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      Additions to Neopestalotiopsis (Amphisphaeriales, Sporocadaceae) fungi: two new species and one new host record from China

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          Abstract

          Background

          In this study, three Neopestalotiopsis taxa were identified, associated with leaves of Zingiber officinale , Elaeagnus pungens and Salacca zalacca .

          New information

          Based on morphology and multi–gene analyses of the internal transcribed spacer (ITS), beta-tubulin (TUB2) and translation elongation factor 1–alpha (TEF1), the five strains of Neopestalotiopsis represent two novel and one known species. They are introduced with descriptions, illustrations and notes herein.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

              T.J White, T. Bruns, S. Lee … (1990)
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                Author and article information

                Contributors
                Yong Wang
                Journal
                Journal ID (nlm-ta): Biodivers Data J
                Journal ID (iso-abbrev): Biodivers Data J
                Journal ID (publisher-id): 1
                Journal ID (index): urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Title: Biodiversity Data Journal
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-2836
                ISSN (Electronic): 1314-2828
                Publication date Collection: 2022
                Publication date (Electronic): 28 September 2022
                Volume: 10
                Electronic Location Identifier: e90709
                Affiliations
                [1 ] Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand
                [2 ] Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang, 550025, China Department of Plant Pathology, Agriculture College, Guizhou University Guiyang, 550025 China
                [3 ] School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand School of Science, Mae Fah Luang University Chiang Rai 57100 Thailand
                Author notes
                Corresponding author: Yong Wang ( yongwangbis@ 123456aliyun.com ).

                Academic editor: Ning Jiang

                Author information
                https://orcid.org/0000-0003-3043-0493
                https://orcid.org/0000-0001-5549-1028
                https://orcid.org/0000-0003-1341-1004
                https://orcid.org/0000-0001-7702-4885
                Article
                Publisher ID: 90709 Publisher-manuscript ID: 20445
                DOI: 10.3897/BDJ.10.e90709
                PMC ID: 9848506
                PubMed ID: 36761578
                SO-VID: 408731c7-f9da-4675-a8ad-c049257ba667
                Copyright © Yu-Ke He, Qi Yang, Ya-Ru Sun, Xiang-Yu Zeng, Ruvishika S. Jayawardena, Kevin D. Hyde, Yong Wang
                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.

                History
                Date received : 22 July 2022
                Date accepted : 19 September 2022
                Page count
                Figures: 4, Tables: 3, References: 52
                Funding
                Funded by: National Natural Science Foundation of China 501100001809 http://doi.org/10.13039/501100001809
                Categories
                Subject: Taxonomy & Inventories
                Subject: Fungi
                Subject: Ascomycota
                Subject: Pezizomycetes
                Subject: Taxonomy

                Keywords: morphology,pestalotiod,phylogeny,taxonomy,zingiberaceae
                Data availability:
                Keywords: morphology, pestalotiod, phylogeny, taxonomy, zingiberaceae

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