Multilocus phylogenetic reconstruction of the Clavariaceae (Agaricales) reveals polyphyly of agaricoid members

Literature cited

• BirkebakJMMayorJRRybergMMathenyPB. 2013. A systematic, morphological and ecological overview of the Clavariaceae (Agaricales). Mycologia 105:896–911, doi:10.3852/12-070
   Web of Science ®Google Scholar
• BonordenHF. 1851. Handbuch der allgemeinen Mykologie. Stuttgart: E. Schweiyerbart. 336 p.
   Google Scholar
• CastresanaJ. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552, doi:10.1093/oxfordjournals.molbev.a026334
   PubMed Web of Science ®Google Scholar
• DentingerBTMMcLaughlinDJ. 2006. Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new segregate genus from Clavaria. Mycologia 98:746–762, doi:10.3852/mycologia.98.5.746
   Web of Science ®Google Scholar
• GardesMBrunsTD. 1993. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118, doi:10.1111/j.1365-294X.1993.tb00005.x
   PubMed Web of Science ®Google Scholar
• GouyMGuindonSGascuelO. 2010. SeaView 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224, doi:10.1093/molbev/msp259
   PubMed Web of Science ®Google Scholar
• HeimR. 1966. Breves diagnoses latinae novitatum generico-rum specificorumque nuper descriptiorum. Rev Mycol 30:231–238.
   Google Scholar
• JustoAHibbettDS. 2011. Phylogenetic classification of Trametes (Basidiomycota, Polyporales) based on a five-marker dataset. Taxon 60:1567–1583.
   Web of Science ®Google Scholar
• KautmanováITomšovskýDueñasMMartínMP. 2012. European species of Clavaria (Agaricales, Agaricomycetes) with dark basidiomata—a morphological and molecular study. Persoonia 29:133–145, doi:10.3767/003158512X661543
   Google Scholar
• KnudsenHVesterholtJ. 2012. Funga Nordica: Agaricoid, Boletoid, Clavarioid, Cyphelloid and Gastroid genera. Copenhagen: Nordsvamp. 1083 p.
   Google Scholar
• KornerupAWanscherJH. 1967. Methuen handbook of colour. 2nd ed. London: Methuen. 243 p.
   Google Scholar
• LanfearRCalcottBKainerDMayerCStamatakisA. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol 14:82, doi:10.1186/1471-2148-14-82
   PubMed Web of Science ®Google Scholar
• LarkinMABlackshieldsGBrownNPChennaRMcGettiganPAMcWilliamsHValentinFWallaceIMWilmALopezRThompsonJDGibsonTJHigginsDG. 2007. ClustalW and ClustalX 2.0. Bioinformatics 23:2947–2948, doi:10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• LarssonKH. 2007. Re-thinking the classification of corticioid fungi. Mycol Res 111:1040–1063, doi:10.1016/j.mycres.2007.08.001
   PubMed Web of Science ®Google Scholar
• LebelTTonkinJE. 2007. Australasian species of Macowanites are sequestrate species of Russula (Russulaceae, Basidiomycota). Aust Syst Bot 20:355–381, doi:10.1071/SB07007
   Web of Science ®Google Scholar
• MaddisonDRMaddisonWP. 2005. MacClade 4: analysis of phylogeny and character evolution. Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• MathenyPB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phylogenet Evol 35:1–20, doi:10.1016/j.ympev.2004.11.014
   PubMed Web of Science ®Google Scholar
• MathenyPBCurtisJMHofstetterVAimeMCMoncalvoJMGeZWYangZLSlotJCAmmiratiJFBaroniTJBougherNLHughesKWLodgeDJKerriganRWSeidlMTAanenDKDeNitisMDanieleGDesjardinDEKroppBRNorvellLLParkerAVellingaECVilgalysRHibbettDS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982–995, doi:10.3852/mycologia.98.6.982
   PubMed Web of Science ®Google Scholar
• MoserM. 1978. Band IIb/2, Die Röhrlinge und Blätterpilze (Polyporales, Boletales, Agaricales, Russulales). 4th ed. In: GamsH, ed. Kleine Kryptogamenflora. Stuttgart-New York: Gustav Fischer Verlag. p 90–91.
   Google Scholar
• PeintnerUMoserMVilgalysR. 2002. Thaxterogaster is a taxonomic synonym of Cortinarius: new combinations and new names. Mycotaxon 81:177–184.
   Web of Science ®Google Scholar
• PetersenRH. 1988. The clavarioid fungi of New Zealand. DSIR Bull 236:1–170.
   Google Scholar
• RonquistFHuelsenbackJTeslenkoM. 2011. MrBayes3.2. http://mrbayes.sourceforge.net
   Google Scholar
• ShimodairaH. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492–508, doi:10.1080/10635150290069913
   PubMed Web of Science ®Google Scholar
• ShimodairaHHasegawaM. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246–1247, doi:10.1093/bioinformatics/17.12.1246
   PubMed Web of Science ®Google Scholar
• SilvestroDMichalakI. 2012. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12:335–337, doi:10.1007/s13127-011-0056-0
   Web of Science ®Google Scholar
• StamatakisA. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690, doi:10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• TalaveraGCastresanaJ. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564–577, doi:10.1080/10635150701472164
   PubMed Web of Science ®Google Scholar
• VellingaECKuyerTWAmmiratiJDesjardinDEHallingREJustoALaessoeTLebelTLodgeDJMathenyPBMethvenASMoreauPAMuellerGMNoordeloosMENuytinckJOvreboCLVerbekenA. 2015. Six simple guidelines for introducing new genera of fungi. IMA Fungus 6:65–68.
   Web of Science ®Google Scholar
• WhiteTJBrunsTTaylorLS. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: InnisMAGelfandDHSninskyJJWhiteTJ, eds. PCR Protocols: a guide to methods and application. London: Academic Press. p 315–322.
   Google Scholar