Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations
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{"title"=>"Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations", "type"=>"journal", "authors"=>[{"first_name"=>"Danielle A.", "last_name"=>"Badro", "scopus_author_id"=>"36645563500"}, {"first_name"=>"Bouchra", "last_name"=>"Douaihy", "scopus_author_id"=>"54792875200"}, {"first_name"=>"Marc", "last_name"=>"Haber", "scopus_author_id"=>"7102207183"}, {"first_name"=>"Sonia C.", "last_name"=>"Youhanna", "scopus_author_id"=>"26431676000"}, {"first_name"=>"Angélique", "last_name"=>"Salloum", "scopus_author_id"=>"54793675800"}, {"first_name"=>"Michella", "last_name"=>"Ghassibe-Sabbagh", "scopus_author_id"=>"36898347500"}, {"first_name"=>"Brian", "last_name"=>"Johnsrud", "scopus_author_id"=>"39861651500"}, {"first_name"=>"Georges", "last_name"=>"Khazen", "scopus_author_id"=>"24314780000"}, {"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"=>"Chris", "last_name"=>"Tyler-Smith", "scopus_author_id"=>"7006076653"}, {"first_name"=>"Daniel E.", "last_name"=>"Platt", "scopus_author_id"=>"7201719040"}, {"first_name"=>"Pierre A.", "last_name"=>"Zalloua", "scopus_author_id"=>"6701479746"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84873811629", "doi"=>"10.1371/journal.pone.0054616", "pui"=>"368227136", "pmid"=>"23382925", "scopus"=>"2-s2.0-84873811629", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"55fe1886-685e-3d03-9848-77ff54b53977", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/ychromosome-mtdna-genetics-reveal-significant-contrasts-affinities-modern-middle-eastern-populations", "reader_count"=>89, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>15, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>34, "Student > Postgraduate"=>4, "Other"=>10, "Student > Master"=>12, "Student > Bachelor"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>15, "Student > Doctoral Student"=>4, "Student > Ph. D. 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  • {"files"=>["https://ndownloader.figshare.com/files/498481"], "description"=>"<p>mtDNA vs. Y-chromosome AMOVA results contrasting mtDNA and Y dendrogram-based classifications.</p>", "links"=>[], "tags"=>["y-chromosome", "amova", "contrasting", "mtdna", "dendrogram-based"], "article_id"=>168976, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_mtDNA_vs_Y_chromosome_AMOVA_results_contrasting_mtDNA_and_Y_dendrogram_based_classifications_/168976", "title"=>"mtDNA vs. Y-chromosome AMOVA results contrasting mtDNA and Y dendrogram-based classifications.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-30 02:29:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/498005"], "description"=>"<p>Frequencies distribution from the current study and from the published data <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054616#pone.0054616-Gonzalez1\" target=\"_blank\">[30]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054616#pone.0054616-AlZahery1\" target=\"_blank\">[31]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054616#pone.0054616-Pereira1\" target=\"_blank\">[35]</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054616#pone.0054616-Cerny1\" target=\"_blank\">[48]</a> as reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054616#pone-0054616-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["mtdna"], "article_id"=>168514, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.g001", "stats"=>{"downloads"=>4, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_distribution_of_mtDNA_haplogroups_/168514", "title"=>"Geographic distribution of mtDNA haplogroups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:21:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/498530"], "description"=>"<p>mtDNA Haplogroup frequencies of 1509 newly sequenced Levantine samples and 3665 samples collected from the literature.</p>", "links"=>[], "tags"=>["haplogroup", "frequencies", "1509", "sequenced", "levantine", "samples", "3665"], "article_id"=>169027, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.t001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_mtDNA_Haplogroup_frequencies_of_1509_newly_sequenced_Levantine_samples_and_3665_samples_collected_from_the_literature_/169027", "title"=>"mtDNA Haplogroup frequencies of 1509 newly sequenced Levantine samples and 3665 samples collected from the literature.