Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit
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{"title"=>"Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit", "type"=>"journal", "authors"=>[{"first_name"=>"Mari", "last_name"=>"Järve", "scopus_author_id"=>"35078643800"}, {"first_name"=>"Lev A.", "last_name"=>"Zhivotovsky", "scopus_author_id"=>"7003737918"}, {"first_name"=>"Siiri", "last_name"=>"Rootsi", "scopus_author_id"=>"6506947123"}, {"first_name"=>"Hela", "last_name"=>"Help", "scopus_author_id"=>"57199575179"}, {"first_name"=>"Evgeny I.", "last_name"=>"Rogaev", "scopus_author_id"=>"35391858800"}, {"first_name"=>"Elza K.", "last_name"=>"Khusnutdinova", "scopus_author_id"=>"35381528600"}, {"first_name"=>"Toomas", "last_name"=>"Kivisild", "scopus_author_id"=>"55804366500"}, {"first_name"=>"Juan J.", "last_name"=>"Sanchez", "scopus_author_id"=>"7403998988"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"70349696186", "pmid"=>"19789645", "pui"=>"355371512", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-70349696186", "doi"=>"10.1371/journal.pone.0007276", "issn"=>"19326203"}, "id"=>"a8a24321-dbc6-3244-a572-478edffe17e2", "abstract"=>"BACKGROUND: Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.\\n\\nPRINCIPAL FINDINGS: In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.\\n\\nCONCLUSIONS: Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.", "link"=>"http://www.mendeley.com/research/decreased-rate-evolution-y-chromosome-str-loci-increased-size-repeat-unit", "reader_count"=>36, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>4, "Agricultural and Biological Sciences"=>26, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>2, "Brazil"=>1, "United Kingdom"=>1, "Malaysia"=>1, "Australia"=>2, "France"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/881646"], "description"=>"<p>Coalescence age estimates, based on penta/hexanucleotide and tri/tetranucleotide repeats and the respective mutation rates, and ancestral haplotypes (estimated as the weighted median number of repeats at each locus) of Y chromosome haplogroups. SNP-based age estimates from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone.0007276-Karafet1\" target=\"_blank\">[24]</a> are reported for comparison. Multicopy markers DYF411S1 and DYS385a/b were excluded from the calculations.</p>", "links"=>[], "tags"=>["estimates", "ancestral", "haplotypes", "chromosome"], "article_id"=>552096, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coalescence_age_estimates_and_ancestral_haplotypes_of_Y_chromosome_haplogroups_/552096", "title"=>"Coalescence age estimates and ancestral haplotypes of Y chromosome haplogroups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-30 00:34:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/881695"], "description"=>"<p>Penta- and hexanucleotide markers shown in italics. Multicopy markers DYF411S1 and DYS385a/b were excluded from the calculations.</p>1<p>Europe, 14 R1a+14 R1b1b2 samples.</p>2<p>8 balanced samples.</p>3<p>8 R+4 Q samples.</p>4<p>12 P+4 NO+1 L samples.</p>5<p>27 samples, incl 17 K.</p><p>α–proportion of the average variance of the younger (<.3) versus older (≥.7) clades relative to their respective age estimates. α = [mean variance(R1a, R1b1b2)/mean variance(P,K,F)]/[age(R1a, R1b1b2)/age(P,K,F)].</p>*<p>p<0.05.</p>**<p>p<0.01.</p>", "links"=>[], "tags"=>["str", "locus", "variances", "haplogroup"], "article_id"=>552141, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.t004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_dynamics_of_different_STR_loci_8211_time_series_of_STR_locus_variances_by_haplogroup_age_estimates_/552141", "title"=>"Temporal dynamics of different STR loci–time series of STR locus variances by haplogroup age estimates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-30 00:35:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/881606"], "description"=>"<p>Multicopy markers DYF411S1 and DYS385a/b, in which cases it was impossible to unambiguously distinguish the two copies, were excluded from the calculations.</p>*<p>Haplogroups R1a and R1b1b were represented by the same samples as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone-0007276-g001\" target=\"_blank\">Figures 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone-0007276-g002\" target=\"_blank\">2</a> (4 samples from R1a and 3 from R1b1b, marked with grey shading in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone.0007276.s001\" target=\"_blank\">Table S1</a>).</p>", "links"=>[], "tags"=>["variance"], "article_id"=>552062, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.t002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_average_repeat_variance_and_diversity_between_penta_hexa_and_tri_tetra_markers_/552062", "title"=>"Comparison of the average repeat variance and diversity between penta/hexa and tri/tetra markers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-30 00:34:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/881314"], "description"=>"<p>Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 9 penta- and hexanucleotide STR markers and SNPs; B network based solely on the data of the 9 penta- and hexanucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS448, DYS596, Y PENTA 1, Y PENTA 2, DYS438, DYS594, DYS643, DYS645, DYF411S1.