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Thursday, May 4, 2017

Darra-i-Kur specimen about 25,000 years younger than previously thought


Very disappointing, because of the dearth of pre-Neolithic samples from Central Asia, but interesting nonetheless. The sample belongs to mtDNA haplogroup H2a, which has also been found in remains from the Eneolithic and Bronze Age Pontic-Caspian Steppe (see here). So there's a chance that it harbors Khvalynsk-like or Yamnaya-like ancestry from ancient Eastern Europe. Hopefully the genome-wide data is coming soon.

Abstract: The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced.

Douka et al., Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone, Journal of Human Evolution, Volume 107, June 2017, Pages 86–93, https://doi.org/10.1016/j.jhevol.2017.03.003

49 comments:

Nirjhar007 said...

or can be just poor coverage...

Nirjhar007 said...

But if H2a is there , there will be R1a also ...

Davidski said...

They got quite a bit of endogenous DNA from the petrous bone in the skull, and the mito-genome has a coverage of 181.9, which is ridiculously good.

There's definitely some decent genome-wide data from this sample on the way. And yes, R1a might turn up as well.

Nirjhar007 said...

There will be R1a in mature Harappan , there is no doubt now.

Olympus Mons said...

@Nirjhar,
Just great how our bias work, isnt it? Its just so funny.

So H2a that we have from Kum6 (4800bc) in Anatolia, shows up in Afganisthan by 2500bc and is steppe or R1a, or whatever?

So, you have an aquarium, so you are Gay. Just like the Joke. lol.

Nirjhar007 said...

Oly,

if we see the pattern of H2 mtdna , its typically West Eurasian and IINW is also high in R1a centered places . Its high in Northern Europe IINW. We need a confirmation from someone who knows Mtdna better .

Davidski said...

@Olympus Mons

There is no evidence of direct Neolithic Anatolian input into South Central Asian populations, and H2a seems to be pretty common in ancient steppe DNA, so it's possible, although granted far from certain, that H2a arrived in Afghanistan ~4,500 years ago from the steppe.

Nirjhar007 said...


David,
I don't think so buddy , but we will see.

Alberto said...

Isn't 2500 BC in Afghanistan a bit too early to come from the steppe? I thought there's more or less consensus that anything before 2000-1800 BC. should be local, with steppe intrusions being possible only after that date.

Nirjhar007 said...

Yes .

Davidski said...

The ~2,500 year estimate is probably rough. In any case, Afanasievo is older and Poltavka_outlier (the one with the oldest Z93 to date) just as old.

But like I say, I'm just guessing about the steppe ancestry based on the H2a, which is definitely a western lineage (not native to Central Asia).

Nirjhar007 said...

Steppe theory will fall if they have R1a etc from period before 2000 BC , people didn't travel by planes those days.

But lets see .

Davidski said...

Steppe theory will fall if they have R1a etc from period before 2000 BC, people didn't travel by planes those days.

It can't fail if the R1a comes with a very clear signal of steppe genome-wide ancestry.

It's not Voodoo Magic that we're dealing with here. It can be scientifically tested and demonstrated.

Jaydeep said...

India has H2a1 and that too among Upper Caste Dravidians. The Indian subgroup is shared with Armenians.

Hence, the H2a1 in South Asia could be present since the Neolithic.

If we consider it to have come from the steppe, that would mean that we are arguing for a 2500 BC or earlier period entry of Indo-Iranians in South Asia. This again rules out the Steppe MLBA as a source for the steppe related ancestry in South Asia.

All the theories of Anthony, Kuzmina et al for South Asian history are going to bite the dust. But let us first wait for more ancient DNA from South Asia.

Is there a way to access the text ?

Nirjhar007 said...


It can't fail if the R1a comes with a very clear signal of steppe genome-wide ancestry.

It's not Voodoo Magic that we're dealing with here. It can be scientifically tested and demonstrated.


