Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha
Tài liệu tham khảo
Alfaro, 2003, Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence, Molecular Biology and Evolution, 20, 255, 10.1093/molbev/msg028
Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F, 2009. A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Systematic Biology, in press.
Arx, 1975, A re-evaluation of the bitunicate ascomycetes with keys to families and genera, Studies in Mycology, 9, 1
Barr, 1979, A classification of Loculoascomycetes, Mycologia, 71, 935, 10.2307/3759283
Birky, 2001, The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models, Annual Review of Genetics, 35, 125, 10.1146/annurev.genet.35.102401.090231
Coppins, 1989, Notes on the Arthoniaceae in the British Isles, Lichenologist, 21, 195, 10.1017/S0024282989000435
2006, Myconet, 12, 1
Eriksson, 1993, Outline of the Ascomycetes — 1993, Systema Ascomycetum, 12, 51
Eriksson, 1997, Supraordinal taxa of Ascomycota, Myconet, 1, 1
Follmann, 2003, Lichenicolous fungi occurring on Roccellaceae (Arthoniales). I. New species from South America, Journal of the Hattori Botanical Laboratory, 94, 261
Gargas, 1995, Multiple origins of lichen symbioses in fungi suggested by SSUrDNA phylogeny, Science, 268, 1492, 10.1126/science.7770775
Grube, 1998, Classification and phylogeny in the Arthoniales (lichenized ascomycetes), Bryologist, 101, 377, 10.1639/0007-2745(1998)101[377:CAPITA]2.0.CO;2
Grube, 1996, Studies on some species of Arthothelium occurring in the western Mediterranean, Lichenologist, 28, 15, 10.1006/lich.1996.0003
Grube, 1995, A preliminary account of the lichenicolous Arthonia species with reddish, K+ reactive pigments, Lichenologist, 27, 25, 10.1006/lich.1995.9999
Hafellner, 1988, Principles of classification and main taxonomic groups, 41
Hawksworth, 1986, The names of accepted orders of ascomycetes, Systema Ascomycetum, 5, 175
Hawksworth, 1995
Henssen, 1974
Hibbett, 2007, A higher-level phylogenetic classification of the Fungi, Mycological Research, 111, 509, 10.1016/j.mycres.2007.03.004
Hofstetter, 2007, Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota), Molecular Phylogenetics and Evolution, 44, 412, 10.1016/j.ympev.2006.10.016
Huelsenbeck, 2001, MRBAYES: Bayesian inference of phylogeny, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754
Kirk, 2001
Kjer, 1995, Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs, Molecular Phylogenetics and Evolution, 4, 314, 10.1006/mpev.1995.1028
Körber, 1855, Systema Lichenum Germaniae, Die Flechten Deutschlands, mikroskopisch geprüft, kritisch gesichtet, charakteristisch beschrieben und systematisch geordnet, Breslau Verlag von Trewendt & Granier
Lawrey, 2003, Lichenicolous fungi: interactions, evolution, and biodiversity, Bryologist, 106, 80, 10.1639/0007-2745(2003)106[0080:LFIEAB]2.0.CO;2
Lee, 1993, Uniparental inheritance and replacement of mitochondrial DNA in Neurospora tetrasperma, Genetics, 134, 1063, 10.1093/genetics/134.4.1063
Liu, 1999, Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit, Molecular Biology and Evolution, 16, 1799, 10.1093/oxfordjournals.molbev.a026092
Luttrell, 1973, Loculoascomycetes, 59
Lutzoni, 2004, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits, American Journal of Botany, 91, 1446, 10.3732/ajb.91.10.1446
Maddison, 2002
Mallet, 2005, Hybridization as an invasion of the genome, Trends in Ecology and Evolution, 20, 229, 10.1016/j.tree.2005.02.010
Mason-Gamer, 1996, Testing for phylogenetic conflict among molecular datasets in the tribe Triticeae (Gramineae), Systematic Biology, 45, 524, 10.1093/sysbio/45.4.524
Matzer, 1996
Miadlikowska, 2000, Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal DNA data, International Journal of Plant Sciences, 161, 925, 10.1086/317568
Miadlikowska, 2002, Pseudocyphellaria perpetua, a new lichen from Western North America, Bryologist, 105, 1, 10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2