</p>", "links"=>[], "tags"=>["str", "haplotypes", "penta-", "hexanucleotide"], "article_id"=>551764, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Networks_of_STR_haplotypes_based_on_penta_and_hexanucleotide_STRs_with_and_without_SNPs_/551764", "title"=>"Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-30 00:29:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/881512"], "description"=>"<p>Median joining network of all the samples belonging to haplogroups R1a and R1b1b, based on the data of all the 24 markers used in this study. Open circles represent haplotypes of haplogroup R1a, black those of haplogroup R1b1b2, grey those of haplogroup R1b1b1. 13 nearly identical Altaian and Tuva samples form a separate branch within R1a, indicated by a red circle.</p>", "links"=>[], "tags"=>["r1a", "r1b1b", "str", "haplotypes"], "article_id"=>551960, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.g003", "stats"=>{"downloads"=>9, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_of_R1a_and_R1b1b_STR_haplotypes_based_on_the_data_of_all_the_markers_/551960", "title"=>"Network of R1a and R1b1b STR haplotypes based on the data of all the markers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-30 00:32:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/881578"], "description"=>"<p>Repeat units of the markers, GenBank accession numbers with the positions of the beginning of the forward primer and the end of the reverse primer in the GenBank sequence, and the primers used to amplify the markers. The ‘gtt’ or ‘gttt’ at the 5′ end of three of the reverse primers denotes a non-specific primer ‘tail’.</p>*<p>novel markers.</p>**<p>DYF411S1 was sequenced from the opposite strand of DNA compared to what was described by <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone.0007276-Kayser2\" target=\"_blank\">[7]</a>. Complex repeats are presented as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007276#pone.0007276-Kayser2\" target=\"_blank\">[7]</a>, but only the variable penta/hexanucleotide repeats were counted (n repeats).</p>", "links"=>[], "tags"=>["markers", "analysed", "included"], "article_id"=>552028, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_markers_analysed_in_this_study_not_included_in_the_AmpFlSTR_174_Yfiler_8482_Kit_/552028", "title"=>"The markers analysed in this study not included in the AmpFlSTR® Yfiler™ Kit.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-30 00:33:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/436989"], "description"=>"<div><h3>Background</h3><p>Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.</p><h3>Principal Findings</h3><p>In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.</p><h3>Conclusions</h3><p>Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.</p></div>", "links"=>[], "tags"=>["decreased", "chromosome", "str", "loci"], "article_id"=>146168, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276", "stats"=>{"downloads"=>6, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Decreased_Rate_of_Evolution_in_Y_Chromosome_STR_Loci_of_Increased_Size_of_the_Repeat_Unit/146168", "title"=>"Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-30 01:42:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/881420"], "description"=>"<p>Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 15 tri- and tetranucleotide STR markers and SNPs; B network based solely on the data of the 15 tri- and tetranucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS439, DYS456, DYS458, DYS635, Y GATA H4.</p>", "links"=>[], "tags"=>["str", "haplotypes", "tri-", "tetranucleotide"], "article_id"=>551873, "categories"=>["Evolutionary Biology"], "users"=>["Mari Järve", "Lev A. Zhivotovsky", "Siiri Rootsi", "Hela Help", "Evgeny I. Rogaev", "Elza K. Khusnutdinova", "Toomas Kivisild", "Juan J. Sanchez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007276.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Networks_of_STR_haplotypes_based_on_tri_and_tetranucleotide_STRs_with_and_without_SNPs_/551873", "title"=>"Networks of STR haplotypes based on tri- and tetranucleotide STRs, with and without SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-30 00:31:13"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
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  • {"unique-ip"=>"20", "full-text"=>"20", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"8", "full-text"=>"11", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
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  • {"unique-ip"=>"12", "full-text"=>"17", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"18", "full-text"=>"20", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
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Relative Metric

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