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. 2013;8(1):e54616.
doi: 10.1371/journal.pone.0054616. Epub 2013 Jan 30.

Y-chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations With European and African Populations

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Y-chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations With European and African Populations

Danielle A Badro et al. PLoS One. .
Free PMC article


The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of F(ST)'s, R(ST)'s, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Conflict of interest statement

Competing Interests: IBM has no marketed products associated with the contents of this paper. IBM has no income derived from contracts related to consultancy or capital or intellectual assets in this research. The affiliation of an author (DP) with IBM does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.


Figure 1
Figure 1. Geographic distribution of mtDNA haplogroups.
Frequencies distribution from the current study and from the published data , , – as reported in Table 1.
Figure 2
Figure 2. Populations comparison based on mtDNA haplogroups.
a) Principal Component Analysis of relative frequencies of haplogroups within populations, b) with mean-linkage (UPGMA) dendrogram determined from Euclidean distances.
Figure 3
Figure 3. Nonmetric Multidimensional Scaling.
a) mtDNA FST and b) Y-STR RST distances with c) mtDNA FST and d) Y-STR RST mean-linkage dendrogram.
Figure 4
Figure 4. Heatmap of the Y(Y+mtDNA) distances.
The heatmap shows the normalized ratio of the Y FST distance with respect to the total distance (Y RST+mtDNA FST distances). The dendrograms are obtained using complete linkage hierarchical clustering with the Euclidean distance measure.

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The Genographic Project is supported by funding from the National Geographic Society, IBM and the Waitt Family Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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