Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group

第868回千葉医学会例会・第8回磯野外科例会

matK sequences matri

Making Carex monophyletic (Cyperaceae, tribe Cariceae): a new broader circumscription

Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments.We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natural Sciences and Engineering Research Council, Canada (NSERC) to MJW and JRS; University of Mainz to BG; JSPS KAKENHI Grant no. 25840136 to OY; Korea National Arboretum to SK; CGL2012- 38744 project from the Spanish Ministry of Economy and Competitiveness to ML; project 30870178 from the National Natural Science Foundation of China to SRZ, and a University of Wisconsin-Madison Raper Travel Grant to DS. The figures were prepared with invaluable technical advice from H. C. Rimmer.Peer reviewe

Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

Jiménez Mejías, Pedro [et al.]We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.Funding for this work was provided by the National Science Foundation (Award #1255901 to ALH and MJW and Award #1256033 to EHR), the Natural Sciences and Engineering Research Council of Canada (funding to JRS and MJW) the German Science Foundation (funding to SG and MHH, project numbers HO2213/3-1, HO2213/3-2), and the Spanish Ministry of Science and Technology (funding to ML, CGL2012-38744).Peer reviewe

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

Pham, Kasey K. [et al.]Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group.Funding for this work was provided by the National Science Foundation (Award #1255901 to ALH andMJWand Award #1256033 to EHR), including an REU supplement that supported KKP’s work.Peer reviewe