Myllys, 1998, A comparison of SSU rDNA data and morphological data in Arthoniales (Euascomycetes) phylogeny, Bryologist, 101, 70, 10.1639/0007-2745(1998)101[70:ACOSRD]2.0.CO;2
Myllys, 1999, Applicability of ITS data in Roccellaceae (Arthoniales, Euascomycetes) phylogeny, Lichenologist, 31, 461, 10.1017/S0024282999000626
Nylander, 1863, Lichenes, Annales des Sciences Naturelles, Botanique, sér, 4, 286
Pentecost, 1983, Key to Opegrapha in Great Britain, British Lichen Society Bulletin, 53, 27
Pentecost, 1992, Opegrapha, 404
Poelt, 1973, Classification, 599
Posada, 1998, Modeltest: testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817
Redinger, 1938, Restitution und kritische Revision der Flechtengattungen Enterographa Fée und Sclerophyton Eschw, Feddes Repertorium specierum novarum regni vegetabilis, 43, 49, 10.1002/fedr.19380430103
Rehner, 1994, Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences, Mycological Research, 98, 625, 10.1016/S0953-7562(09)80409-7
Reich, 1966, Replication and inheritance of mitochondrial DNA, Proceedings of the National Academy of Sciences USA, 55, 1600, 10.1073/pnas.55.6.1600
Rieseberg, 1991, Phylogenetic consequences of cytoplasmic gene flow in plants, Evolutionary Trends in Plants, 5, 65
Rodríguez, 1990, The general stochastic model of nucleotide substitution, Journal of Theoretical Biology, 142, 485, 10.1016/S0022-5193(05)80104-3
Röhr, 1999, Recombination: organelle DNA of plants and fungi: inheritance and recombination, 39, 10.1007/978-3-642-59940-8_2
Ronquist, 2003, MRBAYES 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180
Schneider, 1898
Smith JE, Sowerby J, 1807. English Botany, or Coloured Figures of British Plants with Their Essential Characters, Synonymes and Places of Growth. Vol. 25. Richard Taylor and Co., London, tab. 1790.
Sparrius, 2004, A monograph of Enterographa and Sclerophyton, Bibliotheca Lichenologica, 89, 1
Spatafora, 2006, A five-gene phylogeny of Pezizomycotina, Mycologia, 98, 1018, 10.3852/mycologia.98.6.1018
Staiger, 2006, Phylogeny and phenotypic variation in the lichen family Graphidaceae (Ostropomycetidae, Ascomycota), Mycological Research, 110, 765, 10.1016/j.mycres.2006.05.003
Stamatakis, 2005, Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, 21, 456, 10.1093/bioinformatics/bti191
Swofford, 2002
Tehler, 1983, The genera Dirina and Roccellina, Opera Botanica, 70, 1
Tehler, 1990, A new approach to the phylogeny of Euascomycetes with a cladistic outline of Arthoniales focussing on Roccellaceae, Canadian Journal of Botany, 68, 2458, 10.1139/b90-312
Tehler, 1993, Schismatomma and three new or reinstated genera, a reassessment of generic relationships in Arthoniales, Cryptogamic Botany, 3, 139
Tehler, 1995, Arthoniales phylogeny as indicated by morphological and rDNA sequence data, Cryptogamic Botany, 5, 82
Tehler, 1995, Morphological data, molecular data, and total evidence in phylogenetic analysis, Canadian Journal of Botany (Supp 1), 73, 667, 10.1139/b95-309
Tehler, 1997, The phylogeny of Lecanactis (Opegraphaceae), Lichenologist, 29, 397, 10.1006/lich.1997.0095
Tehler, 2007, Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota), Cladistics, 23, 1, 10.1111/j.1096-0031.2007.00156.x
Torrente, 1989, La familia Opegraphaceae en el área Mediterránea de la Península Ibérica y norte de Africa, Bibliotheca Lichenologica, 32, 1
Tsitrone, 2003, A model for chloroplast capture, Evolution, 57, 1776, 10.1111/j.0014-3820.2003.tb00585.x
Vilgalys, 1990, Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species, Journal of Bacteriology, 172, 4238, 10.1128/jb.172.8.4238-4246.1990
Yoshimura, 2002, Isolation and culture of lichen photobionts and mycobionts, 3
Zoller, 1999, PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes, Lichenologist, 31, 511, 10.1017/S0024282999000663