An overview of the genus Glyphium and its phylogenetic placement in Patellariales

Literature cited

• AltschulSFGishWMillerWMyersEWLipmanDJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.
   PubMed Web of Science ®Google Scholar
• BarrME. 1975. The genus Ostreichnion. Mycotaxon 3:81–88.
   Google Scholar
• BarrME. 1987. Prodromus to class Loculoascomycetes. Hamilton I. Newell Inc., Amherst, Massachusetts: M.E. Barr Bigelow.
   Google Scholar
• BarrME. 1990. Melanommatales (Loculoascomycetes) II. North American Flora II. 13:1–129.
   Google Scholar
• BarrMEBlackwellM. 1980. A new genus in the Lophiaceae. Mycologia 72:1224–1227.
   Google Scholar
• BisbyGREllisMB. 1952. Lophium elatum Grev. Trans Br Mycol Soc 35:299–303.
   Google Scholar
• BoehmEWASchochCLSpataforaJW. 2009a. On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes. Mycol Res 113:461–479.
   PubMed Web of Science ®Google Scholar
• BoehmEWAMugambiGKMillerANMMarincowitzSSpataforaJWSchochCL. 2009b. A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species. Stud Mycol 64:49–83.
   Google Scholar
• CashE. 1943. Some new or rare Florida Discomycetes and Hysteriales. Mycologia 35:595–603.
   Google Scholar
• ChenCYHsiehWH. 1996. Two new species and some new records of ascomycetes from Taiwan. Bot Bull Acad Sin 37:219–227.
   Google Scholar
• DarkerGD. 1963. A new genus of the Lophiaceae. Can J Bot 41:1383–1388.
   Google Scholar
• EarleSF. 1901. Fungi from Colorado and New Mexico. Plantae Bakerianae 2:1–30.
   Google Scholar
• EdgarRC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797.
   PubMed Web of Science ®Google Scholar
• EllisJB. 1881. New ascomycetous fungi. Bull Torrey Bot Club 8:123–125.
   Google Scholar
• ErikssonOE. 1994. Problems in the classification of fissitunicate ascomycetes. In: HawksworthDL, ed. Ascomycete systematics: problems and perspectives in the nineties. NATO ASI series. Vol. 269. New York and London: Plenum Press. p 341–348.
   Google Scholar
• ErtzDTehlerA. 2011. The phylogeny of Arthoniales (Pezizomycotina) inferred from nucLSU and RPB2 sequences. Fungal Divers 49:47–71.
   Web of Science ®Google Scholar
• GoreeH. 1974. Glyphium in western Canada and United States. Can J Bot 52:1265–1269.
   Google Scholar
• GrevilleRK. 1825. Scottish Cryptogamic Flora III., Edinburgh.
   Google Scholar
• GrigorievIVCullenDGoodwinSBHibbettDJeffriesTWKubicekCPKuskeCMagnusonJKMartinFSpataforaJWTsangABakerSE. 2011. Fueling the future with fungal genomics. Mycology 2:192–209.
   Google Scholar
• GueidanCRuibalCVde HoogGSGorbushinaAAUntereinerWALutzoniF. 2008. A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages. Stud Mycol 61:111–119.
   PubMed Web of Science ®Google Scholar
• HafellnerJ. 1979. Karschia: Revision einer Sammelgattung an der Grenze von lichenisierten und nichtlichenisierten Ascomyceten. Beih Nova Hedwigia 62:1–248.
   Google Scholar
• HawksworthDLErikssonOE. 1988. Proposals to conserve 11 family names in the Ascomycotina (Fungi). Taxon 37:190–193.
