Francois M. Lutzoni | Scholars@Duke

Francois M. Lutzoni
Professor of Biology

Current Appointments & Affiliations

Professor of Biology, Biology, Trinity College of Arts & Sciences 2015

Contact Information

357 Bio Sci Bldg, Durham, NC 27708
Box 90338, Durham, NC 27708-0338
francois.lutzoni@duke.edu (919) 660-7261
Lab website

Background
Education, Training, & Certifications
- Ph.D., Duke University 1995
- M.S., Ottawa University 1990
- B.S., Grinnel College and University of Laval 1987
Duke Appointment History
- Associate Professor of Biology, Biology, Trinity College of Arts & Sciences 2005 - 2015
- Assistant Professor of Biology, Biology, Trinity College of Arts & Sciences 2001 - 2004
Recognition
In the News
- JUL 22, 2016 New York Times
  
  Two's company, three's a lichen?
- SEP 15, 2015
  
  Lutzoni Receives NSF Grant for Fungal Genealogy
Awards & Honors
Expertise
Global Scholarship
- Research
Research
Selected Grants
- Molecular Mycology and Pathogenesis Training Program awarded by National Institutes of Health 2019 - 2024
- Collaborative Research: Leveraging historical collections and new surveys to characterize foundational shifts in vital symbioses in the threatened Arctic awarded by National Science Foundation 2020 - 2023
- Digitization TCN: Collaborative Research: Building a global consortium of bryophytes and lichens: keystones of cryptobiotic communities awarded by National Science Foundation 2020 - 2023
- Spatio-temporal factors shaping symbiotic networks: a case study with cyanolichens awarded by National Science Foundation 2019 - 2022
- Collaborative Research: Filling the largest phylogenetic void of the fungal genealogy of life and integrating symbiotic, environmental and physiological data awarded by National Science Foundation 2016 - 2021
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- SG: Combining phylogenetic and network analyses for the study of symbiotic systems: a case study using lichens awarded by National Science Foundation 2016 - 2019
- DISSERTATION RESEARCH: Assessing the Importance of Trophic Lability for Fungal Endophytism Using the Moss Dicranum scoparium and its Associated Fungi awarded by National Science Foundation 2017 - 2018
- Dimensions: Collaborative Research: An Interdisciplinary Study of Hyperdiverse Endophytic Fungi and Their Function in Boreal Forests awarded by National Science Foundation 2011 - 2016
- Digitization TCN: Collaborative Research: North American Lichens and Bryophytes: Sensitive Indicators of Environmental Quality and Change awarded by National Science Foundation 2011 - 2016
- REVSYS: Phylogenetic Revision of the Lichen-Forming Genus Peltigera (Ascomycota): Dissentangling Cryptic Speciation, Phenotypic Plasticity, and Hybridization awarded by National Science Foundation 2010 - 2015
- A multilocus phylogenetic study of the Teloschistales (Ascomycota) and the evolution of symbiotic systems awarded by National Science Foundation 2009 - 2013
- Collaborative Research: Assembling the Fungal Tree of Life: Resolving the Evolutionary History of the Fungi awarded by National Science Foundation 2007 - 2012
- DISSERTATION RESEARCH: A phylogenetic characterization of the lichen microbiome awarded by National Science Foundation 2010 - 2012
- Collaborative Research: Hyperdiverse endolichenic and endophytic fungi: A large-scale, multi-gene phylogenetic survey and estimation of trophic transition networks awarded by National Science Foundation 2007 - 2010
- Dissertation Research: Molecular phylogeny of Verrucariales (Fungi, Ascomycota) and the evolution of nutritional modes. awarded by National Science Foundation 2005 - 2007
- ATOL: Collaborative Research: Assembling the Fungal Tree of Life awarded by National Science Foundation 2003 - 2007
- Career: Using Multigene Phylogenies to Solve Early Euascomycete Relationships awarded by National Science Foundation 2001 - 2007
- Collaborative Research: Assembling the fungal tree of life awarded by National Science Foundation 2003 - 2006
- DISSERTATION RESEARCH: Phylogenetics of Nostoc and the Evolution of Specificity and Selectivity in Cyanolichen Symbioses awarded by National Science Foundation 2003 - 2005
- DISSERTATION RESEARCH: Phylogeny, reconstruction of ancestral states and divergence times of lichen-forming fungi Acarosporaceae and Acrospora (Valerie Reeb) awarded by National Science Foundation 2001 - 2004
- Phylogeny in the Genus Omphalina and the Evolutionary Consequences of Mutualism awarded by National Science Foundation 1994 - 1996
External Relationships
- Elsevier
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Cornet, L., N. Magain, D. Baurain, and F. Lutzoni. “Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens (Accepted).” Molecular Phylogenetics and Evolution 162 (September 1, 2021). https://doi.org/10.1016/j.ympev.2021.107100.
