Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria
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{"title"=>"Coalescent simulations reveal hybridization and incomplete lineage sorting in mediterranean Linaria", "type"=>"journal", "authors"=>[{"first_name"=>"José Luis", "last_name"=>"Blanco-Pastor", "scopus_author_id"=>"54390838700"}, {"first_name"=>"Pablo", "last_name"=>"Vargas", "scopus_author_id"=>"35270381000"}, {"first_name"=>"Bernard E.", "last_name"=>"Pfeil", "scopus_author_id"=>"6701678419"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "pmid"=>"22768061", "doi"=>"10.1371/journal.pone.0039089", "pui"=>"365133243", "issn"=>"19326203", "sgr"=>"84863085677", "scopus"=>"2-s2.0-84863085677"}, "id"=>"dc9ac409-f57a-3711-9385-5ab8c3dfdee0", "abstract"=>"We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnL(UAG), trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.", "link"=>"http://www.mendeley.com/research/coalescent-simulations-reveal-hybridization-incomplete-lineage-sorting-mediterranean-linaria", "reader_count"=>111, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>31, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>40, "Student > Postgraduate"=>5, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>31, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>40, "Student > Postgraduate"=>5, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>96, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2, "Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>96}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>5}}, "reader_count_by_country"=>{"New Zealand"=>1, "Canada"=>1, "Sweden"=>2, "United States"=>5, "Brazil"=>2, "South Africa"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/616086"], "description"=>"<p>Divergence dates of parental lineages of hybrid species presented as mean age of divergence and 95% highest posterior density (HPD) intervals based on the *BEAST multilabelled species tree analysis (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g005\" target=\"_blank\">Figure 5</a>).</p>", "links"=>[], "tags"=>["dates", "lineages", "hybrid", "presented", "divergence", "highest", "posterior", "intervals", "multilabelled"], "article_id"=>286572, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t007", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_dates_of_parental_lineages_of_hybrid_species_presented_as_mean_age_of_divergence_and_95_highest_posterior_density_HPD_intervals_based_on_the_BEAST_multilabelled_species_tree_analysis_Figure_5_/286572", "title"=>"Divergence dates of parental lineages of hybrid species presented as mean age of divergence and 95% highest posterior density (HPD) intervals based on the *BEAST multilabelled species tree analysis (Figure 5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:49:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/616188"], "description"=>"<p>Morphological key traits of the subsections proposed for section <i>Supinae</i> regarding the results obtained in the *BEAST species tree analysis of ITS, AGT1 and cpDNA sequences (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g004\" target=\"_blank\">Figure 4</a>).</p>", "links"=>[], "tags"=>["subsections", "agt1", "cpdna", "sequences"], "article_id"=>286682, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t004", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_key_traits_of_the_subsections_proposed_for_section_Supinae_regarding_the_results_obtained_in_the_BEAST_species_tree_analysis_of_ITS_AGT1_and_cpDNA_sequences_Figure_4_/286682", "title"=>"Morphological key traits of the subsections proposed for section <i>Supinae</i> regarding the results obtained in the *BEAST species tree analysis of ITS, AGT1 and cpDNA sequences (Figure 4).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:51:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/615718"], "description"=>"<p>An example illustrating the method used for the detection of potential hybrids. It is shown the effect of the exclusion of <i>L. glauca</i> ssp. <i>olcadium</i> on the differences between base line and observed distributions of tree distances.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>286213, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_potential_hybrids_/286213", "title"=>"Detection of potential hybrids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:43:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/616159"], "description"=>"<p>Divergence dates of clades of <i>Linaria</i> sect <i>Supinae</i>, presented as mean crown ages and 95% highest posterior density (HPD) intervals based on the *BEAST species tree analysis (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g004\" target=\"_blank\">Figure 4</a>).</p>", "links"=>[], "tags"=>["dates", "clades", "sect", "presented", "crown", "ages", "highest", "posterior", "intervals"], "article_id"=>286644, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_dates_of_clades_of_Linaria_sect_Supinae_presented_as_mean_crown_ages_and_95_highest_posterior_density_HPD_intervals_based_on_the_BEAST_species_tree_analysis_Figure_4_/286644", "title"=>"Divergence dates of clades of <i>Linaria</i> sect <i>Supinae</i>, presented as mean crown ages and 95% highest posterior density (HPD) intervals based on the *BEAST species tree analysis (Figure 4).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:50:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/615887"], "description"=>"<p>Maximum clade credibility tree obtained in the multilabelled *BEAST species tree analysis by including the presumed hybrids connected in two labels (L1 and L2) representing the two parental lineages of hybrid species. Node bars represent the 95% highest posterior density intervals for the divergence time estimates of nodes with posterior probabilities above 0.50 (only divergence time estimates for <i>Supinae</i> lineages are shown). Values above branches indicate Bayesian posterior probabilities. A hyphen (-) indicates posterior probability below 0.50. Colors and tree labels represent the systematic nomenclature for <i>Supinae</i> as established in this paper. Species labels of putative hybrids produced by the cross of the two main <i>Supinae</i> clades are highlighted in grey.