   Google Scholar
• HydeKDJonesEBGLiuJKAriyawansaHBoehmEBoonmeeSBraunUChomnuntiPCrousPWDaiDQDiederichPDissanayakeADoilomMDoveriFHongsananSJayawardenaRLawreyJDLiYMLiuYXLückingRMonkaiJMuggiaLNelsenMPPangKLPhookamsakRSenanayakeICShearerCASuetrongSTanakaKThambugalaKMWijayawardeneNNWikeeSWuHXZhangYAguirre-HudsonBAliasSAAptrootABahkaliAHBezerraJLBhatDJCamporesiEChukeatiroteEGueidanCHawksworthDLHirayamaKDe HoogSKangJCKnudsenKLiWJLiXHLiuZYMapookAMcKenzieEHCMillerANMortimerPEPhillipsAJLRajaHAScheuerCSchummFTaylorJETianQTibprommaSWanasingheDNWangYXuJCYacharoenSYanJYZhangM. 2013. Families of Dothideomycetes. Fungal Divers 63:1–313.
   Web of Science ®Google Scholar
• KatohKAsimenosGTohH. 2009. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537:39–64.
   PubMedGoogle Scholar
• KirschsteinW. 1924. Beiträge zur Kenntnis der Ascomyceten. Verh Bot Vereins Prov Brandenburg 66:23–29.
   Google Scholar
• KorfRP. 1962. A synopsis of the Hemiphacidiaceae, a family of the Helotiales (Discomycetes) causing needle blights of conifers. Mycologia 54:12–33.
   Web of Science ®Google Scholar
• KutorgaEHawksworthDL. 1997. A reassessment of the genera referred to the family Patellariaceae (Ascomycota). Syst Ascomycetum 15:1–110.
   Google Scholar
• LindemuthRWirtzNLumbschHT. 2001. Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports the view that loculoascomycetes (Ascomycota) are not monophyletic. Mycol Res 105:1176–1181.
   Web of Science ®Google Scholar
• LiuKRaghavanSNelesenSLinderCRWarnowT. 2009. Rapid and accurate large-scale co-estimation of sequence alignments and phylogenetic trees. Science 324:1561–1564.
   PubMed Web of Science ®Google Scholar
• LohmanML. 1933a. Hysteriaceae: Life histories of certain species. Pap Michigan Acad 17:229–288.
   Google Scholar
• LohmanML. 1933b. Septonema toruloideum: a stage of Mytilidion scolecosporum. Mycologia 25:34–43.
   Google Scholar
• LorenzoLEMessutiMI.2005. Glyphium elatum (Ascomycota) in Patagonia (Argentina). Bol Soc Argent Bot 40:13–16.
   Google Scholar
• LumbschHTSchmittILindemuthRMillerAMangoldAFernandoFHuhndorfS. 2005. Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol Phylogenet Evol 34:512–524.
   PubMed Web of Science ®Google Scholar
• MathiassenG. 1993. Corticolous and lignicolous Pyrenomycetes s. lat. (Ascomycetes) on Salix along a mid-Scandinavian transect. Sommerfeltia 20:1–180.
   Google Scholar
• MillerMPfeifferWSchwartzT. 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. Proceedings of the Gateway computing environments workshop (GCE), New Orleans, p 1–8.
   Google Scholar
• MoncalvoJMRehnerSAVilgalysR. 1993. Systematics of Lyophyllum section Difformia based on evidence from culture studies and ribosomal DNA sequences. Mycologia 85:788–794.
   Web of Science ®Google Scholar
• NordénBAppelquistTBarckLLöhmusM. 1997. An ecological field study of wood living pyrenomycetes in a Swedish hardwood forest. Windahlia 22:57–64.
   Google Scholar
• RéblováMUntereinerWARéblováK. 2013. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure. PLoS ONE 85:e63547.
   Google Scholar
• RehnerSASamuelsGJ. 1994. Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol Res 98:625–634.
   Web of Science ®Google Scholar
• SaccardoPA. 1902. Sylloge Fungorum hucusque cognitorum, 16:1–1291.
   Google Scholar
• SamuelsGJMüllerE. 1979. Life-history studies of Brazilian ascomycetes. 7. Rhytihysteron rufulum and the genus Eutryblidiella. Sydowia 32:277–292.
   Google Scholar
• SchochCLShoemakerRASeifertKAHambletonSSpataforaJWCrousPW. 2006. A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041–1052.
