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Yuan Q, Zhao C. Morphology and multigene phylogeny revealed four new species of Xylodon (Schizoporaceae, Basidiomycota) from southern China. MycoKeys 2024; 107:161-187. [PMID: 39169988 PMCID: PMC11336394 DOI: 10.3897/mycokeys.107.128223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Fungi are one of the most diverse groups of organisms on Earth, amongst which wood-inhabiting fungi play a crucial role in ecosystem processes and functions. Four new wood-inhabiting fungi, Xylodoncremeoparinaceus, X.luteodontioides, X.poroides and X.wumengshanensis are proposed, based on morphological features and molecular evidence. Xylodoncremeoparinaceus is distinguished by a cream hymenial surface with a pruinose hymenophore, a monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonluteodontioides is characterised by flavescens hymenophore surface with odontioid hymenophore, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonporoides bears coriaceous basidiomata with a poroid hymenophore surface, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonwumengshanensis is a distinct taxon by its grandinoid hymenophore surface, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed using the Maximum Likelihood, Maximum Parsimony, and Bayesian Inference methods. The phylogram, based on the ITS+nLSU rDNA gene regions, included three genera within the Schizoporaceae as Fasciodontia, Lyomyces and Xylodon. The four new species were grouped into the genus Xylodon. The topology, based on the ITS sequences, revealed that Xylodoncremeoparinaceus was grouped closely with X.pruinosus, X.detriticus and X.ussuriensis. The taxon X.luteodontioides was sister to X.nesporii. The species X.poroides separated from X.pseudotropicus, while X.wumengshanensis was grouped with four taxa: X.patagonicus, X.radula, X.subtropicus and X.taiwanianus.
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Affiliation(s)
- Qi Yuan
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Changlin Zhao
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
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Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
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Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M. Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C. Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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Fernández‐López J, Telleria MT, Dueñas M, May T, Martín MP. DNA barcode analyses improve accuracy in fungal species distribution models. Ecol Evol 2021. [DOI: 10.1002/ece3.7737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Javier Fernández‐López
- Department of Mycology Real Jardín Botánico‐CSIC Madrid Spain
- Department of Biology University of Massachusetts Boston Boston MA USA
| | | | | | - Tom May
- Royal Botanic Gardens Victoria Melbourne Vic. Australia
| | - María P. Martín
- Department of Mycology Real Jardín Botánico‐CSIC Madrid Spain
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Wang XW, May TW, Liu SL, Zhou LW. Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales ( Basidiomycota). J Fungi (Basel) 2021; 7:jof7060478. [PMID: 34204800 PMCID: PMC8231612 DOI: 10.3390/jof7060478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia;
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Correspondence:
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Fernández-López J, Telleria MT, Dueñas M, Laguna-Castro M, Schliep K, Martín MP. Linking morphological and molecular sources to disentangle the case of Xylodon australis. Sci Rep 2020; 10:22004. [PMID: 33319784 PMCID: PMC7738490 DOI: 10.1038/s41598-020-78399-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
The use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.
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Affiliation(s)
- Javier Fernández-López
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain. .,Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM-CSIC-JCCM), Ciudad Real, Spain.
| | - M Teresa Telleria
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Margarita Dueñas
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Mara Laguna-Castro
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain.,Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial Esteban Terradas, Torrejón de Ardoz, Spain
| | | | - María P Martín
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
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Morphologically similar but not closely related: the long-spored species of Subulicystidium (Trechisporales, Basidiomycota). Mycol Prog 2020. [DOI: 10.1007/s11557-020-01587-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractSpecies boundaries and geographic distribution of corticioid fungi (resupinate Basidiomycota) are often poorly known. Our recent study on Subulicystidium showed that species diversity in this genus is at least twice as high as previously recognized. This re-estimation of the species diversity was based on a study of only a part of the genus. The present study sheds light on molecular and morphological diversity of three more species. We generated 27 ITS and 24 28S nuclear ribosomal DNA sequences from 49 specimens labelled as Subulicystidium cochleum, S. longisporum and S. perlongisporum and collected in distant geographic localities. We assessed pairwise dissimilarities and phylogenetic relationships of DNA sequences with Bayesian and maximum likelihood methods. We correlated phylogenetic information with morphological data on spores and cystidia. We found that the three species are not closely related, despite their similarity in spore shape and size. In one of the species, S. perlongisporum, we detected the presence of two sympatric lineages. These lineages are not morphologically distinct, except for a small difference in the mean length of cystidia. Our study provides a further example of transoceanic species distribution in Agaricomycetes.
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