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  - Crous, P. W., M. Hernández-Restrepo, R. K. Schumacher, D. A. Cowan, G. Maggs-Kölling, E. Marais, M. J. Wingfield, et al. “New and Interesting Fungi. 4.” Fungal Systematics and Evolution 7 (June 2021): 255–343. https://doi.org/10.3114/fuse.2021.07.13.
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  - Oita, Shuzo, Alicia Ibáñez, François Lutzoni, Jolanta Miadlikowska, József Geml, Louise A. Lewis, Erik F. Y. Hom, Ignazio Carbone, Jana M. U’Ren, and A Elizabeth Arnold. “Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale.” Communications Biology 4, no. 1 (March 9, 2021): 313. https://doi.org/10.1038/s42003-021-01826-7.
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  - Haridas, S., R. Albert, M. Binder, J. Bloem, K. LaButti, A. Salamov, B. Andreopoulos, et al. “101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.” Studies in Mycology 96 (June 2020): 141–53. https://doi.org/10.1016/j.simyco.2020.01.003.
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  - Magain, N., B. Goffinet, A. Simon, J. S. S. Seelan, I. D. Medeiros, F. Lutzoni, and J. Miadlikowska. “Peltigera serusiauxii (Lecanoromycetes, Ascomycota), a new species from Papua New Guinea and Malaysia.” Plant and Fungal Systematics 65, no. 1 (June 1, 2020): 139–46. https://doi.org/10.35535/pfsyst-2020-0009.
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  - Miadlikowska, J., N. Magain, W. R. Buck, R. V. Castillo, G. T. Barlow, C. J. Pardo-De la Hoz, S. LaGreca, and F. Lutzoni. “Peltigera hydrophila (Lecanoromycetes, Ascomycota), a new semi-aquatic cyanolichen species from Chile.” Plant and Fungal Systematics 65, no. 1 (June 1, 2020): 210–18. https://doi.org/10.35535/pfsyst-2020-0016.
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  - Darnajoux, Romain, Nicolas Magain, Marie Renaudin, François Lutzoni, Jean-Philippe Bellenger, and Xinning Zhang. “Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests.” Proceedings of the National Academy of Sciences of the United States of America 116, no. 49 (December 2019): 24682–88. https://doi.org/10.1073/pnas.1913314116.
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  - U’Ren, Jana M., François Lutzoni, Jolanta Miadlikowska, Naupaka B. Zimmerman, Ignazio Carbone, Georgiana May, and A Elizabeth Arnold. “Host availability drives distributions of fungal endophytes in the imperilled boreal realm.” Nature Ecology & Evolution 3, no. 10 (October 2019): 1430–37. https://doi.org/10.1038/s41559-019-0975-2.
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  - Armaleo, Daniele, Olaf Müller, François Lutzoni, Ólafur S. Andrésson, Guillaume Blanc, Helge B. Bode, Frank R. Collart, et al. “The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.” Bmc Genomics 20, no. 1 (July 23, 2019): 605. https://doi.org/10.1186/s12864-019-5629-x.
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  - Carbone, Ignazio, James B. White, Jolanta Miadlikowska, A Elizabeth Arnold, Mark A. Miller, Nicolas Magain, Jana M. U’Ren, and François Lutzoni. “T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.” Microbiology Resource Announcements 8, no. 29 (July 18, 2019). https://doi.org/10.1128/mra.00328-19.
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  - Chagnon, P. L., N. Magain, J. Miadlikowska, and F. Lutzoni. “Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera.” Journal of Ecology 107, no. 4 (July 1, 2019): 1645–61. https://doi.org/10.1111/1365-2745.13207.
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  - Chen, Ko-Hsuan, Hui-Ling Liao, Jean-Philippe Bellenger, and François Lutzoni. “Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium.” Environmental Microbiology 21, no. 7 (July 2019): 2273–89. https://doi.org/10.1111/1462-2920.14605.
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  - Lutzoni, François, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A Elizabeth Arnold, et al. “Contemporaneous radiations of fungi and plants linked to symbiosis.” Nature Communications 9, no. 1 (December 21, 2018): 5451. https://doi.org/10.1038/s41467-018-07849-9.
