Interannual variation and host affiliations of endophytic fungi associated with ferns at La Selva, Costa Rica

Literature cited

• AbramoffMMagelhaesPRamS. 2004. Image processing with Image J. Biophotonics Int 11:36–42.
   Google Scholar
• AltschulSGishWMillerWMyersELipmanD. 1990. Basic local alignment search tool. J Mol Biol 215:403–410.
   PubMed Web of Science ®Google Scholar
• ArnoldAE. 2007. Understanding the diversity of foliar endophytic fungi: progress, challenges and frontiers. Fungal Biol Rev 21:51–66, doi:10.1016/j.fbr.2007.05.003
   Google Scholar
• ArnoldAE. 2008. Endophytic fungi: hidden components of tropical community ecology. In: SchnitzerSCarsonW, eds. Tropical forest community ecology. Oxford, UK: Wiley-Blackwell. p 254–271.
   Google Scholar
• ArnoldAEHenkDAEellsRLLutzoniFVilgalysR. 2007. Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99: 185–206, doi:10.3852/mycologia.99.2.185
   PubMed Web of Science ®Google Scholar
• ArnoldAEHerreEA. 2003. Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95:388–98, doi:10.2307/3761880
   PubMed Web of Science ®Google Scholar
• ArnoldAELutzoniF. 2007. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549, doi:10.1890/05-1459
   PubMed Web of Science ®Google Scholar
• ArnoldAEMaynardZGilbertGSColeyPDKursarTA. 2000. Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274, doi:10.1046/j.1461-0248.2000.00159.x
   Web of Science ®Google Scholar
• ArnoldAEMaynardZGilbertGS. 2001. Fungal endophytes in dicotyledonous Neotropical trees: patterns of abundance and diversity. Mycol Res 105:1502–1507, doi:10.1017/S0953756201004956
   Web of Science ®Google Scholar
• ArnoldAEMejíaLCKylloDRojasEIMaynardZRobbinsNHerreEA. 2003. Fungal endophytes limit pathogen damage in a tropical tree. P Natl Acad Sci USA 100: 15649–54, doi:10.1073/pnas.2533483100
   PubMed Web of Science ®Google Scholar
• ArnoldAEMiadlikowskaJHigginsKLSarvateSDGuggerPWayAHofstetterVKauffFLutzoniF. 2009. A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283–97, doi:10.1093/sysbio/syp001
   PubMed Web of Science ®Google Scholar
• BarnettHLHunterBB. 1998. Ilustrated genera of imperfect fungi. St Paul, Minnesota: APS Press. 218 p.
   Google Scholar
• BauerROberwinklerFVánkyK. 1999. Ustilaginomycetes on Osmunda. Mycologia 91:669–675, doi:10.2307/3761254
   Web of Science ®Google Scholar
• BerndtR. 2008. The rust fungi (Uredinales) on ferns in South Africa. Mycol Prog 7:7–19, doi:10.1007/s11557-007-0548-7
   Google Scholar
• BlackwellM. 2011. The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–38, doi:10.3732/ajb.1000298
   PubMed Web of Science ®Google Scholar
• BorcardDGilletFLegendreP. 2011. Numerical ecology with R. Use R! Series. New York: Springer. 306 p.
   Google Scholar
• CannonPFSimmonsCM. 2002. Diversity and host preference of leaf endophytic fungi in the Iwokrama forest reserve, Guyana. Mycologia 94:210–220, doi:10.2307/3761797
   PubMed Web of Science ®Google Scholar
• CarrollG. 1995. Forest endophytes: pattern and process. Can J Bot 73:S1316–S1324, doi:10.1139/b95-393
   Google Scholar
• ChapelaIHPetriniOPetriniLE. 1990. Unusual ascospore germination in Hypoxylon fragiforme: first steps in the establishment of an endophytic symbiosis. Can J Bot 68: 2571–2575, doi:10.1139/b90-324
   Google Scholar
• ChaverriPGazisRO. 2011. Linking ex planta fungi with their endophytic stages: Perisporiopsis, a common leaf litter and soil fungus, is a frequent endophyte of Hevea spp. and other plants. Fungal Ecol 4:94–102, doi:10.1016/j.funeco.2010.09.003
   Google Scholar
• ClarkeKR. 1993. Nonparametric multivariate analyses of changes in community structure. Aust J Ecol 18:117–143, doi:10.1111/j.1442-9993.1993.tb00438.x
   Google Scholar
• ColwellRK. 2005. EstimateS 7.5: statistical estimation of species richness and shared species from samples. http://purl.oclc.org/estimates
   Google Scholar
• DomschKGamsWAndersonT. 1993. Compendium of soil fungi. Germany: IHW-Verlag Press. 1264 p.
