Multilocus phylogenetic and coalescent-based methods reveal dilemma in generic limits, cryptic species, and a prevalent intercontinental disjunct distribution in Geopyxis (Pyronemataceae s. l., Pezizomycetes)

Literature cited

• Alvarado PMoreno GManjón JLGelpi CKaounas VKonstantinidis GBarseghyan GSVenturella G.2011. First molecular data on Delastria rosea, Fischerula macrospora and Hydnocystis piligera. Bot Soc Micol Madrid 35:31–37.
   Google Scholar
• Ané CLarget BBaum DASmith SDRokas A.2007. Bayesian estimation of concordance among gene trees. Mol Biol Evol 24:412– 426 doi:10.1093/molbev/msl170
   PubMed Web of Science ®Google Scholar
• Arpin N.1968. Les caroténoïdes des Discomycètes: essai chimotaxinomique. [doctoral dissertation].Lyon, France: University of Lyon. 169 p.
   Google Scholar
• Benkert D.2008. Emendation der gattung Kotlabaea (Ascomycota, Pezizales). Österr Z Pilzk 17:173–221.
   Google Scholar
• Bonito GGryganskyi APTrappe JMVilgalys R.2010. A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal. Mol Ecol 19:4994–5008 doi:10.1111/j.1365-294X.2010.04855.x
   PubMed Web of Science ®Google Scholar
• Boudier E.1907. Histoire et classification des discomycetes D’Europe. Paris: Librairei des Sciences Naturelles. 120 p.
   Google Scholar
• Castellano MATrappe JMLuoma DL.2004. Sequestrate fungi. In: Mueller GMBills GFFoster MS eds. Biodiversity of Fungi: inventory and monitoring methods. Amsterdam: Elsevier. p 197–213.
   Google Scholar
• Cooke MC.1875. Mycographia seu Icones Fungorum. Vol. I. Discomycetes, Part I. London: Williams and Norgate. 267 p.
   Google Scholar
• Dennis KWG.1975. New or interesting British microfungi, III. Kew Bull 30:345–365 doi:10.2307/4103162
   Google Scholar
• Dennis KWG.1978. British Ascomycetes. Vaduz, Germany: J. Cramer. 585 p.
   Google Scholar
• Dettman JRJacobson DJTaylor JW.2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57:2703–2720 doi:10.1111/j.0014-3820.2003.tb01514.x
   PubMed Web of Science ®Google Scholar
• Dimitrova EGyosheva M.2009. Bulgarian Pezizales: diversity, distribution and ecology. Phytol Balcan 15:13–28.
   Google Scholar
• Du XHZhao QO’Donnell KRooney APYang ZL.2012. Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China. Fungal Genet Biol 49:455–469 doi:10.1016/j.fgb.2012.03.006
   PubMed Web of Science ®Google Scholar
• Eckblad F-E.1968. The genera of the operculate discomycetes. A re-evaluation of their taxonomy, phylogeny and nomenclature. Nytt Magasin for Botanikk 1:1–191.
   Google Scholar
• Egger KN. 1986. Substrate hydrolysis patterns of post-fire ascomycetes (Pezizales). Mycologia 78:771–780 doi:10.2307/3807522
   Web of Science ®Google Scholar
• Egger KNPaden JW.1986. Biotrophic associations between lodgepole pine seedlings and postfire ascomycetes (Pezizales) in monoxenic culture. Can J Bot 64:2719–2725 doi:10.1139/b86-359
   Google Scholar
• Engel HHanff B.1984. Neue Ascomyceten-funde 1983 in Nordwestoberfranken. Pilzflora Nordwestoberfrankens 8:31–57.
   Google Scholar
• Feng BXu JWu GHosen IZeng NKLi YCBau TKost GWYang ZL.2012. DNA Sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms. PLoS One 7:e37567 doi:10.1371/journal.pone.0037567
   PubMed Web of Science ®Google Scholar
• Fries EM.1851. Novae symbolae mycologicae. Uppsala, Sweden. 120 p.
