Taxonomy and phylogeny of the basidiomycetous hyphomycete genus <i>Hormomyces</i>

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Abstract

The taxonomy of the genus Hormomyces, typified by Hormomyces aurantiacus, which based on circumstantial evidence was long assumed to be the hyphomycetous asexual morph of Tremella mesenterica ( Tremellales, Tremellomycetes) or occasionally Dacrymyces ( Dacrymycetales, Dacrymycetes) , is revised. Phylogenies based on the three nuc rDNA markers [internal transcribed spacers (ITS), 28S large ribosomal subunit nrDNA (28S) and 18S small ribosomal subunit nrDNA (18S)], based on cultures from Canada and the United States, suggest that the genus is synonymous with Tulasnella ( Cantharellales, Agaricomycetes) rather than Tremella or Dacrymyces. Morphological studies of 38 fungarium specimens of Hormomyces, including the type specimens of H. callorioides, H. fragiformis, H. paridiphilus and H. peniophorae and examination of the protologues of H. abieticola, H. aurantiacus and H. pezizoideus suggest that H. callorioides and H. fragiformis are conspecific with H. aurantiacus while the remaining species are unlikely to be related to Tulasnella. The conidial chains produced by H. aurantiacus are similar to monilioid cells of asexual morphs of Tulasnella species formerly referred to the genus Epulorhiza. The new combination Tulasnella aurantiaca is proposed and the species is redescribed, illustrated and compared with similar fungi. The ecological niche of T. aurantiaca and its possible relationship to orchid root endophytes is discussed. A key to asexual genera with similar conidium ontogeny to T. aurantiaca is provided.

Citation: Mack J, Assabgui RA, Seifert KA (2021). Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces. Fungal Systematics and Evolution 7: 177–196. doi: 10.3114/fuse.2021.07.09

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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

R. C. Edgar (2004)

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

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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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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

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Author and article information

Journal

Journal ID (nlm-ta): Fungal Syst Evol

Journal ID (iso-abbrev): Fungal Syst Evol

Journal ID (publisher-id): FUSE

Title: Fungal Systematics and Evolution

Publisher: Westerdijk Fungal Biodiversity Institute

ISSN (Print): 2589-3823

ISSN (Electronic): 2589-3831

Publication date (Electronic): 12 February 2021

Publication date (Print): June 2021

Volume: 7

Pages: 177-196

Affiliations

Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada.

Author notes

#Current address: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.

*Corresponding author: jonathan.mack2@ 123456canada.ca

Corresponding editor: P.W. Crous

Article

DOI: 10.3114/fuse.2021.07.09

PMC ID: 8166209

SO-VID: b6f17624-7d85-4590-951f-cc1be42e50a3

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Fungal Systematics and Evolution is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Taxonomy and phylogeny of the basidiomycetous hyphomycete genus Hormomyces

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Most cited references 107

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

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