An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales

Literature cited

• AbascalFZardoyaRPosadaD. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104–2105, doi:10.1093/bioinformatics/bti263
   PubMed Web of Science ®Google Scholar
• AltekarGDwarkadasSHuelsenbeckJPRonquistF. 2004. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415, doi:10.1093/bioinformatics/btg427
   PubMed Web of Science ®Google Scholar
• BakerRHDeSalleR. 1997. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst Biol 46:654–673, doi:10.1093/sysbio/46.4.654
   PubMed Web of Science ®Google Scholar
• BenjaminRK. 1959. The merosporangiferous Mucorales. Aliso 4:321–433.
   Google Scholar
• BenjaminRK. 1961. Addenda to “The merosporangiferous Mucorales”. Aliso 5:11–19.
   Google Scholar
• BenjaminRK. 1979. Zygomycetes and their spores. The whole fungus 2:573–622.
   Google Scholar
• BennyGL. 2005. Zygomycetes. Published on the Internet at http://www.zygomycetes.org
   Google Scholar
• BollbackJP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88, doi:10.1186/1471-2105-7-88
   PubMed Web of Science ®Google Scholar
• BrainAPRJeffriesPYoungTWK. 1982. Ultrastructure of septa in Tieghemiomyces californicus. Mycologia 74:173–181, doi:10.2307/3792883
   Google Scholar
• CafaroMJ. 1999. Baltomyces, a new genus of gut-inhabiting fungus in an isopod. Mycologia 91: 517–519, doi:10.2307/3761352
   Web of Science ®Google Scholar
• ChuangS-CHoH-MBennyGLeeC-F. 2013. Two new Ramicandelaber species from Taiwan. Mycologia 105: 320–334, doi:10.3852/11-219
   Web of Science ®Google Scholar
• DarribaDTaboadaGLDoalloRPosadaD. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772–772, doi:10.1038/nmeth.2109
   PubMed Web of Science ®Google Scholar
• EdgarRC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797, doi:10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• FarrDFLichtwardt RobertW. 1967. Some cultural and ultrastructural aspects of Smittium culisetae (Trichomycetes) from mosquito larvae. Mycologia 59:172–182, doi:10.2307/3756952
   Web of Science ®Google Scholar
• FelsensteinJ. 1974. The evolutionary advantage of recombination. Genetics 78:737–756.
   PubMed Web of Science ®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
• GoloboffPAFarrisJSKällersjöMOxelmanBRamírezMJSzumikCA. 2003. Improvements to resampling measures of group support. Cladistics 19:324–332, doi:10.1111/j.1096-0031.2003.tb00376.x
   Web of Science ®Google Scholar
• GoloboffPAFarrisJSNixonKC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774–786, doi:10.1111/j.1096-0031.2008.00217.x
   Web of Science ®Google Scholar
• GottliebAMLichtwardtRW. 2001. Molecular variation within and among species of Harpellales. Mycologia 93: 66–81, doi:10.2307/3761606
   Web of Science ®Google Scholar
• GruberARLorenzRBernhartSHNeuböckRHofackerIL. 2008. The Vienna RNA Websuite. Nucleic Acids Res 36:W70–W74, doi:10.1093/nar/gkn188
   PubMed Web of Science ®Google Scholar
• GuindonSGascuelO. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704, doi:10.1080/10635150390235520
   PubMed Web of Science ®Google Scholar
• HibbettDSBinderMBischoffJFBlackwellMCannonPFErikssonOEHuhndorfSJamesTKirkPMLückingRThorsten LumbschHLutzoniFMathenyPBMcLaughlinDJPowellMJRedheadSSchochCLSpataforaJWStalpersJAVilgalysRAimeMCAptrootABauerRBegerowDBennyGLCastleburyLACrousPWDaiYCGamsWGeiserDMGriffithGWGueidanCHawksworthDLHestmarkGHosakaKHumberRAHydeKDIronsideJEKõljalgUKurtzmanCPLarssonKHLichtwardtRLongcoreJMiadlikowskaJMillerAMoncalvoJMMozley-StandridgeSOberwinklerFParmastoEReebVRogersJDRouxCRyvardenLSampaioJPSchüsslerASugiyamaJThornRGTibellLUntereinerWAWalkerCWangZWeirAWeissMWhiteMMWinkaKYaoYJZhangN. 2007. A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509–547, doi:10.1016/j.mycres.2007.03.004
   PubMed Web of Science ®Google Scholar
• HuelsenbeckJPRonquistF. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755, doi:10.1093/bioinformatics/17.8.754
   PubMed Web of Science ®Google Scholar
• HumberRA. 2012. Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi. Mycotaxon 120:477–492, doi:10.5248/120.477