   Google Scholar
• Ganley RJNewcombe G.2006. Fungal endophytes in seeds and needles of Pinus monticola. Mycol Res 110:318–327 doi:10.1016/j.mycres.2005.10.005
   PubMedGoogle Scholar
• Garnweidner ELohmeyer TRMarxmüller H.1991. Geopyxis foetida Vel., Geopyxis alpina v. Höhnel und nahestehende Taxa – mehr Fragen als Antworten. Z Mykol 57:201–214.
   Google Scholar
• Geml JTimling IRobinson CHLennon NNusbaum HCBrochmann CNoordeloos METaylor DL.2012. An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA. J Biogeogr 39:74–88 doi:10.1111/j.1365-2699.2011.02588.x
   Web of Science ®Google Scholar
• Grelet L-J.1937. Les Discomycètes de France d’après la classification de Boudier. Bull Soc Bot Centre-Ouest 6:41–60.
   Google Scholar
• Groves JWHoare SC.1954. Notes on fungi from northern Canada. I. Hypocreales and Discomycetes. Can Field Nat 68:1–8.
   Google Scholar
• Hambäck PAWeingartner EEricson LFors LCassel-Lundhagen AStenberg JABergsten J.2013. Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host. BMC Evol Biol 13:92 doi:10.1186/1471-2148-13-92
   Web of Science ®Google Scholar
• Hansen KLæssøe TPfister DH.2002. Phylogenetic diversity in the core group of Peziza inferred from ITS sequences and morphology. Mycol Res 106:879–902 doi:10.1017/S0953756202006287
   Google Scholar
• Hansen KOlariaga I.2015. Species limits and relationships within Otidea inferred from multiple gene phylogenies. Persoonia 35:148–165 doi:10.3767/003158515X687993
   PubMed Web of Science ®Google Scholar
• Hansen KPerry BADranginis AWPfister DH.2013. A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits. Mol Phylogenet Evol 67:311–335 doi:10.1016/j.ympev.2013.01.014
   PubMed Web of Science ®Google Scholar
• Hansen KPfister DHHibbett DS.1999. Phylogenetic relationships among species of Phillipsia inferred from molecular and morphological data. Mycologia 91:299–314 doi:10.2307/3761375
   Web of Science ®Google Scholar
• Harmaja H. 1974. The generic limit between Otidea and Tarzetta (Pustularia auct.). Karstenia 14:138–142.
   Google Scholar
• Harrower EBougher NLHenkel TWHorak EMatheny PB.2015. Long-distance dispersal and speciation of Australasian and American species of Cortinarius sect. Cortinarius. Mycologia 107:697–709 doi:10.3852/14-182
   Web of Science ®Google Scholar
• Higgins KLArnold AEMiadlikowska JSarvate SDLutzoni F.2007. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol Phylogenet Evol 42:543–555 doi:10.1016/j.ympev.2006.07.012
   PubMed Web of Science ®Google Scholar
• Hoffman MTArnold AE.2010. Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes. Appl Eviron Microbiol 76:4063–4075 doi:10.1128/AEM.02928-09
   PubMed Web of Science ®Google Scholar
• Höhnel FXR von.1906 (“1905”). Mycologische Fragmente CVI-CXVII. Ann Mycologici 3:548–560.
   Google Scholar
• Huelsenbeck JPBull JJCunningham CW.1996. Combining data in phylogenetic analysis. Trends Ecol Evol 11:152–158 doi:10.1016/0169-5347(96)10006-9
   PubMed Web of Science ®Google Scholar
• Huhtinen S.1984. Additions to the ascomycetous flora of the Canadian north. Karstenia 24:1–11.
   Google Scholar
• Huhtinen S.1985. Mycoflora of Poste-de-la-Baleine, Northern Québec. Ascomycetes. Naturaliste Can (Rev Écol Syst) 112:473–524.
