DOI: 10.3897/mycokeys.138.205866

Authors: Shen-Xian Zhou, Jia-Hui Huang, Shi-Qiang Chen, Qian Deng, Cai-Hua Shi, Quan-Zhou Wen, Pian-Pian Yan, Jian-Xin Deng

Abstract: The genus Alternaria (Pleosporales, Pleosporaceae) is globally distributed, occurs on a wide variety of substrates, and comprises saprobic, endophytic, and pathogenic species. In this study, four unidentified Alternaria isolates were obtained from symptomatic leaves of cowpea (Vigna unguiculata) in Hainan Province, China. These Alternaria spp. were characterized based on morphological features and phylogenetic analysis with multiple loci (GAPDH, RPB2, Alt a 1, EndoPG, and OPA10-2). Based on the combined morphological and phylogenetic evidence, two novel species in Alternaria sect. Alternaria are described: A. unguiculatae sp. nov. and A. hainanensis sp. nov. This study expands the known diversity of Alternaria associated with Fabaceae, particularly cowpea, in China.

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DOI: 10.3897/mycokeys.110.136048

Authors: R. Henrik Nilsson, Arnold Tobias Jansson, Christian Wurzbacher, Sten Anslan, Pauline Belford, Natàlia Corcoll, Alexandra Dombrowski, Masoomeh Ghobad-Nejhad, Mikael Gustavsson, Daniela Gómez-Martínez, Faheema Kalsoom Khan, Maryia Khomich, Charlotte Lennartsdotter, David Lund, Breyten Van Der Merwe, Vladimir Mikryukov, Marko Peterson, Teresita M. Porter, Sergei Põlme, Alice Retter, Marisol Sanchez-Garcia, Sten Svantesson, Patrik Svedberg, Duong Vu, Martin Ryberg, Kessy Abarenkov, Erik Kristiansson

Abstract: Journal impact factors were devised to qualify and compare university library holdings but are frequently repurposed for use in ranking applications, research papers, and even individual applicants in mycology and beyond. The widely held assumption that mycological studies published in journals with high impact factors add more to systematic mycology than studies published in journals without high impact factors nevertheless lacks evidential underpinning. The present study uses the species hypothesis system of the UNITE database for molecular identification of fungi and other eukaryotes to trace the publication history and impact factor of sequences uncovering new fungal species hypotheses. The data show that journal impact factors are poor predictors of discovery potential in systematic mycology. There is no clear relationship between journal impact factor and the discovery of new species hypotheses for the years 2000–2021. On the contrary, we found journals with low, and even no, impact factor to account for substantial parts of the species hypothesis landscape, often discovering new fungal taxa that are only later picked up by journals with high impact factors. Funding agencies and hiring committees that insist on upholding journal impact factors as a central funding and recruitment criterion in systematic mycology should consider using indicators such as research quality, productivity, outreach activities, review services for scientific journals, and teaching ability directly rather than using publication in high impact factor journals as a proxy for these indicators.

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DOI: 10.3897/mycokeys.96.102669

Authors: R. Henrik Nilsson, Martin Ryberg, Christian Wurzbacher, Leho Tedersoo, Sten Anslan, Sergei Põlme, Viacheslav Spirin, Vladimir Mikryukov, Sten Svantesson, Martin Hartmann, Charlotte Lennartsdotter, Pauline Belford, Maryia Khomich, Alice Retter, Natàlia Corcoll, Daniela Gómez Martinez, Tobias Jansson, Masoomeh Ghobad-Nejhad, Duong Vu, Marisol Sanchez-Garcia, Erik Kristiansson, Kessy Abarenkov

Abstract: Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community – that the current situation is satisfactory and that no change is needed to “the code” – and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

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DOI: 10.3897/mycokeys.96.100037

Authors: Maonian Xu, Yingkui Liu, Erik Möller, Scott LaGreca, Patricia Moya, Xinyu Wang, Einar Timdal, Hugo de Boer, Eva Barreno, Lisong Wang, Holger Thüs, Ólafur Andrésson, Kristinn Pétur Magnússon, Elín Soffia Ólafsdóttir, Starri Heiðmarsson

