<i>Youngiahangii</i> (Asteraceae, Crepidinae), a new species from Hubei, China

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Abstract

Youngia hangii T.Deng, D.G.Zhang, Qun Liu & Z.M.Li, sp. nov., a new species of Asteraceae , is described and illustrated. It was collected in Wufeng County, Hubei Province, Eastern Central China. Youngia hangii is morphologically most similar to Y. rubida , but can be easily distinguished from the latter by capitula with 8–10 florets and the hairy leaf surface. Phylogenetic analyses, based on the internal transcribed spacers (ITS) and one chloroplast marker ( rps16), showed that Y. hangii and Y. rubida were sister species with good support. The results of both phylogenetic analysis and the morphological data support the specific rank of Y. hangii .

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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Precision Farming: Technologies and Information as Risk-Reduction Tools

Franklin Hall (1999)

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SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

Gaurav Vaidya, David Lohman, Rudolf Meier (2011)

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.

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Author and article information

Contributors

Qun Liu: Role: Formal analysisRole: Writing - original draftRole: Writing - review and editing

Dai-Gui Zhang: Role: Formal analysis

Jian-Wen Zhang:

ORCID: https://orcid.org/0000-0002-4735-168X

Role: Formal analysis

Tao Deng

Journal

Journal ID (nlm-ta): PhytoKeys

Journal ID (iso-abbrev): PhytoKeys

Journal ID (publisher-id): 3

Journal ID (index): urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD

Title: PhytoKeys

Publisher: Pensoft Publishers

ISSN (Print): 1314-2011

ISSN (Electronic): 1314-2003

Publication date Collection: 2021

Publication date (Electronic): 14 September 2021

Volume: 182

Pages: 27-38

Affiliations

[1 ] School of Life Sciences, Yunnan Normal University, Kunming 650092, Yunnan, China Yunnan Normal University Kunming China

[2 ] Rare Plants Research Institute of Yangtze River, Three Gorges Corporation, Yichang 443133, Hubei, China Rare Plants Research Institute of Yangtze River Yichang China

[3 ] College of Biology and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China Jishou University Jishou China

[4 ] CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China Kunming Institute of Botany, Chinese Academy of Sciences Kunming China

Author notes

Corresponding authors: Tao Deng ( dengtao@ 123456mail.kib.ac.cn ), Zhi-Min Li ( lizhimin_vip@ 123456163.com )

Academic editor: Alexander Sennikov

Author information

Jian-Wen Zhang https://orcid.org/0000-0002-4735-168X

Article

Publisher ID: 71063

DOI: 10.3897/phytokeys.182.71063

PMC ID: 8455504

SO-VID: d727bd3b-0579-40ac-9ee0-61c725a8f08f

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Youngiahangii (Asteraceae, Crepidinae), a new species from Hubei, China

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Most cited references 34

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Precision Farming: Technologies and Information as Risk-Reduction Tools

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

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