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  - Miadlikowska, J., N. Magain, C. J. Pardo-De La Hoz, D. Niu, T. Goward, E. Sérusiaux, and F. Lutzoni. “Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision.” Plant and Fungal Systematics 63, no. 2 (December 1, 2018): 45–64. https://doi.org/10.2478/pfs-2018-0007.
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  - Hoz, C. J. P. D. L., N. Magain, F. Lutzoni, T. Goward, S. Restrepo, and J. Miadlikowska. “Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera.” Frontiers in Microbiology 9, no. NOV (November 16, 2018). https://doi.org/10.3389/fmicb.2018.02770.
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  - Korotkin, Hailee B., Rachel A. Swenie, Otto Miettinen, Jessica M. Budke, Ko-Hsuan Chen, François Lutzoni, Matthew E. Smith, and P Brandon Matheny. “Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.” American Journal of Botany 105, no. 11 (November 2018): 1869–87. https://doi.org/10.1002/ajb2.1183.
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  - Magain, N., C. Truong, T. Goward, D. Niu, B. Goffinet, E. Sérusiaux, O. Vitikainen, F. Lutzoni, and J. Miadlikowska. “Species delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in peltigera section peltigera (Lichenized ascomycota: Lecanoromycetes).” Taxon 67, no. 5 (October 1, 2018): 836–70. https://doi.org/10.12705/675.3.
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  - Lu, Jade, Nicolas Magain, Jolanta Miadlikowska, Jessica R. Coyle, Camille Truong, and François Lutzoni. “Bioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen-forming genus Peltigera.” American Journal of Botany 105, no. 7 (July 12, 2018): 1198–1211. https://doi.org/10.1002/ajb2.1119.
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  - Chagnon, P. L., N. Magain, J. Miadlikowska, and F. Lutzoni. “Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera.” Oecologia 187, no. 3 (July 2018): 767–82. https://doi.org/10.1007/s00442-018-4159-6.
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  - Chen, Ko-Hsuan, Hui-Ling Liao, A Elizabeth Arnold, Gregory Bonito, and François Lutzoni. “RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi.” The New Phytologist 218, no. 4 (June 2018): 1597–1611. https://doi.org/10.1111/nph.15092.
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  - Kauff, F., A. Bachran, M. Schultz, V. Hofstetter, F. Lutzoni, and B. Büdel. “Molecular data favours a monogeneric Peltulaceae (Lichinomycetes).” Lichenologist 50, no. 3 (May 1, 2018): 313–27. https://doi.org/10.1017/S0024282918000105.
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  - Magain, Nicolas, Jolanta Miadlikowska, Olaf Mueller, Michael Gajdeczka, Camille Truong, Asaf A. Salamov, Inna Dubchak, et al. “Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.” Molecular Phylogenetics and Evolution 117 (December 2017): 10–29. https://doi.org/10.1016/j.ympev.2017.08.013.
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  - Heiđmarsson, S., C. Gueidan, J. Miadlikowska, and F. Lutzoni. “Multi-locus phylogeny supports the placement of endocarpon pulvinatum within staurothele s. Str. (lichenised ascomycetes, eurotiomycetes, verrucariaceae).” Phytotaxa 306, no. 1 (May 5, 2017): 37–48. https://doi.org/10.11646/phytotaxa.306.1.3.
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  - Carbone, Ignazio, James B. White, Jolanta Miadlikowska, A Elizabeth Arnold, Mark A. Miller, Frank Kauff, Jana M. U’Ren, Georgiana May, and François Lutzoni. “T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.” Bioinformatics (Oxford, England) 33, no. 8 (April 2017): 1160–68. https://doi.org/10.1093/bioinformatics/btw808.
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  - Darnajoux, Romain, Xinning Zhang, Darcy L. McRose, Jolanta Miadlikowska, François Lutzoni, Anne M. L. Kraepiel, and Jean-Philippe Bellenger. “Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates.” The New Phytologist 213, no. 2 (January 2017): 680–89. https://doi.org/10.1111/nph.14166.
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  - Hestmark, G., F. Lutzoni, and J. Miadlikowska. “Photobiont associations in co-occurring umbilicate lichens with contrasting modes of reproduction in coastal Norway.” Lichenologist 48, no. 5 (September 1, 2016): 545–57. https://doi.org/10.1017/S0024282916000232.