Abstract: The fungal mitochondrial small subunit (mtSSU) ribosomal DNA is one of the most commonly used loci for phylogenetic analysis of lichen-forming fungi, but their primer specificity to mycobionts has not been evaluated. The current study aimed to design mycobiont-specific mtSSU primers and highlights their utility with an example from the saxicolous lichen-forming fungal genus Melanelia Essl. in Iceland. The study found a 12.5% success rate (3 out of 24 specimens with good-quality mycobiont mtSSU sequences) using universal primers (i.e. mrSSU1 and mrSSU3R), not including off-target amplification of environmental fungi, e.g. Cladophialophora carrionii and Lichenothelia convexa. New mycobiont-specific primers (mt-SSU-581-5’ and mt-SSU-1345-3’) were designed by targeting mycobiont-specific nucleotide sites in comparison with environmental fungal sequences, and assessed for mycobiont primer specificity using in silico PCR. The new mycobiont-specific mtSSU primers had a success rate of 91.7% (22 out of 24 specimens with good-quality mycobiont mtSSU sequences) on the studied Melanelia specimens. Additional testing confirmed the specificity and yielded amplicons from 79 specimens of other Parmeliaceae mycobiont lineages. This study highlights the effectiveness of designing mycobiont-specific primers for studies on lichen identification, barcoding and phylogenetics.

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DOI: 10.3897/mycokeys.87.73082

Authors: Yukito Tochihara, Tsuyoshi Hosoya

Abstract: The genus Erioscyphella Kirschst., which was morphologically confused with Lachnum, was herein examined. Based on molecular phylogenetic analyses using a combined dataset of ITS, LSU, mtSSU, and RPB2 and morphological examinations, Erioscyphella was distinguished from Lachnum and redefined by longer ascospores and the presence of apical amorphous materials and/or resinous materials equipped on hairs. Species boundaries recognized by morphology/ecology and phylogenetic analyses were cross-checked using species delimitation analyses based on DNA barcode sequences downloaded from UNITE, resulting in that species’ taxonomic problems being uncovered. Six new species (E. boninensis, E. insulae, E. otanii, E. papillaris, E. paralushanensis, and E. sasibrevispora) and two new combinations (E. hainanensis and E. sinensis) were proposed.

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DOI: 10.3897/mycokeys.86.76053

Authors: Kessy Abarenkov, Erik Kristiansson, Martin Ryberg, Sandra Nogal-Prata, Daniela Gómez-Martínez, Katrin Stüer-Patowsky, Tobias Jansson, Sergei Põlme, Masoomeh Ghobad-Nejhad, Natàlia Corcoll, Ruud Scharn, Marisol Sánchez-García, Maryia Khomich, Christian Wurzbacher, R. Henrik Nilsson

Abstract: The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.

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DOI: 10.3897/mycokeys.26.14591

Authors: R. Henrik Nilsson, Marisol Sánchez-García, Martin K. Ryberg, Kessy Abarenkov, Christian Wurzbacher, Erik Kristiansson

Abstract: DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

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DOI: 10.3897/mycokeys.14.9244

Authors: Taavi Riit, Leho Tedersoo, Rein Drenkhan, Eve Runno-Paurson, Harri Kokko, Sten Anslan

Abstract: Microbial metabarcoding studies using high throughput sequencing technologies generate unprecedented amounts of DNA sequence data and make it possible to determine not only the composition of the communities but also the underlying factors powering the evolution of these communities. Despite the potential of community level studies in helping to better understand the ecology of pathogens and to manage the losses caused by them, very few oomycete addressing metabarcoding studies have been carried out and with highly variable results. The aim of this study was to develop new oomycete-specific ITS region PCR primers with improved specificity for metabarcoding and identification of oomycetes. The modified ITS1oo and the newly developed ITS3oo primers show improved in silico specificity for oomycetes and when paired with the universal ITS4 successfully amplified the DNA from all eleven tested oomycete species from six genera. High throughput sequencing of 20 soil samples from forest nurseries and bordering areas, using the primer pair ITS1oo/ITS4, recovered more than 400 oomycete OTUs, which is a significant increase over previous studies, and indicates the ability of the new method to detect various oomycete groups from complex substrates. The average fraction of oomycete reads per soil samples was 32–36%, with a maximum of 69%. The recovered oomycete OTUs represented the groups Lagenidiales, Peronosporales, Pythiales and Saprolegniales, with Pythiales dominating in all samples. In addition, the new primers were successfully used in identifying pathogens directly from infected plant tissues with Sanger sequencing. The pathogen was identified to the species or genus level in four samples out of six. In conclusion, the developed oomycete-specific primers provide a reliable method for the identification and metabarcoding of oomycetes.