   Google Scholar
• Kaya AUzun YKaracan IHYakar S.2016. Contributions to Turkish Pyronemataceae from Gaziantep Province. Turk J Bot 40:298–307 doi:10.3906/bot-1508-4
   Web of Science ®Google Scholar
• Khalid ANQadeer NIqbal SH.2000. Additions to the Discomycetes of Pakistan. Pak J Bot 32:27–34.
   Web of Science ®Google Scholar
• Kornerup AWanscher JH.1961. Farver i farver. Copenhagen: Politikens Forlag. 248 p.
   Google Scholar
• Kotlaba F.1969. Podzimní exkurze čs. mykologů na Karlštejn r. 1968. Česka Mykologie 23:203–206.
   Google Scholar
• Læssøe THansen K.2007. Truffle trouble: what happened to the Tuberales? Mycol Res 111:1075–1099.
   PubMedGoogle Scholar
• Larget BRKotha SKDewey CNAné C.2010. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910–2911 doi:10.1093/bioinformatics/btq539
   PubMed Web of Science ®Google Scholar
• Larsen HJDenison WC.1978. A checklist of the operculate cup-fungi (Pezizales) of North America west of the Great Plains. Mycotaxon 7:68–90.
   Web of Science ®Google Scholar
• Leaché ADFujita MK.2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc Biol Sci 277:3071–3077 doi:10.1098/rspb.2010.0662
   PubMed Web of Science ®Google Scholar
• Lindemann UVega MAlvarado P.2015. Revision der gattung Kotlabaea: K. deformis, K. delectans und K. benkertii. Z Mykol 81:372–402.
   Google Scholar
• Liu CYZhuang WY.2006. Relationships among some members of the genus Otidea (Pezizales, Pyronemataceae). Fungal Divers 23:181–192.
   Web of Science ®Google Scholar
• Liu YJWhelen SBenjamin DH.1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799–1808 doi:10.1093/oxfordjournals.molbev.a026092
   PubMed Web of Science ®Google Scholar
• McNeill JBarrie FRBuck WRDemoulin VGreuter WHawksworth DLHerendeen PSKnapp SMarhold KPrado JPrud’homme van Reine WFSmith GFWiersema JHTurland NJ eds. 2012. International Code of Nomenclature for algae, fungi, and plants (Melbourne Code) adopted by the Eighteenth International Botanical Congress, Melbourne, Australia, Jul 2011. [Regnum Vegetabile No. 154.] Königstein, Germany: Koeltz Scientific Books. 240 p.
   Google Scholar
• Mihál IGlejdura SBlanár D.2011. Makromycéty (Zygomycota, Ascomycota, Basidiomycota) v masíve Kohúta (Stolické vrchy). Reussia 6( 1–2): 1–44.
   Google Scholar
• O’Donnell KRooney APMills GLKuo MWeber NSRehner SA.2011. Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic. Fungal Genet Biol 48:252–265 doi:10.1016/j.fgb.2010.09.006
   PubMed Web of Science ®Google Scholar
• Peck CH.1873. Fungi. In: Annual report of the United States Geological Survey of the territories 6:792.
   Google Scholar
• Peck CH.1879. Reports of the botanist. Annual Report of the New York State Museum of Natural History 31:19–60.
   Google Scholar
• Perry BAHansen KPfister DH.2007. A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales). Mycol Res 111:549–571 doi:10.1016/j.mycres.2007.03.014
   PubMedGoogle Scholar
• Petersen PM.1970. Danish fireplace fungi—an ecological investigation on fungi on burns. Dansk Botanisk Arkiv 27( 3): 1–97.
   Google Scholar
• Raymundo TBautista-HernándezAguirre-Acosta EAguilar SValenzuela R.2012. Nuevos registros de Pezizales (Pezizomycetes, Ascomycota) en México. Bol Soc Micol Madrid 36:13–21.
