Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales, Ascomycota)
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{"title"=>"Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera cudonia and spathularia (Rhytismatales, Ascomycota)", "type"=>"journal", "authors"=>[{"first_name"=>"Zai Wei", "last_name"=>"Ge", "scopus_author_id"=>"25960591500"}, {"first_name"=>"Zhu L.", "last_name"=>"Yang", "scopus_author_id"=>"35331478800"}, {"first_name"=>"Donald H.", "last_name"=>"Pfister", "scopus_author_id"=>"7005653944"}, {"first_name"=>"Matteo", "last_name"=>"Carbone", "scopus_author_id"=>"35483245400"}, {"first_name"=>"Tolgor", "last_name"=>"Bau", "scopus_author_id"=>"30367511200"}, {"first_name"=>"Matthew E.", "last_name"=>"Smith", "scopus_author_id"=>"9737056100"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84928206547", "pmid"=>"25084276", "pui"=>"373776109", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84928206547", "doi"=>"10.1371/journal.pone.0103457", "issn"=>"19326203"}, "id"=>"89b06b25-cba7-391f-b006-ca4a3b2adf35", "abstract"=>"The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the \"earth tongue fungi\" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.", "link"=>"http://www.mendeley.com/research/multigene-molecular-phylogeny-biogeographic-diversification-earth-tongue-fungi-genera-cudonia-spathu", "reader_count"=>15, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>8, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>8, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>14}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "Japan"=>1, "United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1618576", "https://ndownloader.figshare.com/files/1618577", "https://ndownloader.figshare.com/files/1618578", "https://ndownloader.figshare.com/files/1618579", "https://ndownloader.figshare.com/files/1618580", "https://ndownloader.figshare.com/files/1618581", "https://ndownloader.figshare.com/files/1618582", "https://ndownloader.figshare.com/files/1618583", "https://ndownloader.figshare.com/files/1618584", "https://ndownloader.figshare.com/files/1618585"], "description"=>"<div><p>The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera <i>Cudonia</i> and <i>Spathularia</i>. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within <i>Cudonia</i> and <i>Spathularia</i> using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, <i>rpb2</i> and <i>tef-1α</i> sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus <i>Cudonia</i> and the family Cudoniaceae are supported as monophyletic groups, while the genus <i>Spathularia</i> is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of <i>Cudonia</i> and <i>Spathularia</i> in eastern Asia, with 16 (out of 21) species-level clades of <i>Cudonia</i> and 8 (out of 11) species-level clades of <i>Spathularia</i>. We estimate that the divergence time of the <i>Cudoniaceae</i> was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of <i>Cudonia</i> and <i>Spathularia</i> and highlights the need for more molecular studies on collections from Europe and North America.</p></div>", "links"=>[], "tags"=>["biogeography", "Evolutionary biology", "Evolutionary systematics", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "ascomycetes", "multigene", "molecular", "phylogeny", "biogeographic", "diversification", "genera"], "article_id"=>1124724, "categories"=>["Biological Sciences"], "users"=>["Zai-Wei Ge", "Zhu L. Yang", "Donald H. Pfister", "Matteo Carbone", "Tolgor Bau", "Matthew E. Smith"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0103457.s001", "https://dx.doi.org/10.1371/journal.pone.0103457.s002", "https://dx.doi.org/10.1371/journal.pone.0103457.s003", "https://dx.doi.org/10.1371/journal.pone.0103457.s004", "https://dx.doi.org/10.1371/journal.pone.0103457.s005", "https://dx.doi.org/10.1371/journal.pone.0103457.s006", "https://dx.doi.org/10.1371/journal.pone.0103457.s007", "https://dx.doi.org/10.1371/journal.pone.0103457.s008", "https://dx.doi.org/10.1371/journal.pone.0103457.s009", "https://dx.doi.org/10.1371/journal.pone.0103457.s010"], "stats"=>{"downloads"=>13, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multigene_Molecular_Phylogeny_and_Biogeographic_Diversification_of_the_Earth_Tongue_Fungi_in_the_Genera_Cudonia_and_Spathularia_Rhytismatales_Ascomycota_/1124724", "title"=>"Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera <i>Cudonia</i> and <i>Spathularia</i> (Rhytismatales, Ascomycota)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-01 03:10:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1618570"], "description"=>"<p>ML bootstrap support values are shown above the internal branches. Sequences from Asia are in black text, sequences from North America are in blue text, and sequences from Europe are in red text. Mislabeled sequences from GenBank and sequences from misidentified herbarium collections are shown in purple text.