New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0
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{"title"=>"New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0", "type"=>"journal", "authors"=>[{"first_name"=>"Vanesa", "last_name"=>"Álvarez-Iglesias", "scopus_author_id"=>"17343352900"}, {"first_name"=>"Ana", "last_name"=>"Mosquera-Miguel", "scopus_author_id"=>"23493010800"}, {"first_name"=>"Maria", "last_name"=>"Cerezo", "scopus_author_id"=>"23481403300"}, {"first_name"=>"Beatriz", "last_name"=>"Quintáns", "scopus_author_id"=>"6507149467"}, {"first_name"=>"Maria Teresa", "last_name"=>"Zarrabeitia", "scopus_author_id"=>"7004208162"}, {"first_name"=>"Ivon", "last_name"=>"Cuscó", "scopus_author_id"=>"24173216300"}, {"first_name"=>"Maria Victoria", "last_name"=>"Lareu", "scopus_author_id"=>"7004398060"}, {"first_name"=>"Óscar", "last_name"=>"García", "scopus_author_id"=>"7102412860"}, {"first_name"=>"Luis", "last_name"=>"Pérez-Jurado", "scopus_author_id"=>"7004218993"}, {"first_name"=>"Ángel", "last_name"=>"Carracedo", "scopus_author_id"=>"7006062179"}, {"first_name"=>"Antonio", "last_name"=>"Salas", "scopus_author_id"=>"7102443063"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"64549148932", "pui"=>"354461656", "pmid"=>"19340307", "issn"=>"19326203", "scopus"=>"2-s2.0-64549148932", "doi"=>"10.1371/journal.pone.0005112"}, "id"=>"5e6da808-f30e-3c7b-ba7b-76e771c5b2e9", "abstract"=>"BACKGROUND: R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (approximately 40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6+/-8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).\\n\\nCONCLUSIONS/SIGNIFICANCE: In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.", "link"=>"http://www.mendeley.com/research/new-population-phylogenetic-features-internal-variation-within-mitochondrial-dna-macrohaplogroup-r0", "reader_count"=>56, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>7, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>7, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>41, "Medicine and Dentistry"=>3, "Social Sciences"=>2, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>41}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>4, "Australia"=>1, "Spain"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/902971"], "description"=>"<p>Dots in the map of H* indicate the location of the populations used. Codes for populations are: <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Achilli1\" target=\"_blank\">[1]</a> Galicia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-AbuAmero1\" target=\"_blank\">[2]</a> Cantabria, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Loogvli1\" target=\"_blank\">[3]</a> Catalonia (present study); <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Roostalu1\" target=\"_blank\">[4]</a> Volga-Ural, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Torroni1\" target=\"_blank\">[5]</a> Finland, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Brandsttter1\" target=\"_blank\">[6]</a> Estonia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Quintns1\" target=\"_blank\">[7]</a> Eastern Slavs, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-lvarezIglesias1\" target=\"_blank\">[8]</a> Slovakia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-lvarezIglesias2\" target=\"_blank\">[9]</a> France, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Coble1\" target=\"_blank\">[10]</a> Balkans, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Kong1\" target=\"_blank\">[11]</a> Central Asia <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Loogvli1\" target=\"_blank\">[3]</a>; <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Achilli2\" target=\"_blank\">[12]</a> Turkey, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Behar1\" target=\"_blank\">[13]</a> Armenia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Achilli3\" target=\"_blank\">[14]</a> Georgia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Brandsttter2\" target=\"_blank\">[15]</a> Northwest Caucasus, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Salas1\" target=\"_blank\">[16]</a> Daghestan, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Salas2\" target=\"_blank\">[17]</a> Ossetia, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-MacaMeyer1\" target=\"_blank\">[18]</a> Karatchians-Balkarians, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Pereira1\" target=\"_blank\">[19]</a> Syria, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Andrews1\" target=\"_blank\">[20]</a> Lebanon, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-vanOven1\" target=\"_blank\">[21]</a> Jordan, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Achilli4\" target=\"_blank\">[22]</a> Arabian Peninsula <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Roostalu1\" target=\"_blank\">[4]</a>; <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Torroni2\" target=\"_blank\">[23]</a> Austria <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Brandsttter1\" target=\"_blank\">[6]</a>; <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Bandelt1\" target=\"_blank\">[24]</a> Tuscani <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Achilli3\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["maps", "haplogroup", "frequencies", "haplogroups"], "article_id"=>573420, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005112.g003", "stats"=>{"downloads"=>28, "page_views"=>509, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_maps_of_haplogroup_frequencies_for_haplogroups_H_H1_H2a_H3_H4_H5a_H6a_H7_H8_H11_/573420", "title"=>"Geographic maps of haplogroup frequencies for haplogroups H*, H1, H2a, H3, H4, H5a, H6a, H7, H8, H11.