But it will not matter since the whole paradigm of Steppe Hypothesis will be demolished , as it is ruled by a certain time frame and archaeological appearance in Asia , you do realize that do you?.

Davidski said...

India has H2a1 and that too among Upper Caste Dravidians. The Indian subgroup is shared with Armenians.

Well, duh, Aryans from the steppe, both in India and Armenia (Mitanni elite).

You can access the text if you have academic access or if you're somewhat creative.

Davidski said...

But it will not matter since the whole paradigm of Steppe Hypothesis will be demolished, as it is ruled by a certain time frame and archaeological appearance in Asia, you do realize that do you?

Right, so evidence of an migration from the steppe will demolish the steppe hypothesis? And I thought you said that there was no archaeological evidence in South Central Asia backing up the steppe hypothesis? So what does it matter?

In any case, like I say, the dating is not precise.

Nirjhar007 said...

Well, duh, Aryans from the steppe, both in India and Armenia (Mitanni elite).

You should cool down, have a little drink . Today is exciting . :)

Nirjhar007 said...

Right, so evidence of an migration from the steppe will demolish the steppe hypothesis? And I thought you said that there was no archaeological evidence in South Central Asia backing up the steppe hypothesis? So what does it matter?

Because it will not be steppe ancestry anymore , it will change to Central Eurasian . There is no trace of anything ''Steppish'' in that period there , it comes only around SC Asia(not Afghan.) after BMAC disintegration, with scanty traces from Andronovo .

Davidski said...

If it came from the steppe, then it's steppe ancestry.

Nirjhar007 said...

As I said , it will not be any longer steppe ancestry , it will be Central Eurasian , appearing both in E Europe and SC Asia from a middle zone/Central Asia.

Davidski said...

As I said , it will not be any longer steppe ancestry , it will be Central Eurasian , appearing both in E Europe and SC Asia from a middle zone/Central Asia.

If that Afghan sample has R1a and EHG/CHG steppe ancestry, then it has ancestry from Bronze Age Eastern Europe, not any middle zone.

Nirjhar007 said...

No because around middle 3rd millennium BC , its an archaeological impossibility , it will either mean its local of SC Asia or came very early both to Yamnaya area and SC Asia around `3000 BC from somewhere else .

It will also mean mature harappan will show R1a .

Alberto said...

The paper itself doesn't say anything about the dating being unreliable:

"AMS 14C dating of the Darra-i-Kur sample produced a conventional radiocarbon age of 3989 ± 31 BP (OxA-31781). When calibrated using the latest INTCAL13 calibration curve (Reimer et al., 2013) and OxCal v4.2 software (Bronk Ramsey, 2009) this converts to an age ranging between 4530 and 4410 cal BP/2580-2460 BCE at 95.4% probability."

But anyway, it's very speculative that this sample will be Yamnaya-like or have R1a-Z93. Seems wiser to wait for the results than to speculate about some early offshoot from the steppe to Afghanistan.

About H2a, why is it definitely not Central Asian? Shouldn't we get (more) ancient DNA from the area to know?

Davidski said...

The EHG/CHG mixture can't be local to SC Asia and it can't be foreign to Eastern Europe.

We have evidence of it happening on the Pontic-Caspian Steppe in Eastern Europe gradually during the Eneolithic, with samples that carry R1a.

If this Afghan sample shows EHG/CHG ancestry and R1a, and looks obviously steppe admixed, then it has recent ancestry from Eastern Europe.

WTF?

Davidski said...

Btw, H2a is not native to Central Asia. It's native to the Near East.

It arrived on the steppe with admixture from the Near East.

Nirjhar007 said...

People are already suggesting local ancestry or deeper ancestry which create the Yamnaya type ancestry, which is not from Yamnaya .