</p>", "links"=>[], "tags"=>["biogeography", "Evolutionary biology", "Evolutionary systematics", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "ascomycetes", "phylogeny", "127", "ribosomal", "dna"], "article_id"=>1124718, "categories"=>["Biological Sciences"], "users"=>["Zai-Wei Ge", "Zhu L. Yang", "Donald H. Pfister", "Matteo Carbone", "Tolgor Bau", "Matthew E. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103457.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogeny_of_Cudonia_and_Spathularia_species_based_on_127_ITS_ribosomal_DNA_sequences_/1124718", "title"=>"Maximum likelihood phylogeny of <i>Cudonia</i> and <i>Spathularia</i> species based on 127 ITS ribosomal DNA sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-01 03:10:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1618568"], "description"=>"<p>A. <i>Cudonia circinans</i> (M. Carbone 313); B. <i>Cudonia confusa</i> (M. Carbone 314); C. <i>Cudonia</i> sp1 (Z.-W. Ge 729); D. <i>Cudonia lutea</i> (Z.-W. Ge 1634); E. <i>Cudonia</i> sp10 (Z. L. Yang 4297); F. <i>Cudonia</i> sp9 (X. H. Wang 2324); G. <i>Cudonia</i> sp12 (Z.-W. Ge 829); H. <i>Spathularia</i> sp5 (Z. L. Yang 5385); I. <i>Spathularia</i> sp4 (L. P. Tang 252); J. <i>Spathularia velutipes</i> (Z.-W. Ge 2232); K. <i>Spathularia rufa</i> (M. Carbone 309); L. <i>Spathularia flavida</i> (M. Carbone 313); M. Hymenium of <i>Spathularia flavida</i> (Z.-W. Ge 3348); N. Asci and paraphyses of <i>Spathularia flavida</i> (Z.-W. Ge 3348); O. Ascospores of <i>Spathularia flavida</i> (Z.-W. Ge 3348).</p>", "links"=>[], "tags"=>["biogeography", "Evolutionary biology", "Evolutionary systematics", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "ascomycetes", "microscopic", "morphological"], "article_id"=>1124716, "categories"=>["Biological Sciences"], "users"=>["Zai-Wei Ge", "Zhu L. Yang", "Donald H. Pfister", "Matteo Carbone", "Tolgor Bau", "Matthew E. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103457.g001", "stats"=>{"downloads"=>5, "page_views"=>53, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macroscopic_and_microscopic_morphological_features_of_Cudonia_and_Spathularia_species_/1124716", "title"=>"Macroscopic and microscopic morphological features of <i>Cudonia</i> and <i>Spathularia</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-01 03:10:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1618573"], "description"=>"<p>Estimated mean divergence times and 95% highest posterior density of resolved nodes in phylogenetic analyses are summarized in the upper left panel. Geological time scale according to Gradstein et al. (2004) is shown along the bottom for scale.</p>", "links"=>[], "tags"=>["biogeography", "Evolutionary biology", "Evolutionary systematics", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "ascomycetes", "reconstruction", "chronogram", "clade", "node"], "article_id"=>1124721, "categories"=>["Biological Sciences"], "users"=>["Zai-Wei Ge", "Zhu L. Yang", "Donald H. Pfister", "Matteo Carbone", "Tolgor Bau", "Matthew E. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103457.g004", "stats"=>{"downloads"=>7, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ancestral_area_reconstruction_and_chronogram_of_clade_of_Cudonia_and_Spathularia_based_on_BEAST_analyses_using_Cudonia_stem_65_03_0_29_MYA_node_1_as_calibration_/1124721", "title"=>"Ancestral area reconstruction and chronogram of clade of <i>Cudonia</i> and <i>Spathularia</i> based on BEAST analyses using <i>Cudonia</i> stem (65.03 ± 0.29 MYA, node 1) as calibration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-01 03:10:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1618571"], "description"=>"<p>Bootstrap support values from ML (1000 bootstrap replicates) analyses are shown above the internal branches. Bayesian posterior probabilities (BPP) greater than 0.95 are indicated by thickened branches. Branch lengths are proportional to the average number of substitutions per site except for dashed lines, which indicate longer branches that are not shown to scale.</p>", "links"=>[], "tags"=>["biogeography", "Evolutionary biology", "Evolutionary systematics", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "ascomycetes", "phylogeny", "depicting", "phylogenetic", "relationships", "58", "sequences"], "article_id"=>1124719, "categories"=>["Biological Sciences"], "users"=>["Zai-Wei Ge", "Zhu L. Yang", "Donald H. Pfister", "Matteo Carbone", "Tolgor Bau", "Matthew E. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0103457.g003", "stats"=>{"downloads"=>13, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Four_locus_ITS_nrLSU_rpb2_and_tef_1_945_maximum_likelihood_ML_phylogeny_depicting_phylogenetic_relationships_among_58_sequences_of_Cudonia_and_Spathularia_/1124719", "title"=>"Four-locus (ITS, nrLSU, <i>rpb2</i> and <i>tef-1α</i>) maximum likelihood (ML) phylogeny depicting phylogenetic relationships among 58 sequences of <i>Cudonia</i> and <i>Spathularia</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-01 03:10:57"}

PMC Usage Stats | Further Information

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Relative Metric

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