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Hypotrachyna neohorrescens , a new species in the subgenus Parmelinopsis ( Parmeliaceae ) from Brazil

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Abstract

This study describes a new species of Hypotrachyna subgenus Parmelinopsis from the south-eastern Cerrado (Brazilian savannah), a biodiversity hotspot. The species is especially common in open vegetation, including urban environments. Hypotrachyna neohorrescens sp. nov. is morphologically and chemically similar to H. horrescens . Nevertheless, phylogenetic analyses of the nuITS and mtSSU regions revealed that H. neohorrescens is a distinct species and closely related to the North American H. mcmulliniana , differing by the size of the laciniae and ascospores.

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Four primers for the amplification of mitochondrial DNA of lichen-forming 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 anserina. 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.
Article
Hypotrachyna virginica was long considered to be an endemic Appalachian macrolichen until it was recently reported from the Caribbean. Here we show that Neotropical material identified as H. virginica is morphologically distinct from that species and instead is conspecific with H. exsecta, a species widespread in the Paleotropics. Both species have also previously been confused with H. laevigata, which is widespread in the Americas and Europe. A revision of the three species is presented, including descriptions, illustrations, distribution maps, and global IUCN red-list assessments.
Article
We have designed two taxon-selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1-F and ITS4-B, were intended to be specific to fungi and basidiomycetes, respectively. We have tested the specificity of these primers against 13 species of ascomycetes, 14 of basidiomycetes, and 15 of plants. Our results showed that ITS4-B, when paired with either a ‘universal’ primer ITS1 or the fungal-specific primer ITS1-F, efficiently amplified DNA from all basidiomycetes and discriminated against ascomycete DNAs. The results with plants were not as clearcut. The ITS1-F/ITS4-B primer pair produced a small amount of PCR product for certain plant species, but the quantity was in most cases less than that produced by the ‘universal’ ITS primers. However, under conditions where both plant and fungal DNAs were present, the fungal DNA was amplified to the apparent exclusion of plant DNA. ITS1-F/ITS4-B preferential amplification was shown to be particularly useful for detection and analysis of the basidiomycete component in ectomycorrhizae and in rust-infected tissues. These primers can be used to study the structure of ectomycorrhizal communities or the distribution of rusts on alternate hosts.
Article
The species delimitation in fungi is currently in flux. A growing body of evidence shows that the morphology-based species circumscription underestimates the number of existing species. The large and ever growing number of DNA sequence data of fungi makes it possible to use these to identify potential cases of hidden species, which then need to be studied with extensive taxon samplings. We used Parmeliaceae, one of the largest families of lichenized fungi as a model. Intra- and interspecific distances derived from maximum-likelihood phylogenetic trees inferred from 491 nuclear ITS rDNA sequences were examined for five major clades of parmelioid lichens. The intra- and interspecific distances were well separated in most cases allowing the calculation of a threshold, with exceptions of highly deviating distances in a few cases. These situations are shown to be taxa in which the current delimitation needs revision. Thus the analysis of the distance distributions is shown to be a powerful tool for identifying species complexes.
Article
Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
Article
The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.
A família Parmeliaceae na localidade de Fazenda da Estrela, município de Vacaria
  • L Canêz
Canêz L (2005) A família Parmeliaceae na localidade de Fazenda da Estrela, município de Vacaria, Rio Grande do Sul, Brasil. MSc. thesis, Instituto de Botânica (São Paulo).
Hypotrachyna (Parmeliaceae, lichenized fungi)
  • Sipman
A família Parmeliaceae (fungos liquenizados) em fragmentos de cerrados do Estado de São Paulo
  • P Jungbluth
Jungbluth P (2006) A família Parmeliaceae (fungos liquenizados) em fragmentos de cerrados do Estado de São Paulo. MSc. thesis, Instituto de Botânica (São Paulo).
Pequenas Parmelia s. l. (Liquens: Ascomycotina) ciliadas dos cerrados brasileiros
  • M P Marcelli
Marcelli MP (1993) Pequenas Parmelia s. l. (Liquens: Ascomycotina) ciliadas dos cerrados brasileiros. Acta Botanica Brasilica 7, 25-70.
A bibliography on Brazilian lichenology
  • M P Marcelli
  • Pereira
  • M Iacomini
Marcelli MP, Pereira EC and Iacomini M (1998) A bibliography on Brazilian lichenology. In Marcelli MP and Seaward MRD (eds), Lichenology in Latin America: History, Current Knowledge and Applications. São Paulo: CETESB, pp. 47-63.
Modeling fuel loads dynamics and fire spread probability in the Brazilian Cerrado. Forest Ecology and Management 482, 118889. Orange A, James PW and White FJ (2010) Microchemical Methods for the Identification of Lichens
  • U Oliveira
  • B Soares-Filho
  • Souza Costa
  • W L Gomes
  • L Bustamante
  • M Miranda
Oliveira U, Soares-Filho B, Souza Costa WL, Gomes L, Bustamante M and Miranda H (2021) Modeling fuel loads dynamics and fire spread probability in the Brazilian Cerrado. Forest Ecology and Management 482, 118889. Orange A, James PW and White FJ (2010) Microchemical Methods for the Identification of Lichens. London: British Lichen Society.
Hypotrachyna (Parmeliaceae, lichenized fungi)
  • Hjm Sipman
  • Elix
  • T H Nash
  • Iii
Sipman HJM, Elix JA and Nash TH, III (2009) Hypotrachyna (Parmeliaceae, lichenized fungi). Flora Neotropica Monograph 104, 1-176.
The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny
  • Swofford
  • J Sullivan
Swofford DL and Sullivan J (2003) Phylogeny inference based on parsimony and other methods using PAUP*. In Salemi M and Vandamme AM (eds), The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny. Cambridge: Cambridge University Press, pp. 160-206.
Microchemical Methods for the Identification of Lichens
  • A Orange
  • James
  • White
Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)
  • G Singh
  • Dal Grande
  • F Divakar
  • Pk
  • J Otte
  • Leavitt
  • Sd
  • K Szczepanska
  • A Crespo
  • Rico
  • Vj
  • A Aptroot
  • M Cáceres