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

Pham, Kasey K. [et al.]

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

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

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.

Carex sect. Rhynchocystis (Cyperaceae): a Miocene subtropical relict in the Western Palaearctic showing a dispersal‐derived Rand Flora pattern

Aim To evaluate how Cenozoic climate changes shaped the evolution and distribution of Carex section Rhynchocystis. Location Western Palaearctic and Afrotropical regions (Rand Flora pattern). Methods DNA regions ITS, ETS (nuclear), matK and rpl32-trnLUAG (plastid) were amplified for 86 samples of species from section Rhynchocystis. Phylogenetic and phylogeographical relationships were inferred using maximum parsimony, Bayesian inference and coalescent-based species tree approaches. Divergence times and ancestral areas were also inferred. Results Carex section Rhynchocystis is a clade that diversified during the middle Miocene in Europe. Most cladogenesis events date to the middle and late Mi…

Megaphylogenetic Specimen-level Approaches to the <I>Carex</I> (Cyperaceae) Phylogeny Using ITS, ETS, and <I>matK</I> Sequences: Implications for Classification

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…

An updated checklist of the vascular flora native to Italy

AbstractAn updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented. The checklist includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms, and 1551 angiosperms. 157 taxa are archaeophytes and 1440 neophytes. The alien taxa currently established in Italy are 791 (570 naturalized and 221 invasive), while 705 taxa are casual aliens, 4 are not assessed, 7 are of unknown regional distribution, 47 have not been confirmed in recent times, 3 are considered extinct or possibly extinct in the country, and 40 are doubtfully occurring in…

Notulae to the Italian alien vascular flora: 11

Publisher Copyright: © This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited In this contribution, new data concerning the distribution of vascular flora alien to Italy are presented. It includes new records, confirmations, exclusions, and status changes for Italy or for Italian administrative regions. Nomenclatural and distribution updates published elsewhere are provided as Suppl. material 1. Peer rev…

Notulae to the Italian native vascular flora: 12

In this contribution, new data concerning the distribution of native vascular flora in Italy are presented. It includes new records, confirmations, exclusions, and status changes to the Italian administrative regions. Nomenclatural and distribution updates, published elsewhere, and corrigenda are provided as Suppl. material 1.

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

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 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 mis…

Supplementary material 1 from: Bartolucci F, Domina G, Argenti C, Bacchetta G, Ballelli S, Banfi E, Barberis D, Barberis G, Bertolli A, Bolpagni R, Bonari G, Bonini F, Briozzo I, Brundu G, Bruschi T, Calbi M, Callegari M, Calvia G, Campoccia D, Cancellieri L, Cangelmi G, Carfagno S, Carruggio F, Casazza G, Cavallaro V, Cherchi S, Ciocia B, Conti F, Crisafulli A, Dagnino D, Vecchia AD, De Fine G, Del Nero V, Di Filippo A, Dunkel FG, Festi F, Filibeck G, Fois M, Forte L, Fratolin F, Galasso G, Gigante D, Gottschlich G, Gubellini L, Hofmann N, Jiménez-Mejías P, Laface VLA, Lonati M, Lozano V, Mainetti A, Mariotti M, Mei G, Minutillo F, Minuto L, Musarella CM, Nota G, Orsenigo S, Pallanza M, Passalacqua NG, Pazienza G, Pinzani L, Pittarello M, Podda L, Prosser F, Enri SR, Riva G, Santi F, Scoppola A, Selvaggi A, Selvi F, Spampinato G, Stinca A, Tomaselli V, Tomasi G, Tondi G, Turcato C, Wilhalm T, Lastrucci L (2021) Notulae to the Italian native vascular flora: 12. Italian Botanist 12: 85-103. https://doi.org/10.3897/italianbotanist.12.78038

Supplementary data