If such ancestry is already there in SC Asia at mature harappan time, a time period which shows evidence of trade wise relation between BMAC and Indian Civilization , its clearly obvious that it had nothing to do a to steppe . Now Dave is acting like a child , but he should realize that already Andronovo is ruled out by geneticists , it was already ruled out by archaeology, so genetics only followed what archaeology suggested many years before .

So,2500 BC-2300 BC Yamnaya type ancestry +R1a from SC Asia and India is the end of steppe hypothesis which was on the cards for a long time .

Nirjhar007 said...

I can't comment on H2a , we need a specialist , who will tell about its occurrence through space and time.

Nirjhar007 said...

But IIRC Yuzhnyy Oleni Ostrov of Karelia had H2a .

Nirjhar007 said...

aha! from Mtdna Guru Kristiina ;) :
''Olympus, Balkans are very interesting from the metallurgy point of view and it will be very interesting if we get ancient yDNA from Vinča culture (5700–4500 BC) which provides the earliest known example of copper metallurgy. What archaeological culture do you have in mind when you point to a population movement from the north Balkans to Anatolia and Caucasus by 8000/7000 BC?

It is a pity that I cannot find information as to if Kumtepe (4700 BC) is H2a1 or H2a2, because as I said above, mtDNA H2a has been detected as follows: Early Eneolithic Smyadovo, Bulgaria (4500–3000 BC) H2a2, Early Eneolithic Vinogradnoe Moldova (4500–3000 BC) and Remedello Italy (3483-3107 BC) H2a (H2a2?). Instead, H2a from Khvalynsk II Samara Eneolithic (5200-4000 BC) is H2a1, and it is this Samara line which is detected in Areni-1 from Armenia (4330-3060 BC). From the point of view of the origin of H2a it is important that the oldest H2a2 is from Karelia as we have Yuzhnyy Oleni Ostrov, Karelia (5500 BC) H2a2b.

If Kumteke (4700 BC) is H2a2 it could have arrived to Anatolia from nearby Bulgaria and it could also explain why it is Sardinian and Oetzi like. However, I know that there are people who want everything to have originated in the Near East. In any case, Kumtepe site is said to be near Troy on the western coast of Turkey which means that it is very close to Bulgaria.''
http://eurogenes.blogspot.in/2016/08/on-origins-of-first-farmers-in-anatolia.html?showComment=1470469327017#c7507729229237847435

Kristiina said...

Nirj, I recall that Yuzhnyy Oleni Ostrov has been recently reassigned to mtDNA R1b or something similar. This is a very quick and hasty comment from me so please check this!

Nirjhar007 said...

I see. But still its present from ~5000 BC Samara . Perhaps as Jaydeep suggested us , its already there in Neolithic period .

Nirjhar007 said...

Seems wiser to wait for the results than to speculate

Yeah lets do that .

Rob said...

@ Davidski

To date: The earliest H2a is from Samara/Karelia. The earliest H from Near East is H5.
The earleist H from Caucasus (Kotias) is H13.

jv said...

@ Rob
The earliest H6 is Israel, Wadi el Makkukh, approximately 4000 BCE. So I guess? H6 would be considered a Near Eastern line. But I've read that H6 may have been in Mesolithic Russia. I wish I knew how mtDNA H6a arrived on the PC Steppe...........

ak2014b said...

The BAM file of the 6700 year old female kumtepe 6 sample (4700 bce) has it looking like H2a3, notably also matching G16274A in the up to date Phylotree build.