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  - Nieuwenhuijzen, E. J. van, J. M. Miadlikowska, J. A. M. P. Houbraken, O. C. G. Adan, F. M. Lutzoni, and R. A. Samson. “Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni.” Studies in Mycology 85 (September 2016): 107–24. https://doi.org/10.1016/j.simyco.2016.11.008.
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  - Chagnon, Pierre-Luc, Jana M. U’Ren, Jolanta Miadlikowska, François Lutzoni, and A. E. Arnold. “Erratum to: Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.” Oecologia 181, no. 2 (June 2016): 633. https://doi.org/10.1007/s00442-016-3589-2.
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  - U’Ren, Jana M., Jolanta Miadlikowska, Naupaka B. Zimmerman, François Lutzoni, Jason E. Stajich, and A Elizabeth Arnold. “Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).” Molecular Phylogenetics and Evolution 98 (May 2016): 210–32. https://doi.org/10.1016/j.ympev.2016.02.010.
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  - Chagnon, Pierre-Luc, Jana M. U’Ren, Jolanta Miadlikowska, François Lutzoni, and A Elizabeth Arnold. “Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.” Oecologia 180, no. 1 (January 2016): 181–91. https://doi.org/10.1007/s00442-015-3457-5.
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  - Darnajoux, Romain, François Lutzoni, Jolanta Miadlikowska, and Jean-Philippe Bellenger. “Determination of elemental baseline using peltigeralean lichens from Northeastern Canada (Québec): Initial data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in Canada.” The Science of the Total Environment 533 (November 2015): 1–7. https://doi.org/10.1016/j.scitotenv.2015.06.030.
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  - Oono, Ryoko, Emilie Lefèvre, Anita Simha, and François Lutzoni. “A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).” Fungal Biology 119, no. 10 (October 2015): 917–28. https://doi.org/10.1016/j.funbio.2015.07.003.
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  - Gaya, Ester, Samantha Fernández-Brime, Reinaldo Vargas, Robert F. Lachlan, Cécile Gueidan, Martín Ramírez-Mejía, and François Lutzoni. “The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift.” Proceedings of the National Academy of Sciences of the United States of America 112, no. 37 (September 2015): 11600–605. https://doi.org/10.1073/pnas.1507072112.
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  - Chen, Ko-Hsuan, Jolanta Miadlikowska, Katalin Molnár, A Elizabeth Arnold, Jana M. U’Ren, Ester Gaya, Cécile Gueidan, and François Lutzoni. “Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.” Molecular Phylogenetics and Evolution 85 (April 2015): 117–30. https://doi.org/10.1016/j.ympev.2015.01.008.
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  - Gueidan, C., D. J. Hill, J. Miadlikowska, and F. Lutzoni. “Pezizomycotina: Lecanoromycetes,” January 1, 2015, 89–120. https://doi.org/10.1007/978-3-662-46011-5_4.
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  - Miadlikowska, Jolanta, Frank Kauff, Filip Högnabba, Jeffrey C. Oliver, Katalin Molnár, Emily Fraker, Ester Gaya, et al. “A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.” Molecular Phylogenetics and Evolution 79 (October 2014): 132–68. https://doi.org/10.1016/j.ympev.2014.04.003.
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  - Oono, Ryoko, François Lutzoni, A Elizabeth Arnold, Laurel Kaye, Jana M. U’Ren, Georgiana May, and Ignazio Carbone. “Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.” American Journal of Botany 101, no. 8 (August 15, 2014): 1362–74. https://doi.org/10.3732/ajb.1400141.
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  - Miadlikowska, Jolanta, David Richardson, Nicolas Magain, Bernard Ball, Frances Anderson, Robert Cameron, James Lendemer, Camille Truong, and François Lutzoni. “Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).” American Journal of Botany 101, no. 7 (July 11, 2014): 1141–56. https://doi.org/10.3732/ajb.1400267.
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  - Darnajoux, Romain, Jérôme Constantin, Jolanta Miadlikowska, François Lutzoni, and Jean-Philippe Bellenger. “Is vanadium a biometal for boreal cyanolichens?” The New Phytologist 202, no. 3 (May 2014): 765–71. https://doi.org/10.1111/nph.12777.
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  - Fernández-Brime, S., X. Llimona, F. Lutzoni, and E. Gaya. “Phylogenetic study of Diploschistes (lichen-forming Ascomycota: Ostropales: Graphidaceae), based on morphological, chemical, and molecular data.” Taxon 62, no. 2 (April 20, 2013): 267–80. https://doi.org/10.12705/622.10.
