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.

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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.
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pgen-1003316-g003: 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.

Mentions: The previous analyses are based on linkage disequilibrium (LD) pruned data (r2<0.4) since LD can bias cluster analysis. However, identification of haplotypes shared between groups is a valuable tool to infer population history events [12]–[15]. Thus, we phased our data and generated a coancestry matrix using ChromoPainter [16] which reconstruct the haplotype of every individual using the haplotypes of each of the other individuals as possible donors. ChromoPainter computes a similarity measure which is the number of haplotype “chunks” used to reconstruct the recipient individual from each donor individual. We then used fineSTRUCTURE [16] which employ model-based Bayesian clustering to construct a tree that infer population relationships and similarities using ChromoPainter's coancestry matrix. The population tree (Figure 3A) splits Levantine populations in two branches: one leading to Europeans and Central Asians that includes Lebanese, Armenians, Cypriots, Druze and Jews, as well as Turks, Iranians and Caucasian populations; and a second branch composed of Palestinians, Jordanians, Syrians, as well as North Africans, Ethiopians, Saudis, and Bedouins. The tree shows a correlation between religion and the population structures in the Levant: all Jews (Sephardi and Ashkenazi) cluster in one branch; Druze from Mount Lebanon and Druze from Mount Carmel are depicted on a private branch; and Lebanese Christians form a private branch with the Christian populations of Armenia and Cyprus placing the Lebanese Muslims as an outer group. The predominantly Muslim populations of Syrians, Palestinians and Jordanians cluster on branches with other Muslim populations as distant as Morocco and Yemen. It should be noted here that the results depend significantly on populations included in the analysis as well as recent admixture events, and so should be treated as an approximate guide to similarity, rather than a full population history.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003316-g003: 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.
Mentions: The previous analyses are based on linkage disequilibrium (LD) pruned data (r2<0.4) since LD can bias cluster analysis. However, identification of haplotypes shared between groups is a valuable tool to infer population history events [12]–[15]. Thus, we phased our data and generated a coancestry matrix using ChromoPainter [16] which reconstruct the haplotype of every individual using the haplotypes of each of the other individuals as possible donors. ChromoPainter computes a similarity measure which is the number of haplotype “chunks” used to reconstruct the recipient individual from each donor individual. We then used fineSTRUCTURE [16] which employ model-based Bayesian clustering to construct a tree that infer population relationships and similarities using ChromoPainter's coancestry matrix. The population tree (Figure 3A) splits Levantine populations in two branches: one leading to Europeans and Central Asians that includes Lebanese, Armenians, Cypriots, Druze and Jews, as well as Turks, Iranians and Caucasian populations; and a second branch composed of Palestinians, Jordanians, Syrians, as well as North Africans, Ethiopians, Saudis, and Bedouins. The tree shows a correlation between religion and the population structures in the Levant: all Jews (Sephardi and Ashkenazi) cluster in one branch; Druze from Mount Lebanon and Druze from Mount Carmel are depicted on a private branch; and Lebanese Christians form a private branch with the Christian populations of Armenia and Cyprus placing the Lebanese Muslims as an outer group. The predominantly Muslim populations of Syrians, Palestinians and Jordanians cluster on branches with other Muslim populations as distant as Morocco and Yemen. It should be noted here that the results depend significantly on populations included in the analysis as well as recent admixture events, and so should be treated as an approximate guide to similarity, rather than a full population history.

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