Ancestral Journeys is keeping track of aDNA. The oldest H2 samples in the aDNA so far are:

Samara Eneolithic 5200-4000 BCE H2a1
4700 BCE kum6 sample Anatolia H2a (female) from a 7000 YBP settlement.
Armenia 4330-3060 BCE H2a1
Remedello 3483-3107 BC H2a
3 samples 3400 - 3000 BC Germany were H2 (2012, not further resolved?)
Yamnaya 3010-2622 BC H2b
Germany Eulau 2568-2518 BC H2a1 (Eulau was inhabited by the people implicated in the massacre of CWC males)
Bell Beaker Culture Germany H2a1e (no date)

Later ones are,
Vatya Hungary 2000-1500 BC H2a1
Unetice Germany 1982-1942 BC H2a1a3
Srubnaya 1850-1600 BC - H2b
Kazakhstan 900-700 BC H2a1
Lithuania 908-485 BC H2a2
Russia 500-200 BC H2a1f
Scythian Russia H2a1


The range of dates for the H2a1 Samara Eneolithic sample is 5200-4000 BCE. This includes the 4700 BCE of the Kum6 H2a sample, which is possibly H2a3. And the fact that each instance is possibly not immediately derived from the other also allows a wider presence of H2a before this period.


Omrak et al 2015 states

Kum6 shows a strong population continuity with present-day Sardinia

Kum6 expresses connections to the central Eurasian gene pool

Kum6 shares notable affinity with the Iceman, a 5,300-year-old southern European

Genetic affinities to both East and West suggest continuous contact with Anatolia


Maybe their second bullet point, on Kum6's connections to central Eurasia, meant to cover the tentative mtDNA association? I'll search for some additional papers on modern Iran and South Central Asia mtDNA.

ak2014b said...

I had a look through several mtDNA papers on Iran to South Asia. H2a3 is not very common, but H2 in general doesn't seem to be either.

Schönberg et al 2011 covering Caucasus and West Asia populations, 147 samples in total covering Georgia, Armenia, Azeri, Iran, Turkey,
1 x H2 in Turkic speaking Azeri
1 x H2, 1 x H2a3 in Armenian
1 x H2a1a, 1 x H1e1 in Turkey
1 x H1 in Georgian

Farjadian et al 2011 sampled 14 ethnic populations of Iran, 718 samples in total, and found one instance of H2. It was H2a1 and it was detected in a Turkmen sample (T) from Gonbad in North Iran. Since the number of Turkmen samples was 55, this was a frequency of 1.8% among Iran's Turkmen population.

In this paper, the Zoroastrians samples (Z) were all from Yazd, and they had no H2a1 among them. Nor did any of the remaining ethnic populations in Iran.


Derenko et al, 2013 had 353 Iranian samples, with the following 3 instances of H2
1 x H2a1* in an Armenian sample from Isfahan in central Iran
2 x H2a1h. One in a Persian another in a Turkic speaking Qashqai. Both from Kerman province in Iran's southeast.


In Pakistan, there are no instances of any H2 among 85 Saraiki samples (Punjab), nor among a sampling of 100 Makrani persons.

It would be useful to have papers focusing on Baloch and on Brahui in Pakistan, but I haven't come across any on either population. However, the Farjadian 2011 paper already had 61 Baloch samples from Iran's southeast and found no H2a1 among them.

115 samples from Sindh contained 0 of H2 or further downstream, but 2 x H1 (H1a, H1a1)

There were a number of different papers on Pashtuns in Pakistan. And the frequency of H2 were different in each.

The first paper consisted of 230 Pathan samples, finding H2a1 at 0.4% (1 sample) but H2b was at 2.6% (6 samples).

The second paper had a total of 100 samples across four tribes, but found 0 of any H2 and 2 x H1 (H1a1, H1a3).

However, the third paper, which contained 165 samples across 5 Pashtun tribes, found H2 quite common among them but described this haplogroup as being of a Southwest Asian or Middle Eastern origin. Although there was no H2a1, there was 5 x H2 and 1 x H2a3. The rest were H2a2: 6 x H2a2a1g, 4 x H2a2a1c, 2 x H2a2a1d, and one sample of H2a2b.


