Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia

Literature cited

• AinsworthAMParfittDRogersHJBoddyL. 2010. Cryptic taxa within European species of Hydnellumand Phellodonrevealed by combined molecular and morphological analysis. Fungal Ecol 3:65–80, 10.1016/j.funeco.2009.07.001
   Google Scholar
• BeatonGPeglerDNYoungTWK. 1984. Gasteroid Basidiomycota of Victoria state, Australia I. Hydnangiaceae. Kew Bull 39:499–508, 10.2307/4108593
   Google Scholar
• BickfordDLohmanDJSodhiNSNgPKLMeierRWinkerKIngramKKDasI. 2007. Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155, 10.1016/j.tree.2006.11.004
   PubMed Web of Science ®Google Scholar
• BougherNLTommerupICMalajczukN. 1993. Broad variation in developmental and mature basidiome morphology of the ectomycorrhizal fungus Hydnangium sublamellatumsp. nov. bridges morhologically based generic concepts of Hydnangium, Podohydnangiumand Laccaria. Mycol Res 97:613–619, 10.1016/S0953-7562(09)81186-6
   Google Scholar
• BrockPMDöringHBidartondoMI. 2009. How to know unknown fungi: the role of a herbarium. New Phytol 181:719–724, 10.1111/j.1469-8137.2008.02703.x
   PubMed Web of Science ®Google Scholar
• CarlsenTEnghIBDecockCRajchenbergMKauserudH. 2011. Multiple cryptic species with divergent substrate affinities in the Serpula himantioidesspecies complex. Fungal Biol 115:54–61, 10.1016/j.funbio.2010.10.004
   Google Scholar
• The Council of Heads of Australasian Herbaria. (1999–). Australia’s Virtual Herbarium www.chah.gov.au/avh
   Google Scholar
• FourmentMGibbsMJ. 2006. Patristic: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6:1, 10.1186/1471-2148-6-1
   PubMedGoogle Scholar
• HarderCBLæssøeTKjøllerRFrøslevTG. 2010. A comparison between ITS phylogenetic relationships and morphological species recognition within Mycenasect. Calodontesin northern europe. Mycol Prog 9:395–405, 10.1007/s11557-009-0648-7
   Web of Science ®Google Scholar
• HarrowerEAmmiratiJFCappuccinoAACeskaOKranabetterJMKroegerPLimSTaylorTBerbeeML. 2011. Cortinariusspecies diversity in British Columbia and molecular phylogenetic comparison with European specimen sequences. Botany 89:799–810, 10.1139/b11-065
   Web of Science ®Google Scholar
• HawksworthDL. 2006. Pandora’s mycological box: molecular sequences vs. morphology in understanding fungal relationships and biodiversity. Rev Iberoam Micol 23: 127–133, 10.1016/S1130-1406(06)70031-6
   Google Scholar
• HibbettDSOhmanAGlotzerDNuhnMKirkPNilssonRH. 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25:38–47, 10.1016/j.fbr.2011.01.001
   Google Scholar
• HosakaKCastellanoMASpataforaJW. 2008. Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota). Mycol Res 112:448–462, 10.1016/j.mycres.2007.06.004
   Google Scholar
• HughesKWPetersenRHLickeyEB. 2009. Using hetero-zygosity to estimate a percentage DNA sequence similarity for environmental species delimitation across basidiomycete fungi. New Phytol 189:795–798, 10.1111/j.1469-8137.2009.02802.x
   Google Scholar
• JombartTBallouxFDrayS. 2010. adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics 26:1907–1909, 10.1093/bioinformatics/btq292
   PubMed Web of Science ®Google Scholar
• JustoAMorgensternIHallen-AdamsHEHibbettDS. 2010. Convergent evolution of sequestrate forms in Amanitaunder Mediterranean climate conditions. Mycologia 102:675–688, 10.3852/09-191
   PubMed Web of Science ®Google Scholar
• KühnerR. 1980. Les Hyménomycètes agaricoïdes. Bull Mens Soc Linn Lyon 49:1–1027.