   Google Scholar
• DreyfussMPetriniO. 1984. Further investigations on the occurrence and distribution of endophytic fungi in tropical plants. Bot Helv 94:33–40.
   Web of Science ®Google Scholar
• DufreneMLegendreP. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr 67:345–366.
   Web of Science ®Google Scholar
• EllettCW. 1989. Curvularia Blight of Ophioglossum vulgatum. Mycologia 81:815–817, doi:10.2307/3759890
   Google Scholar
• EwingBGreenP. 1998. Base-calling of automated sequencer traces using phred II. Error probabilities. Genome Res 8:186–194.
   PubMed Web of Science ®Google Scholar
• EwingBHillierLWendlMGreenP. 1998. Base-calling of automated sequencer traces using phred I. Accuracy assessment. Genome Res 8:175–185, doi:10.1101/gr.8.3.175
   PubMed Web of Science ®Google Scholar
• FelsensteinJ. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791, doi:10.2307/2408678
   PubMed Web of Science ®Google Scholar
• FisherPJ. 1996. Survival and spread of the endophyte Stagonospora pteridiicola in Pteridium aquilinum, other ferns and some flowering plants. New Phytol 132:119–122, doi:10.1111/j.1469-8137.1996.tb04516.x
   Google Scholar
• FisherPJPunithalingamE. 1993. Stagonospora pteridiicola sp. nov., a new endophytic coelomycete in Pteridium aquilinum. Mycol Res 97:661–664, doi:10.1016/S0953-7562(09)80143-3
   Google Scholar
• FisherRACorbetASWilliamsCB. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. J Anim Ecol 12:42–58, doi:10.2307/1411
   Web of Science ®Google Scholar
• FranklandJC. 1966. Succession of fungi on decaying petioles of Pteridium aquilinum. J Ecol 54:41–63, doi:10.2307/2257658
   Web of Science ®Google Scholar
• GamsW. 2000. Phialophora and some similar morphologically little-differentiated anamorphs of divergent ascomycetes. Stud Mycol 45:187–199.
   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
• GazisRChaverriP. 2010. Diversity of fungal endophytes in leaves and stems of wild rubber trees (Hevea brasiliensis) in Peru. Fungal Ecol 3:240–254, doi:10.1016/j.funeco.2009.12.001
   Web of Science ®Google Scholar
• GazisRRehnerSChaverriP. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Mol Ecol 20:3001–3013, doi:10.1111/j.1365-294X.2011.05110.x
   PubMed Web of Science ®Google Scholar
• GilbertsonRLHemmesDE. 1997. Notes on fungi on Hawaiian tree ferns. Mycotaxon 62:465–487.
   Web of Science ®Google Scholar
• GodfreyBES. 1974. Phylloplane mycoflora of bracken, Pteridium aquilinum. T Br Mycol Soc 62:305–311, doi:10.1016/S0007-1536(74)80039-2
   Google Scholar
• GohT-KHydeKD. 1996. Spadicoides cordanoides sp. nov., a new dematiaceous hyphomycete from submerged wood in Australia, with a taxonomic review of the genus. Mycologia 88:1022–1031, doi:10.2307/3761067
   Google Scholar
• GosleeSCUrbanDL. 2007. The ecodist package for dissimilarity-based analysis of ecological data. J Stat Software 22:1–19.
   Web of Science ®Google Scholar
• HammerØHarperDAT. 2006. Paleontological data analysis. Oxford, UK: Blackwell Publishing. 351 p.
   Google Scholar
• HanlinTR. 1998. Illustrated genera of ascomycetes. Vol. 1, 2 combined keys. St Paul, Minnesota: APS Press. 113 p.
   Google Scholar
• HarperDAT, ed. 1999. Numerical palaeobiology: computer-based modeling and analysis of fossils and their distributions. Chichester, UK: John Wiley & Sons. 478 p.
   Google Scholar
• HelferS. 2006. Micro-fungal pteridophyte pathogens. Fern Gazette 17:259–261.
   Google Scholar
• HietzP. 2010. Fern adaptation to xeric environments. In: MehltreterKWalkerLRSharpeJM, eds. Fern ecology. New York: Cambridge Univ. Press. p 140–176.