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DOI: 10.3897/mycokeys.12.7553

Authors: R. Henrik Nilsson, Christian Wurzbacher, Mohammad Bahram, Victor R. M. Coimbra, Ellen Larsson, Leho Tedersoo, Jonna Eriksson, Camila Duarte, Sten Svantesson, Marisol Sánchez-García, Martin K. Ryberg, Erik Kristiansson, Kessy Abarenkov

Abstract: Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.

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DOI: 10.3897/mycokeys.6.3185

Authors: Christian Printzen, Stephanie Domaschke, Fernando Fernández-Mendoza, Sergiо Pérez-Ortega

Abstract: Ecological and historical biogeography of lichens have rarely been studied in a concerted effort, but both aspects have to be taken into consideration when explaining the distributional patterns of species. This review summarizes, partly preliminary, results from a series of studies on phylogeography, ecophysiology and symbiotic interactions of the lichen Cetraria aculeata. This species is not only widespread but also occupies a very wide ecological niche. Evidence suggests that Cetraria aculeata has evolved and diversified in the Northern Hemisphere and colonised the Southern Hemisphere from there. Genetic isolation of populations indicates the absence of ongoing long range dispersal and genetic exchange between geographically isolated populations. We observe a hitherto unrecognized genetic diversity that may indicate ecotypic differentiation and speciation processes. Mediterranean and Polar populations differ not only genetically, but also in ecophysiological properties. Ongoing common garden experiments will have to show whether genetically fixed adaptation or acclimation is responsible for these differences. The genetic structure of the photobiont is best explained by climatic differences between localities, but co-dispersal with the mycobiont plays an important role as well. Taken together, these results indicate that a photobiont switch in the past enabled C. aculeata to widen its ecological niche, with subsequent genetic isolation of populations. Photobiont switches may play a crucial role in speciation processes of lichens. A combination of ecophysiological and phylogeographic studies with experimental approaches is necessary to better understand the reaction of lichens to changing environmental conditions.

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DOI: 10.3897/mycokeys.6.3869

Authors: Jouko Rikkinen

Abstract: Symbioses between cyanobacteria and lichen-forming fungi occur worldwide in a wide range of terrestrial environments, ranging from tropical rainforests to hot and cold deserts. The evolutionary success of these symbioses is evident from the wide range of fungal groups that have established associations with cyanobacteria. The diversity of symbiotic cyanobacteria is also high, and it is obvious that symbioses between different cyanobacteria and different lichen-forming fungi have evolved on multiple occasions. From the late 1990s cyanobacterial lichens have been the subject of a steadily increasing number of molecular investigations. This chronological review examines how these studies have contributed to present knowledge and highlights some conceptual developments that have been instrumental in the process.

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DOI: 10.3897/mycokeys.5.4302

