Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid Nudibranchs
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{"title"=>"Traditional taxonomic groupings mask evolutionary history: A molecular phylogeny and new classification of the chromodorid nudibranchs", "type"=>"journal", "authors"=>[{"first_name"=>"Rebecca Fay", "last_name"=>"Johnson", "scopus_author_id"=>"7407019399"}, {"first_name"=>"Terrence M.", "last_name"=>"Gosliner", "scopus_author_id"=>"6603048131"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84859575431", "issn"=>"19326203", "pmid"=>"22506002", "pui"=>"364605570", "isbn"=>"1932-6203", "sgr"=>"84859575431", "doi"=>"10.1371/journal.pone.0033479"}, "id"=>"9fa7e067-897c-338c-8780-abc0abca80bb", "abstract"=>"Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.", "link"=>"http://www.mendeley.com/research/traditional-taxonomic-groupings-mask-evolutionary-history-molecular-phylogeny-new-classification-chr", "reader_count"=>69, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>18, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>7, "Other"=>3, "Student > Master"=>15, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>18, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>7, "Other"=>3, "Student > Master"=>15, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Agricultural and Biological Sciences"=>58, "Physics and Astronomy"=>1, "Chemistry"=>3, "Social Sciences"=>1, "Earth and Planetary Sciences"=>2, "Biochemistry, Genetics and Molecular Biology"=>2}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>58}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"United States"=>1, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>3, "Italy"=>1, "Mexico"=>1, "Georgia"=>1, "Australia"=>1, "Portugal"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/655257"], "description"=>"<p>Tree is the same Bayesian phylogram as figured in S3A. All specimens, both genes and all characters included.</p>", "links"=>[], "tags"=>["phylogram", "generic"], "article_id"=>325754, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033479.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circle_phylogram_with_current_generic_names_/325754", "title"=>"Circle phylogram with current generic names.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-10 01:35:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/655388"], "description"=>"<p>Tree is the same Bayesian phylogram as figured in S3A. All specimens, both genes and all characters included. Blue = Indo-Pacific, Red = Atlantic and Caribbean, Gold = Eastern Pacific, Green = Sister group, Black = outgroups. Dark grey = Solely eastern Pacific and Atlantic clades. Light grey = Primarily Indo-Pacific clades with eastern Pacific members.</p>", "links"=>[], "tags"=>["mapped"], "article_id"=>325891, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033479.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Biogeography_mapped_on_circle_phylogram_/325891", "title"=>"Biogeography mapped on circle phylogram.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-10 01:38:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/655150"], "description"=>"<p>\n <i>New collections (from this contribution and </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Johnson1\" target=\"_blank\">[<i>28</i>]</a><i> in blue. GenBank specimens in red. Size of circle represents number of specimens collected in each region. Specimen details in Supplementary <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479.s001\" target=\"_blank\">Table S1</a>).</i></p>", "links"=>[], "tags"=>["localities", "numbers"], "article_id"=>325646, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033479.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_collection_localities_and_numbers_of_specimens_/325646", "title"=>"Map of collection localities and numbers of specimens.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-10 01:34:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/337100", "https://ndownloader.figshare.com/files/337219", "https://ndownloader.figshare.com/files/337352", "https://ndownloader.figshare.com/files/337426", "https://ndownloader.figshare.com/files/337500"], "description"=>"<div><p>Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera <em>Verconia</em> and <em>Diversidoris</em> are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.</p> </div>", "links"=>[], "tags"=>["taxonomic", "groupings", "evolutionary", "molecular", "phylogeny", "classification", "chromodorid", "nudibranchs"], "article_id"=>126616, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033479.s001", "https://dx.doi.org/10.1371/journal.pone.0033479.s002", "https://dx.doi.org/10.1371/journal.pone.0033479.s003", "https://dx.doi.org/10.1371/journal.pone.0033479.s004", "https://dx.doi.org/10.1371/journal.pone.0033479.s005"], "stats"=>{"downloads"=>26, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Traditional_Taxonomic_Groupings_Mask_Evolutionary_History_A_Molecular_Phylogeny_and_New_Classification_of_the_Chromodorid_Nudibranchs/126616", "title"=>"Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid Nudibranchs", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-10 01:50:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/655053"], "description"=>"<p>A. ‘Phylogenetic scenario’ for the chromodorid genera modified from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Rudman1\" target=\"_blank\">[5]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Rudman3\" target=\"_blank\">[26]</a>. B. Morphological phylogeny of generic representatives for the Chromodorididae <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Gosliner2\" target=\"_blank\">[13]</a>. C. Combined 16s and COI phylogram of the Chromodorididae from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Turner1\" target=\"_blank\">[27]</a>. D. Combined 16s and COI phylogram of the Chromodorididae and Cadlinidae from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Johnson1\" target=\"_blank\">[28]</a>. Rudman's ‘<i>Chromodoris</i> group’ in red, ‘<i>Hypselodoris</i> group’ in blue, <i>Cadlinella</i> in yellow, <i>Diversidoris</i> (not included in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Rudman1\" target=\"_blank\">[5]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Gosliner2\" target=\"_blank\">[13]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033479#pone.0033479-Rudman3\" target=\"_blank\">[26]</a>), <i>Cadlina</i> in grey and other dorids in black.</p>", "links"=>[], "tags"=>["phylogenetic"], "article_id"=>325554, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033479.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Previous_Phylogenetic_Hypotheses_/325554", "title"=>"Previous Phylogenetic Hypotheses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-10 01:32:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/655523"], "description"=>"<p>Tree is the same Bayesian phylogram as figured in S3A. All specimens, both genes and all characters included.</p>", "links"=>[], "tags"=>["phylogram", "generic", "clade"], "article_id"=>326015, "categories"=>["Physiology", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Rebecca Fay Johnson", "Terrence M. Gosliner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033479.g005", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circle_phylogram_with_new_generic_and_clade_names_/326015", "title"=>"Circle phylogram with new generic and clade names.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-10 01:40:15"}

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Relative Metric

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