   Google Scholar
• HigginsKLColeyPDKursarTAArnoldAE. 2011. Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses. Mycologia 103:247–60, doi:10.3852/09-158
   PubMed Web of Science ®Google Scholar
• HoffmanMTArnoldAE. 2008. Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycol Res 112:331–44, doi:10.1016/j.mycres.2007.10.014
   PubMed Web of Science ®Google Scholar
• HoubrakenJSamsonRA. 2011. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol 70:1–51, doi:10.3114/sim.2011.70.01
   PubMed Web of Science ®Google Scholar
• JohnsonJAWhitneyNJ. 1992. Isolation of fungal endophytes from black spruce (Picea mariana) dormant buds and needles from New Brunswick, Canada. Can J Bot 70:1754–1757, doi:10.1139/b92-217
   Google Scholar
• KamalSingh CS. 1970. Succession of fungi on decaying leaves of some Pteridophytes. Ann I Pasteur Paris 119: 468–482.
   Google Scholar
• KatohKTohH. 2008. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9:212–226, doi:10.1186/1471-2105-9-212
   PubMed Web of Science ®Google Scholar
• KiefferEMoreletM. 2000. The Deuteromycete, mitosporic fungi classification and generic key. Enfield, New Hampshire: Science Publishers. 273 p.
   Google Scholar
• KindtRCoeR. 2005. Tree diversity analysis. A manual and software for common statistical methods for ecological and biodiversity studies. Nairobi, Kenya: World Agroforestry Centre (ICRAF). 196 p.
   Google Scholar
• LarkinMABlackshieldsGBrownNPChennaRMcGettiganPAMcWilliamHValentinFWallaceIMWilmALopezRThompsonJDGibsonTJHigginsDG. 2007. Clustal W and Clustal X 2.0. Bioinformatics 23:2947–2948, doi:10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• LegendrePLegendreL. 1998. Numerical ecology. Amsterdam, the Netherlands: Elsevier. 853 p.
   Google Scholar
• LodgeDJFisherPJSuttonBC. 1996. Endophytic Fungi of Manilkara bidentata leaves in Puerto Rico. Mycologia 88:733–738, doi:10.2307/3760967
   Web of Science ®Google Scholar
• MaddisonDRMaddisonWP. 2010. Chromaseq 0.984: a Mesquite module for analyzing sequence chromatograms. http://mesquiteproject.org/packages/chromaseq
   Google Scholar
• MaddisonWPMaddisonDR. 2007. Mesquite 2.0: a modular system for evolutionary analysis. http://mesquiteproject.org
   Google Scholar
• MarkhamKChalkTStewardCN. 2006. Evaluation of fern and moss protein-based defenses against phytophagous insects. Int J Plant Sci 167:111–117, doi:10.1086/497651
   Google Scholar
• McDadeLAHartshornGS. 1994. La selva biological station. In: McDadeLABawaKSHespenheideHAHartshornGS, eds. La selva: ecology and natural history of a Neotropical rain forest. Chicago: Univ. Chicago Press. p 6–14.
   Google Scholar
• MedelRLorea-HernándezF. 2008. Hyaloscyphaceae (Ascomycota) growing on tree ferns in Mexico. Mycotaxon 106:209–217.
   Google Scholar
• MehltreterK. 2008. Adaptations of tropical ferns to their environment: phenology and habitat preferences. In: RankerTAHauflerCH, eds. Biology of ferns and lycophytes. Cambridge, UK: Cambridge Univ. Press. p 201–221.
   Google Scholar
• MillerMAHolderMTVosRMidfordPELiebowitzTChanLHooverPWarnowT. 2009. The CIPRES Portal: http://www.phylo.org/sub_sections/portal
   Google Scholar
• MoranRC. 2008. Biogeography of ferns and lycophytes. In: HauflerCRankerTA, eds. The biology and evolution of ferns and lycophytes. Cambridge, UK: Cambridge Univ. Press. p 369–396.
   Google Scholar
• MuraliTSSuryanarayananTSVenkatesanG. 2007. Fungal endophyte communities in two tropical forests of southern India: diversity and host affiliation. Mycol Prog 6:191–199, doi:10.1007/s11557-007-0540-2
   Web of Science ®Google Scholar
• NagaoHDoiY. 1996. Discomycetes on decayed tree fern. (1) Lachnum pteridophyllum (Rodway) Spooner New to Japan. Bulletin of the National Science Museum. Series B Botanica 22:19–22.
