Limits...
Genome-wide diversity in the levant reveals recent structuring by culture.

Haber M, Gauguier D, Youhanna S, Patterson N, Moorjani P, Botigué LR, Platt DE, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Bertranpetit J, Tyler-Smith C, Comas D, Zalloua PA - PLoS Genet. (2013)

Bottom Line: Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region.The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations.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.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.

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.

Show MeSH
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.
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pgen-1003316-g001: 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.

Mentions: A multidimensional scaling (MDS) plot based on the identity-by-state (IBS) matrix shows strong stratification in Lebanon by religion, with separate clusters for Christians, Muslims, and Druze, irrespective of their geographic origin (Figure 1). The results suggest endogamous practices among the religious groups of Lebanon within a small geographical area not exceeding 10,452 km2 (half the size of the state of New Jersey or one third the size of Belgium). Christianity in Lebanon dates back to the first century CE, whereas Islam was brought to the Levant through the Islamic expansions in 635 CE. In 986 CE, the Druze faith developed as a movement within Islam, and from 1030 AD, a person could only be Druze if born Druze. This correlation of genetic structure within Lebanon with cultural traits was previously described by Haber et al. [3] based on the religious structuring of Y-chromosomal variation within Lebanon, but here we see it is genome-wide. In order to assess the proportion of putative ancestral components in the Lebanese, an unsupervised clustering method (ADMIXTURE) [10] was applied to the Lebanese dataset (Figure S1A). At K = 2, which showed the lowest cross-validation error (Figure S1B), Christians present one major component (∼82% on average per individual), which is also found in Druze and in lower frequencies in Muslims; in contrast, the second component is almost exclusive to Muslims with a lower representation in Druze. At K = 3 and K = 4, new components most abundant in Lebanese Muslims are shown, probably reflecting recent admixture after the split from the other Lebanese groups.


Genome-wide diversity in the levant reveals recent structuring by culture.

Haber M, Gauguier D, Youhanna S, Patterson N, Moorjani P, Botigué LR, Platt DE, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Bertranpetit J, Tyler-Smith C, Comas D, Zalloua PA - PLoS Genet. (2013)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585000&req=5

pgen-1003316-g001: 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.
Mentions: A multidimensional scaling (MDS) plot based on the identity-by-state (IBS) matrix shows strong stratification in Lebanon by religion, with separate clusters for Christians, Muslims, and Druze, irrespective of their geographic origin (Figure 1). The results suggest endogamous practices among the religious groups of Lebanon within a small geographical area not exceeding 10,452 km2 (half the size of the state of New Jersey or one third the size of Belgium). Christianity in Lebanon dates back to the first century CE, whereas Islam was brought to the Levant through the Islamic expansions in 635 CE. In 986 CE, the Druze faith developed as a movement within Islam, and from 1030 AD, a person could only be Druze if born Druze. This correlation of genetic structure within Lebanon with cultural traits was previously described by Haber et al. [3] based on the religious structuring of Y-chromosomal variation within Lebanon, but here we see it is genome-wide. In order to assess the proportion of putative ancestral components in the Lebanese, an unsupervised clustering method (ADMIXTURE) [10] was applied to the Lebanese dataset (Figure S1A). At K = 2, which showed the lowest cross-validation error (Figure S1B), Christians present one major component (∼82% on average per individual), which is also found in Druze and in lower frequencies in Muslims; in contrast, the second component is almost exclusive to Muslims with a lower representation in Druze. At K = 3 and K = 4, new components most abundant in Lebanese Muslims are shown, probably reflecting recent admixture after the split from the other Lebanese groups.

Bottom Line: Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region.The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations.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.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.

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.

Show MeSH