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, 9 (2), e1003316

Genome-wide Diversity in the Levant Reveals Recent Structuring by Culture

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Genome-wide Diversity in the Levant Reveals Recent Structuring by Culture

Marc Haber et al. PLoS Genet.

Abstract

The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ∼23,700-15,500 years ago during the last glacial period, and diverged from Europeans ∼15,900-9,100 years ago between the last glacial warming and the start of the Neolithic.

Conflict of interest statement

DEP is an employee of IBM. There are no patents or products in development or marketed products to declare. This does not alter the author's adherence to all the PLOS Genetics policies on sharing data and materials. All other authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Multidimensional scaling of >240K SNPs in 1,341 Lebanese samples showing the first four dimensions.
The SNPs were pruned from >500,000 SNPs excluding r2>0.4. The samples were classified by their religion or region of origin.
Figure 2
Figure 2. Multidimensional scaling of >240K SNPs showing the top two dimensions.
Main plot shows global diversity using 50 populations. Inset shows Levantine populations in their regional and religion context. The Levant region includes Lebanon, Syria, Jordan, Israel, Palestine, and often Cyprus and historical Armenia. The Levantine core cluster is shaded in pink.
Figure 3
Figure 3. Population relationships from genome-wide haplotypes.
A) Each tip of the tree corresponds to an individual; numbers of individuals are shown next to their population name at the tip of the branches. Numbers on branches show partition posterior probability. The Levantine populations' tips are highlighted in pink. B) Raw coancestry matrix shows relationships between the Levantines and the world populations. Intensity of the colors reflects the number of haplotype chunks donated to the Levantines. The vertical line is a visual aid to reflect the Levantine split observed in the tree. Horizontal lines distinguish the major geographic regions. C) Principal component analysis using the world coancestry matrix, figure is magnified on West Asia.
Figure 4
Figure 4. Comparisons of the Levantine and Middle Eastern modal components.
A) ADMIXTURE analysis based on 10 constructed ancestral components, with only the Levantine and Middle Eastern components highlighted. B) Frequency of the Middle Eastern component in world populations. C) Frequency of the Levantine component in world populations. Intensity of the colors reflects the frequency of a component in the plotted populations. Maps were produced using a weighted average interpolating algorithm, and therefore should be used as a guide rather than a precise representation of the frequency distribution.

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