadwathi epicenter was one of the thickest population centres for at least past 3000 years for the same time being the one of the highest for R1a1.Could you please explain how can there be a population shift in a such densely populated area of about 200 000 km2.

udaya udaya ranasinghe seneviratne said...

I think there is need for close involvement of Boltoslavicnorse dominated countries in the Kurukshethra genetics analysis by sending more academics to lead the archeological work in Saraswathi basin

Davidski said...

You can use Y-haplogroups as signals of migrations and population shifts, but not to measure population shifts, because Y-haplogroup frequencies can be affected significantly by founder effect and drift.

To measure population shifts you need to use data from the autosomes, which are less susceptible to founder effect.

So the high frequencies of Y-haplogroup R1a today in North India are still possible even if there was only a ~10% contribution from the steppe to this region during the Bronze Age. Many of the local R1a lineages may have significantly risen in frequency during more recent historic times.

udaya udaya ranasinghe seneviratne said...

R1a1 in Kurupanchala region had been shown to be oldest with more than 15 000 age determination and Saraswathi civilization spread has greatest diversity of R1a1 making it impossible to explain this without a incident of total migration of a population to India from Northern Europe which is not possible as climate would have not allowed new migrants to survive in a post Saraswathi climate change in around 2000BC.Please refer to literature on this.

Davidski said...

Most of the scientific literature on R1a in South Asia is wrong because it's based on limited STR data and faulty dating methods.

There's nothing remarkable about the R1a in South Asia; it's basically all Z93, so it shows less diversity than European R1a, which is represented there by L664 in Northwestern Europe, Z282 in East Central Europe, and Z93 in the Volga-Ural.

So that's three major subclades of R1a in Europe vs just one in all of South Asia.

udaya udaya ranasinghe seneviratne said...

It is reported by underwood and lot of others were involved

Davidski said...

You mean Underhill.

Well, Underhill and the others were wrong when they said R1a was native to India. It happens. They wouldn't say the same thing today.

udaya udaya ranasinghe seneviratne said...

What about the mitochondrial DNA inherited through maternal lines.How does they correlate with Stepp Ureimart theory

Davidski said...

There's very little steppe mtDNA in India, but obviously a lot of Z93 and generally quite a bit of steppe autosomal admixture in the Indo-European speaking areas, which suggests that most of the steppe migrants were males.

We'll probably see the same model for India as for Bronze Age Central Europe, but maybe even more extreme.

http://eurogenes.blogspot.com.au/2016/09/male-dominated-conquest-of-europe-by.html

Nishant Gopal said...

Any update on when the results of the dna tests will be published?

MC said...

Any news on the results yet?

Davidski said...

The Rakhigarhi ancient DNA results for about 15-20 samples will be revealed within a few months.

pmreghu said...

david, do you have any new updates on the dna results? have you noticed any interference from the government of India to suppress the DNA results?

udaya udaya ranasinghe seneviratne said...

Latest is a lecture delivered by Dr Vasanth Shinde at New Delhi where he has given some clues on the impending DNA results which are now thoroughly verified and done on multiple samples