Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation
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{"title"=>"Multiple ITS copies reveal extensive hybridization within Rheum (polygonaceae), a genus that has undergone rapid radiation", "type"=>"journal", "authors"=>[{"first_name"=>"Dongshi", "last_name"=>"Wan", "scopus_author_id"=>"22986737300"}, {"first_name"=>"Yongshuai", "last_name"=>"Sun", "scopus_author_id"=>"36194171300"}, {"first_name"=>"Xu", "last_name"=>"Zhang", "scopus_author_id"=>"56148962500"}, {"first_name"=>"Xiaotao", "last_name"=>"Bai", "scopus_author_id"=>"56071337900"}, {"first_name"=>"Jun", "last_name"=>"Wang", "scopus_author_id"=>"55973381700"}, {"first_name"=>"Ailan", "last_name"=>"Wang", "scopus_author_id"=>"23399033500"}, {"first_name"=>"Richard", "last_name"=>"Milne", "scopus_author_id"=>"35240689000"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372629990", "issn"=>"19326203", "pmid"=>"24587023", "doi"=>"10.1371/journal.pone.0089769", "sgr"=>"84896337278", "scopus"=>"2-s2.0-84896337278"}, "id"=>"c80b7318-0a4a-3f82-bf02-33e76c0add05", "abstract"=>"BACKGROUND: During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.\\n\\nCONCLUSIONS: These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.", "link"=>"http://www.mendeley.com/research/multiple-copies-reveal-extensive-hybridization-within-rheum-polygonaceae-genus-undergone-rapid-radia", "reader_count"=>15, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>12, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"Brazil"=>1, "Germany"=>1, "Nepal"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1401333"], "description"=>"<p>*Indicates sequences that were retrieve from GenBank Dateabase (?, not affirmative or reported). Samples were collected in China except <i>R. rhaponticuml</i>.</p><p>Chromosomal numbers reported by Jaretzky (1928), Chin and Youngken (1947), Hu et al. (2007) and Liu et al. (2010).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "taxa", "sources", "materials", "accessions", "sequences"], "article_id"=>946869, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_taxa_and_sources_of_plant_materials_analyzed_and_accessions_of_ITS_sequences_in_GenBank_/946869", "title"=>"List of taxa and sources of plant materials analyzed and accessions of ITS sequences in GenBank.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1401332"], "description"=>"<p>Bootstrap support values from ML analyses using PHYML are given below branches and the corresponding Bayesian posterior probabilities from Bayesian analyses using MrBayes are shown above branches. For simplification, three monophyletic clade A1, A, B, C, D, were marked and also a paraphyletic group A2 on the cpDNA tree. On the ITS tree, four clades and ploidy of each <i>Rheum</i> species was marked and the seven species with multiple clones were also marked with clone serial numbers. The different colours branches were used to mark species with different characters, and the branches of glasshouse species was marked with triangle tag.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "phylogenetic", "trees", "reconstructed", "nrdna", "matrix", "log-likelihood", "cpdna"], "article_id"=>946868, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769.g002", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_phylogenetic_trees_reconstructed_using_maximum_likelihood_method_on_a_basis_of_nrDNA_ITS_matrix_left_Log_likelihood_8202_8202_8722_6967_11_and_cpDNA_matrix_right_Log_likelihood_8202_8202_8722_30277_42_/946868", "title"=>"The phylogenetic trees reconstructed using maximum likelihood method on a basis of nrDNA ITS matrix (left, Log-likelihood  = −6967.11) and cpDNA matrix (right, Log-likelihood  = −30277.42).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1401337"], "description"=>"<div><p>Background</p><p>During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.</p><p>Methodology/Principal Findings</p><p>In this study, we cloned and sequenced ITS regions for 30 species of the genus <i>Rheum</i>, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. <i>Rheum globulosum</i>, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.</p><p>Conclusions</p><p>These findings suggested that hybridization among QTP species of <i>Rheum</i> has been extensive, and that a role of hybridization in diversification of <i>Rheum</i> requires investigation.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "copies", "hybridization", "genus", "undergone"], "article_id"=>946873, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multiple_ITS_Copies_Reveal_Extensive_Hybridization_within_Rheum_Polygonaceae_a_Genus_That_Has_Undergone_Rapid_Radiation/946873", "title"=>"Multiple ITS Copies Reveal Extensive Hybridization within <i>Rheum</i> (Polygonaceae), a Genus That Has Undergone Rapid Radiation", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1401335"], "description"=>"<p>Tandem repeats found from ITS sequences of <i>Rheum</i>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "repeats", "sequences"], "article_id"=>946871, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tandem_repeats_found_from_ITS_sequences_of_Rheum_/946871", "title"=>"Tandem repeats found from ITS sequences of <i>Rheum</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1401334"], "description"=>"<p>p-distances between ITS within and between species, involving species with two divergent versions of ITS.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "involving", "divergent", "versions"], "article_id"=>946870, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_p_distances_between_ITS_within_and_between_species_involving_species_with_two_divergent_versions_of_ITS_/946870", "title"=>"p-distances between ITS within and between species, involving species with two divergent versions of ITS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1401331"], "description"=>"<p>Schematic illustration of the distribution of substitution sites across the entire ITS region obtained from seven species of <i>Rheum</i>, using the <i>R. globulosum</i> ITS region as reference (red  =  T, purple  =  G, green  =  A, blue  =  C, yellow  =  gap).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Comparative genomics", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "genetics", "Plant genetics", "Plant science", "Plant phylogenetics", "Population biology", "substitution", "sites"], "article_id"=>946867, "categories"=>["Biological Sciences"], "users"=>["Dongshi Wan", "Yongshuai Sun", "Xu Zhang", "Xiaotao Bai", "Jun Wang", "Ailan Wang", "Richard Milne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0089769.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_illustration_of_the_distribution_of_substitution_sites_across_the_entire_ITS_region_obtained_from_seven_species_of_Rheum_using_the_R_globulosum_ITS_region_as_reference_red__T_purple__G_green__A_blue__C_yellow__gap_/946867", "title"=>"Schematic illustration of the distribution of substitution sites across the entire ITS region obtained from seven species of <i>Rheum</i>, using the <i>R. globulosum</i> ITS region as reference (red  =  T, purple  =  G, green  =  A, blue  =  C, yellow  =  gap).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 03:21:07"}

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