   Google Scholar
• LebelTTonkinJE. 2007. Australasian species of Macowanitesare sequestrate species of Russula(Russulaceae, Basidiomycota). Aust Syst Bot 20:355–381, 10.1071/SB07007
   Web of Science ®Google Scholar
• LefébureTDouadyCJGouyMGibertJ. 2006. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol 40:435–447, 10.1016/j.ympev.2006.03.014
   PubMed Web of Science ®Google Scholar
• MaddisonWP. 1997. Gene trees in species trees. Syst Biol 46:523–536, 10.1093/sysbio/46.3.523
   Web of Science ®Google Scholar
• MartinFAertsAAhrenDBrunADanchinEGJDuchaussoyFGibonJKohlerALindquistEPeredaVSalamovAShapiroHJWuytsJBlaudezDBueeMBroksteinPCanbackBCohenDCourtyPECoutinhoPMDelaruelleCDetterJCDeveauADiFazioSDuplessisSFraissinet-TachetLLucicEFrey-KlettPFourreyCFeussnerIGayGGrimwoodJHoeggerPJJainPKilaruSLabbeJLinYCLegueVLe TaconFMarmeisseRMelayahDMontaniniBMuratetMNehlsUNiculita-HirzelHOudot-Le SecqMPPeterMQuesnevilleHRajashekarBReichMRouhierNSchmutzJYinTChalotMHenrissatBKuesULucasSvan de PeerYPodilaGKPolleAPukkilaPJRichardsonPMRouzePSandersIRStajichJETunlidATuskanGGrigorievIV. 2008. The genome of Laccaria bicolorprovides insights into mycorrhizal symbiosis. Nature 452:88–92, 10.1038/nature06556
   PubMed Web of Science ®Google Scholar
• MartinFDíezJDellBDelaruelleC. 2002. Phylogeography of the ectomycorrhizal Pisolithusspecies as inferred from nuclear ribosomal DNA ITS sequences. New Phytol 153:345–357, 10.1046/j.0028-646X.2001.00313.x
   Web of Science ®Google Scholar
• MathenyPB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phylogenet Evol 35:1–20, 10.1016/j.ympev.2004.11.014
   PubMed Web of Science ®Google Scholar
• MathenyPBCurtisJMHofstetterVAimeMCMoncalvoJ-MGeZWYangZLSlotJCAmmiratiJFBaroniTJBougherNLHughesKWLodgeDJKerriganRWSeidlMTAanenDKDeNitisMDanieleGMDesjardinDEKroppBRNorvellLLParkerAVellingaECVilgalysRHibbettDS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982–995, 10.3852/mycologia.98.6.982
   PubMed Web of Science ®Google Scholar
• MayTW. 1991. A taxonomic study of the Australian species of Laccaria [doctoral dissertation]. Monash Univ. Press. 339 p.
   Google Scholar
• MayTW. Laccaria. In: GrgurinovicCA. Larger fungi of South Australia. The botanic gardens of Adelaide and state herbarium and the flora and fauna. Adelaide: South Australia Handbooks Committee, 296–310.
   Google Scholar
• MuellerGM. 1992. Systematics of Laccaria (Agaricales) in the continental United States and Canada, with discussions on extralimital taxa and descriptions of extant types. Fieldiana Bot 30:1–158.
   Google Scholar
• MuellerGMHofstenAVAxénAStrackBA. 1993. Basidiospore wall ultrastructure of the false-truffle Hydnangiumand its phylogenetic significance. Mycologia 85:890–893, 10.2307/3760670
   Google Scholar
• MuellerGMPineEM. 1994. DNA data provide evidence on the evolutionary relationships between mushrooms and false truffles. McIlvainea 11:61–74.
   Google Scholar
• NilssonRHKristianssonERybergMHallenbergN. 2008. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform 4:193–201.
