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      Three new species of Cortinarius section Delibuti (Cortinariaceae, Agaricales) from China

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          Abstract

          Three new species of Cortinarius section Delibuti , namely C. fibrillososalor , C. pseudosalor , and C. subtropicus are described as new to science based on morphological and phylogenetic evidences. Cortinarius pseudosalor is extremely morphologically similar to C. salor , but it differs from the latter by smaller coarsely verrucose basidiospores. Cortinarius fibrillososalor can be easily differentiated by its fibrillose pileus. The pileus of C. subtropicus becomes brown without lilac tint at maturity comparing with other members of section Delibuti . A combined dataset of ITS and LSU sequences was used for phylogenetic analysis. The phylogenetic reconstruction of section Delibuti revealed that these three new species clustered and formed independent lineages with full support respectively. A key to the three new species and related species of section Delibuti is provided in this work.

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

          Kazutaka Katoh, Daron Standley (2013)
          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

            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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              MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

              K Tamura, D. Peterson, N. Peterson … (2011)
              Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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                Author and article information

                Contributors
                Pan Long: Role: ConceptualizationRole: Writing - original draftRole: MethodologyRole: Resources
                Song-Yan Zhou: Role: Writing - review and editingRole: Resources
                Sai-Nan Li: Role: Resources
                Fei-Fei Liu: Role: Methodology
                Zuo-Hong Chen: Role: ConceptualizationRole: Writing - review and editingRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: Supervision
                Journal
                Journal ID (nlm-ta): MycoKeys
                Journal ID (iso-abbrev): MycoKeys
                Journal ID (publisher-id): 11
                Journal ID (index): urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:A4FD9303-3F01-45D9-B438-FCCFE465D2F7
                Title: MycoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-4057
                ISSN (Electronic): 1314-4049
                Publication date Collection: 2024
                Publication date (Electronic): 17 January 2024
                Volume: 101
                Pages: 143-162
                Affiliations
                [1 ] College of Life Science, Hunan Normal University, Changsha 410081, China Hunan Normal University Changsha China
                [2 ] Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
                Author notes
                Corresponding author: Zuo-Hong Chen ( chenzuohong@ 123456263.net)

                Academic editor: Bao-Kai Cui

                Article
                Publisher ID: 114705
                DOI: 10.3897/mycokeys.101.114705
                PMC ID: 10809417
                PubMed ID: 38274713
                SO-VID: 6e5c1dc4-dfa6-4b50-8c9c-188c65ef2689
                Copyright © Pan Long, Song-Yan Zhou, Sai-Nan Li, Fei-Fei Liu, Zuo-Hong Chen
                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 : 25 October 2023
                Date accepted : 04 January 2024
                Funding
                This study was financially supported by the National Science Foundation of China (Grant No. 32170016) and the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (Grant No. 2019HJ2096001006).
                Categories
                Subject: Research Article
                Subject: Agaricales
                Subject: Agaricomycetes
                Subject: Cortinariaceae
                Subject: Taxonomy
                Subject: Asia

                Keywords: morphology,new taxa,phylogeny,taxonomy
                Data availability:
                Keywords: morphology, new taxa, phylogeny, taxonomy

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