Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture
Publication Date
February 28, 2013
Journal
PLOS Genetics
Authors
Marc Haber, Dominique Gauguier, Sonia Youhanna, Nick Patterson, et al
Volume
9
Issue
2
Pages
e1003316
DOI
http://doi.org/10.1371/journal.pgen.1003316
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1003316
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23468648
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585000
Europe PMC
http://europepmc.org/abstract/MED/23468648
Web of Science
000315638300061
Scopus
84874762618
Mendeley
http://www.mendeley.com/research/genomewide-diversity-levant-reveals-recent-structuring-culture
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{"title"=>"Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture", "type"=>"journal", "authors"=>[{"first_name"=>"Marc", "last_name"=>"Haber", "scopus_author_id"=>"7102207183"}, {"first_name"=>"Dominique", "last_name"=>"Gauguier", "scopus_author_id"=>"7004461140"}, {"first_name"=>"Sonia", "last_name"=>"Youhanna", "scopus_author_id"=>"26431676000"}, {"first_name"=>"Nick", "last_name"=>"Patterson", "scopus_author_id"=>"7006515330"}, {"first_name"=>"Priya", "last_name"=>"Moorjani", "scopus_author_id"=>"24069108500"}, {"first_name"=>"Laura R.", "last_name"=>"Botigué", "scopus_author_id"=>"24166507300"}, {"first_name"=>"Daniel E.", "last_name"=>"Platt", "scopus_author_id"=>"7201719040"}, {"first_name"=>"Elizabeth", "last_name"=>"Matisoo-Smith", "scopus_author_id"=>"6602155766"}, {"first_name"=>"David F.", "last_name"=>"Soria-Hernanz", "scopus_author_id"=>"8676103200"}, {"first_name"=>"R. Spencer", "last_name"=>"Wells", "scopus_author_id"=>"39863715400"}, {"first_name"=>"Jaume", "last_name"=>"Bertranpetit", "scopus_author_id"=>"7005566413"}, {"first_name"=>"Chris", "last_name"=>"Tyler-Smith", "scopus_author_id"=>"7006076653"}, {"first_name"=>"David", "last_name"=>"Comas", "scopus_author_id"=>"7003976031"}, {"first_name"=>"Pierre A.", "last_name"=>"Zalloua", "scopus_author_id"=>"6701479746"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84874762618", "doi"=>"10.1371/journal.pgen.1003316", "issn"=>"15537390", "pui"=>"368490537", "isbn"=>"1553-7404", "pmid"=>"23468648", "scopus"=>"2-s2.0-84874762618"}, "id"=>"27a19d3b-941e-34cc-8dbd-1bfc343bddbe", "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.", "link"=>"http://www.mendeley.com/research/genomewide-diversity-levant-reveals-recent-structuring-culture", "reader_count"=>112, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Librarian"=>2, "Student > Doctoral Student"=>7, "Researcher"=>25, "Student > Ph. D. Student"=>32, "Student > Postgraduate"=>6, "Student > Master"=>12, "Other"=>6, "Student > Bachelor"=>8, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Librarian"=>2, "Student > Doctoral Student"=>7, "Researcher"=>25, "Student > Ph. D. Student"=>32, "Student > Postgraduate"=>6, "Student > Master"=>12, "Other"=>6, "Student > Bachelor"=>8, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>77, "Arts and Humanities"=>6, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>14, "Medicine and Dentistry"=>1, "Psychology"=>2, "Social Sciences"=>4, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>4}, "Psychology"=>{"Psychology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>6}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>77}, "Computer Science"=>{"Computer Science"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Austria"=>1, "United States"=>2, "Brazil"=>1, "Italy"=>1, "France"=>1, "Portugal"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/973423"], "description"=>"<p>The SNPs were pruned from >500,000 SNPs excluding r<sup>2</sup>>0.4. The samples were classified by their religion or region of origin.</p>", "links"=>[], "tags"=>["scaling", "snps", "lebanese", "samples"], "article_id"=>641808, "categories"=>["Genetics"], "users"=>["Marc Haber", "Dominique Gauguier", "Sonia Youhanna", "Nick Patterson", "Priya Moorjani", "Laura R. Botigué", "Daniel E. Platt", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Jaume Bertranpetit", "Chris Tyler-Smith", "David Comas", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003316.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_scaling_of_gt_240K_SNPs_in_1_341_Lebanese_samples_showing_the_first_four_dimensions_/641808", "title"=>"Multidimensional scaling of >240K SNPs in 1,341 Lebanese samples showing the first four dimensions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 11:07:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/973426"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["scaling", "snps"], "article_id"=>641811, "categories"=>["Genetics"], "users"=>["Marc Haber", "Dominique Gauguier", "Sonia Youhanna", "Nick Patterson", "Priya Moorjani", "Laura R. Botigué", "Daniel E. Platt", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Jaume Bertranpetit", "Chris Tyler-Smith", "David Comas", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003316.