Authors: Dagmar Triebel, Gregor Hagedorn, Gerhard Rambold

Abstract: The megascience platforms Biodiversity Heritage Library (BHL), Catalogue of Life (CoL), Encyclopedia of Life (EOL), Global Biodiversity Information Facility (GBIF), International Barcode of Life (iBOL), International Nucleotide Sequence Database Collaboration (INSDC) and JSTOR Plant Science, all belong to a group of global players that harvest, process, repurpose and provide biodiversity data on all kinds of organisms. Each of these platforms primarily focus on one data domain, for instance, taxonomy and classification, occurrence, morphology, ecology, and molecular data.The present contribution describes aspects of processing and provision of biological research data on these platforms, focusing on the technical implementation of data exchange, copyright issues, and data sharing policies as well as their implications for data custodians, owners, providers, and publishers. With the exception of JSTOR Plant Science, most international initiatives seek long-term business models and funding mechanisms to provide online data openly and free of charge. For example, currently GBIF depends on governmental commitments for its funding, and CoL is financed by EU or national grants, as well as being based on Species 2000, a British non-for-profit company, and ITIS. These business models are compared with that of JSTOR Plant Science, the commercial portal of the Global Plant Initiative (GPI). All initiatives currently meet challenges of sustainability with regard to data curation as well as software development for maintaining the complexity of their services. All platforms discussed here also harvest and provide mycological and lichenological research data.

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DOI: 10.3897/mycokeys.5.3342

Authors: Michel Benatti

Abstract: Descriptions are presented for the seven known Bulbothrix (Parmeliaceae, Lichenized Fungi) species with salazinic acid in the medulla and without vegetative propagules. Bulbothrix continua, previously considered as a synonym of B. hypocraea, is recognized as independent species. The current delimitations are confirmed for B. enormis, B. hypocraea, B. meizospora, B. linteolocarpa, B. sensibilis, and B. setschwanensis. New characteriscs and range extensions are provided.

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DOI: 10.3897/mycokeys.4.3606

Authors: R. Henrik Nilsson, Leho Tedersoo, Kessy Abarenkov, Martin Ryberg, Erik Kristiansson, Martin Hartmann, Conrad L. Schoch, Johan A. A. Nylander, Johannes Bergsten, Teresita M. Porter, Ari Jumpponen, Parag Vaishampayan, Otso Ovaskainen, Nils Hallenberg, Johan Bengtsson-Palme, K. Martin Eriksson, Karl-Henrik Larsson, Ellen Larsson, Urmas Kõljalg

Abstract: Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

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DOI: 10.3897/mycokeys.2.2499

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.2.2471

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.2.2196

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.2067

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.2066

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.2065

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.2064

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.1961

Authors: Sandra Knapp, John McNeill, Nicholas J. Turland

Abstract: Changes to the International Code of Botanical Nomenclature are decided on every 6 years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18-22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank). Draft text of the new articles dealing with electronic publication is provided and best practice is outlined.To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in Botanical Journal of the Linnean Society, BMC Evolutionary Biology, Cladistics, Mycotaxon, MycoKeys, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, PLoS ONE, Systematic Botany and Taxon.

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DOI: 10.3897/mycokeys.1.2062

Authors: David Hawksworth

Abstract: A personal synopsis of the decisions made at the Nomenclature Section meeting of the International Botanical Congress in Melbourne in July 2011 is provided, with an emphasis on those which will affect the working practices of, or will otherwise be of interest to, mycologists. The topics covered include the re-naming of the Code, the acceptance of English as an alternative to Latin for validating diagnoses, conditions for permitting electronic publication of names, mandatory deposit of key nomenclatural information in a recognized repository for the valid publication of fungal names, the discontinuance of dual nomenclature for pleomorphic fungi, and clarification over the typification of sanctioned names, and acceptability of names originally published under the zoological code. Collectively, these changes are the most fundamental to have been enacted at single Congress since the 1950s, and herald the dawn of a new era in the practice of fungal nomenclature.

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DOI: 10.3897/mycokeys.1.2058

Authors: Thorsten Lumbsch, Andrew Miller, Dominik Begerow, Lyubomir Penev

Abstract: The launch of MycoKeys coincided with several revolutionary changes to the International Code of Botanical Nomenclature (ICBN) (Knapp et al. 2011 and Hawksworth 2011, in this volume, Miller et al. 2011) that occurred during the Nomenclature Section of the XVIII International Botanical Congress (IBC2011) in Melbourne, Australia. The path to the present launch, however was paved years ago by the lively discussions on electronic publication and dissemination of biodiversity information in the Internet era (e.g., Knapp 2010, Penev et al. 2010a), as well as by the successful start of its sister journals, PhytoKeys and ZooKeys.

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