The Palanichamy et al 2015 paper had a total of 14198 Indian and Bangladesh mtDNA samples. Compared to 74 basal H samples, there were only 6 samples under H2 at all. All 6 were H2a1 or downstream, with 2 being H2a1a. And out of these 6 samples, 5 were Dravidian speakers from southern India and the other one (H2a1a) was a Tibeto-Burmese speaker from northern India. H2a1's route to the region is far from clear, as it's not really common in Iran and seems rarer in Pakistan, where H when it is found, is usually in the form of H1 derivatives or H2a2. And H2a1 doesn't seem common in northern India either. The four instances of H2a1 in southern India could be the result of endogamy, as the carriers converge in terms of region, language and caste affiliations which may indicate some localised founder effect compared to H2a1's paucity in the rest of south Asia.

For now, assuming an origin for H2a1 in Samara in the Eneolithic or before, this maternal lineage had already entered Armenia in 4330-3060 BCE, where it was found in a male carrying Y L1a-M27. Such an early date argues against an Indo-European dispersal carrying it into Chalcolithic Armenia, and that Y lineage is not Indo-European, which would not be indicative of a male dominated steppe migration into early Armenia. L1a-M27 further turns out to be common in south Asia, particularly in southern Indian Dravidian speakers. Could H2a1 in southern India plausibly be from earlier, associated with a similar route as for L1a-M27? Though making such an association isn't strictly necessary, and I should be following Alberto's advice to wait for the aDNA results rather than speculate.

Rob said...

Thanks Ak2014b

John Smith said...

The problem with it being H2a is that the CRS is H2a. I corrected the paper on Bioxriv that says most Zoroastrians belong to H2a (they do not). It would be interesting if it is H2a but we need to look at the methods because H2a is one of the few haplogroups that is very prone to error because the CRS belongs to it.

Davidski said...

Well, the thought crossed my mind, but Svante Paabo is one of the co-authors, so imagine if he messed up a haplogroup assignment for an mtDNA genome sequenced at 181.9-fold coverage. That'd be really something.

Samuel Andrews said...

@David,

H2a doesn't indicate a connection to the Steppe. It just indicates a connection to the Stone age Near East. Afghanistan could have been something Iran Neo-like in 2500 BC which can explain the H2a.

Davidski said...

Currently, the Darra-i-Kur H2a does suggest a connection to the steppe and also to other parts of Europe, because there's H2a on the ancient steppe and in various ancient European samples but not in ancient Iran. Even the H2a in the Chalcolithic Armenian samples might be linked to the steppe in some way, because of the high level of EHG admix in them.

So at the moment it looks like H2a entered Europe from the Near East during the Neolithic, and then expanded back into Asia via the steppe. There's no evidence right now of an expansion of H2a directly from the Near East to Central Asia.

Samuel Andrews said...

The number of possibly origins for this ancient Afghan H2a are endless. The Steppe is just one possible origin and not the most likely.

Davidski said...

Right now the steppe looks like a good bet.

postneo said...

"H2a entered Europe from the Near East during the Neolithic"

what stops it from spilling over into Iran, some travel ban? MTDNA is very diffuse and at such a young age of 2500 BC H2a would be everywhere.

postneo said...

by young I mean recent

Davidski said...

Just been told that the genome-wide DNA for this sample is publicly available. Here it is...

https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=335708

But it's heavily contaminated, and not treated for deamination. So only the damaged transversion SNPs can be used.

I don't have a clue how to process this.

ak2014b said...

Additional instances of H2 and H1 I missed out recording in my earlier comment. No further H2a1 that I could see, but 3 more of H2a derivatives.

Saraiki did have H2:
Among them, there's an "H2a +152 1631", 1 x H2a2a, and 1 x H2a2a1g. The H2a2a1g, however, was listed in the first table as U2 next to its ht.

115 samples from Sindh contained 0 of H2 or further downstream, but 4 x H1 (H1a, H1a1 and H1ba, H1e2c)

The Pashtun paper with 100 samples from four tribes, had 0 of any H2 and 4 x H1 (2 x H1a1, and H1a3, H1ba).

Nirjhar007 said...

Dave, by any means , process it ...