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Otalora, M. A. G., Martinez, I., Molina, C., Aragon, G., and Lutzoni, F. 2008. Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae). Taxon (in press).

Savic, S., Tibell, L., Gueidan, C., and Lutzoni, F. 2008. Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera. Mycological Research (in press).

Gaya, E., Navarro-Rosinés, P., Llimona, X., Hladun, N., and Lutzoni, F. 2008. Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes). Mycological Research 112:528-546.
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Amtoft, A., Lutzoni, F. and Miadlikowska, J. 2008. Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North America. The Bryologist 111:1-40.
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Gueidan, C., Roux, C., and Lutzoni, F. 2007. Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Eurotiomycetes, Ascomycota). Mycological Research 111:1145-1168.
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Arnold, A. E., Henk, D. A., Eells, R. L., Lutzoni, F. and Vilgalys, R. 2007. Diversity and phylogenic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99:185-206.
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Litaker, R. W., Vandersea, M. W., Kibler, S. R., Reece, K. S., Stokes, N. A., Lutzoni, F. M., Yonish, B. A., Black, M. N. D., and Tester, P. A. 2007. Recognizing dinoflagellate species using ITS rDNA sequences. Journal of Phycology 43:344-355.
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Kauff, F., Cox, C., and Lutzoni, F. 2007. WASABI: An Automated Sequence Processing
System for Multi-Gene Phylogenies. Systematic Biology 56:523-531.
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Hofstetter, V., Miadlikowska, J., Kauff, F., and Lutzoni, F. 2007. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota). Molecular Phylogenetics and Evolution 44:412-426.
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Hibbett, D. S., Binder, M., Bischoff, J. F., Blackwell, M., Cannon, P. F., Eriksson, O., Huhndorf, S., James, T., Kirk, P. M., Lücking, R., Lumbsch, T., Lutzoni, F., Matheny, P. B., McLaughlin, D. J., Powell, M. J., Redhead, S., Schoch, C. L., Spatafora, J. W., Stalpers, J. A., Vilgalys, R., Aime, M. C., Aptroot, A., Bauer, R., Begerow, D., Benny, G. L., Castlebury, L. A., Crous, P. W., Dai, Y.- C., Gams, W., Geiser, D. M., Griffith, G. W., Gueidan, C., Hawksworth, D. L., Hestmark, G., Hosaka, K., Humber, R. A., Hyde, K., Koljalg, U., Kurtzman, C. P., Larsson, K.-H., Lichtward, R., Longcore, J., Miadlikowska, J., Miller, A., Monclavo, J.-M., Mozley- Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J. D., Roux, C., Ryvarden, L., Sampaio, J. P., Schuessler, A., Sugiyama, J., Thorn, R. G., Tibell, L., Untereiner, W. A., Walker, C., Wang, Z., Weir, A., Weiss, M., White, M., Winka, K., Yao, Y.-J., Zhang, N. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111:509-547.
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Rydholm, C., Dyer, P. S., and Lutzoni, F. 2007. DNA sequence characterization and
molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri. Eukaryotic Cell 6:868-874.
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Reeb, V., Haugen, P., Bhattacharya, D. and Lutzoni, F. 2007. Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease. Journal of Molecular Evolution 64:285-298.
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Higgins, K. L., Arnold, A. E., Miadlikowska, J. M., Sarvate, S. D., and Lutzoni, F. 2007. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Molecular Phylogenetics and Evolution 42:543-555.
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Arnold, A.E. and Lutzoni, F. 2007. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541-549.
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Miadlikowska, J., Kauff, F., Hofstetter, V., Fraker, E., Grube, M., Hafellner, J., Reeb, V., Hodkinson, B. P., Kukwa, M., Lücking, R., Hestmark, G., Garcia Otalora, M., Rauhut, A., Büdel, B., Scheidegger, C., Timdal, E., Stenroos, S., Brodo, I., Perlmutter, G., Ertz, D., Diederich, P., Lendemer, J. C., May, P., Schoch, C. L., Arnold, A. E., Gueidan, C., Tripp, E., Yahr, R., Robertson, C., Lutzoni, F. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98:1088-1103.
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Geiser, D. M., Gueidan, C., Miadlikowska, J., Lutzoni, F., Kauff, F., Hofstetter, V., Fraker, E., Schoch, C. L., Tibell, L., Untereiner, W. A., Aptroot, A. 2006. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 98:1053-1064.
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Spatafora, J.W., Johnson, D., Sung, G.-H., Hosaka, K., O’Rourke, B., Serdani, M., Spotts, R., Lutzoni, F., Hofstetter, V., Fraker, E., Gueidan, C., Miadlikowska, J., Reeb, V., Lumbsch, T., Lücking, R., Schmitt, I., Aptroot, A., Roux, C., Miller, A., Geiser, D., Hafellner, J., Hestmark, G., Arnold, A.E., Büdel, B., Rauhut, A., Hewitt, D., Untereiner, W., Cole, M.S., Scheidegger, C., Schultz, M., Sipman., H. and Schoch, C. 2006. A five-gene phylogenetic analysis of the Pezizomycotina. Mycologia 98:1018-1028.
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James, T.Y., Kauff, F., Schoch, C., Matheny, B., Hofstetter, V., Cox, C.J., Celio, G., Guiedan, C., Fraker, E., Miadlikowska, J., Lumbsh, T., Rauhut, A., Reeb, V., Arnold, A., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schueller, A., Longcore, J.E., O Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, D.M., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., Mclaughlin, D.J., Spatafora, J.W., Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822.
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Rydholm, C., Szakacs, G., and Lutzoni, F. 2006. Low genetic variation and no detectable population structure in Aspergillus fumigatus compared to closely related Neosartorya species. Eukaryotic Cell 5:650-657.
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Fernández, F. A., Miller, A. N., Huhndorf, S. M., Lutzoni, F. M., and Zoller, S. 2006. Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa. Mycologia 98:121-130.
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Bhattacharya, D., Reeb, V., Simon, D., and Lutzoni, F. 2005. Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. BMC Evolutionary Biology 5:68.
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O’Brien, H., Miadlikowska, J., and Lutzoni, F. 2005. Assessing host specialization in symbiotic Cyanobacteria associated with four closely related species of the lichen fungus Peltigera. European Journal of Phycology 40:363-378.
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Paoletti, M., Rydholm, C., Schwier, E., Anderson, M. J., Szakacs, G., Lutzoni, F., Debeaupuis, J.-P, Latgé, J.-P., Denning, D. W., Dyer, P. S. 2005. Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus. Current Biology 15:1242-1248.
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Lutzoni, F., Kauff, F., Cox, J. C., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T. Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A. E., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G.-H., Lücking, R., Lumbsch, T., O'Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hansen, K., Harris, R. C., Hosaka, K., Lim, Y.-W., Matheny, B., Nishida, H., Pfister, D., Rogers, J., Rossman, A., Schmitt, I., Sipman, H., Stone, J., Sugiyama, J., Yahr, R., and Vilgalys, R. 2004. Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits. American Journal of Botany 91:1446-1480.
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Reeb, V., Lutzoni, F. and Roux, C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the Pezizomycotina (euascomycetes, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Molecular Phylogenetics and Evolution 32:1036-1060.
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Miadlikowska, J. and Lutzoni F. 2004. Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits. American Journal of Botany 91:449-464 (journal cover).
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Haugen, P., Reeb, V., Lutzoni, F., Bhattacharya, D. 2004. The evolution of homing endonuclease genes and group I introns in nuclear rDNA. Molecular Biology and Evolution 21:105-116.
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Taylor, J. W., Spatafora, J., O’Donnell, K., Lutzoni, F., James, T., Hibbett, D. S., Geiser, D., Bruns, T. D. and Blackwell, M. 2004. The Fungi. Pp. 171-194 In: Assembling the Tree of Life (J. Cracraft and M. J. Donoghue, eds.). Oxford University Press, Oxford, UK.

