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      A phylogenetic overview of the Hydnaceae ( Cantharellales, Basidiomycota) with new taxa from China

      research-article
      1 , 2 , 3 , 1 , 2 , 4 , 1 , 2 ,
      Studies in Mycology
      Westerdijk Fungal Biodiversity Institute
      Cantharellales, Hydnaceae, Multiple-marker phylogeny, Taxonomy, In genus Cantharellus: Cantharellus subgenus Magnus T. Cao & H.S. Yuan, in genus Craterellus: Craterellus subgenus Cariosi T. Cao & H.S. Yuan, subg. Craterellus, subg. Imperforati T. Cao & H.S. Yuan, subg. Lamelles T. Cao & H.S. Yuan, subg. Longibasidiosi T. Cao & H.S. Yuan, subg. Ovoidei T. Cao & H.S. Yuan , in genus Hydnum: Hydnum subgenus Brevispina T. Cao & H.S. Yuan, Cantharellus laevihymeninus T. Cao & H.S. Yuan, Ca. magnus T. Cao & H.S. Yuan, Ca. subminor T. Cao & H.S. Yuan , Craterellus badiogriseus T. Cao & H.S. Yuan, Cr. croceialbus T. Cao & H.S. Yuan, Cr. macrosporus T. Cao & H.S. Yuan, Cr. squamatus T. Cao & H.S. Yuan , Hydnum brevispinum T. Cao & H.S. Yuan, H. flabellatum T. Cao & H.S. Yuan, H. flavidocanum T. Cao & H.S. Yuan, H. longibasidium T. Cao & H.S. Yuan, H. pallidocroceum T. Cao & H.S. Yuan, H. pallidomarginatum T. Cao & H.S. Yuan, H. sphaericum T. Cao & H.S. Yuan, H. tangerinum T. Cao & H.S. Yuan, H. tenuistipitum T. Cao & H.S. Yuan, H. ventricosum T. Cao & H.S. Yuan , Cantharellus anzutake W. Ogawa, N. Endo, M. Fukuda and A. Yamada and Ca. tuberculosporus M. Zang as Ca. yunnanensis W.F. Chiu , Hydnum albomagnum Banker, Hydnum minum Yanaga & N. Maek

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          Abstract

          The family Hydnaceae ( Cantharellales, Basidiomycota) is a group of fungi found worldwide which exhibit stichic nuclear division. The group is highly diverse in morphology, ecology, and phylogeny, and includes some edible species which are popular all over the world. Traditionally, Hydnaceae together with Cantharellaceae, Clavulinaceae and Sistotremataceae are four families in the Cantharellales. The four families were combined and redefined as “ Hydnaceae”, however, a comprehensive phylogeny based on multiple-marker dataset for the entire Hydnaceae sensu stricto is still lacking and the delimitation is also unclear. We inferred Maximum Likelihood and Bayesian phylogenies for the family Hydnaceae from the data of five DNA regions: the large subunit of nuclear ribosomal RNA gene (nLSU), the internal transcribed spacer regions (ITS), the mitochondrial small subunit rDNA gene (mtSSU), the second largest subunit of RNA polymerase II ( RPB2) and the translation elongation factor 1-alpha gene ( TEF1). We also produced three more phylogenetic trees for Cantharellus based on 5.8S, nLSU, mtSSU, RPB2 and TEF1, Craterellus and Hydnum both based on the combined nLSU and ITS. This study has reproduced the status of Hydnaceae in the order Cantharellales, and phylogenetically confirmed seventeen genera in Hydnaceae. Twenty nine new taxa or synonyms are described, revealed, proposed, or reported, including eight new subgenera ( Cantharellus subgenus Magnus, Craterellus subgenus Cariosi, subg. Craterellus, subg. Imperforati, subg. Lamelles, subg. Longibasidiosi, subg. Ovoidei, and Hydnum subgenus Brevispina); seventeen new species ( Ca. laevihymeninus, Ca. magnus, Ca. subminor, Cr. badiogriseus, Cr. croceialbus, Cr. macrosporus, Cr. squamatus, H. brevispinum, H. flabellatum, H. flavidocanum, H. longibasidium, H. pallidocroceum, H. pallidomarginatum, H. sphaericum, H. tangerinum, H. tenuistipitum and H. ventricosum); two synonyms ( Ca. anzutake and Ca. tuberculosporus as Ca. yunnanensis), and two newly recorded species ( H. albomagnum and H. minum). The distinguishing characters of the new species and subgenera as well as their allied taxa are discussed in the notes which follow them. The delimitation and diversity in morphology, ecology, and phylogeny of Hydnaceae is discussed. Notes of seventeen genera which are phylogenetically accepted in Hydnaceae by this study and a key to the genera in Hydnaceae are provided .

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

          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

            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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              MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

              Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
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                Author and article information

                Contributors
                Journal
                Stud Mycol
                Stud Mycol
                Studies in Mycology
                Westerdijk Fungal Biodiversity Institute
                0166-0616
                1872-9797
                23 December 2021
                June 2021
                23 December 2021
                : 99
                : 100121
                Affiliations
                [1 ]CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
                [2 ]University of the Chinese Academy of Sciences, Beijing 100049, PR China
                [3 ]Nanjing Institute of Environmental Sciences, MEE/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, PR China
                [4 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
                Author notes
                [] Correspondence: Hai-Sheng Yuan hsyuan@ 123456iae.ac.cn
                Article
                S0166-0616(21)00008-7 100121
                10.1016/j.simyco.2021.100121
                8717575
                35035603
                c1640e07-8426-42df-a1f8-7c1b816b8667
                © 2021 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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                Research Paper

                Plant science & Botany
                cantharellales,hydnaceae,multiple-marker phylogeny,taxonomy,in genus cantharellus: cantharellus subgenus magnus t. cao & h.s. yuan,in genus craterellus: craterellus subgenus cariosi t. cao & h.s. yuan, subg. craterellus, subg. imperforati t. cao & h.s. yuan, subg. lamelles t. cao & h.s. yuan, subg. longibasidiosi t. cao & h.s. yuan, subg. ovoidei t. cao & h.s. yuan,in genus hydnum: hydnum subgenus brevispina t. cao & h.s. yuan,cantharellus laevihymeninus t. cao & h.s. yuan, ca. magnus t. cao & h.s. yuan, ca. subminor t. cao & h.s. yuan,craterellus badiogriseus t. cao & h.s. yuan, cr. croceialbus t. cao & h.s. yuan, cr. macrosporus t. cao & h.s. yuan, cr. squamatus t. cao & h.s. yuan,hydnum brevispinum t. cao & h.s. yuan, h. flabellatum t. cao & h.s. yuan, h. flavidocanum t. cao & h.s. yuan, h. longibasidium t. cao & h.s. yuan, h. pallidocroceum t. cao & h.s. yuan, h. pallidomarginatum t. cao & h.s. yuan, h. sphaericum t. cao & h.s. yuan, h. tangerinum t. cao & h.s. yuan, h. tenuistipitum t. cao & h.s. yuan, h. ventricosum t. cao & h.s. yuan,cantharellus anzutake w. ogawa, n. endo, m. fukuda and a. yamada and ca. tuberculosporus m. zang as ca. yunnanensis w.f. chiu,hydnum albomagnum banker,hydnum minum yanaga & n. maek

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