Y-DNA from Afghanistan

28 Mar
Hazaras (source)
Afghanistan was one of those potentially key crossroads with only indirect sampling, mostly via ethnic relatives from Pakistan. Therefore we must welcome with a great applause the following paper, which fills a gap in our knowledge (next Burma, please):


Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan’s location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan’s history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia.

Fig. 1 – PCA derived from Y-chromosomal haplogroup frequencies
In my understanding the really interesting stuff is in the supplemental table 4, which lists all the tested haplogroups for the Afghan samples.
Large and medium samples (n>10) simplified (only largest haplogroups):
  • Hazara (n=60): 20 C3 (33%), 10 J2a* (17%), 6 J2a5 (10%), 4 R1a1a (7%), 3 B (5%), 3 E1b1b1c1 (5%),
  • Tajik (n=56): 17 R1a1a (30%) 9 J2a (14%), 5 O (9%), 3 H1a (5%)
  • Pashtun (n=49): 25 R1a1a (51%), 9 Q (18%), 6 L1c (12%), 3 G2c(6%)
  • Uzbek (n=17): 7 C3 (41%), 3 R1a1a (18%), 2 R1b1a2 (12%)
  • Baluch (n=13): 8 L1a (61%), 2 R2a (15%)
Small and tiny samples (n<10):
  • Norestani (n=5): 3 R1a1a, 1 R2a, 1 J2a*
  • Arab (n=3): 2 L1a, 1 R2a
  • Turkmen (n=1): 1 R1a1a
Hazara Y-DNA oddities (B and M1)
The Hazara Country (source) is the center of Afghanistan
I must say that what stroke me the most were the three Y-DNA B Hazaras. This is a lineage almost unreported in Eurasia and much less in a population that shows no other signs of African admixture. 
Supplementary table 1 lists all haplotypes and the three Y-DNA B Hazaras (two from Bamiyan and one from Ghor) have some differences: they are not recent relatives by patrilineage. Whenever the African lineage arrived to the area, it had since then some time to evolve and diverge locally.
Are we before yet another puzzling Out-of-Africa remnant like the East Asian Y-DNA DE (mostly D)? Or is something more recently arrived? If so, how did it reach such high frequencies among the Hazara (and only them)?
The Hazara sample also includes an individual with Y-DNA M1, which is in principle a Melanesian lineage, i.e. another haplogroup which should not be there, but this one from the opposite corner of the Old World.
Dominant lineages
Otherwise it seems evident that Y-DNA R1a1a dominates among Indoeuropean speakers (Pashtun, Tajik and Noristani), C3 among the Uzbek and Hazara and L1a among the Baluch and “Arab” (who seem identical to the Baluch).
J2a (maybe a Neolithic layer) is also important among Tayik and Hazaras, while Q is very important among Pashtuns (Q is most basally diverse in West Asia, in case you do not know, even if it is most frequent among Native Americans).

9 responses to “Y-DNA from Afghanistan

  1. f8017ec0-d7f3-11e0-b6cd-000f20980440

    October 14, 2012 at 2:15 am

  2. Maju

    October 14, 2012 at 3:11 am

  3. MasterBoy

    October 14, 2012 at 7:04 am

  4. MasterBoy

    October 14, 2012 at 7:39 am

  5. Maju

    October 15, 2012 at 10:20 am

  6. Mosart

    May 12, 2013 at 10:39 pm

    Khazar > Hazara Too obvious? Some Hebrew genes mixed with Asiatic in the Khazar Empire, in the silk road trade c.650-1,000CE. Some clues/connections may come from dispersed 'bukharian jews' (, who preserve much of the old culture such as a language cross between Dari Persian and Turkoman.

  7. Maju

    May 12, 2013 at 11:53 pm

    The sound coincidence may be just that: a coincidence. The Khazars anyhow were not Jews by ancestry but Turkic converts. I'm not sure where do you see the "Hebrew lineages" either.

  8. Hasan Malistani

    December 28, 2013 at 2:29 am

    I want to mention something about Hazaras. Firstly, 32% R1b1b1-M73 come Hazaras of Pakistan. They migrated from Southern most part of Hazarajat named Ghazni or exactly Jaghory tribe about 100 years ago to Pakistan. The tribe is one of the largest group of all Hazaras with more mixed features with nearby Pashton or Tajik people and by the migration, this mixing even more evolved. So, no surprising this results for me as a Hazara. Unfortunately, the new study missed this large group of Jaghori or Ghazni Hazaras and only very limited samples have been taken.
    Abut the E and J haplogroups, it is important to consider the direct and historically important religiously relation of hazaras and Iranian, both Persian speaking Shia Muslims. The only local who could inter the the community were Shias mostly religious elders and clerics or Turkik people named Qizilbash. About strange B group also important to note that 3 samples found in the western hazara tribe named Day-zangi, which zangi in Persian means Black, but they are not black people nowadays!

  9. Maju

    December 28, 2013 at 3:51 am

    Hasan: this study is focused in Afghanistan and AFAIK the first one sampling inside this country, so it's only logical that they ignored these groups from Pakistan. There are plenty of genetic studies about Pakistan, including Pashtuns and Hazaras (not sure if that specific group you mention).

    These pops. from Pakistan are shown in some graphics like the PCA, where both Hazara populations are rather close to each other, although it's true that Afghan Hazaras (4) are more outliers than Pakistani ones (18).

    About the “strange” haplogroup B it was later spotted in important frequencies Hormozgan (Iran), so that's probably the direct source. How it reached to Hormuz is another story.

    See: →


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: