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      Multi-gene phylogeny and morphological characters reveal seven new species of Micropsalliota (Agaricales, Agaricaceae) from southern China, with an updated key for the species distributed in China

      research-article
      a , b , c , a , b , c , a , b
      Mycology
      Taylor & Francis
      Agaricaceae, molecular phylogeny, new taxa, taxonomy

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          ABSTRACT

          Species of Micropsalliota generally grow in the tropics and are characterised by small, slender basidiomes, brown basidiospores, and cheilocystidia that vary in shape with capitate or subcapitate apex, and pigmented pileipellis. Based on morphological characters and molecular evidence, here we describe seven new species from southern China, viz. Micropsalliota ferruginea, M. fimbriata, M. gigaspora, M. longicystis, M. nana, M. squarrosa, and M. umbonata. Micropsalliota appendiculata, a species recently described from Vietnam, was first recorded in China. The Maximum likelihood and Bayesian analyses based on multi-locus sequence datasets (the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, nrITS; the D1–D2 domains of nuc 28S rDNA, LSU; partial sequences of the most variable region of the second-largest subunit of RNA polymerase II, rpb2, and a portion of the translation-elongation factor 1-α, tef1) shows that the genus is separated into 11 major clades and subclades. To aid in diagnosis, a key to 32 species of Micropsalliota in China is provided.

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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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            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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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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                Author and article information

                Journal
                Mycology
                Mycology
                Mycology
                Taylor & Francis
                2150-1203
                2150-1211
                3 April 2024
                2024
                3 April 2024
                : 15
                : 3
                : 374-399
                Affiliations
                [a ]CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences; , Kunming, China
                [b ]Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences; , Kunming, China
                [c ]College of Life Sciences, University of Chinese Academy of Sciences; , Beijing, China
                Author notes
                CONTACT Zai-Wei Ge zwge@ 123456mail.kib.ac.cn CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences; , Lanhei Road 132, Kunming 650201, China; Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences; , Kunming 650201, China
                Article
                2323206
                10.1080/21501203.2024.2323206
                11376282
                39247894
                2b9b6a05-fcf8-4e2f-a89b-6970073efede
                © 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

                History
                Page count
                Figures: 10, Tables: 1, References: 53, Pages: 26
                Categories
                Research Article
                Research Article

                agaricaceae,molecular phylogeny,new taxa,taxonomy
                agaricaceae, molecular phylogeny, new taxa, taxonomy

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