   Web of Science ®Google Scholar
• JamesTYKauffFSchochCLMathenyPBHofstetterVCoxCJCelioGGueidanCFrakerEMiadlikowskaJLumbschHTRauhutAReebVArnoldAEAmtoftAStajichJEHosakaKSungGHJohnsonDO’RourkeBCrockettMBinderMCurtisJMSlotJCWangZWilsonAWSchüsslerALongcoreJEO’DonnellKMozley-StandridgeSPorterDLetcherPMPowellMJTaylorJWWhiteMMGriffithGWDaviesDRHumberRAMortonJBSugiyamaJRossmanAYRogersJDPfisterDHHewittDHansenKHambletonSShoemakerRAKohlmeyerJVolkmann-KohlmeyerBSpottsRASerdaniMCrousPWHughesKWMatsuuraKLangerELangerGUntereinerWALückingRBüdelBGeiserDMAptrootADiederichPSchmittISchultzMYahrRHibbettDSLutzoniFMcLaughlinDJSpataforaJWVilgalysR. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822, doi:10.1038/nature05110
   PubMed Web of Science ®Google Scholar
• JeffriesPYoungTWK. 1979. Ultrastructure of septa in Dimargaris cristalligena R.K. Benjamin. J Gen Microbiol 111:303–311, doi:10.1099/00221287-111-2-303
   Google Scholar
• KeelingPJ. 2003. Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of Microsporidia. Fungal Genet Biol 38:298–309, doi:10.1016/S1087-1845(02)00537-6
   PubMed Web of Science ®Google Scholar
• KeelingPJLukerMAPalmerJD. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the Fungi. Mol Biol Evol 17:23–31, doi:10.1093/oxfordjournals.molbev.a026235
   PubMed Web of Science ®Google Scholar
• KuriharaYDegawaYTokumasuS. 2004. Two novel kickxellalean fungi, Mycoëmilia scoparia gen. sp. nov. and Ramicandelaber brevisporus sp. nov. Mycol Res 108: 1143–1152, doi:10.1017/S0953756204000930
   Google Scholar
• LeSQGascuelO. 2008. An improved general amino acid replacement matrix. Mol Biol Evol 25:1307–1320, doi:10.1093/molbev/msn067
   PubMed Web of Science ®Google Scholar
• LichtwardtRWCafaroMJWhiteMM. 2001. The Trichomycetes, fungal associates of arthropods. Revised edition. Published on the Internet: http://www.nhm.ku.edu/~fungi
   Google Scholar
• LiuYLHodsonMHallB. 2006. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol Biol 6:74, doi:10.1186/1471-2148-6-74
   Google Scholar
• LiuYLWhelenSHallBD. 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
• MaddisonWMaddisonD. 2011. Mesquite 2.75: a modular system for evolutionary analysis. ( http://mesquiteproject.org)
   Google Scholar
• MatternDSchlegelM. 2001. Molecular evolution of the small subunit ribosomal DNA in woodlice (Crustacea, Isopoda, Oniscidea) and implications for Oniscidean phylogeny. Mol Phylogenet Evol 18:54–65, doi:10.1006/mpev.2000.0861
   PubMed Web of Science ®Google Scholar
• MossST. 1975. Septal structure in the trichomycetes with special reference to Astreptonema gammari (Eccrinales). Trans Br Mycol Soc 65:115–127, doi:10.1016/S0007-1536(75)80187-2
   Web of Science ®Google Scholar
• MossSTLichtwardtRW. 1977. Zygospores of the Harpellales: an ultrastructural study. Can J Bot 55:3099–3110, doi:10.1139/b77-351
   Google Scholar
• MossSTYoungTWK. 1978. Phyletic considerations of the Harpellales and Asellariales (Trichomycetes, Zygomycotina) and the Kickxellales (Zygomycetes, Zygomycotina). Mycologia 70:944–963, doi:10.2307/3759130
   Web of Science ®Google Scholar
• MullerHJ. 1964. The relation of recombination to mutational advance. Mutat Res-Fund Mol M 1:2–9, doi:10.1016/0027-5107(64)90047-8
   Web of Science ®Google Scholar
• O’DonnellK. 1993. Fusarium and its near relatives. In: ReynoldsRTaylorJW, eds. The fungal holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics. Wallingford, United Kingdom: CAB International. p 225–233.
   Google Scholar
• O’DonnellKCigelnikEBennyGL. 1998. Phylogenetic relationships among the Harpellales and Kickxellales. Mycologia 90:624–639, doi:10.2307/3761222
   Web of Science ®Google Scholar
• OgawaYHayashiSDegawaYYaguchiY. 2001. Ramicandelaber, a new genus of the Kickxellales, Zygomycetes. Mycoscience 42:193–199, doi:10.1007/BF02464137
   Google Scholar
• OgawaYKuriharaYSudaAKusama EguchiKWatanabeKTokumasuS. 2005. Taxonomic position of the genus Ramicandelaber, Kickxellales, inferred from 18SrDNA. Nippon Kingakukai Kaiho 46.