   Google Scholar
• Rifai MA.1968. The Australasian Pezizales in the Herbarium of The Royal Botanic Gardens Kew. Amsterdam: N.V. Noord-Hollandsche Uitgevers Maatschappij. 195 p.
   Google Scholar
• Ronquist FTeslenko Mvan der Mark P, Ayres DLDarling AHohna SLarget BLiu LSuchard MAHeulsenbeck JP.2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542 doi:10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Saccardo PA.1889. Sylloge Fungorum. 8. 1143 p.
   Google Scholar
• Seaver FJ.1928. The North American cup-fungi (Operculates). New York: Published by author. 284 p.
   Google Scholar
• Seaver FJ.1942. The North American cup-fungi (Operculates). Supplemented edition.New York: Hafner Publishing. 377 p.
   Google Scholar
• Seaver FJ.1961. The North American cup-fungi (Operculates). Supplemented edition.New York: Hafner Publishing. 377 p.
   Google Scholar
• Soca-Chafre GRivera-Orduña FNHidalgo-Lara MEHernandez-Rodriguez CMarsch RFlores-Cotera LB.2011. Molecular phylogeny and paclitaxel screening of fungal endophytes from Taxus globosa. Fungal Biol 115:143–156 doi:10.1016/j.funbio.2010.11.004
   PubMed Web of Science ®Google Scholar
• Stamatakis A.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
• Starbäck K.1898. Några märkligare skandinaviska ascomycetfynd. Botaniska Notiser 1898:201–219.
   Google Scholar
• Stark CBabik WDurka W.2009. Fungi from the roots of the common terrestrial orchid. Mycol Res 113:952–959 doi:10.1016/j.mycres.2009.05.002
   PubMed Web of Science ®Google Scholar
• Stielow BHensel GStrobelt DMae Makonde HRohde MDijksterhuis JKlenk HGöker M.2013. Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora. Mycol Prog 12:675–686 doi:10.1007/s11557-012-0875-1
   Web of Science ®Google Scholar
• Svrćek M.1974. New and less known Discomycetes. I. Česká Mykol 28( 3): 129–137.
   Google Scholar
• Svrćek M.1976. A taxonomic revision of Velenovsky’s types of operculate discomycetes (Pezizales) preserved in National Museum, Prague. Acta Musei Nationalis Prague 32B( 2–4): 115–194.
   Google Scholar
• Taskin HBuyukalaca SDogän HHRehner SAO’Donnell K.2010. A multigene molecular phylogenetic assessment of true morels (Morchella) in Turkey. Fungal Genet Biol 47:672–682 doi:10.1016/j.fgb.2010.05.004
   PubMed Web of Science ®Google Scholar
• Taskin HBuyukalaca SHansen KO’Donnell K.2012. Multilocus phylogenetic analysis of true morels (Morchella) reveals high levels of endemics in Turkey relative to other regions of Europe. Mycologia 104:446–461 doi:10.3852/11-180
   PubMed Web of Science ®Google Scholar
• Taylor JWJacobsen DJKroken SKasuga TGeiser DMHibbett DSFisher MC.2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32 doi:10.1006/fgbi.2000.1228
   PubMed Web of Science ®Google Scholar
• Tedersoo LArnold AEHansen K.2013. Novel aspects in the life cycle and biotrophic interactions in Pezizomycetes (Ascomycota, Fungi). Mol Ecol 22:1488–1493 doi:10.1111/mec.12224
   Web of Science ®Google Scholar
• Tedersoo LHansen KPerry BAKjøller R.2006. Molecular and morphological diversity of pezizalean ectomycorrhiza. New Phytol 170:581–596 doi:10.1111/j.1469-8137.2006.01678.x
   Web of Science ®Google Scholar
• Tedersoo LMay TWSmith ME.2010. Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20:217–263 doi:10.1007/s00572-009-0274-x
   PubMed Web of Science ®Google Scholar
• Tedersoo LSmith ME.2013. Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground. Fungal Biol Rev 27( 3–4): 83–99.
