MYCOLENS (65) , 8

, 14 , Teresa Lebel , Teresa 7 (Nuhn et al. (Nuhn 2002). (Eberhardt (Eberhardt . 2002), Lactarius , Machiel E. Noordeloos , Machiel , Thomas Læssøe , Thomas 13 6 However, such phylogenetic analyses phylogenetic such However, molecular-phylogenetic research and the the and research molecular-phylogenetic led has to It trees. phylogenetic resulting cases many in of characters; re-evaluation shown were gastroid forms and sequestrate higher assumed, evolvability have to than genera of such subsumption justifying the genera; existing in example for under 1997), Cortinarius & Bruns (Kretzer Suillus et al (Peintner 2015), Russula 2004, Kirk & Verbeken 2007), Lepiota (Ge & (Lebel Tonkin & Boletus 2013), and Smith 2013). Lichenization had low evolvability low had 2013). Lichenization justifying basidiomycetes, recognitionin for genus as a separate of Lichenomphalia placed previously three in were species that (Redheadgenera et al. hoped was than extent a smaller to have and delimitation of genus problems solved the several that shown recognition. have Analyses such paraphyletic, remain genera well-known , Alfredo Justo , Alfredo 5 , Gregory M. Mueller 2014, 12 , Roy E. Halling 4

16 2015). , Pierre-Arthur Moreau , Pierre-Arthur 11 , Dennis E., Dennis Desjardin The underlying principle for recognition for principle underlying The The floodnew these recent generic of 3 described based newly species on discovered morphological unique with character are latter of the Examples combinations. Rocky the from crocodilinus Cercopemyces Hymenoporus and (USA) Mountains et al. (Baroni China from paradoxus Tkalčec et al. of a genus, or any taxonomic rank for that that for rank taxonomic any or of a genus, 1950, 1965). (Hennig is monophyly matter, difficult to past extremely was this the In of fungi, in number as the demonstrate could be usedmorphological that characters whether also was unknown limited.was It used, such were that characters of the some gastroid or of sequestrate formation as the justifying evolvability, basidiomes, a low had recognition genera, a high as or separate its downplays which then evolvability, context. a phylogenetic in relevance by been mainly has prompted names , Andrew S. Methven , Andrew , and Annemieke Verbeken Annemieke , and , Joe Ammirati , Joe 2 10 15

” for a long time. time. a long ” for , Clark L.Ovrebo , Clark 14 , Thomas W. Kuyper W. , Thomas 1 , P. Brandon Matheny Brandon , P. 9 were proposed. Most of these new of these proposed. Most were , newin Lyophyllaceae , five genera

are for numbers The

Department of Biology, University of Central Oklahoma, Edmond, OK 73034, USA of Central of Biology, University Department of Biology, K.L. Department Ledeganckstraat Belgium 35, 9000 Gent, University, Ghent Département des Sciences Végétales et Fongiques, Faculté des sciences pharmaceutiques et biologiques, Université de Lille, 59006 Lille, et biologiques, France Université pharmaceutiques des sciences Faculté et Fongiques, des Sciences Végétales Département Cook 1000 Lake Road,Chicago Glencoe, IL Garden, Botanic 60022, USA Netherlands 9517, 2300 RA Box Leiden, The P.O. Biodiversity Centre, Naturalis Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN USA 37996-1610, Knoxville, of Tennessee, of Ecology Biology,Department University Evolutionary and IL 61920, USA Charleston, of Biological University, Illinois Department Sciences, Eastern Center for Forest Mycology Research, Northern Research Station, USDA-Forest Service, PR Luquillo, 00773-1377, USA USDA-Forest Station, Research Mycology Northern Research, Forest for Center Department of Botany, Institute of Biology, National Autonomous University of Mexico, 04510 Mexico City, Mexico City, 04510 Mexico of Mexico, University Autonomous of Biology, National Institute of Botany, Department 15, 2100 Copenhagen Denmark Ø, of Copenhagen, Universitetsparken University of Denmark, of Biology/Natural History Museum Department 3004, Australia Melbourne Victoria, Ave, Birdwood Royal Gardens Botanic Department of Soil Quality, Wageningen University, P.O. Box 47, 6700 AA Wageningen, The Netherlands; corresponding author e-mail:[email protected] author corresponding Netherlands; The 47, 6700 AA Wageningen, Box P.O. University, Wageningen of Soil Quality, Department 98195-1800, USA WA Seattle, of Washington, of Biology, University Department CA 94132, USA Francisco, San Avenue, 1600 Holloway University, State of Biology, Francisco San Department Boulevard, NY Bronx, 10458, USA 2900 Southern Botanical Garden, York New Botany, of Systematic Institute Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720-3102, USA; corresponding author e-mail: CA ecvellinga@comcast. USA; 94720-3102, author corresponding Berkeley, Berkeley, at of California Biology, Microbial and University of Plant Department generic names encompass species that occur occur species that encompass names generic have that and Europe and America North in been called “Boletus . The Psathyrellaceae new in ones three and not , was Cortinarius far, largest by genus probably 6–7 some In contrast, affected. under been now subsumed have genera new generic many . With Cortinarius well-known for introduced being names species, it comes as larger even surprise an very few were new genera there that note to In 2014 and the first six months of six months first the 2014 and In 20 new in genera than 2015 alone, more Boletaceae 25 new comparable: around counted we time same published names that generic in white-spored, with period, of them most six new species for used genera call to we Clitocybe INTRODUCTION

