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Afghan Hindu Kush: where Eurasian sub-continent gene flows converge

. 2013 Oct 18;8(10):e76748. doi: 10.1371/journal.pone.0076748. eCollection 2013. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge Erwan Pennarun, Stéphane Mazières, Natalie M Myres, Alice A Lin, Shah Aga Temori, Mait Metspalu, Ene Metspalu, Michael Witzel, Roy J King, Peter A Underhill, Richard Villems, Jacques Chiaroni

Affiliations

Affiliation

¹ Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France.

PMID: 24204668
PMCID: PMC3799995
DOI: 10.1371/journal.pone.0076748

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Afghan Hindu Kush: where Eurasian sub-continent gene flows converge

Julie Di Cristofaro et al. PLoS One. 2013.

. 2013 Oct 18;8(10):e76748. doi: 10.1371/journal.pone.0076748. eCollection 2013. Authors Julie Di Cristofaro¹, Erwan Pennarun, Stéphane Mazières, Natalie M Myres, Alice A Lin, Shah Aga Temori, Mait Metspalu, Ene Metspalu, Michael Witzel, Roy J King, Peter A Underhill, Richard Villems, Jacques Chiaroni Affiliation

¹ Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France.

PMID: 24204668
PMCID: PMC3799995
DOI: 10.1371/journal.pone.0076748

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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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures
Figure 1. Samples collection locations. Blue dots…

Figure 1. Samples collection locations. Blue dots indicate locations where samples were collected in Afghanistan…
Figure 1. Samples collection locations. Blue dots indicate locations where samples were collected in Afghanistan and analyzed for mt DNA, Y-chromosome and GWA, red dot indicates Afghan capital, Kabul.

Black dots indicate locations where samples were collected in Iran, Kyrgyzstan, Mongolia and Pakistan (HGDP-CEPH) and analyzed for Y-chromosome (see further description in Table S1). Red squares indicate samples locations used for the autosomal analyses (PCA, Fst, structure-like ADMIXTURE) (see further description in Table S2).

Figure 2. Spatial distribution of Ancestry Components…

Figure 2. Spatial distribution of Ancestry Components based on the admixture analysis results at K…
Figure 2. Spatial distribution of Ancestry Components based on the admixture analysis results at K = 9.

Frequency data (ancestry fractions) were converted by applying the Kriging algorithm using the software Surfer v8.00. The color for the respective ACs matches that of Figures S1 and S2.

Figure 3. First and second components of…

Figure 3. First and second components of the Principal Component Analysis based on autosomal data.
Figure 3. First and second components of the Principal Component Analysis based on autosomal data.

The corresponding colored dots for the Central Asian populations are shown on the lower right corner. The colored “arrows” on the background represent the frequency gradients as seen as on Figures S1 and S2 and follow the same color code. It shall be stressed that they DO NOT represent actual gene flow, PCA analysis does not permit to reveal such movements. _Pak and _Afg stand for Pakistan and Afghanistan respectively.

Figure 4. First and second components of…

Figure 4. First and second components of the Factorial Correspondence Analysis based on the frequencies…
Figure 4. First and second components of the Factorial Correspondence Analysis based on the frequencies of 84 well-defined Y chromosome haplogroups in 37 populations from Afghanistan, Iran, Kyrgyzstan, Pakistan, and Mongolia.

In Figure 4-A, populations are colored according to their language (Altaic and Indo-European speaking populations). Figure 4-B differentiates populations according to their respective country.