Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex

Literature cited

• AanenDKKuyperTWHoekstraRF. 2001. A widely distributed ITS polymorphism within a biological species of the ectomycorrhizal fungus Hebeloma velutipes. Mycol Res 105:284–290, doi:10.1017/S0953756201003628
   Google Scholar
• AdamčíkS. 2002. Taxonomy of the Russula xerampelina group 2. Taxonomic and nomenclatural study of Russula xerampelina and R. erythropoda. Mycotaxon 82: 241–267.
   Google Scholar
• AdamčíkS. 2003. Russula faginea and similar taxa. Czech Mycol 54:177–191.
   Google Scholar
• AdamčíkS. 2004. Studies on Russula clavipes and related taxa of Russula sect. Xerampelinae with predominantly olivaceous pileus. Persoonia 18:393–409.
   Google Scholar
• AdamčíkSBuyckB. 2014. Type studies in Russula subsection Nigricantes from the eastern United States. Cryptog Mycol 35:293–309, doi:10.7872/crym.v35.iss3.2014.293
   Google Scholar
• AdamčíkSJančovičováS. 2013. Type studies in Russula subsection Maculatinae: four species typified by H. Romagnesi. Sydowia 65:201–222.
   Google Scholar
• AdamčíkSKnudsenH. 2004. Red-capped species of Russula sect. Xerampelinae associated with dwarf scrub. Mycol Res 108:1463–1475.
   Google Scholar
• AdamčíkSMarholdK. 2000. Taxonomy of the Russula xerampelina group I. Morphometric study of the Russula xerampelina group in Slovakia. Mycotaxon 76: 463–479.
   Google Scholar
• BuyckB. 1989. Valeur taxonomique du bleu de crésyl pour le genre Russula. Bull Soc Mycol Fr 105:1–6.
   Google Scholar
• BuyckB. 1991. The study of microscopic features in Russula 2. Sterile cells of the hymenium. Russulales News 1: 62–85.
   Google Scholar
• BuyckBAdamčíkS. 2013a. Type studies in Russula subsection Lactarioideae from North America and a tentative key to North American species. Cryptog Mycol 34: 259–279.
   Web of Science ®Google Scholar
• BuyckBAdamčíkS. 2013b. The Russula xerampelina complex (Russulales, Agaricomycotina) in North America. Scripta Bot Belg 51:117–131.
   Google Scholar
• den BakkerHCZuccarelloGCKuyperTWNoordeloosME. 2007. Phylogeographic patterns in Leccinum sect. Scabra and the status of the arctic-alpine species L. rotundifoliae. Mycol Res 107:663–672.
   Google Scholar
• EberhardtU. 2012. Methods for DNA Barcoding of Fungi. In: KressWJEricksonDL, eds. DNA barcodes. Methods in molecular biology. Vol. 858:183–205. Humana Press.
   Google Scholar
• EberhardtUBekerHJVesterholtJ. 2015. Decrypting the Hebeloma crustuliniforme complex: European species of Hebeloma section Denudata subsection Denudata (Agaricales). Persoonia 35:101–147, doi:10.3767/003158515X687704
   Web of Science ®Google Scholar
• FlotJ-F. 2010. SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Mol Ecol Resour 10:162–166, doi:10.1111/j.1755-0998.2009.02732.x
   PubMed Web of Science ®Google Scholar
• FlotJ-FTillierASamadiSTillierS. 2006. Phase determination from direct sequencing of length-variable DNA regions. Mol Ecol Notes 6:627–630, doi:10.1111/j.1471-8286.2006.01355.x
   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
• GemlJLaursenGATimlingIMcfarlandJMBoothMGLennonNNusbaumCTaylorDL. 2009. Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA. Mol Ecol 18:2213–2227.
   PubMed Web of Science ®Google Scholar
• HughesKWPetersenRHLodgeDJBergemannSEBaumgartnerKTullossRE. 2013. Evolutionary consequences of putative intra- and interspecific hybridization in agaric fungi. Mycologia 105:1577–1594, doi:10.3852/13-041
   Web of Science ®Google Scholar
• JurkeitWKrauchFHampeFGrauwinkerBAlbersJ. 2011. Russula-Forschung in Mitteleuropa III, Drei neue Russula-Arten aus Nordrhein-Westfalen und Niedersachsen (Deutschland). Z Mykol 77:19–43.