fungi Six simple guidelines for introducing new genera of genera new for introducing guidelines Six simple net volume 6 · no. 2 16 12 13 14 15 9 10 11 6 7 8 3 4 5 1 2 Else C. Vellinga Else Jorinde Nuytinck Jorinde basidiomycetes, molecular systematics, nomenclature, phylogenetics, , phylogenetics, nomenclature, molecular basidiomycetes, Key systematics, words: We formulate five guidelines for introducing new genera, plus one recommendation how to publish the results of scientific research. We recommend that that We recommend research. of scientific results the to publish how new recommendation one five genera, plus introducing guidelines for formulate We Abstract: discussed. The properly are solutions final the and results the is solid, that and research underlying the that propose guidelines. these to editors and adhere reviewers We recognized are: are of species, geographic (1) all shouldsix criteria that number genera be should in tree be wide coverage phylogenetic monophyletic; (2) the of the the for options support; (4) different statistical sufficient have to has trees coverage, phylogenetic study; type of the and branching under genera species (3) the of the justified; final phylogenetic shouldthe shoulddecision the evidence be and discussed (5) be classification based on a formal into tree phylogenetic of the translation new proposed, taxa which the in this are and should publication be the included in gene; one background information than evidence and more (6) all and supporting should be peer-reviewed.publication D. Jean Lodge Jean D. as Boletus (Nuhn et al. 2013, Wu et al., 2014) not. In the case of the boletes, inclusion use these guidelines, but also that reviewers and Psathyrella (e.g, Padamsee et al. 2008). of more sequences from more taxa may and editors of taxonomic journals use these Dealing with the issue of paraphyly then set impact the phylogeny, as the resolution criteria in their assessments of submitted the mycological community on two, rather of the phylogeny of Boletaceae is low manuscripts. divergent, paths. These divergent approaches at many branches (Nuhn et al. 2013, The sixth criterion concerns the way the mirrored old distinctions of splitters and Wu et al. 2014). We strongly advocate results are published and presented to the lumpers. One pathway was to take small that different options are explored and scientific world. MYCOLENS monophyletic groups as the basis for new discussed, instead of using a boilerplate genera, without too much concern about model in which every monophyletic 1. All genera that are recognized the remainder of the original genus. This is clade is translated into a genus. should be monophyletic, not only a practice clearly shown by the treatment of (2) Several of the new genera are erected the one that is the focus of the study, Boletus and Clitocybe. Separation of one small solely based on phylogenetic evidence but also the group from which it is monophyletic group often set into motion a provided by one or two gene regions, separated and the group to which it splitting snowball, as in Xerocomellus (Gelardi sometimes only nrITS sequences that is added (the reciprocal monophyly et al. 2015, Vizzini 2015). Unfortunately, do not lend themselves to higher level criterion). recognition of such small genera sometimes phylogenies (Bruns 2001). contributed to the formation of paraphyletic (3) More and more rapid on-line, non- Examples: genera, as in the case of Resupinatus peer-reviewed publications appear (i) When Macrolepiota was split into a which became paraphyletic because of the without any supporting evidence for monophyletic core Macrolepiota with recognition of R. vetlinianus in a separate the newly described taxa. M. procera as its type species, and a genus Lignomyces (Petersen et al. 2015). The second group containing M. rachodes, second approach was taken in Entoloma and We therefore have formulated and present the latter was moved to