   Google Scholar
• OkaneILumyongSNakagiriAItoT. 2003. Extensive host range of an endophytic fungus, Guignardia endophyllicola (anamorph: Phyllosticta capitalensis). Mycoscience 44:353–363, doi:10.1007/S10267-003-0128-X
   Google Scholar
• OkaneISrikitikulchaiPTabuchiYSivichaiSNakagiriA. 2012. Recognition and characterization of four Thai xylariaceous fungi inhabiting various tropical foliage as endophytes by DNA sequences and host plant preference. Mycoscience 53:122–132, doi:10.1007/S10267-011-0149-9
   Web of Science ®Google Scholar
• OksanenJBlanchetFGKindtRLegendrePMinchinPRO’HaraRBSimpsonGLSolymosPStevensMHHWagnerH. 2011. Package vegan 2.0-2. http://cran.r-project.org/web/packages/vegan/index.html
   Google Scholar
• PageCN. 2002. Ecological strategies in fern evolution: a neopteridological overview. Rev Palaeobot Palyno 119: 1–33, doi:10.1016/S0034-6667(01)00127-0
   Web of Science ®Google Scholar
• PetersSDraegerSAustHSchulzB. 1998. Interactions in dual cultures of endophytic fungi with host and non-host plant calli. Mycologia 90:360–367, doi:10.2307/3761393
   Google Scholar
• PetriniOCarrollGC. 1981. Endophytic fungi in foliage of some Cupressaceae in Oregon. Can J Bot 59:629–636, doi:10.1139/b81-089
   Google Scholar
• PetriniOFisherPJPetriniLE. 1992. Fungal endophytes of bracken (Pteridium aquilinum), with some reflections on their use in biological control. Sydowia 44:282–293.
   Google Scholar
• PosadaDCrandallKA. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics 14:817–818, doi:10.1093/bioinformatics/14.9.817
   PubMed Web of Science ®Google Scholar
• RaitviirASchnellerJ. 2007. Some new Helotiales on ferns from South Africa. Sydowia 59:255–265.
   Google Scholar
• RambautADrummondAJ. 2009. Tracer 1.5. http://beast.bio.ed.ac.uk/Tracer
   Google Scholar
• RichardsonKACurrahRS. 1995. The fungal community associated with the roots of some rainforest epiphytes of Costa Rica. Selbyana 16:49–73.
   Google Scholar
• RobertsDW. 2010. labdsv: ordination and multivariate analysis for ecology. http://CRAN.R-project.org/package5labdsv
   Google Scholar
• RodriguesFK. 1994. The foliar fungal endophytes of the Amazonian palm Euterpe oleracea. Mycologia 86:376–385, doi:10.2307/3760568
   Web of Science ®Google Scholar
• RogersJD. 1984. Xylaria cubensis and its anamorph Xylocoremium flabelliforme, Xylaria allantoidea and Xylaria poitei in continental United States. Mycologia 76:912–923, doi:10.2307/3793147
   Web of Science ®Google Scholar
• RonquistFHuelsenbeckJP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574, doi:10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• RowellCHFRowell-RahierMBrakerHECooper-DriverGGomezLD. 1983. The palatability of ferns and the ecology of two tropical forest grasshoppers. Biotropica 15:207–216, doi:10.2307/2387830
   Google Scholar
• SaikkonenK. 2007. Forest structure and fungal endophytes. Fungal Biol Rev 21:67–74, doi:10.1016/j.fbr.2007.05.001
   Google Scholar
• SanfordRLPaabyPLuvallJCPhillipsE. 1994. Climate, geomorphology and aquatic systems. In: McCadeLABawaKSHespenheideHAHartshornGS, eds. La selva: ecology and natural history of a Neotropical rainforest. Chicago: Univ. Chicago Press. p 19–33.
   Google Scholar
• SchmidEOberwinklerFGómezLD. 1995. Light and electron microscopy of a host-fungus interaction in the roots of some endophytic ferns from Costa Rica. Can J Bot 73:991–996, doi:10.1139/b95-107
   Google Scholar
• SchneiderHSchuettpelzEPryerKMCranfillRMagallónSLupiaR. 2004. Ferns diversified in the shadow of angiosperms. Nature 428:553–557, doi:10.1038/nature02361
   PubMed Web of Science ®Google Scholar
• SchuettpelzEPryerK. 2009. Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy. P Natl Acad Sci USA 106:11200–11205, doi:10.1073/pnas.0811136106
   PubMed Web of Science ®Google Scholar
• SeifertKA. 2009. Progress toward DNA barcoding of fungi. Mol Ecol Resources 9 Suppl. s1:83–9, doi:10.1111/j.1755-0998.2009.02635.x
   Google Scholar
• SharpeJMMehltreterK. 2010. Ecological insights from fern population dynamics. In: MehltreterKWalkerLRSharpeJM, eds. Fern ecology. Cambridge, UK: Cambridge Univ. Press. p 61–110.