   Google Scholar
• KärcherR. 2002. Beitrag zur Kenntnis der Täublinge. Russula Studien, Teil 8. Vorschlag zur Neuordnung der dominant grünen Heringstäublinge unter Laubbäumen. Z Mykol 68:165–182.
   Google Scholar
• KatohKKumaKTohHMiyataT. 2005. MAFFT 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518, doi:10.1093/nar/gki198
   PubMed Web of Science ®Google Scholar
• KatohKStandleyDM. 2013. MAFFT multiple sequence alignment software 7: improvements in performance and usability. Mol Biol Evol 30:772–780, doi:10.1093/molbev/mst010
   PubMed Web of Science ®Google Scholar
• KleckaWR. 1980. Discriminant analysis. Sage University papers. Beverly Hills, California: Quantitative Application in the Social Science. 72 p.
   Google Scholar
• KnudsenHRuotsalainenJVaurasJ. 2008. Russula Pers. In: KnudsenHVesterholtJ, eds. Funga Nordica, Agaricoid, boletoid and cyphelloid genera. Copenhagen: Nordsvamp. p. 107–148.
   Google Scholar
• KõljalgUNilssonRHAbarenkovKTedersooLTaylorAFSBahramMBatesSTBrunsTDBengtsson-PalmeJCallaghanTMDouglasBDrenkhanTEberhardtUDueñasMGrebencTGriffithGWHartmannMKirkPMKohoutPLarssonELindahlBDLückingRMartínMPMathenyPBNguyenNHNiskanenTOjaJPeayKGPeintnerUPetersonMPõldmaaKSaagLSaarISchüßlerAScottJASenésCSmithMESuijaATaylorDLTelleriaMTWeißMLarssonK-H. 2013. Toward a unified paradigm for sequence-based identification of Fungi. Mol Ecol 22:5271–5277, doi:10.1111/mec.12481
   PubMed Web of Science ®Google Scholar
• KrzanowskiWJ. 1990. Principles of multivariate analysis. Oxford, UK: Clarendon Press. 608 p.
   Google Scholar
• KühnerR. 1975. Agaricales de la zone alpine: Genre Russula Pers. Bull Soc Mycol Fr 91:324–345.
   Google Scholar
• LegendrePLegendreL. 1998. Numerical ecology. 2nd ed. Amsterdam, The Netherlands: Elsevier. 852 p.
   Google Scholar
• LiYJioLYaoY-J. 2013. Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis. Mol Phylog Evol 68:373–379, doi:10.1016/j.ympev.2013.04.010
   Google Scholar
• LindnerDLBanikMT. 2011. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 103:731–740, doi:10.3852/10-331
   PubMed Web of Science ®Google Scholar
• LindnerDLCarlsenTNilssonRHDaveyMSchumacherTKauserudH. 2013. Employing 454 amplicon pyrose-quencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecol Evol 3:1751–1764, doi:10.1002/ece3.586
   Google Scholar
• LiimatainenKNiskanenTDimaBKytovuoriIAmmiratiJFFrøslevTG. 2014. The largest type study of Agaricales species to date: bringing identification and nomenclature of Phlegmacium (Cortinarius) into the DNA era. Persoonia 33:98–140, doi:10.3767/003158514X684681
   PubMed Web of Science ®Google Scholar
• LindahlBDNilssonRHTedersooLAbarenkovKCarlsenTKjøllerRKõljalgUPennanenTRosendahlSStenlidJKauserudH. 2013. Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide. New Phytol 199:288–299, doi:10.1111/nph.12243.
   PubMed Web of Science ®Google Scholar
• MeyerCPPaulayG. 2005. DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3:e422.
   PubMed Web of Science ®Google Scholar
• MillerMAPfeifferWSchwartzT. 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway computing environments workshop (GCE), New Orleans, Louisiana. 2010:1–8.
   Google Scholar
• MorgadoLNSemenovaTAWelkerJMWalkerMDSmetsEGemlJ. 2014. Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in arctic Alaska. Global Change Biol 21:959–972, doi:10.1111/gcb.12716
   Google Scholar
• ReumauxPBidaudAMoënne-LoccozP. 1996. Russules rares ou méconues. Editions Federation Mycologique Dauphiné, Savoy, Frangy. 296 p.