   Google Scholar
• OmanSJWhiteMM. 2012. Extended studies of Baltomyces styrax in Idaho and expanded distribution of this isopod gut fungus in USA. Mycologia 104:313–320, doi:10.3852/11-204
   Web of Science ®Google Scholar
• OttMZolaJStamatakisAAluruS. 2007. Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. In: Proceedings of the 2007 ACM/IEEE conference on Supercomputing. ACM. 4 p.
   Google Scholar
• PeñaCWahlbergNWeingartnerEKodandaramaiahUNylinSFreitasAVLBrowerAVZ. 2006. Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data. Mol Phylogenet Evol 40:29–49, doi:10.1016/j.ympev.2006.02.007
   PubMed 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
• SaikawaM. 1989. Ultrastructure of the septum in Ballocephala verrucospora (Entomophthorales, Zygomycetes). Can J Bot 67:2484–2488, doi:10.1139/b89-318
   Google Scholar
• SaikawaMOguchiMRuizRFC. 1997a. Electron microscopy of two nematode-destroying fungi, Meristacrum asterospermum and Zygnemomyces echinulatus (Meristacraceae, Entomophthorales). Can J Bot 75:762–768, doi:10.1139/b97-086
   Google Scholar
• SaikawaMSugiuraKSatoH. 1997b. Electron microscopy of two trichomycetous fungi attached to the hindgut lining of pill bugs. Can J Bot 75:1479–1484, doi:10.1139/b97-862
   Google Scholar
• SchmittICrespoADivakarPKFankhauserJDHerman-SackettEKalbKNelsenMPNelsonNARivas-PlataEShimpADWidhelmTLumbschHT. 2009. New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23:35–40, doi:10.3767/003158509X470602
   PubMed Web of Science ®Google Scholar
• SchochCLSeifertKAHuhndorfSRobertVSpougeJLLevesqueCAChenWBolchacovaEVoigtKCrousPWMillerANWingfieldMJAimeMCAnKDBaiFYBarretoRWBegerowDBergeronMJBlackwellMBoekhoutTBogaleMBoonyuenNBurgazARBuyckBCaiLCaiQCardinaliGChaverriPCoppinsBJCrespoACubasPCummingsCDammUde BeerZWde HoogGSDel-PradoRDentingerBDiéguez-UribeondoJDivakarPKDouglasBDueñasMDuongTAEberhardtUEdwardsJEElshahedMSFliegerovaKFurtadoMGarcíaMAGeZWGriffithGWGriffithsKGroenewaldJZGroenewaldMGrubeMGryzenhoutMGuoLDHagenFHambletonSHamelinRCHansenKHarroldPHellerGHerreraCHirayamaKHirookaYHoHMHoffmannKHofstetterVHögnabbaFHollingsworthPMHongSBHosakaKHoubrakenJHughesKHuhtinenSHydeKDJamesTJohnsonEMJohnsonJEJohnstonPRJonesEBKellyLJKirkPMKnappDGKõljalgUKovácsGMKurtzmanCPLandvikSLeavittSDLiggenstofferASLiimatainenKLombardLLuangsa-ArdJJLumbschHTMagantiHMaharachchikumburaSSMartinMPMayTWMcTaggartARMethvenASMeyerWMoncalvoJMMongkolsamritSNagyLGNilssonRHNiskanenTNyilasiIOkadaGOkaneIOlariagaIOtteJPappTParkDPetkovitsTPino-BodasRQuaedvliegWRajaHARedeckerDRintoulTLRuibalCSarmiento-RamírezJMSchmittISchüßlerAShearerCSotomeKStefaniFOStenroosSStielowBStockingerHSuetrongSSuhSOSungGHSuzukiMTanakaKTedersooLTelleriaMTTretterEUntereinerWAUrbinaHVágvölgyiCVialleAVuTDWaltherGWangQMWangYWeirBSWeißMWhiteMMXuJYahrRYangZLYurkovAZamoraJCZhangNZhuangWYSchindelD. 2012. Nucle-arribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci 109:6241–6246, doi:10.1073/pnas.1117018109
   PubMed Web of Science ®Google Scholar
• ShimodairaH. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492–508, doi:10.1080/10635150290069913
   PubMed Web of Science ®Google Scholar
• ShimodairaHHasegawaM. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116, doi:10.1093/oxfordjournals.molbev.a026201
   Web of Science ®Google Scholar
• ShimodairaHHasegawaM. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247, doi:10.1093/bioinformatics/17.12.1246
   PubMed Web of Science ®Google Scholar
• SorensonMDFranzosaEA. 2007. TreeRot 3. Boston University.