Søchting, U., and Lutzoni, F. 2003. Molecular phylogenetic studies at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae). Mycological Research 107:1266-1276.
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Miadlikowska, J., Lutzoni, F. , Goward, T. , Zoller, S. , and Posada, D. 2003. New approach to an old problem: Incorporating signal from gap-rich regions of ITS and nrDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex. Mycologia 95:1181-1203 (journal cover).
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Zoller, S., and Lutzoni, F. 2003. Slow algae, fast fungi: Exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa. Molecular Phylogenetics and Evolution 29:629-640.
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Gaya, E., Lutzoni, F., Zoller, S. and Navarro-Rosinés, P. 2003. Phylogenetic study of Fulgensia and allied Caloplaca, and Xanthoria species (Teloschistaceae, lichen-forming Ascomycota). American Journal of Botany 90:1095-1103.
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McDonald, T., Miadlikowska, J. and Lutzoni, F. 2003. The lichen genus Sticta in the Great Smoky Mountains: A phylogenetic study of morphological, chemical, and molecular data. The Bryologist 106:61-79 (journal cover).
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Alfaro, M, Zoller, S., and Lutzoni, F. 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 20:255-266.
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Kauff, F. and Lutzoni, F. 2002. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Molecular Phylogenetics and Evolution 25:138-156.
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Barker, F. K., and Lutzoni, F. 2002. The utility of the incongruence length difference test. Systematic Biology 51:625-637.
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Pagel, M. and Lutzoni, F. 2002. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. Pp. 151-164. In: Biological Evolution and Statistical Physics. M. Laessig and A. Valleriani (Eds.), Springer Verlag, Berlin, Germany.
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Lutzoni, F. 2002. Lichens. In: Encyclopedia of Evolution. Vol. 2. M. Pagel (Ed.), Oxford University Press, Oxford, UK.

