Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
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{"title"=>"Broad phylogenomic sampling and the sister lineage of land plants", "type"=>"journal", "authors"=>[{"first_name"=>"Ruth E.", "last_name"=>"Timme", "scopus_author_id"=>"8911044400"}, {"first_name"=>"Tsvetan R.", "last_name"=>"Bachvaroff", "scopus_author_id"=>"6506378208"}, {"first_name"=>"Charles F.", "last_name"=>"Delwiche", "scopus_author_id"=>"7003339797"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22253761", "doi"=>"10.1371/journal.pone.0029696", "sgr"=>"84855858792", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84855858792", "issn"=>"19326203", "pui"=>"364092933"}, "id"=>"6933079c-eacf-3be0-a182-87d43335ed8e", "abstract"=>"The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that ‘stoneworts,’ or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as “pond scum”) as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1) the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2) the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.", "link"=>"http://www.mendeley.com/research/broad-phylogenomic-sampling-sister-lineage-land-plants", "reader_count"=>148, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>7, "Researcher"=>40, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>44, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>7, "Researcher"=>40, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>44, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>1, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>114, "Neuroscience"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>114}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Czechia"=>1, "United States"=>4, "United Kingdom"=>1, "Switzerland"=>1, "Spain"=>4, "India"=>1, "New Zealand"=>1, "Canada"=>2, "Sweden"=>1, "Serbia and Montenegro"=>1, "Brazil"=>4, "Mexico"=>2, "France"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/692443"], "description"=>"<p>Phylogenetic analyses are summarized by a BI (CAT-Poisson model) consensus tree with branch support values from both BI and ML analyses (ML bootstrap/Bayesian posterior probabilities).</p>", "links"=>[], "tags"=>["relationships", "14", "viridiplantae", "taxa", "160", "concatenated"], "article_id"=>362881, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029696.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_14_Viridiplantae_taxa_determined_by_160_concatenated_proteins_/362881", "title"=>"Phylogenetic relationships of 14 Viridiplantae taxa determined by 160 concatenated proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-13 00:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/352255", "https://ndownloader.figshare.com/files/352314"], "description"=>"<div><p>The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that ‘stoneworts,’ or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as “pond scum”) as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1) the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2) the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.</p> </div>", "links"=>[], "tags"=>["phylogenomic", "sampling", "lineage", "plants"], "article_id"=>129637, "categories"=>["Genetics", "Cell Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029696.s001", "https://dx.doi.org/10.1371/journal.pone.0029696.s002"], "stats"=>{"downloads"=>10, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Broad_Phylogenomic_Sampling_and_the_Sister_Lineage_of_Land_Plants/129637", "title"=>"Broad Phylogenomic Sampling and the Sister Lineage of Land Plants", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-01-13 02:40:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/692551"], "description"=>"<p>The earliest branching streptophytes (<i>Mesostigma</i> and <i>Chlorokybus</i>) were unicellular, flagellate, and isogamous. Multicellularity in the form of unbranched filaments evolved in the common ancestor of the remaining streptophytes and is represented in the Klebsormidiales. The most recent common ancestor of Charales+Coleochaetales+Zygnematales+LP most likely was an alga with plant-like cell division (phragmoplast), branched filaments, and oogamous sexual reproduction. The Charales went on to independently evolve a complex macrophytic form. The Coleochaetales independently acquired parenchymatous tissue and maternally retained zygotes. However, the Zygnematales went the route of reduction: loss of flagellate cells (reproduction via conjugation), loss of multicelluarity (Desmids), and loss of the phragmoplast.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "Evolutionary biology"], "article_id"=>363001, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029696.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypothesis_of_character_evolution_in_the_Charophytes_/363001", "title"=>"Hypothesis of character evolution in the Charophytes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-13 00:50:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/692326"], "description"=>"<p>This diagram outlines the steps used for identifying orthologous genes for phylogenetic analysis. <b>A</b>) Unresolved phylogenetic scheme relating chlorophytes, charophytes, and embryophytes with a list of the six taxa with fully sequenced genomes used for the core ortholog determination. <b>B</b>) Core ortholog prediction from the previous six taxa. <b>C</b>) Charophyte orthog prediction. The core orthologs were then used to search for proteins in each of the eight charophyte transcriptomes. We filtered for good taxon sampling and removed orthologs with significant amino acid bias, resulting in 160 aligned proteins. These were concatenated onto one large multigene data matrix for phylogenetic analysis.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "Evolutionary biology"], "article_id"=>362777, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029696.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ortholog_identification_method_/362777", "title"=>"Ortholog identification method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-13 00:46:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/692641"], "description"=>"<p>Genes present for each charophyte taxon in the multigene alignment (160 total).</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "Evolutionary biology"], "article_id"=>363085, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029696.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_missing_data_/363085", "title"=>"Summary of missing data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-13 00:51:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/692671"], "description"=>"<p>Unigenes are contigs with a putative coding region.</p>", "links"=>[], "tags"=>["clustering"], "article_id"=>363119, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Ruth E. Timme", "Tsvetan R. Bachvaroff", "Charles F. Delwiche"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029696.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primary_sequence_data_and_summary_of_clustering_results_/363119", "title"=>"Primary sequence data and summary of clustering results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-13 00:51:59"}

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Relative Metric

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