Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

Julie Di Cristofaro,Michael Witzel,Jacques Chiaroni,Alice A Lin,Peter A Underhill,Richard Villems,Roy J King,Natalie M Myres,Erwan Pennarun,Mait Metspalu,Shah Aga Temori,Ene Metspalu,Stéphane Mazières

doi:10.1371/journal.pone.0076748

Abstract

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

Highlights

The Hindu Kush covers the mountainous regions of Afghanistan and north Pakistan, including areas on the western borders of the Pamir Mountains; since ancient times it has been the crossroad of the more densely settled regions of South and Central Asia and of historical Persia
Sampling A total of 516 samples of blood obtained by venipuncture were collected from 5 ethnically distinct populations in the Hindu Kush region of Afghanistan: Hazara, Tajik, Uzbek, Turkmen, and Pashtun (Figure 1 and Table S1). 478 additional original samples were collected for Y- chromosome analysis from Iran, Kyrgyzstan and Mongolia as well as 177 updated Pakistani samples (HGDP-CEPH) [47] (Figure 1 and Table S1)
Autosomal analyses Autosomal variation in Eurasian populations was analyzed via genetic structure in a dataset of over 232,000 genome-wide SNPs, depicted by a structure-like clustering approach implemented in ADMIXTURE

Summary

Introduction

The Hindu Kush covers the mountainous regions of Afghanistan and north Pakistan, including areas on the western borders of the Pamir Mountains; since ancient times it has been the crossroad of the more densely settled regions of South and Central Asia and of historical Persia. The unknown BMAC language can be triangulated from the loan words that it transmitted to Old Iranian (Avestan, Old Persian), Old Indian (Vedic) and Tocharian; the latter was spoken in westernmost China (Xinjiang) [6,7,8,9]. This language seems related to North Caucasian in the west and to Burushaski from the high Pamirs in the east, both form part of the Macro-Caucasian language family that includes Basque [10,11]

Methods

Results

Discussion

Conclusion