April 30, 2015

Kalash origins

This is an open access paper.

AJHG http://dx.doi.org/10.1016/j.ajhg.2015.03.012

The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection

Qasim Ayub et al.

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.

Link

16 comments:

bellbeakerblogger said...

Related topics out this week:

Strontium Isotope analysis of first generation Harappan and Farmana immigrants of the Indus Valley...

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123103

From two weeks ago:

Four Harappans excavated by a South Korean team to undergo full genomic sequence...

http://www.archaeology.org/news/3209-150415-india-harappan-skeletons

aniasi said...

I would like to ask two questions here:

1) If the Kalash represent ANE in South-Central asia, then why are so many of their male lineages either indigenous to South Asia or representative of Bronze Age migrations?

2) By the same token, surely this undermines the two way ANI-ASI model. ASI clearly was not the isolated homogenous population it was previously made out to be. Interestingly enough, Eurogenes has featured a new study that indicates West Eurasian mitochondrial clades amongst southern lower and middle castes from the epipaleolithic.

This surely throws out the idea of a 60,000 year old unrelated population, and forces a reconsideration of population flow into South Asia before the late neolithic?

Kurti said...

I have been saying on Eupedia that Kalash are most likely the remnant of ancient Proto ANE people from South_Central Asia since more than a year.

Kalash have significant frequncy of Haplogroups such as R*, R1*, R1a*, R2*.

My hypothesis is that this "Siberian" individual original stems from a population which was inhabiting the regon between South_Central Asia, Iran , North Asia and Sibiria. However ultimately they stem from somewhere in between South_Central Asia and Iran.

People seem to forget that beside Amerindians the South_Central Asians such as Kalash have the highest frequency of ANE.

Imagine how strong this ANE component will be among ancient South_Central Asians if even modern once(who have been the target of many farmer/herder waves) are still that strong in this component.

To be honest I don't even think this "ANE" is the "real deal", simply because Mal'ta might himself had absorbed some "other" admixture. I am not denying that ANE is very ancient I am simply speculating that some ancient R* individuals in other parts of the world, as example in South_Central Asia, could be autosomally slightly different.

Nirjhar007 said...

Awesome Stuff.

sykes.1 said...

When did these people show up in the Hindu Kush? If they are Indo-European speakers, they can't have arrived much before 4,000 BC.

sykes.1 said...

PS. Eurogenes thinks there is an error in their technique.

http://eurogenes.blogspot.com

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capra internetensis said...

@aniasi

Among Kalash male lineages, only H1a1-M82 (20%) is properly South Asian. Even their R1a is Z2125, the more Central Asian type.

That said you are surely right, people with a variety of G, H, J, L, and young R clades can hardly be the product of ancient isolation on the male side.

ASI is not supposed to have been a homogeneous population. In fact Moorjani et al specifically note evidence for differences in ASI within different Indian populations - that for some Onge is more closely related than for others.

That said, I agree with you that South Asia is unlikely to have been totally isolated from everyone for the whole of the Upper Paleolithic.

andrew said...

"When did these people show up in the Hindu Kush? If they are Indo-European speakers, they can't have arrived much before 4,000 BC"

An Indo-European language means significant cultural contact in the last 6,000 years, but doesn't say anything more about their ancestral genetics than, for example, that fact that many pure blooded Native Americans and indigenous Australians speak English or Spanish or Portuguese.

Unknown said...

The term Indo-European is so overplayed that it has outlived its usefullness. Its reality began as language influenced but in the same vein the NE Afghan Nuristanis (my favourite baseline group) do speak an Iranic languange (Dari and even Pashto) as inhabitants of a nation state but whose original 'language' gave way to numbers and culture of greater identity (demographics and location of the larger society). Kalash and bottleneck survival of an intitial origin group who 'lost' their way but whose greater elements are /have become the seed group of earlier out of Asia migration to the Fertile Crescent and even the forerunner of Eropean population dispersal!

aniasi said...

@Capra

Isn't L also heavily concentrated in the western side of South Asia?

Could you guide me to Moorjani's analysis of ASI differentiation? Until now, I have only heard of it as one population.

I am glad to see that there is someone else who finds the notion of SA Paleolithic isolation absurd.

aniasi said...

@Capra

Isn't L also heavily concentrated in the western side of South Asia?

Could you guide me to Moorjani's analysis of ASI differentiation? Until now, I have only heard of it as one population.

I am glad to see that there is someone else who finds the notion of SA Paleolithic isolation absurd.

Nirjhar007 said...

Kurti,
Good Points.
Andrew,
// many pure blooded Native Americans and indigenous Australians speak English or Spanish or Portuguese.//
Yeah but the Situation of the Subcontinent and its cultural back ground with recorded history doesn't make that a good point:).
Capra,
//South Asia is unlikely to have been totally isolated from everyone for the whole of the Upper Paleolithic.//
Yes not totally but before 6 th century bc to the middle 5th millennium bc at least there don't seem to be any kind of significant migrations into at all.

terryt said...

@ aniasi:

"This surely throws out the idea of a 60,000 year old unrelated population, and forces a reconsideration of population flow into South Asia before the late neolithic?"

Have you seen this:

http://www.unz.com/gnxp/agriculture-came-with-men-to-the-indian-subcontinent/

Many interesting ideas presented but I found this particularly so:

"More or less all South Asian populations are a fusion between a deeply indigenous strain which distant affinities to the peoples of eastern Eurasia (ASI), and a group very close to the ones typically found in Western Eurasia (ANI). There are no pure indigenes".

There is very little evidence of any 'deeply indigenous strain'. And the ASI element looks by no means indigenous to India. This would indicate the idea that South Asia provided a major route east during the early Paleolithic.

Pakistani Warrior said...

Fool, majority Kalash are haplogroup L, they also have a lot of Z93, H, and R2 also, 98% are South Asian origin who way before came from Siberia, their features are de pigmented North Indians, not European, they're dard speaking people who are what original North Indians looked like, all Northern Indian languages are related to Persian more than dravidian for a reason.

Pakistani Warrior said...

The majority of Kalasha are haplogroup L, which is South Asian the next majority are from R2, which is South Asian,their R1a1 is also Z-93, their language is Indo Aryan dard, their religion is from Proto rig veda, they're indo aryan with less asi mixture, they look like de pigmented North Indians not similar to european people.