Multigene Phylogeny of Choanozoa and the Origin of Animals
Publication Date
May 07, 2008
Journal
PLOS ONE
Authors
Kamran Shalchian Tabrizi, Marianne A. Minge, Mari Espelund, Russell Orr, et al
Volume
3
Issue
5
Pages
e2098
DOI
https://dx.plos.org/10.1371/journal.pone.0002098
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0002098
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18461162
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346548
Europe PMC
http://europepmc.org/abstract/MED/18461162
Web of Science
000261642400020
Scopus
47749123501
Mendeley
http://www.mendeley.com/research/multigene-phylogeny-choanozoa-origin-animals
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{"title"=>"Multigene phylogeny of Choanozoa and the origin of animals", "type"=>"journal", "authors"=>[{"first_name"=>"Kamran", "last_name"=>"Schalchian-Tabrizi", "scopus_author_id"=>"24475129900"}, {"first_name"=>"Marianne A.", "last_name"=>"Minge", "scopus_author_id"=>"14020208700"}, {"first_name"=>"Mari", "last_name"=>"Espelund", "scopus_author_id"=>"6603237518"}, {"first_name"=>"Russell", "last_name"=>"Orr", "scopus_author_id"=>"25959242800"}, {"first_name"=>"Torgeir", "last_name"=>"Ruden", "scopus_author_id"=>"6604022730"}, {"first_name"=>"Kjetill S.", "last_name"=>"Jakobsen", "scopus_author_id"=>"7005413513"}, {"first_name"=>"Thomas", "last_name"=>"Cavalier-Smith", "scopus_author_id"=>"7005140375"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"47749123501", "doi"=>"10.1371/journal.pone.0002098", "pui"=>"352025100", "pmid"=>"18461162", "scopus"=>"2-s2.0-47749123501", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)"}, "id"=>"b65819e2-c510-3969-84b2-ba714a98d875", "abstract"=>"Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.", "link"=>"http://www.mendeley.com/research/multigene-phylogeny-choanozoa-origin-animals", "reader_count"=>179, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>13, "Researcher"=>52, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>35, "Student > Postgraduate"=>4, "Student > Master"=>24, "Other"=>5, "Student > Bachelor"=>16, "Professor"=>14}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>13, "Researcher"=>52, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>35, "Student > Postgraduate"=>4, "Student > Master"=>24, "Other"=>5, "Student > Bachelor"=>16, "Professor"=>14}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>10, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>19, "Agricultural and Biological Sciences"=>130, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>130}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Argentina"=>1, "United States"=>8, "Uruguay"=>1, "United Kingdom"=>2, "Switzerland"=>1, "Portugal"=>1, "Spain"=>6, "Russia"=>1, "Canada"=>1, "Czech Republic"=>1, "Netherlands"=>1, "Norway"=>4, "Finland"=>1, "Brazil"=>4, "Italy"=>1, "France"=>3, "Australia"=>1, "Chile"=>1, "Germany"=>5}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/932149"], "description"=>"<p>Phylogenetic distribution of annotated animal-like signaling and cell adhesion components within Choanozoa.</p>", "links"=>[], "tags"=>["annotated", "animal-like", "adhesion", "components"], "article_id"=>602587, "categories"=>["Molecular Biology", "Microbiology", "Developmental Biology", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Kamran Shalchian-Tabrizi", "Marianne A. Minge", "Mari Espelund", "Russell Orr", "Torgeir Ruden", "Kjetill S. Jakobsen", "Thomas Cavalier-Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002098.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distribution_of_annotated_animal_like_signaling_and_cell_adhesion_components_within_Choanozoa_/602587", "title"=>"Phylogenetic distribution of annotated animal-like signaling and cell adhesion components within Choanozoa.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-07 00:43:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/932073"], "description"=>"<p>The five choanozoan classes (bold) form at least four distinct clades, one probably related to fungi and the others to animals. Innovations in pseudopod character and their multiple losses with the origin of cell walls during nutritional shifts from engulfing prey (phagotrophy) to saprotrophy or parasitism are indicated by bars. In the common ancestor of animals and choanoflagellates a subset of the filozoan actin-supportd tentacles aggregated as a collar around the cilium ( = flagellum) for filter feeding. Epithelia and connective tissue made the first animals: the filter-feeding sponges.</p>", "links"=>[], "tags"=>["relationships", "animals", "fungi", "unicellular", "relatives"], "article_id"=>602510, "categories"=>["Molecular Biology", "Microbiology", "Developmental Biology", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Kamran Shalchian-Tabrizi", "Marianne A. Minge", "Mari Espelund", "Russell Orr", "Torgeir Ruden", "Kjetill S. Jakobsen", "Thomas Cavalier-Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002098.