   Google Scholar
• RomagnesiH. 1967. Les Russules d’Europe et d’Afrique du Nord. Bordas. Paris. 998 p.
   Google Scholar
• SarnariM. 2005. Monografia illustrata del Genere Russula in Europa. Vol. 2. A.M.B. FondazioneCentro Studi Micologici, Trento, Italy. 768 p.
   Google Scholar
• SchnabelGAshJSBrysonPK. 2005. Identification and characterization of Armillaria tabescens from the southeastern United States. Mycol Res 109:1208–1222, doi:10.1017/S0953756205003916
   PubMedGoogle Scholar
• SchochCLSeifertKAHuhndorfSRobertVSpougeJLLevesqueCAChenW, Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109:6241–6246, doi:10.1073/pnas.1117018109
   PubMed Web of Science ®Google Scholar
• SlovákMMarholdK. 2007. Morphological evaluation of Picris hieracioides L. (Compositae) in Slovakia. Phyton-Ann Rei Bot A 47:73–102.
   Google Scholar
• SneathPHASokalRR. 1973. Numerical taxonomy. Principles and practice of numerical classification. San Francisco, California: W.H. Freeman & Co. 588 p.
   Google Scholar
• StamatakisA. 2014. RAxML 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313, doi:10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• StephensMDonnellyP. 2003. A comparison of Bayesian methods for haplotype reconstruction. AM J Hum Genet 73:1162–1169, doi:10.1086/379378
   PubMed Web of Science ®Google Scholar
• StephensMSmithNJDonnellyP. 2001. A new statistical method for haplotype reconstruction from population data. AM J Hum Genet 68:978–989, doi:10.1086/319501
   PubMed Web of Science ®Google Scholar
• SwoffordDL. 2003. PAUP* 4: phylogenetic analysis using parsimony (*and other methods). Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• TeacherAGFGriffithsDJ. 2011. HapStar: automated haplotype network layout and visualization. Mol Ecol Resour 11:151–153, doi:10.1111/j.1755-0998.2010.02890.x
   PubMed Web of Science ®Google Scholar
• TedersooLBahramMPõlmeSKõljalgUYorouNSWijesunderaRVillarreal RuizLVascoPalaciosAMThuPQSuijaASmithMESharpCSaluveerESaittaARosasMRiitTRatkowskyDPritschKPõldmaaKPiepenbringMPhosriCPetersonMPartsKPärtelKOtsingENouhraENjouonkouALNilssonRHMorgadoLNMayorJMayTWMajuakimLLodgeDJLeeSSLarssonKHKohoutPHosakaKHiiesaluIHenkelTWHarendHGuoLGreslebinAGreletGGemlJGatesGDunstanWDunkCDrenkhanRDearnaleyJKeselADe DangTChenXBueggerFBrearleyFQBonitoGAnslanSAbellAAbarenkovK. 2014. Global diversity and geography of soil fungi. Science 346:1256688.
   PubMed Web of Science ®Google Scholar
• TedersooLJairusTHortonBMAbarenkovKSuviTSaarIKõljalgU. 2008. Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytol 180:479–490, doi:10.1111/j.1469-8137.2008.02561.x
   PubMed Web of Science ®Google Scholar
• TedersooLMettMIshidaTABahramM. 2013. Phylogenetic relationships among host plants explain differences in fungal species richness and community composition in ectomycorrhizal symbiosis. New Phytol 199:822–831, doi:10.1111/nph.12328
   Web of Science ®Google Scholar
• ThiersB. [continuously updated]. Index herbariorum: a global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium (http://sweetgum.nybg.org/ih/).
   Google Scholar
• TimlingIDahlbergAWalkerDAGardesMCharcossetJYWelkerJMTaylorDL. 2012. Distribution and drivers of ectomycorrhizal fungal communities across the North American arctic. Ecosphere 3:111.
   Web of Science ®Google Scholar
• WhiteTJBrunsTDLeeSTaylorJW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: InnisMAGelfandHSninskyJSWhiteTJ, eds. PCR protocols: a guide to methods and applications. New York: Academic Press. p. 315–322.
   Google Scholar