   PubMed Web of Science ®Google Scholar
• SchochCLCrousPWGroenewaldJZBoehmEWBurgessTIde GruyterJde HoogGSDixonLJGrubeMGueidanCHaradaYHatakeyamaSHirayamaKHosoyaTHuhndorfSMHydeKDJonesEBKohlmeyerJKruysALiYMLückingRLumbschHTMarvanovaLMbatchouJSMcVayAHMillerANMugambiGKMuggiaLNelsenMPNelsonPOwensbyCAPhillipsAJPhongpaichitSPointingSBPujade-RenaudVRajaHAPlataERRobbertseBRuibalCSakayarojJSanoTSelbmannLShearerCAShirouzuTSlippersBSuetrongSTanakaKVolkmann-KohlmeyerBWingfieldMJWoodARWoudenbergJHYonezawaHZhangYSpataforaJW. 2009a. A class-wide phylogenetic assessment of Dothideomycetes. Stud Mycol 64:1–15.
   PubMed Web of Science ®Google Scholar
• SchochCLSungGHLopez-GiraldezFTownsendJPMiadlikowskaJHofstetterVRobbertseBMathenyPBKauffFWangZGueidanCAndrieRMTrippeKCiufettiLMWynnsAFrakerEHodkinsonBPBonitoGGroenewaldJZArzanlouMde HoogGSCrousPWHewittDPfisterDHPetersonKGryzenhoutMWingfieldMJAptrootASuhSOBlackwellMHillisDMGriffithGWCastleburyLARossmanAYLumbschHTLückingRBudelBRauhutADiederichPErtzDGeiserDMHosakaKInderbitzinPKohlmeyerJVolkmann-KohlmeyerBMostertLO’DonnellKSipmanHRogersJDShoemakerRASugiyamaJSummerbellRCUntereinerWJohnstonPRStenroosSZuccaroADyerPSCrittendenPDColeMSHansenKTrappeJMYahrRLutzoniFSpataforaJW. 2009b. The Ascomycota Tree of Life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol 58:224–239.
   PubMed Web of Science ®Google Scholar
• SchochCLGrubeM. 2014. Pezizomycotina: Dothideomycetes and Arthoniomycetes In: McLaughlinDJSpataforaJW, eds. The Mycota. Vol. VII, Part B. Berlin, Germany: Springer Verlag, p. 143–178.
   Google Scholar
• StamatakisA. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
   PubMed Web of Science ®Google Scholar
• StamatakisAHooverPRougemontJ. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771.
   PubMed Web of Science ®Google Scholar
• SuetrongSSchochCLSpataforaJWKohlmeyerJVolkmann-KohlmeyerBSakayarojJPhongpaichitSTanakaKHirayamaKJonesEB. 2009. Molecular systematics of the marine Dothideomycetes. Stud Mycol 64:155–173.
   PubMed Web of Science ®Google Scholar
• SuttonBC. 1970. Glyphium leptothecium (Earle) comb. nov., G. schizosporum (Maire) Zogg, and their imperfect states. Trans Br Mycol Soc 54:255–264.
   Google Scholar
• TamuraKStecherGPetersonDFilipskiAKumarS. 2013. MEGA 6: molecular evolutionary genetics analysis Mol Biol Evol 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• TsunedaADaveyMLCurrahRS. 2011. A new endoconidial black meristematic genus, Atramixtia, associated with declining white spruce and phylogenetically allied to a lineage of dothidealean conifer pathogens. Botany 89:323–338.
   Google Scholar
• VasilyevaLN. 2001. Hysteriaceous fungi in the Russian Far East IV. Glyphium, Lophium and Mytilinidion. Mikolog Fitopatol 35:15–18.
   Google Scholar
• VilgalysRHesterM. 1990. Rapid identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246.
   PubMed Web of Science ®Google Scholar
• von ArxJAMüllerE. 1975. A re-evaluation of the bitunicate Ascomycetes with keys to families and genera. Stud Mycol 9:1–159.
   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
• ZoggH. 1962. Die Hysteriaceae s. str. und Lophiaceae, unter besonderer Berücksichtigung der mitteleuropäischen Formen. Beiträge zur Kryptogamenflora der Schweiz, Band 11:1–190.
   Google Scholar