Chlorophyllum Clitopilus (Co-David et al. 2009), where here criteria by which the phylogenetic that in itself was only monophyletic by deliberately a broad genus concept was chosen studies and the publications that present also including Endoptychum agaricoides (though other authors opted for smaller genera the data from those studies should be tested (Vellinga et al. 2003) and all necessary (e.g. Largent 1994, Kluting et al. 2014). Other before being accepted. nomenclatorial changes were made examples are Amanita ( Justo et al. 2010) (Vellinga 2002. Vellinga & de Kok and Cortinarius (Peintner et al. 2001) where 2002). sequestrate and gastroid species were included PROPOSED GUIDELINES (ii) The genusPorpoloma was found to be in genera with predominantly agaricoid highly polyphyletic and split into four basidiomes. It is an interesting question how Some of our proposed guidelines are genera (Sánchez-Garcia et al. 2014). this divergence should be explained; certainly, so self-explanatory and obvious to us It was essential for the application the existing taxonomy of the group in question that it seems superfluous to present of names to clades to sequence plays a big role. In the boletes, for instance, them here; nevertheless, examples the type species of Porpoloma (see many previously published generic names for that are in conflict with these Recommendation 2). well supported genera, such as Leccinum and recommendations are surprisingly Strobilomyces, were already available, and the easy to find. The examples we Unfortunately, many studies do not reach proposal of new genera was (consequently) present show how easy it is to meet this standard, as it is very easy to expel considered acceptable. these standards. We realize that species from a genus, without taking into practical issues, such as lost original account the monophyly of the target group. type specimens, or material that Especially in cases of poor resolution PRINCIPLE CONCERNS does not easily yield DNA sequences in a phylogeny, erection of very small may interfere with perfection, monophyletic genera will create more and We find several of the recent trends in but one should at least try, and ever more messy paraphyletic units, from mycological taxonomic research on discuss failures. We emphasize the which the next separation of a new genus basidiomycete fungi disturbing: importance of exploring different can already be predicted. (1) In several groups, the translation from classification options and giving a phylogenetic tree into a classification arguments for the proposed new 2. The coverage of the phylogenetic is taken into extremes, where every taxonomies. The examples we tree has to be broad. single clade is recognized as a separate present are taken from the literature genus. This does not increase insight on basidiomycete fungi, but could Coverage needs to be broad in terms of the: in the evolutionary history of the equally have been chosen from the (a) number of species – it is important to group in question, only inflates the ascomycete literature. remember that a phylogenetic tree only gives taxonomic framework. From a formal The first five criteria relate to the information on those taxa that are included phylogenetic perspective it may not underlying science; the first two criteria in it, and that all statements on relationships matter whether we have one family (e.g. are equally important, and we put less are relative, and not absolute, unless all Boletaceae), with more than a hundred emphasis on the next three. Nevertheless, known taxa are included; (b) geographic genera, or whether we have one it goes without saying that contradiction distribution of the taxa – a phylogeny based genus (e.g. Boletus s. lat.) with many of any of these criteria should be avoided. on species from temperate areas of North infrageneric units, formally named or We recommend first of all that researchers America and Europe, is not informative

