The Genetics of the Kalash People

In an early worldwide survey of this kind, division into five clusters unsurprisingly identified (1) Africans, (2) a widespread group including Europeans, Middle Easterners, and South Asians, (3) East Asians, (4) Oceanians, and (5) Native Americans. However, division into six groups led to a more surprising finding: the sixth group consisted of a single population, the Kalash. The Kalash are an isolated South Asian population of Indo-European speakers residing in the Hindu Kush mountain valleys in northwest Pakistan, near the Afghan frontier. With a reported census size of 5,000 individuals, they represent a religious minority with unique and rich cultural traditions.

From a new open access paper in the Journal Cell on their autosomal genetics.  This outlier status could, however, be due to sustained genetic isolation and inbreeding in a small population which can create a very unique and uniform autosomal genetic profile with isolated mutations that looks more exotic than it seems.

They are also one of the few populations in the world that are non-Hindu pagans religiously, as opposed to having a revived "neo-pagan" or monotheistic religion.

They are some of the most "white" looking people of South Asia (despite their lack of close genetic affinity to Europeans), which led to historically inaccurate myths that the were descendants of Alexander the Great's troops that marched into the general vicinity in ancient times.  As their language illustrates, however, they have had, at least, significant cultural contact with Indo-European people at some point in deep history.  They are also lactose tolerant, although due to genes different than those found in Europeans.

Some of the analysis in the paper is controversial and I will update this post to discuss those issues and the detailed conclusions of the genetic analysis if I have time to do so.

One key point that is not particularly controversial is that the Kalash people show closer affinity to ancient DNA from Ma'alta boy, an Upper Paleolithic individual from near the Altai Mountains whose Y-DNA is a very basal version of haplogroup R, than any other extant modern population.

UPDATE May 3, 2015:

For convenience sake, I will reproduce below the pertinent part of a post at Wash Park Prophet on the subject on March 3, 2011:

The Kalash people in a remote part of the Hindu Kush Mountain range are one of the most genetically distinct populations in the world. When one has a computer break the world's autosomal genetics into the most distinct possible seven clusters, the clusters that you get are: African, European, South Asian, East Asian, Papuan, indigenous American and Kalash.  

Their Y-DNA haplogroups (from a sample of about 43 people) are as follows: 

* L3a 22.7% (most common in Pakistan)

* H1* 20.5% (most common in South Asia)

* R1a 18.2% (most common in Eastern Europe and South Asia)

* G 18.2% (most common in Southern Europe, Anatolia, Druze, Brahui and Pashtuns)

* J2 9.1% (most common in Anatolia and where Indo-Europeans have had an impact)

* R* 6.8% (most common in Thailand, Indonesia, the Phillipines and Australian aborigines)

* R1* 2.3% (most common in indigenous Americans)  

* L* 2.3%. (most common in South Asia) 

Their mtDNA haplogroups (from a sample of 44 people) are as follows: 

* pre-HV 22.7% (most common in Socotri, North Africa, Iran and Arabia)

* HV* 4.5%

* H 4.5% (the modal haplogroup of Europe)

* U2e 15.9% (most common in South Asia)

* U4 34.1% (most common in Central Asia) 

* U7 2.3% (most common in South Asia)

* J1 2.3%

* J2 9.1% 

* T* 4.5%  

They speak a language from the Dardic branch of the Indo-European family (one of the more basal of the Indo-Iranian part of the late language family), and practice a polytheistic religion. 

They are between areas that areas typically Central Asian and areas that are typically South Asian in genetic makeup. Their traditions place them as a lost contingent of Alexander the Great's army, but given their uniparental markers, the genetic makeup, their particularly contingent would have had to have picked up members mostly from the area from Anatolia to the Hindu Kush. Their Dardic language is also an anomaly for an isolated community claiming to descend from the Greeks, they lack common distinctively Greek uniparental markers, and their religion is close to Hinduism than it is to Greek pantheistic beliefs. An origin a millennium or two earlier (if not much more ancient) would seem to be a better fit for the facts. 

Given their autosomal makeup, any new arrivals in the region from somewhere would have had to either admixed substantially with a relict population that was largely wiped out or overwhelmed genetically elsewhere such as Europe and Central Asia's pre-Neolithic hunter-gatherers, or South Asian hunter-gatherer populations disrupted by Munda, Dravidian, and Indo-Aryan populations respectively. Alternately, they might have undergone significant selectively driven evolution analogous to that found in Tibetans as a result of living at high altitudes. The case for incorporation of a relict Central Asian hunter-gatherer population is most strongly supported by the modal mtDNA haplogroup U4, which was one of the second most common types found in ancient DNA from Central Asian hunter-gatherers.