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-30 02:30:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/498220"], "description"=>"<p>a) mtDNA <i>F<sub>ST</sub></i> and b) Y-STR <i>R<sub>ST</sub></i> distances with c) mtDNA <i>F<sub>ST</sub></i> and d) Y-STR <i>R<sub>ST</sub></i> mean-linkage dendrogram.</p>", "links"=>[], "tags"=>["multidimensional"], "article_id"=>168726, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nonmetric_Multidimensional_Scaling_/168726", "title"=>"Nonmetric Multidimensional Scaling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:25:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/498383"], "description"=>"<p>The heatmap shows the normalized ratio of the Y <i>F<sub>ST</sub></i> distance with respect to the total distance (Y <i>R<sub>ST</sub></i>+mtDNA <i>F<sub>ST</sub></i> distances). The dendrograms are obtained using complete linkage hierarchical clustering with the Euclidean distance measure.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>168888, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_of_the_Y_Y_mtDNA_distances_/168888", "title"=>"Heatmap of the Y(Y+mtDNA) distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:28:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/498143"], "description"=>"<p>a) Principal Component Analysis of relative frequencies of haplogroups within populations, b) with mean-linkage (UPGMA) dendrogram determined from Euclidean distances.</p>", "links"=>[], "tags"=>["mtdna"], "article_id"=>168651, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054616.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Populations_comparison_based_on_mtDNA_haplogroups_/168651", "title"=>"Populations comparison based on mtDNA haplogroups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:24:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/479893", "https://ndownloader.figshare.com/files/479896", "https://ndownloader.figshare.com/files/479898", "https://ndownloader.figshare.com/files/479899", "https://ndownloader.figshare.com/files/479901", "https://ndownloader.figshare.com/files/479903", "https://ndownloader.figshare.com/files/479905", "https://ndownloader.figshare.com/files/479906", "https://ndownloader.figshare.com/files/479907", "https://ndownloader.figshare.com/files/479908", "https://ndownloader.figshare.com/files/479911"], "description"=>"<div><p>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 <em>F<sub>ST</sub></em>'s, <em>R<sub>ST</sub></em>'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.</p> </div>", "links"=>[], "tags"=>["y-chromosome", "mtdna", "genetics", "contrasts", "affinities", "populations", "european", "african", "populations"], "article_id"=>154898, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Danielle A. Badro", "Bouchra Douaihy", "Marc Haber", "Sonia C. Youhanna", "Angélique Salloum", "Michella Ghassibe-Sabbagh", "Brian Johnsrud", "Georges Khazen", "Elizabeth Matisoo-Smith", "David F. Soria-Hernanz", "R. Spencer Wells", "Chris Tyler-Smith", "Daniel E. Platt", "Pierre A. Zalloua"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0054616.s001", "https://dx.doi.org/10.1371/journal.pone.0054616.s002", "https://dx.doi.org/10.1371/journal.pone.0054616.s003", "https://dx.doi.org/10.1371/journal.pone.0054616.s004", "https://dx.doi.org/10.1371/journal.pone.0054616.s005", "https://dx.doi.org/10.1371/journal.pone.0054616.s006", "https://dx.doi.org/10.1371/journal.pone.0054616.s007", "https://dx.doi.org/10.1371/journal.pone.0054616.s008", "https://dx.doi.org/10.1371/journal.pone.0054616.s009", "https://dx.doi.org/10.1371/journal.pone.0054616.s010", "https://dx.doi.org/10.1371/journal.pone.0054616.s011"], "stats"=>{"downloads"=>78, "page_views"=>59, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Y_Chromosome_and_mtDNA_Genetics_Reveal_Significant_Contrasts_in_Affinities_of_Modern_Middle_Eastern_Populations_with_European_and_African_Populations__/154898", "title"=>"Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-30 01:21:38"}

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Relative Metric

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