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>286382, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.g005", "stats"=>{"downloads"=>1, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reticulate_evolution_in_Supinae_/286382", "title"=>"Reticulate evolution in <i>Supinae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:46:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/616119"], "description"=>"<p>Morphological key traits of species with putative hybrid origin produced by the cross between subsect <i>Saxatile</i> + subsect <i>Arvenses</i> (<i>ssSax+ssArv</i>) and subsect <i>Supinae</i> (<i>ssSup</i>) parental lineages based on the results obtained in the *BEAST multilabelled species tree analysis (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g005\" target=\"_blank\">Figure 5</a>).</p>", "links"=>[], "tags"=>["putative", "hybrid", "produced", "subsect", "lineages", "multilabelled"], "article_id"=>286607, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t006", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_key_traits_of_species_with_putative_hybrid_origin_produced_by_the_cross_between_subsect_Saxatile_subsect_Arvenses_ssSax_ssArv_and_subsect_Supinae_ssSup_parental_lineages_based_on_the_results_obtained_in_the_BEAST_multilabelled_species_tree_/286607", "title"=>"Morphological key traits of species with putative hybrid origin produced by the cross between subsect <i>Saxatile</i> + subsect <i>Arvenses</i> (<i>ssSax+ssArv</i>) and subsect <i>Supinae</i> (<i>ssSup</i>) parental lineages based on the results obtained in the *BEAST multilabelled species tree analysis (Figure 5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:50:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/615643"], "description"=>"<p>Frequency distribution of tree-to-tree distances between 20 representative trees from the stable posterior distribution of the Bayesian analysis (ITS (A), AGT1 (B) and cpDNA (C)) and 100 simulated gene trees obtained by coalescent simulations (baseline distributions). Blue, green and red bars represent baseline distributions under <i>L. glacialis</i>, <i>L. elegans</i> and <i>L. simplex</i> N<sub>e</sub> estimates respectively. Black and white bars represent the distances between gene trees (observed distributions).</p>", "links"=>[], "tags"=>["observed", "distributions"], "article_id"=>286141, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Baseline_and_observed_distributions_of_tree_distances_/286141", "title"=>"Baseline and observed distributions of tree distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:42:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/616280"], "description"=>"<p><b><i>A L. glacialis</i></b><b> N<sub>e</sub>:</b> Nuclear N<sub>e</sub> = 190000, Plastid N<sub>e</sub> = 95000.</p><p><b><i>B L. elegans</i></b><b> N<sub>e</sub>:</b> Nuclear N<sub>e</sub> = 320000, Plastid N<sub>e</sub> = 160000.</p><p><b><i>C L. simplex</i></b><b> N<sub>e</sub>,</b> Nuclear N<sub>e</sub> = 680000, Plastid N<sub>e</sub> = 340000.</p>*<p>Individuals of putative hybrid origin that were excluded from the analysis in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g004\" target=\"_blank\">Figure 4</a>.</p>§<p>Calculation plotted as an example in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g003\" target=\"_blank\">Fig. 3</a>.</p>", "links"=>[], "tags"=>["taxa", "exclusion", "differences", "simulated", "observed", "distributions", "numbers", "steps", "approximation"], "article_id"=>286766, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_taxa_exclusion_on_the_differences_between_base_line_from_simulated_trees_and_observed_distributions_of_tree_distances_numbers_indicate_steps_while_negative_and_positive_values_indicate_approximation_and_separation_between_distributions_respecti/286766", "title"=>"Effect of taxa exclusion on the differences between base line (from simulated trees) and observed distributions of tree distances, numbers indicate steps while negative (-) and positive (+) values indicate approximation and separation between distributions, respectively.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:52:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/320191", "https://ndownloader.figshare.com/files/320243", "https://ndownloader.figshare.com/files/320313", "https://ndownloader.figshare.com/files/320356", "https://ndownloader.figshare.com/files/320393"], "description"=>"<div><p>We examined the phylogenetic history of <em>Linaria</em> with special emphasis on the Mediterranean sect. <em>Supinae</em> (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (<em>rpl32-trnL<sup>UAG</sup></em>, <em>trnS-trnG</em>). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.</p> </div>", "links"=>[], "tags"=>["coalescent", "simulations", "hybridization", "incomplete", "lineage", "sorting", "mediterranean"], "article_id"=>123210, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039089.s001", "https://dx.doi.org/10.1371/journal.pone.0039089.s002", "https://dx.doi.org/10.1371/journal.pone.0039089.s003", "https://dx.doi.org/10.1371/journal.pone.0039089.s004", "https://dx.doi.org/10.1371/journal.pone.0039089.s005"], "stats"=>{"downloads"=>8, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Coalescent_Simulations_Reveal_Hybridization_and_Incomplete_Lineage_Sorting_in_Mediterranean_Linaria_/123210", "title"=>"Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean <em>Linaria</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-29 00:53:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/616234"], "description"=>"*<p>≤0.05, support for rejection of H<sub>1.