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      Integrative taxonomy confirms three species of Coniocarpon (Arthoniaceae) in Norway

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          Abstract

          Abstract

          We have studied the highly oceanic genus Coniocarpon in Norway. Our aim has been to delimit species of Coniocarpon in Norway based on an integrative taxonomic approach. The material studied comprises 120 specimens of Coniocarpon , obtained through recent collecting efforts (2017 and 2018) or received from major fungaria in Denmark, Finland, Norway and Sweden, as well as from private collectors. We have assessed (1) species delimitations and relationships based on Bayesian and maximum likelihood phylogenetic analyses of three genetic markers (mtSSU, nucITS and RPB2), (2) morphology and anatomy using standard light microscopy, and (3) secondary lichen chemistry using high-performance thin-layer chromatography. The results show three genetically distinct lineages of Coniocarpon , representing C. cinnabarinum , C. fallax and C. cuspidans comb. nov. The latter was originally described as Arthonia cinnabarina f. cuspidans and is herein raised to species level. All three species are supported by morphological, anatomical and chemical data.

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          How many bootstrap replicates are necessary?

          Nicholas D Pattengale, Masoud Alipour, Olaf Bininda-Emonds … (2010)
          Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.
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            Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

            Christoph Sperisen, Stefan Zoller, Christoph Scheidegger (1999)
            Four primers for the amplification of mitochondrial DNA of lichenforming ascomycetes are presented. The primers match the conserved regions U2, U4, and U6, respectively, of mitochondrial small subunit (SSU) ribosomal DNA (rDNA). Polymerase chain reaction using different combinations of the primers produced single amplification products from DNA of eight lichen-forming fungal species but did not amplify DNA of two axenic cultured algal species. The amplification product obtained from Lobaria pulmonaria was sequenced and the 894-bp sequence was compared with the mitochondrial SSU rDNA sequence of Podospora anserine . The two sequences revealed more than 76% identity in the conserved regions U3 to U5 demonstrating that we amplified mitochondrial DNA. The primers matching U2 and U6 yielded amplification products of 800–1000 bp depending on the species examined. The variation observed suggests that mitochondrial SSU rDNA may be useful for phylogenetic analyses of lichen-forming ascomycetes.
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              Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes.

              Inmaculada Larena, Oscar M Salazar, Vicente B González … (1999)
              A primer able to amplify the internal transcribed spacers (ITS) of the ribosomal DNA (rDNA), having enhanced specificity for ascomycetes, was identified by reviewing fungal ribosomal DNA sequences deposited in GenBank. The specificity of the primer, named ITS4A, was tested with DNA extracted from several species of ascomycetes, basidiomycetes, zygomycetes, mastigomycetes and mitosporic fungi (formerly deuteromycetes) and also from plants. The PCR annealing temperature most specific for ascomycetes was found to be 62 degrees C and 64 degrees C for the primer pairs ITS5 + ITS4A and ITS1F + ITS4A, respectively. At these annealing temperatures, all ascomycetous DNA samples were amplified efficiently with the ITS4A primer. The sensitivity limit was in the range 10(-14) g of DNA. This primer could also provide useful tools in suggesting the affinities of many mitosporic fungi with their perfect states.
              Article 0 comments Cited 60 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Mika Bendiksby
                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
                Title: MycoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-4057
                ISSN (Electronic): 1314-4049
                Publication date Collection: 2020
                Publication date (Electronic): 23 January 2020
                Volume: 62
                Pages: 27-51
                Affiliations
                [1 ] NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
                [2 ] Institute of Plant Sciences, Karl-Franzens-University Graz, Holteigasse 6, 8010 Graz, Austria
                Author notes
                Corresponding author: Mika Bendiksby ( mika.bendiksby@ 123456ntnu.no )

                Academic editor: T. Lumbsch

                Article
                Publisher ID: 48480
                DOI: 10.3897/mycokeys.62.48480
                PMC ID: 6992689
                SO-VID: b9ed0860-c3be-4353-b939-2b52f20675b3
                Copyright © Andreas Frisch, Victoria Stornes Moen, Martin Grube, Mika Bendiksby
                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 : 14 November 2019
                Date accepted : 23 December 2019
                Categories
                Subject: Research Article
                Subject: Arthoniaceae
                Subject: Biodiversity & Conservation
                Subject: DNA barcoding
                Subject: Identification key
                Subject: Molecular systematics
                Subject: Nomenclature
                Subject: Phylogeny
                Subject: Taxonomy
                Subject: British Isles
                Subject: Norway incl. Finnmark
                Subject: Rwanda
                Subject: Sweden
                Subject: Uganda

                Keywords: arthoniales ,bayesian inference,maximum likelihood,morphology,mtssu,nucits,phylogeny,rpb2,fungi,arthoniales,arthoniaceae
                Data availability:
                Keywords: arthoniales , bayesian inference, maximum likelihood, morphology, mtssu, nucits, phylogeny, rpb2, fungi, arthoniales, arthoniaceae

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