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_among_animals_and_fungi_and_their_closest_unicellular_relatives_Choanozoa_Protozoa_/602510", "title"=>"Evolutionary relationships among animals and fungi and their closest unicellular relatives (Choanozoa, Protozoa).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-07 00:41:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/931842"], "description"=>"<p>Numbers beside the internal nodes are maximum likelihood bootstrap values obtained from RaxML and Bayesian MCMC posterior probabilities. Black circles indicate 100% bootstrap support and 1.00 posterior probability values.</p>", "links"=>[], "tags"=>["choanozoa", "unikont", "eukaryotes", "reconstructed", "78", "protein-coding"], "article_id"=>602275, "categories"=>["Molecular Biology", "Microbiology", "Developmental Biology", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Kamran Shalchian-Tabrizi", "Marianne A. Minge", "Mari Espelund", "Russell Orr", "Torgeir Ruden", "Kjetill S. Jakobsen", "Thomas Cavalier-Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002098.g001", "stats"=>{"downloads"=>3, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_the_Choanozoa_and_other_unikont_eukaryotes_reconstructed_by_the_maximum_likelihood_method_for_78_protein_coding_genes_/602275", "title"=>"Phylogeny of the Choanozoa and other unikont eukaryotes reconstructed by the maximum likelihood method for 78 protein-coding genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-07 00:37:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/931963"], "description"=>"<p>A: hedgehog and B: Notch homologues. The illustrated domains are some of those found by searches against the Conserved Domain Database. Numbers at the species names are accession numbers, protein IDs from the Joint Genome Institute (JGI) and references where annotation recently have been presented. Domain structure identified in <i>Ministeria</i> is compared with animals - Porifera (<i>Amphimedon</i> and <i>Oscarella</i>), Cnidaria (<i>Nematostella</i>) and Chordata (<i>Homo</i>) - and the choanoflagellate <i>Monosiga</i>. Abbreviations: Hh-signal domain, N-terminal hedgehog domain; Hint cleavage site, cleavage site of the C-terminal hedgehog domain; Hint domain, C-terminal hedgehog domain; Notch(DSL), Notch domain also called Delta Serrate Ligand; EGF, epidermal growth factor domain; NL, domain found in Notch and Lin-12; NOD, NOD region; NODP, NODP region; ANK, ankyrin reapeats; PTP, protein tyrosine phosphatase.</p>", "links"=>[], "tags"=>["annotated"], "article_id"=>602404, "categories"=>["Molecular Biology", "Microbiology", "Developmental Biology", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Kamran Shalchian-Tabrizi", "Marianne A. Minge", "Mari Espelund", "Russell Orr", "Torgeir Ruden", "Kjetill S. Jakobsen", "Thomas Cavalier-Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002098.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Domain_structure_of_selected_annotated_sequences_/602404", "title"=>"Domain structure of selected annotated sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-07 00:40:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/459246", "https://ndownloader.figshare.com/files/459300"], "description"=>"<div><p>Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on <em>Ministeria vibrans</em>, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of <em>Ministeria</em> protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that <em>Ministeria</em> is not sister to animals or choanoflagellates (themselves sisters to animals), but to <em>Capsaspora</em>, another protozoan with thread-like (filose) tentacles. The <em>Ministeria</em>/<em>Capsaspora</em> clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.</p></div>", "links"=>[], "tags"=>["multigene", "phylogeny", "choanozoa", "animals"], "article_id"=>150489, "categories"=>["Molecular Biology", "Microbiology", "Developmental Biology", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Kamran Shalchian-Tabrizi", "Marianne A. Minge", "Mari Espelund", "Russell Orr", "Torgeir Ruden", "Kjetill S. Jakobsen", "Thomas Cavalier-Smith"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0002098.s001", "https://dx.doi.org/10.1371/journal.pone.0002098.s002"], "stats"=>{"downloads"=>8, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multigene_Phylogeny_of_Choanozoa_and_the_Origin_of_Animals/150489", "title"=>"Multigene Phylogeny of Choanozoa and the Origin of Animals", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-05-07 00:08:09"}

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Relative Metric

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