Phylogenomics Reshuffles the Eukaryotic Supergroups
Publication Date
August 29, 2007
Journal
PLOS ONE
Authors
Fabien Burki, Kamran Shalchian Tabrizi, Marianne Minge, Åsmund Skjæveland, et al
Volume
2
Issue
8
Pages
e790
DOI
https://dx.plos.org/10.1371/journal.pone.0000790
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000790
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17726520
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949142
Europe PMC
http://europepmc.org/abstract/MED/17726520
Web of Science
000207455400007
Scopus
40749116835
Mendeley
http://www.mendeley.com/research/phylogenomics-reshuffles-eukaryotic-supergroups
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{"title"=>"Phylogenomics reshuffles the eukaryotic supergroups", "type"=>"journal", "authors"=>[{"first_name"=>"Fabien", "last_name"=>"Burki", "scopus_author_id"=>"57191566814"}, {"first_name"=>"Kamran", "last_name"=>"Shalchian-Tabrizi", "scopus_author_id"=>"6505831131"}, {"first_name"=>"Marianne", "last_name"=>"Minge", "scopus_author_id"=>"14020208700"}, {"first_name"=>"Åsmund", "last_name"=>"Skjæveland", "scopus_author_id"=>"23977146200"}, {"first_name"=>"Sergey I.", "last_name"=>"Nikolaev", "scopus_author_id"=>"7005282328"}, {"first_name"=>"Kjetill S.", "last_name"=>"Jakobsen", "scopus_author_id"=>"7005413513"}, {"first_name"=>"Jan", "last_name"=>"Pawlowski", "scopus_author_id"=>"7103199199"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"40749116835", "doi"=>"10.1371/journal.pone.0000790", "pui"=>"351377326", "pmid"=>"17726520", "scopus"=>"2-s2.0-40749116835", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"ddedb43c-b913-34a7-a4f3-efbd4e84b725", "abstract"=>"BACKGROUND: Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. METHODOLOGY/PRINCIPLE FINDINGS: Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. CONCLUSIONS: This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name 'SAR' (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.", "link"=>"http://www.mendeley.com/research/phylogenomics-reshuffles-eukaryotic-supergroups", "reader_count"=>282, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>16, "Researcher"=>78, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>60, "Student > Postgraduate"=>8, "Student > Master"=>45, "Other"=>3, "Student > Bachelor"=>27, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>17}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>16, "Researcher"=>78, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>60, "Student > Postgraduate"=>8, "Student > Master"=>45, "Other"=>3, "Student > Bachelor"=>27, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>3, "Professor"=>17}, "reader_count_by_subject_area"=>{"Unspecified"=>17, "Agricultural and Biological Sciences"=>195, "Arts and Humanities"=>1, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>2, "Earth and Planetary Sciences"=>8, "Environmental Science"=>21, "Biochemistry, Genetics and Molecular Biology"=>31, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Unspecified"=>{"Unspecified"=>17}, "Environmental Science"=>{"Environmental Science"=>21}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>8}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>195}, "Computer Science"=>{"Computer Science"=>2}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>31}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>6, "Egypt"=>1, "Russia"=>1, "Malta"=>1, "Austria"=>1, "Ireland"=>1, "China"=>1, "Brazil"=>3, "France"=>4, "Chile"=>1, "Croatia"=>1, "Colombia"=>2, "Argentina"=>1, "United Kingdom"=>5, "Spain"=>4, "New Zealand"=>1, "Venezuela"=>1, "Canada"=>4, "Czech Republic"=>2, "Norway"=>1, "Mexico"=>1, "Italy"=>1, "Peru"=>2, "Germany"=>7, "Estonia"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/946390"], "description"=>"<p>Numbers at nodes represent the result of the bootstrap analysis (underlined numbers; hundred bootstrap pseudoreplicates were performed) and Bayesian posterior probabilities. Black dots represent values of 100% bootstrap support (BP) and Bayesian posterior probabilities (BiPP) of 1.0. Nodes without numbers correspond to supports weaker than 50% BP and 0.8 BiPP.</p>", "links"=>[], "tags"=>["eukaryotes", "10", "trees", "searching"], "article_id"=>616735, "categories"=>["Evolutionary Biology"], "users"=>["Fabien Burki", "Kamran Shalchian-Tabrizi", "Marianne Minge", "Åsmund Skjæveland", "Sergey I. Nikolaev", "Kjetill S. Jakobsen", "Jan Pawlowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000790.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Best_maximum_likelihood_tree_of_eukaryotes_found_using_TREEFINDER_with_10_starting_trees_obtained_with_the_global_tree_searching_procedure_/616735", "title"=>"Best maximum likelihood tree of eukaryotes found using TREEFINDER, with 10 starting trees obtained with the global tree searching procedure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-29 01:52:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/946475"], "description"=>"<p>A, B) Comparison between topology A (best tree, corresponding to the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000790#pone-0000790-g001\" target=\"_blank\">Figure 1</a>) and the alternative topology B (corresponding to the best tree when Rhizaria are forced not to be monophyletic with S and A, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000790#pone.0000790.s003\" target=\"_blank\">Figure S3</a>).</p><p>C, D, E) Comparisons between topology C (best tree) and the alternative topologies D and E.</p><p>Abbreviations are as follows: A = alveolates; S = stramenopiles; R = Rhizaria</p><p>Underlined number corresponds to the significant <i>P</i> value of the rejected topology.</p>a<p>Approximate Unbiased Test.</p>b<p>Log likelihood difference.</p>", "links"=>[], "tags"=>["au"], "article_id"=>616826, "categories"=>["Evolutionary Biology"], "users"=>["Fabien Burki", "Kamran Shalchian-Tabrizi", "Marianne Minge", "Åsmund Skjæveland", "Sergey I. Nikolaev", "Kjetill S. Jakobsen", "Jan Pawlowski"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000790.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Likelihood_AU_Tests_of_Alternative_Tree_Topologies_/616826", "title"=>"Likelihood AU Tests of Alternative Tree Topologies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-08-29 01:53:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/469714", "https://ndownloader.figshare.com/files/469773", "https://ndownloader.figshare.com/files/469820", "https://ndownloader.figshare.com/files/469856", "https://ndownloader.figshare.com/files/469861", "https://ndownloader.figshare.com/files/469863"], "description"=>"<div><h3>Background</h3><p>Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial.</p><h3>Methodology/Principle Findings</h3><p>Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history.</p><h3>Conclusions</h3><p>This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.</p></div>", "links"=>[], "tags"=>["phylogenomics", "reshuffles", "eukaryotic", "supergroups"], "article_id"=>152591, "categories"=>["Evolutionary Biology"], "users"=>["Fabien Burki", "Kamran Shalchian-Tabrizi", "Marianne Minge", "Åsmund Skjæveland", "Sergey I. Nikolaev", "Kjetill S. Jakobsen", "Jan Pawlowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000790.s001", "https://dx.doi.org/10.1371/journal.pone.0000790.s002", "https://dx.doi.org/10.1371/journal.pone.0000790.s003", "https://dx.doi.org/10.1371/journal.pone.0000790.s004", "https://dx.doi.org/10.1371/journal.pone.0000790.s005", "https://dx.doi.org/10.1371/journal.pone.0000790.s006"], "stats"=>{"downloads"=>21, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenomics_Reshuffles_the_Eukaryotic_Supergroups/152591", "title"=>"Phylogenomics Reshuffles the Eukaryotic Supergroups", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-08-29 00:43:11"}

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Relative Metric

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