   Google Scholar
• StamatakisA. 2006a. Phylogenetic models of rate heterogeneity: a high performance computing perspective. In: Parallel and distributed processing symposium 2006. IPDPS 2006. 20th International. IEEE. 8 p.
   Google Scholar
• StamatakisA. 2006b. 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
• StamatakisAHooverPRougemontJ. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758–771, doi:10.1080/10635150802429642
   PubMed Web of Science ®Google Scholar
• StöverBCMüllerKF. 2010. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7, doi:10.1186/1471-2105-11-7
   PubMed Web of Science ®Google Scholar
• SwoffordDL. 2003. PAUP* 4: phylogenetic analysis using parsimony (*and other methods). Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• TanabeYO’DonnellKSaikawaMSugiyamaJ. 2000. Molecular phylogeny of parasitic Zygomycota (Dimargaritales, Zoopagales) based on nuclear small subunit ribosomal DNA sequences. Mol Phylogenet Evol 16: 253–262, doi:10.1006/mpev.2000.0775
   Web of Science ®Google Scholar
• TanabeYSaikawaMWatanabeMMSugiyamaJ. 2004. Molecular phylogeny of Zygomycota based on EF-1α and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol Phylogenet Evol 30:438–449, doi:10.1016/S1055-7903(03)00185-4
   Web of Science ®Google Scholar
• TretterEDJohnsonEMWangYKandelPWhiteMM. 2013. Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: comparing MCM7, TSR1 and rRNA genes for single- and multigene analyses of the Kickxellomycotina. Persoonia 30:106–125, doi:10.3767/003158513X666394
   Google Scholar
• ValleLGCafaroMJ. 2008. First report of zygospores in Asellariales and new species from the Caribbean. Mycologia 100:122–131, doi:10.3852/mycologia.100.1.122
   Web of Science ®Google Scholar
• ValleLGSantamariaS. 2005. Zygospores as evidence of sexual reproduction in the genus Orphella. Mycologia 97:1335–1347, doi:10.3852/mycologia.97.6.1335
   Web of Science ®Google Scholar
• VilgalysRHesterM. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246.
   PubMed Web of Science ®Google Scholar
• WalkerWF. 1984. 5S ribosomal RNA sequences from Zygomycotina and evolutionary implications. Syst Appl Microbiol 5:448–456, doi:10.1016/S0723-2020(84)80002-8
   Web of Science ®Google Scholar
• WangYTretterELichtwardtRWWhiteMM. 2013. Overview of 75 y of Smittium research, establishing a new genus for Smittium culisetae and prospects for future revisions of the “Smittium” clade. Mycologia 105:90–111, doi:10.3852/11-311
   Web of Science ®Google Scholar
• WhislerHC. 1963. Observations on some new and unusual enterophilous Phycomycetes. Can J Bot 41:887–900, doi:10.1139/b63-074
   Google Scholar
• WhiteMM. 1999. Legerioides, a new genus of Harpellales in isopods and other Trichomycetes from New England, USA. Mycologia 91:1021–1030, doi:10.2307/3761634
   Web of Science ®Google Scholar
• WhiteMM. 2002. Taxonomic and molecular systematic studies of the Harpellales (Trichomycetes) toward understanding the diversity, evolution and dispersal of gut fungi [doctoral dissertation]. Lawrence: Univ. Kansas. 177 p.
   Google Scholar
• WhiteMM. 2006. Evolutionary implications of a rRNA-based phylogeny of Harpellales. Mycol Res 110:1011–1024, doi:10.1016/j.mycres.2006.06.006
   Google Scholar
• WhiteMMSiriALichtwardtRW. 2006a. Trichomycete insect symbionts in Great Smoky Mountains National Park and vicinity. Mycologia 98:333–352, doi:10.3852/mycologia.98.2.333
   Web of Science ®Google Scholar
• WhiteMMJamesTYO’DonnellKCafaro MatíasJTanabeYSugiyamaJ. 2006b. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98: 872–884, doi:10.3852/mycologia.98.6.872
   PubMed Web of Science ®Google Scholar
• WhiteTJBrunsTDLeeSTaylorJW. 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
• WilgenbuschJCWarrenDLSwoffordDL. 2004. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference.
   Google Scholar
• WilliamRTStrongmanDB. 2012. Two new genera of fungal trichomycetes, Bactromyces and Laculus (Harpellales), from Nova Scotia, Canada. Botany 90:101–111, doi:10.1139/b11-086
   Google Scholar
• YoungTWK. 1969. Ultrastructure of aerial hyphae in Linderina pennispora. Ann Bot 33:211–216.
   Web of Science ®Google Scholar