   Web of Science ®Google Scholar
• Tedersoo LSuvi TJairus TOstonen IPõlme S.2009. Revisiting ectomycorrhizal fungi of the genus Alnus: differential host specificity, diversity and determinants of the fungal community. New Phytol 182:727–735 doi:10.1111/j.1469-8137.2009.02792.x
   Web of Science ®Google Scholar
• Thind KSKaushal SC.1981. Nomenclature and systematics of Geopyxis with taxonomic notes on its Himalayan species. Acta Bot Indica 9:115–121.
   Google Scholar
• Trappe JM.1979. The orders, families, and genera of hypogeous Ascomycotina (truffles and their relatives). Mycotaxon 9:297–340.
   Web of Science ®Google Scholar
• Turnau K.1984. Investigation on post-fire Discomycetes: Geopyxis rehmii sp. nov. and G. carbonaria (Alb. & Schw. ex Fr.) Sacc. Nova Hedwigia 40:157–170.
   Web of Science ®Google Scholar
• Tylutki EE.1993. Mushrooms of Idaho and the Pacific Northwest. Vol. 1. Discomycetes. Moscow: Univ. Idaho Press. 133 p.
   Google Scholar
• U’Ren JMLutzoni FMiadlikowska JArnold AE.2010. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microb Ecol 60:340–353 doi:10.1007/s00248-010-9698-2
   PubMed Web of Science ®Google Scholar
• U’Ren JMLutzoni FMiadlikowska JLaetsch ADArnold AE.2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. Am J Bot 99:898–914 doi:10.3732/ajb.1100459
   PubMed Web of Science ®Google Scholar
• U’Ren JMRiddle JMMonacell JTCarbone IMiadlikowska JArnold AE.2014. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Mol Ecol Resour 14:1032–1048.
   Web of Science ®Google Scholar
• Velenovský J.1922. České Houby. Parts 4–5:633–950. Prague.
   Google Scholar
• Velenovský J.1934. Monographia Discomycetum Bohemiae. Prague. 436 p.
   Google Scholar
• Vrålstad THolst-Jensen ASchumacher T.1998. The postfire discomycete Geopyxis carbonaria (Ascomycota) is a biotrophic root associate with Norway spruce (Picea abies) in nature. Mol Ecol 7:609–616 doi:10.1046/j.1365-294x.1998.00365.x
   Web of Science ®Google Scholar
• Wijeratne EMKBashyal BPLiu MXRocha DDGunaherath GMKBU’Ren JMGunatilaka MKArnold AEWhitesell LGunatilaka AAL.2012. Geopyxins A–E, ent-kaurane diterpenoids from endolichenic fungal strains Geopyxis aff. majalis and Geopyxis sp. AZ0066: structure-activity relationships of Geopyxins and their analogues. J Nat Prod 75:361–369 doi:10.1021/np200769q
   PubMed Web of Science ®Google Scholar
• Yang ZH. 2015. The BPP program for species tree estimation and species delimitation. Curr Zool 61:854–865 doi:10.1093/czoolo/61.5.854
   Web of Science ®Google Scholar
• Yang ZHRannala B.2010. Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A 107:9264–9269 doi:10.1073/pnas.0913022107
   PubMed Web of Science ®Google Scholar
• Zhang CZhang D-XZhu TYang Z.2011. Evaluation of a Bayesian coalescent method of species delimitation. Syst Biol 60:747–761 doi:10.1093/sysbio/syr071
   PubMed Web of Science ®Google Scholar
• Zhuang WYLiu HY.2006. A new species of Geopyxis (Pezizales, Pyronemataceae) with ornamented ascospores from China. Nova Hedwigia 83:177–186 doi:10.1127/0029-5035/2006/0083-0177
   Web of Science ®Google Scholar