   Google Scholar
• SmithARPryerKMSchuettpelzEKorallPSchneiderHWolfPG. 2006. A classification for extant ferns. Taxon 55:705–731, doi:10.2307/25065646
   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
• SuryanarayananTSMuraliTSVenkatesanG. 2002. Occurrence and distribution of fungal endophytes in tropical forests across a rainfall gradient. Can J Bot 80: 818–826, doi:10.1139/b02-069
   Google Scholar
• SuryanarayananTSVenkatesanGMuraliTS. 2003. Endophytic fungal communities in leaves of tropical forest trees: diversity and distribution patterns. Curr Sci India 85:489–493.
   Web of Science ®Google Scholar
• SwoffordDL. 2001. PAUP*4.b10: phylogenetic analysis using parsimony. Sunderland, Massachusetts: Sinauer associates.
   Google Scholar
• TaylorJEHydeKDGJEB. 1999. Endophytic fungi associated with the temperate palm, Trachycarpus fortunei, within and outside its natural geographic range. New Phytol 142:335–346, doi:10.1046/j.1469-8137.1999.00391.x
   Web of Science ®Google Scholar
• TotiLViretOChapelaIHPetriniO. 1992. Differential attachment by conidia of the endophyte, Discula umhrinella (Berk. & Br.) Morelet, to host and non-host surfaces. New Phytol 121:469–475, doi:10.1111/j.1469-8137.1992.tb02947.x
   Web of Science ®Google Scholar
• U’RenJMDallingJWGalleryREMaddisonDRDavisECGibsonCMArnoldAE. 2009. Diversity and evolutionary origins of fungi associated with seeds of a Neotropical pioneer tree: a case study for analyzing fungal environmental samples. Mycol Res 113:432–49, doi:10.1016/j.mycres.2008.11.015
   Web of Science ®Google Scholar
• U’RenJMLutzoniFMiadlikowskaJArnoldAE. 2010. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microb Ecol 60:340–53, doi:10.1007/s00248-010-9698-2
   PubMed Web of Science ®Google Scholar
• VilgalysRHesterM. 1990. Rapid genetic identifcation and mapping of enzymatically amplifed ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246.
   PubMed Web of Science ®Google Scholar
• WangBQiuY-L. 2006. Phylogenetic distribution and evolution of mycorrhiza in land plants. Mycorrhiza 16: 299–363, doi:10.1007/s00572-005-0033-6
   PubMed Web of Science ®Google Scholar
• WangZNilssonRHLopez-GiraldezFZhuangWYDaiYCJohnstonPRTownsendJP. 2011. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. PLoS ONE 6: e19039, doi:10.1371/journal.pone.0019039
   Google Scholar
• WhiteTJBrunsTLeeSBTaylorJW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: InnisMAGelfandDHSninskyJJWhiteTJ, eds. PCR protocols: a guide to methods and application. San Diego, California: Academic press. p 315–322.
   Google Scholar
• WintherJLFriedmanWE. 2007. Arbuscular mycorrhizal symbionts in Botrychium (Ophioglossaceae). Am J Bot 94:1248–1255, doi:10.3732/ajb.94.7.1248
   Google Scholar
• XiaoQMcPhersonEGUstinSLGrismerME. 2000. A new approach to modeling tree rainfall interception. J Geophys Res 105:29173–88, doi:10.1029/2000JD900343
   Web of Science ®Google Scholar
• YuJHolderMT. 2012. SATé 2.0.3. http://phylo.bio.ku.edu/software/sate/sate.html
   Google Scholar
• ZhangYGuoLDLiuRJ. 2004. Arbuscular mycorrhizal fungi associated with common pteridophytes in Dujiangyan, southwest China. Mycorrhiza 14:25–30, doi:10.1007/s00572-003-0272-3
   PubMed Web of Science ®Google Scholar
• ZubekSPiatekKNaksPHeiseWWaydaMMleczkoP. 2010. Fungal root endophyte colonization of fern and lycophyte species from the Celaque National Park in Honduras. Am Fern J 100:126–136, doi:10.1640/0002-8444-100.2.126
   Google Scholar