WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

2021

Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all…

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

2016

Pham, Kasey K. [et al.]

A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles

2021

New Insights into the Systematics of the Schoenoxiphium Clade (Carex, Cyperaceae)

2017

The Spanish Ministry of Science and Technology supported this research through the project CGL2012-38744 and CGL2016- 77401-P to M. Luceño (Principal Investigator), E. Maguilla, M. Escudero, S. Martín-Bravo, and T. Villaverde and an FPU fellowship (AP2012-2189) from the Spanish Government (Ministry of Education, Culture, and Sport) and a Synthesys grant (GB-TAF-2523) by the European Community Research Infrastructure Program to E.Maguilla.

Megaphylogenetic Specimen-level Approaches to the <I>Carex</I> (Cyperaceae) Phylogeny Using ITS, ETS, and <I>matK</I> Sequenc…

2016

Abstract 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, histo…

MakingCarexmonophyletic (Cyperaceae, tribe Cariceae): a new broader circumscription

2015

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 Natu…

Data from: Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classi…

2017

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 mis…

Data from: Specimens at the center: an informatics workflow and toolkit for specimen-level analysis of public DNA database data

2017

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…