(66) ima MYCOLENS (67) : (2014) recognized new genera the Peer review, though not waterproof, though not waterproof, review, Peer . 2015); and of course, whole genome whole of course, . 2015); and All supporting evidence and and evidence 6. All supporting be should information background which in publication the in included new taxathe proposed; are and be should publication this secondly, peer-reviewed. partthis first of The prompted guideline is of very appearance short publications the by official of the one taxon associated with supporting any without sites, registration with sometimes illustrations, evidence nor web personal, often a link another, to information supporting the where site be (e.g. can found. tree) a phylogenetic is of science results of the Communication of A basic principle event. not a one-time by verifiable are results the is that science go back cannot researchers future in If others. that information, and set of data whole the to be applied. This cannot situation principle where studies as experimental same in is the not preserved used are thereby cultures the unrepeatable, experiments the rendering are vouchers no where reports field in and past of the publications retained. Paper a source provide to continue and provided be consulted; always can that of information official line in on information that putting library as extra such JSTOR is an depositories safe guard. debated (see always and e.g., http://www. nature.com/nature/peerreview/debate/) before asis recommended quality control of reviewpeer The publication. function is novelties case of taxonomic the in of taxonomic censorship exercise not to judge to decisions, but new against genera mycological which the to principles these should adhere. community computers, the answer is: taxa and more answer the computers, phylogenies based on genes.more However, only include and rare still genomeswhole are of species (e.g. Dentinger number a small et al will be same faced the comparisons with phylogenies as the basedissues hand-full a on of genes. Example nSSU, loci (nLSU, of three analysis an In range rpb2a wide and genes) of taxa from Sánchez-Garcia clade, tricholomatoid the in et al. and Pogonoloma, , Albomagister, Corneriella all full with statistical Pseudotricholoma support. . 2012), and it. 2012), and , ultimately lat., ultimately s. . . (2015) tested different different . (2015) tested . (2014) discussed options . (2014) discussed options . (2008) presented and and . (2008) presented et al et al : Justo & Hibbett (2014), and Justo Justo and (2014), & Hibbett Justo options different (2014) discussed the of recognizing consequences and for one just genus or five or genera ten Trametes within opting for a one-genus solution. for opting of circumscription the for options of that delimitation and Boletellus ; these regard Heimioporus to in genus form species included that the authors Boletellus base core a grade the of the at of describing instead genus, that within new each clade. for genera the for options 15 different tested clades different of the phylogeny , before Russula and in Lactarius up of breaking solution the on settling two genera, into Lactarius Lactarius recognizing, and Lactifluus and Russula as a separate sect. Ochricompactae Multifurca. genus, Lodge et al for recognition of one or three genera genera recognitionfor three or of one and Porpolomopsis, Gliophorus, for Neohygrocybe performs this role generally role this well because of performs between related large variation sufficiently not all, but fungal many, species within species-level that for pay groups; we price the over is unalignable nrITS accuracy is that 2001). taxa (Bruns related distantly more better, was past, debated it was what the In taxa/collections more analysed or have to genes taxa fewer more for (Greybeal 1998); faster and costs sequencing lower with The phylogenetic evidence has to has evidence phylogenetic 5. The gene, one than be more based on in genes coding protein preferably SSU- of the regions gene to addition ITS-LSU repeat. arecommonly that regions gene The different all classifications used basidiomycete in and histories, evolutionary different have power resolving different they have hence levels.Phylogenies basedonly different at be not only to sequences have nrITS on large a dose of skepticism, with approached fact in should no longer bebut accepted basis as new the for genera.marker This barcode fungal for universal speciesis the recognition (Schoch et al classification with monophyletic groups. monophyletic with classification should be options different Therefore discussed. and presented Examples (i) (ii) Halling (iii) Buyck (iv) , . s. lat.; s.