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_scaling_of_gt_240K_SNPs_showing_the_top_two_dimensions_/641811", "title"=>"Multidimensional scaling of >240K SNPs showing the top two dimensions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 11:08:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/973429"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["relationships", "genome-wide"], "article_id"=>641814, "categories"=>["Genetics"], "users"=>["Marc Haber", "Dominique Gauguier", "Sonia Youhanna", "Nick Patterson", "Priya Moorjani", "Laura R. Botigué", "Daniel E. Platt", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Jaume Bertranpetit", "Chris Tyler-Smith", "David Comas", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003316.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_relationships_from_genome_wide_haplotypes_/641814", "title"=>"Population relationships from genome-wide haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 11:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/973434"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["levantine", "modal"], "article_id"=>641818, "categories"=>["Genetics"], "users"=>["Marc Haber", "Dominique Gauguier", "Sonia Youhanna", "Nick Patterson", "Priya Moorjani", "Laura R. Botigué", "Daniel E. Platt", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Jaume Bertranpetit", "Chris Tyler-Smith", "David Comas", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003316.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_the_Levantine_and_Middle_Eastern_modal_components_/641818", "title"=>"Comparisons of the Levantine and Middle Eastern modal components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 11:10:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/973448", "https://ndownloader.figshare.com/files/973450", "https://ndownloader.figshare.com/files/973454", "https://ndownloader.figshare.com/files/973458", "https://ndownloader.figshare.com/files/973464", "https://ndownloader.figshare.com/files/973467", "https://ndownloader.figshare.com/files/973471", "https://ndownloader.figshare.com/files/973472", "https://ndownloader.figshare.com/files/973473", "https://ndownloader.figshare.com/files/973474"], "description"=>"<div><p>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.</p> </div>", "links"=>[], "tags"=>["genome-wide", "levant", "reveals", "structuring", "culture"], "article_id"=>641829, "categories"=>["Genetics"], "users"=>["Marc Haber", "Dominique Gauguier", "Sonia Youhanna", "Nick Patterson", "Priya Moorjani", "Laura R. Botigué", "Daniel E. Platt", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Jaume Bertranpetit", "Chris Tyler-Smith", "David Comas", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003316.s001", "https://dx.doi.org/10.1371/journal.pgen.1003316.s002", "https://dx.doi.org/10.1371/journal.pgen.1003316.s003", "https://dx.doi.org/10.1371/journal.pgen.1003316.s004", "https://dx.doi.org/10.1371/journal.pgen.1003316.s005", "https://dx.doi.org/10.1371/journal.pgen.1003316.s006", "https://dx.doi.org/10.1371/journal.pgen.1003316.s007", "https://dx.doi.org/10.1371/journal.pgen.1003316.s008", "https://dx.doi.org/10.1371/journal.pgen.1003316.s009", "https://dx.doi.org/10.1371/journal.pgen.1003316.s010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Diversity_in_the_Levant_Reveals_Recent_Structuring_by_Culture__/641829", "title"=>"Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-01 11:12:44"}

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biogeography", "average_usage"=>[321, 494, 634, 734, 850, 962, 1060, 1140, 1226, 1319, 1409, 1493, 1559]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Paleontology", "average_usage"=>[605, 959, 1140, 1273, 1412, 1552, 1709, 1830, 1959, 2077, 2241, 2360, 2456]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[269, 448, 558, 658, 744, 830, 914, 995, 1068, 1139, 1214, 1284, 1349]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[296, 488, 620, 717, 828, 938, 1038, 1130, 1230, 1328, 1414, 1502, 1592]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[284, 475, 603, 722, 826, 928, 1026, 1129, 1225, 1310, 1390, 1468, 1549]}, {"subject_area"=>"/Ecology and environmental sciences/Biogeography", "average_usage"=>[320, 517, 642, 738, 850, 955, 1039, 1136, 1226, 1315, 1406, 1495, 1565]}]}
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