   PubMed Web of Science ®Google Scholar
• NylanderJAAWilgenbuschJCWarrenDLSwoffordDL. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583, 10.1093/bioinformatics/btm388
   PubMed Web of Science ®Google Scholar
• OsmundsonTWCrippsCLMuellerGM. 2005. Morphological and molecular systematics of Rocky Mountain alpine Laccaria. Mycologia 97:949–972, 10.3852/mycologia.97.5.949
   PubMed Web of Science ®Google Scholar
• PeintnerUBougherNLCastellanoMAMoncalvoJMMoserMMTrappeJMVilgalysR. 2001. Multiple origins of sequestrate fungi related to Cortinarius(Cortinariaceae). Am J Bot 88:2168–2179, 10.2307/3558378
   PubMed Web of Science ®Google Scholar
• Van de PutteKNuytinckJDasKVerbekenA. 2012. Exposing hidden diversity by concordant genealogies and morphology—a study of the Lactifluus volemus(Russulales) species complex in Sikkim Himalaya (India). Fungal Divers 55:171–194, 10.1007/s13225-012-0162-0
   Web of Science ®Google Scholar
• Van de PutteKNuytinckJStubbeDLeHTVerbekenA. 2010. Lactarius volemussensu lato (Russulales) from northern Thailand: morphological and phylogenetic species concepts explored. Fungal Divers 45: 99– 130, 10.1007/s13225-010-0070-0
   Google Scholar
• RehnerSABuckleyE. 2005. A Beauveriaphylogeny inferred from nuclear ITS and EF1-a sequences: evidence for cryptic diversification and links to Cordycepsteleomorphs. Mycologia 97:84–98, 10.3852/mycologia.97.1.84
   PubMed Web of Science ®Google Scholar
• RonquistFHuelsenbeckJP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574, 10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• RozenRSkaletskyHJ. 2000. Primer3 on the WWW for general users and for biologist programmers. In: KrawetzSMisenerS, eds. Bioinformatics methods and protocols: methods in molecular biology. Totowa, New Jersey: Humana Press. p 365–386.
   Google Scholar
• RybergMMathenyPB. 2012. Asynchronous origins of ectomycorrhizal clades of Agaricales. P Roy Soc B-Biol Sci 279:2003–2011, 10.1098/rspb.2011.2428
   Google Scholar
• RybergMNilssonRHKristianssonETöpelMJacobssonSLarssonE. 2008. Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe(Basidiomycota). BMC Evol Biol 8:50, 10.1186/1471-2148-8-50
   PubMed Web of Science ®Google Scholar
• SchlossPDWestcottSLRyabinTHallJRHartmannMHollistersEBLesniewskiRAOakleyBBParksDHRobinsonCJSahlJWStresBThallingerGGvan HornDJWeberCF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541, 10.1128/AEM.01541-09
   PubMed Web of Science ®Google Scholar
• SingerR. 1986. The Agaricales in modern taxonomy. 4th ed. Koenigstein, Germany: Koeltz Scientific Books. 981 p.
   Google Scholar
• StamatakisAHooverPRougemontJ. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771, 10.1080/10635150802429642
   PubMed Web of Science ®Google Scholar
• StielowBBratekZOrczánAKIRudnoySHenselGHoffmannPKlenkH-PGökerM. 2011. Species delimitation in taxonomically difficult fungi: the case of Hymenogaster. PloS ONE 6:e15614, 10.1371/journal.pone.0015614
   Google Scholar
• StubbeDLeHTWangX-HNuytinckJVan de PutteKVerbekenA. 2011. The Australasian species of Lactariussubgenus Gerardii(Russulales). Fungal Divers 52:141–167, 10.1007/s13225-011-0111-3
   Google Scholar
• SwoffordDL. 1998. PAUP* 4: phylogenetic analysis using parsimony (*and other methods). Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• TamuraKDudleyJNeiMKumarS. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software. Mol Biol Evol 24:1596–1599, 10.1093/molbev/msm092
   PubMed Web of Science ®Google Scholar
• TaylorJWJacobsonDJKrokenSKasugaTGeiserDMHibbettDSFisherMC. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32, 10.1006/fgbi.2000.1228
   PubMed Web of Science ®Google Scholar
• TedersooLGatesGDunkCWLebelTMayTWKõljalgUJairusT. 2009. Establishment of ectomycorrhizal fungal community on isolated Nothofagus cunninghamii seedlings regenerating on dead wood in Australian wet temperate forests: Does fruit-body type matter? Mycorrhiza 19:403–416, 10.1007/s00572-009-0244-3
   PubMed Web of Science ®Google Scholar
• ThiersHD. 1984. The secotioid syndrome. Mycologia 76:1–8, 10.2307/3792830
   Web of Science ®Google Scholar
• ThompsonJDHigginsDGGibsonTJ. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680, 10.1093/nar/22.22.4673
   PubMed Web of Science ®Google Scholar
• VincenotLNaraKSthultzCLabbéJDuboisM-PTedersooLMartinFSelosseM-A. 2011. Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystinacomplex. Mol Ecol 21: 281– 299, 10.1111/j.1365-294X.2011.05392.x
   Google Scholar
• WhiteTJBrunsTLeeSTaylorJ. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: InnisMAGelfandDHSninskyJJWhiteTJ, eds. PCR protocols: a guide to methods and applications. New York: Academic Press. p 315–322.
   Google Scholar