Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genus  Cheiromycina

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ABSTRACT

The genus Cheiromycina is one of the few genera of lichenized hyphomycetes for which no sexual reproductive stages have been observed. The genus includes species from boreal to temperate regions of the Northern Hemisphere where it is found growing on bark or wood. Congeners in Cheiromycina are characterized by a noncorticate thallus, nearly immersed in the substrate and presenting powdery unpigmented sporodochia, and containing chlorococcoid photobionts. The relationships of members of Cheiromycina with other fungi are not known. Here we inferred the phylogenetic placement of Cheiromycina using three loci (nuSSU, nuLSU, and mtSSU) representing C. flabelliformis, the type species for the genus, C. petri, and C. reimeri. Our results revealed that the genus Cheiromycina is found within the family Malmideaceae (Lecanorales) where members formed a monophyletic clade sister to the genera Savoronala and Malmidea. This phylogenetic placement and the relationships of Cheiromycina with other lichenized hyphomycetous taxa are here discussed.

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TreeView: an application to display phylogenetic trees on personal computers.

R D Page (1996)

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A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora.

Jeremy R Dettman, David J Jacobson, John Taylor (2003)

To critically examine the relationship between species recognized by phylogenetic and reproductive compatibility criteria, we applied phylogenetic species recognition (PSR) to the fungus in which biological species recognition (BSR) has been most comprehensively applied, the well-studied genus Neurospora. Four independent anonymous nuclear loci were characterized and sequenced from 147 individuals that were representative of all described outbreeding species of Neurospora. We developed a consensus-tree approach that identified monophyletic genealogical groups that were concordantly supported by the majority of the loci, or were well supported by at least one locus but not contradicted by any other locus. We recognized a total of eight phylogenetic species, five of which corresponded with the five traditional biological species, and three of which were newly discovered. Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species. Despite previous suggestions of hybridization between N. crassa and N. intermedia in nature, and the fact that several putative hybrid individuals were included in this study, no molecular evidence in support of recent interspecific gene flow or the existence of true hybrids was observed. The sequence data from the four loci were combined and used to clarify how the species discovered by PSR were related. Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting.

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Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.

Claude Roux, François Lutzoni, Valérie Reeb (2004)

Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).

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Author and article information

Journal

Journal ID (nlm-ta): Mycologia

Journal ID (iso-abbrev): Mycologia

Journal ID (archive): UMYC

Journal ID (publisher-id): umyc20

Title: Mycologia

Publisher: Taylor & Francis

ISSN (Print): 0027-5514

ISSN (Electronic): 1557-2536

Publication date Collection: 2017

Publication date (Electronic): 06 December 2017

Volume: 109

Issue: 4

Pages: 588-600

Affiliations

[ ^a ] Department of Life Sciences, University of Trieste , via Giorgieri 10, 34127 Trieste, Italy

[ ^b ] Institute of Environmental Sciences CML, Leiden University , Einsteinweg 2, 2333 CC, Leiden, The Netherlands

[ ^c ] Department of Natural History, University Museum, University of Bergen , Allegt. 41, 7800, N-5020 Bergen, Norway

[ ^d ] Department of Plant Taxonomy and Nature Conservation, University of Gdańsk , Wita Stwosza 59, 80-308 Gdańsk, Poland

[ ^e ] Institute of Botany, Academy of Science of Czech Republic , Zámek 1, CZ-25243 Průhonice, Czech Republic

[ ^f ] Department of Botany, Faculty of Natural Sciences, Charles University , Benátská 2, CZ-12801 Praha, Czech Republic

Author notes

CONTACT Lucia Muggia lmuggia@ 123456units.it ; lucia_muggia@ 123456hotmail.com

Color versions of one or more of the figures in this article can be found online at www.tandfonline.com/umyc.

Author information

Lucia Muggia http://orcid.org/0000-0003-0390-6169

Riccardo Mancinelli http://orcid.org/0000-0003-2402-1669

Martin Kukwa http://orcid.org/0000-0003-1560-909X

Article

Publisher ID: 1397476

DOI: 10.1080/00275514.2017.1397476

PMC ID: 5769673

PubMed ID: 29211626

SO-VID: c1f18725-a0d1-4dad-8e19-6cee0f41c0fa

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License ( http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.

History

Date received : 02 May 2017

Date accepted : 24 October 2017

Page count

Figures: 3, Tables: 1, References: 93, Pages: 13

Funding

Funded by: Akademie Věd České Republiky 10.13039/501100004240

Award ID: RVO67985939

Funded by: Austrian Science Fund 10.13039/501100002428

Award ID: P24114-B16

Funded by: Polish-Norwegian Research Programme

Award ID: Pol-Nor/196829/87/2013

L.M. was financially supported by the Austrian Science Fund (FWF project P24114-B16). M.K. has received financial support by the Polish-Norwegian Research Programme operated by the National Centre for Research and Development under the Norwegian Financial Mechanism 2009–2014 in the frame of project contract no. Pol-Nor/196829/87/2013. L.M. and T.T. are grateful to the National Park Service (NPS) and to the Southwest Alaska Network Anchorage for funding. Z.P. acknowledges the development project no. RVO67985939 from the Czech Academy of Sciences and institutional resources of the Ministry of Education, Youth and Sports of the Czech Republic for the support of science and research.

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genus Cheiromycina

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ABSTRACT

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Genes & Diseases

Most cited references 82

TreeView: an application to display phylogenetic trees on personal computers.

A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora.

Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.

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