when when 2014). 2013).

2015). was determined by by determined was (Jenkinson et al. 2013). . (2012) refrained from introducing introducing . (2012) refrained from : : type that all of species are genera et al was shown to to shown was Anamika The genus fall middle the of in specimens from Australia were added were Australia from specimens based mainly phylogeny the on to species (Rees et al. Eurasian type the species including Only by phylogenetic the in of Pachylepyrium of P. position couldanalyses, the funariophilum P. and carbonicola beunambiguously determined et al. (Matheny sect. of Marasmius The position Hygrometrici included the explicitly that analyses (and types Marasmius genus of the sect.) and of sect.hence Marasmius Hygrometrici always always The type of Rubinoboletus the , hence Chalciporus with clusters Chalciporus into is subsumed genus et al. (Nuhn volume 6 · no. 2 Phylogenetic methods often allow, even in even allow, often methods Phylogenetic formal one than more trees, well-resolved A list of options should be should 4. A list of options should options different discussed, final the for arguments and be tested, given. decision occupies and isolated an warneri Lenzites Trametes within position unsupported Weak support (or even absence of statistical of statistical absence even (or support Weak of proposedsupport) new indicates genera be cannot classifications alternative that is:rejected. advice so the ‘in dubiis And from doubt refrain in when abstine”, new. genera proposing Example Welti Welti species, this for as it alsoa new name generic morphological discriminating does not have (2011) also & Hibbett did Justo characters. but not recognize either, genus it as a separate of Trametes concept their included it within et al of Welti that than which is broader (2012). The branching of the phylogenetic phylogenetic the of branching 3. The and sufficient have should trees support. statistical strong (i) if the group in question is represented by is represented question in group if the Africa, Asia, species tropical in more many base should data the (c) Australia; and and include type of the included,being placement as the a genus. for species use to decides which name Examples (ii) (iii) (iv) CORRESPONDENCE (69) , 69: and and species and and Massee Massee ima fUNGUS 55: 47–64. 63: 993–1007. Fungal Diversity Fungal 95: 442–456. ). (Agaricaceae Czern. 88: 415–417. . Mycotaxon 244. 51: 563–564. Proceedings of the National Academy of Academy National of the . Proceedings Sciences, USA 109: 6241–6246. gen. nov., et sp. paradoxus (2015) Hymenoporus fungus family Omphalotaceae of the a striking tubular ) with (Agaricales, 204: 203–212. Phytotaxa hymenophore. Chlorophyllum Chlorophyllum conserveto name the against Endoptychum Ta xon of Macrolepiota taxonomy and Phylogeny ). Mycologia (Agaricaceae Spouge JL, Levesque CA, Chen W, Fungal Fungal Spouge JL, Levesque CA, W, Chen (2012) Nuclear Consortium Barcoding (ITS) spacer transcribed internal ribosomal for barcoderegion marker DNA as a universal Fungi 93–115. Hosen MI & Yang ZL (2014) Molecular MI & Yang Hosen major seven redefine analyses phylogenetic reveal the and clades in 22 new clades generic fungal family Boletaceae. . of Anamika status generic the do not support 105: 1043–1058. Mycologia Tricholomataceae the DJ (2014) Deconstructing new genera of the introduction ) and (Agaricales , Pogonoloma , Corneriella Albomagister Molecular Molecular Psathyrella. genus the polyphyly of 46: 415–429. Evolution and Phylogenetics Thaxterogaster of synonym is a taxonomic new and names. : new combinations Cortinarius 81: 177–184. Mycotaxon (2015) Lignomyces KW S, Hughes Arslanov P, . a new of pleurotoid genus 107: 1045–1054. Mycologia of agarics: (2002).Phylogeny partial systematics the in genera omphalinoid core for solutions 83: 19–57. Mycotaxon (euagarics). Agaricales (2013) Morphological DA and Orlovich Hebeloma Australian for molecular data . TaPseudotricholoma xon Fungorum S, L Lesage-Meessen Taussac D, M, Navarro of Trametes phylogeny (2012) Molecular of a new genus genera,related description and Diversity. Fungal Leiotrametes Tkalčec Z, Mešić A, Den C-Y, Pleše B, Ćetković H B, Ćetković Pleše Tkalčec Z, A, Mešić C-Y, Den in combinations EC (2002) New Vellinga EC, RPJ de Kok (2002) (1539) Proposal Vellinga TD (2003) Bruns EC, RPJ, de Kok Vellinga Schoch CL, Seifert KA, Huhndorf S, Robert V, Schoch CL, S, Robert Seifert KA, V, Huhndorf Wu G, Feng B, Xu J, Zhu X-T, Li Y-C, Zeng N-K, Zeng N-K, Li Y-C, X-T, Zhu J, B, Xu G, Feng Wu Sánchez-Garcia M, Matheny PB, Palfner G, Lodge PB, Palfner Sánchez-Garcia M, Matheny Peintner U, Moser MM,Vilgalys Moser R (2002) [“2001”] U, Peintner I, Chachuła Zmitrovich N, RH, Psurtseva Petersen Vilgalys J-M, R Moncalv RedheadSA, F, Lutzoni A, A, Perkins Rees Midgley BJ, Marchant DJ, Index Index novelties. Vizzini A (2015) Nomenclatural A, R, Courtecuisse OA, Favel S, Haon Moreau Welti

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MYCOLENS (68)