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-02 00:57:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/902794"], "description"=>"<p>An expanded view of the haplogroup H phylogeny is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone-0005112-g002\" target=\"_blank\">Figure 2</a>. Underlined positions signal parallel mutations, while @ indicates a back mutation. In bold are the control region variants, whereas dots indicate the SNPs selected and genotyped in the present study.</p>", "links"=>[], "tags"=>["haplogroup"], "article_id"=>573242, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005112.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_haplogroup_R0_/573242", "title"=>"Phylogeny of haplogroup R0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-02 00:54:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/902870"], "description"=>"<p>See legend of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone-0005112-g001\" target=\"_blank\">Figure 1</a> for more details.</p>", "links"=>[], "tags"=>["haplogroup"], "article_id"=>573320, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005112.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_haplogroup_H_/573320", "title"=>"Phylogeny of haplogroup H.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-02 00:55:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/446921", "https://ndownloader.figshare.com/files/447102", "https://ndownloader.figshare.com/files/447214", "https://ndownloader.figshare.com/files/447258", "https://ndownloader.figshare.com/files/447275", "https://ndownloader.figshare.com/files/447295", "https://ndownloader.figshare.com/files/447305"], "description"=>"<div><h3>Background</h3><p>R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (∼40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.</p><h3>Methodology/Principal Findings</h3><p>We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (∼57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6±8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).</p><h3>Conclusions/Significance</h3><p>In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.</p></div>", "links"=>[], "tags"=>["phylogenetic", "features", "mitochondrial", "dna", "macro-haplogroup", "r0"], "article_id"=>148085, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005112.s001", "https://dx.doi.org/10.1371/journal.pone.0005112.s002", "https://dx.doi.org/10.1371/journal.pone.0005112.s003", "https://dx.doi.org/10.1371/journal.pone.0005112.s004", "https://dx.doi.org/10.1371/journal.pone.0005112.s005", "https://dx.doi.org/10.1371/journal.pone.0005112.s006", "https://dx.doi.org/10.1371/journal.pone.0005112.s007"], "stats"=>{"downloads"=>36, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/New_Population_and_Phylogenetic_Features_of_the_Internal_Variation_within_Mitochondrial_DNA_Macro_Haplogroup_R0/148085", "title"=>"New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-04-02 02:14:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/903138"], "description"=>"<p><i>N</i> = sample size, <i>k</i> = number of different haplotypes (divided by <i>N</i> in brackets).</p><p><i>S</i> = Number of polymorphic (segregating) sites.</p><p><i>N<sub>mut</sub></i> = total number of mutations.</p><p><i>H</i> = haplotype diversity and standard error.</p><p>π = nucleotide diversity and standard error.</p><p><i>M</i> = average number of nucleotide differences.</p><p><i>V</i><sub>O</sub>(<i>M</i>) = observed variance of <i>M</i>.</p><p><i>r</i> = Harpending's (raggedness) index.</p><p><i>D</i> = Tajima's test of selective neutrality.</p><p><i>FL</i> = Fu and Li's D* statistics.</p><p>Statistical significance: *, <i>P</i>-value<0.05.</p>**<p><i>P</i>-value<0.02.</p>*1<p>Present study.</p>*2<p>Loogväli et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Loogvli1\" target=\"_blank\">[3]</a>.</p>*3<p>Roostalu et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Roostalu1\" target=\"_blank\">[4]</a>.</p>*4<p>Brandstätter et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005112#pone.0005112-Brandsttter2\" target=\"_blank\">[15]</a>.</p>", "links"=>[], "tags"=>["hvs-i", "sequences", "iberian", "populations", "european"], "article_id"=>573583, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005112.t001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_HVS_I_sequences_in_the_North_Iberian_populations_analyzed_in_the_present_article_and_other_European_populations_/573583", "title"=>"Summary statistics of HVS-I sequences in the North Iberian populations analyzed in the present article and other European populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-02 00:59:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/903069"], "description"=>"<p>Phylogeny of haplogroup H2a5.</p>", "links"=>[], "tags"=>["haplogroup"], "article_id"=>573518, "categories"=>["Genetics"], "users"=>["Vanesa Álvarez-Iglesias", "Ana Mosquera-Miguel", "María Cerezo", "Beatriz Quintáns", "Maria Teresa Zarrabeitia", "Ivon Cuscó", "María Victoria Lareu", "Óscar García", "Luis Pérez-Jurado", "Ángel Carracedo", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005112.g004", "stats"=>{"downloads"=>0, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_haplogroup_H2a5_/573518", "title"=>"Phylogeny of haplogroup H2a5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-02 00:58:38"}

PMC Usage Stats | Further Information

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Relative Metric

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