</sub></p>**<p>≤10, very strong evidence for rejection of H<sub>1.</sub></p>", "links"=>[], "tags"=>["shimodaira-hasegawa", "bayes", "factors", "observed", "log-likelihood", "s-h", "marginal", "bayesian", "analyses", "bf", "unconstrained", "monophyly", "constrained", "agt1", "cpdna", "datasets"], "article_id"=>286711, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t003", "stats"=>{"downloads"=>2, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_Shimodaira_Hasegawa_S_H_test_and_Bayes_Factors_BF_test_with_observed_log_likelihood_difference_obtained_in_Maximum_Likelihood_analyses_S_H_test_statistics_mean_values_of_marginal_likelihood_of_the_Bayesian_analyses_and_BF_test_statistics_2xlnB/286711", "title"=>"Results of Shimodaira-Hasegawa (S-H) test and Bayes Factors (BF) test with observed log-likelihood difference obtained in Maximum Likelihood analyses, S-H test statistics, mean values of marginal likelihood of the Bayesian analyses and BF test statistics (2xlnBF) for the unconstrained analysis (H<sub>0</sub>) and the analysis with monophyly of <i>Supinae</i> constrained in AGT1 and cpDNA datasets (H<sub>1</sub>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:51:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/616047"], "description"=>"*<p>Although not explicitly discussed, incongruence due to incomplete lineage sorting is also apparent among gene trees in this paper.</p>", "links"=>[], "tags"=>["phylogenetic", "studies", "mediterranean", "plants", "supported", "incongruence", "articles", "hybridization", "incomplete", "lineage", "sorting", "causes", "topological"], "article_id"=>286533, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t008", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Previous_phylogenetic_studies_of_Mediterranean_plants_with_highly_supported_incongruence_among_gene_trees_we_indicate_those_articles_that_claim_hybridization_and_or_incomplete_lineage_sorting_as_major_causes_of_topological_inconsistency_/286533", "title"=>"Previous phylogenetic studies of Mediterranean plants with highly supported incongruence among gene trees, we indicate those articles that claim hybridization and/or incomplete lineage sorting as major causes of topological inconsistency.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/616311"], "description"=>"<p>p.p. = <i>pro parte</i>.</p><p>p.p.max = <i>pro parte maxima</i>.</p><p>p.p.min = <i>pro parte minima</i>.</p>", "links"=>[], "tags"=>["classification", "sect", "suggested"], "article_id"=>286806, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.t001", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Systematic_classification_of_Linaria_sect_Supinae_suggested_in_this_study_and_its_relation_with_previous_classifications_/286806", "title"=>"Systematic classification of <i>Linaria</i> sect <i>Supinae</i> suggested in this study and its relation with previous classifications.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-29 01:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/615796"], "description"=>"<p>Maximum clade credibility tree obtained in the *BEAST species tree analysis after excluding potential hybrids and using allelic data of ITS, AGT1 and cpDNA datasets. Node bars represent the 95% highest posterior density intervals for the divergence time estimates of nodes with posterior probabilities above 0.50. Values above branches indicate Bayesian posterior probabilities. <i>Linaria</i> sections following Sutton (1988) are shown. Colors and clade labels represent the systematic nomenclature for <i>Supinae</i> as suggested in this paper.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>286291, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.g004", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_tree_of_Linaria_/286291", "title"=>"Species tree of <i>Linaria.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:44:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/615554"], "description"=>"<p>Phylogenetic relationships of 47 samples representing 46 <i>Linaria</i> species and one individual of <i>Antirrhinum</i> as the outgroup. One species of sect. <i>Macrocentrum</i>, three species of sect. <i>Versicolores</i>, five species of sect <i>Linaria</i>, four species of sect. <i>Speciosae</i> and 28 species of sect. <i>Supinae</i> are represented. 50% Mayority-rule consensus tree obtained in the Bayesian analysis of ITS (A), AGT1 (B) and cpDNA (C) sequences are shown. Numbers above branches represent Bayesian posterior probabilities. Phylogenetic trees are based on one sample and one allele per species, when the two alleles were not sister we used the most incongruent one respecting the other two genes. <i>Linaria</i> sections following Sutton <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone.0039089-Sutton1\" target=\"_blank\">[45]</a> are shown in capital letters. Colors represent the systematic nomenclature for <i>Supinae</i> clades as suggested in this paper (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g004\" target=\"_blank\">Fig. 4</a>). Species with key traits from two <i>Supinae</i> clades (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039089#pone-0039089-g004\" target=\"_blank\">Fig. 4</a>) are represented in grey.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>286049, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["José Luis Blanco-Pastor", "Pablo Vargas", "Bernard E. Pfeil"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039089.g001", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_trees_/286049", "title"=>"Gene trees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:40:49"}

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Relative Metric

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