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      Multi-gene phylogenetic evidence indicates that Pleurodesmospora belongs in Cordycipitaceae (Hypocreales, Hypocreomycetidae) and Pleurodesmospora lepidopterorum sp. nov. on pupa from China

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          A new species, Pleurodesmospora lepidopterorum , isolated from a pupa, is introduced. Morphological comparisons and phylogenetic analyses based on multigene datasets (ITS+RPB1+RPB2+TEF) support the establishment of the new species. Pleurodesmospora lepidopterorum is distinguished from P. coccorum by its longer conidiogenous pegs located in the terminal or lateral conidiophores, and smaller subglobose or ellipsoidal conidia. A combined dataset of RPB1, RPB2, and TEF confirmed the taxonomic placement of Pleurodesmospora in Cordycipitaceae for the first time.

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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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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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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.

                Author and article information

                Role: Formal analysisRole: Funding acquisitionRole: Writing - original draft
                Role: Funding acquisitionRole: Writing - review and editing
                Role: Funding acquisitionRole: MethodologyRole: Writing - review and editing
                Role: Funding acquisitionRole: Project administrationRole: Resources
                Role: Writing - review and editing
                Pensoft Publishers
                07 May 2021
                : 80
                : 45-55
                [1 ] Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China Guizhou University of Traditional Chinese Medicine Guiyang China
                [2 ] Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China Guizhou University Guiyang China
                Author notes
                Corresponding author: Yan-Feng Han ( swallow1128@ 123456126.com )

                Academic editor: T. Lumbsch

                Wan-Hao Chen, Yan-Feng Han, Jian-Dong Liang, Wei-Yi Tian, Zong-Qi Liang

                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.

                This work was supported by the National Natural Science Foundation of China (Grant No. 31860002), High-level Innovative Talents Training Object in Guizhou Province (No. Qiankehepingtairencai [2020]6005), Science and Technology Foundation of Guizhou Province (No. Qiankehejichu [2020]1Y060), Program of Innovative Scientific and technological Talent Team of Guizhou Province(2020-5010) and Construction Program of Guizhou Engineering Research Center (Qian Fa Gai Gao Ji 2020-896) and National Survey of Traditional Chinese Medicine Resources (No. Caishe [2017]66, 216).
                Research Article
                Anamorphic Fungi
                Molecular Systematics


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