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       Actinostephanus (Gesneriaceae), a new genus and species from Guangdong, South China

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          Abstract

          Actinostephanus , a new genus from southern China, is described and colorfully illustrated with a single species, A. enpingensis . This new genus is morphologically most similar to Boeica and Leptoboea , nevertheless, it can be easily distinguished from the latter two by the following characteristics, such as leaves in whorls of three, all closely clustered at the top; corolla bowl-shaped, 5-lobed, actinomorphic; capsule hard, oblong-ovoid, short, 3–4 mm long, densely appressed villous, wrapped by persistent densely pubescent calyx lobes, style persistent. The new genus and related genera were sequenced using the next-generation sequencing technique. The whole plastid genome of the new genus is 154, 315 – 154, 344 bp in length. We reconstructed phylogenetic trees using the dataset of 80 encoded protein genes of the whole plastid genome from 47 accessions based on ML and BI analyses. The result revealed that the new genus was recovering in a polytomy including Boeica , Rhynchotechum , and Leptoboea with strong support, congruent to the morphological evidence. A global conservation assessment was also performed and classifies A. enpingensis as Least Concern (LC). In addition, after a review of recently described species of Gesneriaceae , we propose that plant enthusiasts, especially Gesneriad fans, have been playing an increasingly important role in the process of new taxa-discoveries.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              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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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: Project administration
                Role: Data curation
                Role: Investigation
                Role: Formal analysis
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Writing - review and editing
                Role: Funding acquisitionRole: Project administrationRole: Writing - review and editing
                Role: MethodologyRole: SoftwareRole: Writing - original draft
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2022
                22 March 2022
                : 193
                : 89-106
                Affiliations
                [1 ] Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, CN-541006 Guilin, China
                [2 ] Gesneriad Committee of China Wild Plant Conservation Association, National Gesneriaceae Germplasm Bank of GXIB, Gesneriad Conservation Center of China (GCCC), Guilin Botanical Garden, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, CN-541006 Guilin, China
                [3 ] School of Resources and Environmental Engineering, Anhui University, Hefei, CN–230601, Anhui Province, China
                [4 ] Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, CN-650201, Kunming, Yunnan Province, China
                [5 ] Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, CN-650201, Kunming, Yunnan Province, China
                [6 ] Management Office, Guangdong Enping Qixingkeng Provincial Nature Reserve, CN-529400, Enping, China
                [7 ] Guangzhou Linfang Ecology Co., Ltd., Guangzhou, CN-510520, Guangdong Province, China
                [8 ] The Gesneriad Society, 2030 Fitzwater Street, Philadelphia, PA. 19146-1333 USA
                Author notes
                Corresponding authors: Yi-Gang Wei ( weiyigang@ 123456aliyun.com ), Long-Fei Fu ( longfeifu@ 123456126.com )

                Academic editor: E. Fischer

                Author information
                https://orcid.org/0000-0002-3889-8835
                https://orcid.org/0000-0002-0062-6930
                https://orcid.org/0000-0002-9251-2745
                https://orcid.org/0000-0001-8708-4718
                Article
                80715
                10.3897/phytokeys.193.80715
                9849016
                36760839
                949760fe-fae3-463f-a4fb-bad6240d283d
                Fang Wen, Zi-Bing Xin, Xin Hong, Lei Cai, Xiao-Yun Chen, Jun-Jie Liang, Hui-Feng Wang, Stephen Maciejewski, Yi-Gang Wei, Long-Fei Fu

                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.

                History
                : 18 January 2022
                : 04 March 2022
                Categories
                Research Article
                Gesneriaceae
                Taxonomy
                Asia
                China

                Plant science & Botany
                boeica ,didymocarpoideae,flora of china,iucn, leptoboea ,phylogeny
                Plant science & Botany
                boeica , didymocarpoideae, flora of china, iucn, leptoboea , phylogeny

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