Redhead, S. A., Lutzoni, F., Moncalvo, J.-M. and Vilgalys, R . 2002. Phylogeny of agarics: partial systematics solutions for core omphalinoid genera in the Agaricales (Euagarics). Mycotaxon 83:19-57.
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Redhead, S. A., Moncalvo, J.-M., Vilgalys, R. and Lutzoni, F. 2002. Phylogeny of agarics: partial systematics solutions for bryophilous omphalinoid agarics outside of the Agaricales (Euagarics). Mycotaxon 82: 151-168.
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Miadlikowska, J., McCune, B. and Lutzoni, F. 2002. Pseudocyphellaria perpetua, a new lichen from Western North America. The Bryologist 105:1-10.
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Lutzoni, F., Pagel, M., Reeb, V. 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937-940.
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O'Donnell, K., Lutzoni, F., Ward, T., and Benny G. 2001. Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia 93:286-296.
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Bhattacharya, D., Lutzoni, F., Reeb, V., Simon, D., Fernandez, F. 2000. Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. Molecular Biology and Evolution 17:1971-1984.
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Lutzoni, F., Wagner, P., Reeb V., and Zoller, S. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49:628-651.
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Downloadable PC version of INAASE(ZIP file)
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Downloadable Insect 16S mtrDNA data set (Stuffit file)
Downloadable Crocodile 12S mtrDNA data set (Stuffit file)

Miadlikowska, J., and Lutzoni, F. 2000. Phylogenetic revision of the genus Peltigera (lichen-forming ascomycetes) based on morphological, chemical and large subunit nuclear ribosomal DNA data. International Journal of Plant Sciences 161:925-958.
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Wu, Q.-X., Mueller, G. M., Lutzoni, F. M., Huang, Y.-Q., and Guo, S.-Y. 2000. Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (Fungi) as inferred from ITS sequences of nuclear ribosomal RNA ITS sequences. Molecular Phylogenetics and Evolution 17:37-47.
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Moncalvo, J.-M., Lutzoni, F. M., Rehner, S. A., Johnson, J., and Vilgalys, R. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Systematic Biology 49:278-305.
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Zoller, S., Lutzoni F., and Scheidegger, C. 1999. Genetic variability within and among populations of the threatened foliose lichen Lobaria pulmonaria (L.) Hoffm. in Switzerland. Molecular Ecology 8:2049-2060.
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Lutzoni, F., and Barker, F. K. 1999. Sampling confidence envelopes of phylogenetic trees for combinability testing: A reply to Rodrigo. Systematic Biology 48: 596-603.
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Fernandez, A.,Lutzoni, F. and Huhndorf, S. M. 1999. Teleomorph-anamorph connections: the new pyrenomycetous genus Carpoligna and its Pleurothecium anamorph. Mycologia 91:251-262.
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Kranner, I., and Lutzoni, F. 1999. Evolutionary consequences of transition to a lichen symbiotic state and physiological adaptation to oxidative damage associated with poikilohydry. 591-628. In: Plant response to environmental stresses: From phytohormones to genome reorganization. H. R. Lerner (ed.). Marcel Dekker, New York.

Lutzoni, F., and Pagel, M. 1997. Accelerated evolution as a consequence of transitions to mutualism. Proc. Natl. Acad. Sci. 94:11422-11427.
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Lutzoni, F. 1997. Phylogeny of lichen- and non lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Systematic Biology 46:373-406 (journal cover).
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Lutzoni, F., and Vilgalys, R. 1995. Integration of morphological and molecular datasets in estimating fungal phylogenies. Canadian Journal of Botany 73(Suppl. 1):S649-S659.
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Lutzoni, F., and Vilgalys, R. 1995. Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichenized fungi. Special Issue of Cryptogamic Botany 5:82-97.

Lutzoni, F., and Brodo, I. M. 1995. A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized Ascomycotina). Systematic Botany 20: 224-258.
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Lutzoni, F. 1994. Ionaspis alba (Ascomycotina, Hymeneliaceae), a new lichen species from eastern North America. The Bryologist 97(4):393-395.
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Lutzoni, F. M. and Brodo, I. M. 1994. Proposal to conserve the name Gyalecta suaveolens Fr. (lichenized Ascomycota) with a conserved type. Taxon 43:657-659.
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Grandtner, M. M. and Lutzoni, F. 1991. References on the vegetation of Québec. Excerpta Botanica Sec. B. Bd. 29(1):1-24.

Sirois, L., Lutzoni, F. and Grandtner, M. M. 1988. Les lichens sur serpentine et amphibolite du plateau du mont Albert, Gaspésie, Québec. Canadian Journal of Botany 66:851-862.
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