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  - McDonald, Tami R., Olaf Mueller, Fred S. Dietrich, and François Lutzoni. “High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.” Bmc Genomics 14 (April 4, 2013): 225. https://doi.org/10.1186/1471-2164-14-225.
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  - O’Brien, Heath E., Jolanta Miadlikowska, and François Lutzoni. “Assessing population structure and host specialization in lichenized cyanobacteria.” The New Phytologist 198, no. 2 (April 2013): 557–66. https://doi.org/10.1111/nph.12165.
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  - McDonald, T. R., E. Gaya, and F. Lutzoni. “Twenty-five cultures of lichenizing fungi available for experimental studies on symbiotic systems.” Symbiosis 59, no. 3 (March 1, 2013): 165–71. https://doi.org/10.1007/s13199-013-0228-0.
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  - Fernández Brime, S., X. Llimona, F. Lutzoni, and E. Gaya. “Phylogenetic study of Diploschistes (Graphidaceae, Ostropales, lichen-forming Ascomycota), based on morphological, chemical and molecular data (Accepted).” Taxon, 2013.
  - Hodkinson, B. P., J. L. Allen, L. Forrest, B. Goffinet, E. Sérusiaux, Ó. S. Andrésson, V. Miao, J. P. Bellenger, and F. Lutzoni. “Lichen-symbiotic Cyanobacteria have an alternative vanadium-dependent nitrogen fixation system (Submitted).” New Phytologist, 2013.
  - Gazis, R., J. Miadlikowska, F. Lutzoni, A. E. Arnold, and P. Chaverri. “Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes.” Molecular Phylogenetics and Evolution 65, no. 1 (October 2012): 294–304. https://doi.org/10.1016/j.ympev.2012.06.019.
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  - Green, M. S., B. Ball, F. Lutzoni, H. Zi-Min, and J. M. Lopez-Bautista. “TRENTEPOHLIALES (ULVOPHYCEAE, CHLOROPHYTA) FROM COASTAL SOUTH CAROLINA.” Journal of Phycology 48 (August 2012): S15–S15.
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  - Liwa, L., J. Miadlikowska, B. D. Redelings, K. Molnar, and F. Lutzoni. “Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic?” Bryologist 115, no. 2 (June 1, 2012): 265–77. https://doi.org/10.1639/0007-2745-115.2.265.
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  - Gaya, Ester, Filip Högnabba, Angela Holguin, Katalin Molnar, Samantha Fernández-Brime, Soili Stenroos, Ulf Arup, et al. “Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).” Molecular Phylogenetics and Evolution 63, no. 2 (May 2012): 374–87. https://doi.org/10.1016/j.ympev.2012.01.012.
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  - U’Ren, Jana M., François Lutzoni, Jolanta Miadlikowska, Alexander D. Laetsch, and A Elizabeth Arnold. “Host and geographic structure of endophytic and endolichenic fungi at a continental scale.” American Journal of Botany 99, no. 5 (May 2012): 898–914. https://doi.org/10.3732/ajb.1100459.
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  - Geml, József, Frank Kauff, Christian Brochmann, François Lutzoni, Gary A. Laursen, Scott A. Redhead, and D Lee Taylor. “Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).” Fungal Biology 116, no. 3 (March 2012): 388–400. https://doi.org/10.1016/j.funbio.2011.12.009.
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  - Hodkinson, Brendan P., Neil R. Gottel, Christopher W. Schadt, and François Lutzoni. “Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.” Environmental Microbiology 14, no. 1 (January 2012): 147–61. https://doi.org/10.1111/j.1462-2920.2011.02560.x.
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  - McDonald, Tami R., Fred S. Dietrich, and François Lutzoni. “Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.” Mol Biol Evol 29, no. 1 (January 2012): 51–60. https://doi.org/10.1093/molbev/msr123.
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  - Prieto, María, Isabel Martínez, Gregorio Aragón, Cécile Gueidan, and François Lutzoni. “Molecular phylogeny of Heteroplacidium, Placidium, and related catapyrenioid genera (Verrucariaceae, lichen-forming Ascomycota).” American Journal of Botany 99, no. 1 (January 2012): 23–35. https://doi.org/10.3732/ajb.1100239.
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  - Schmull, Michaela, Jolanta Miadlikowska, Monika Pelzer, Elfie Stocker-Wörgötter, Valerie Hofstetter, Emily Fraker, Brendan P. Hodkinson, et al. “Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota).” Mycologia 103, no. 5 (September 2011): 983–1003. https://doi.org/10.3852/10-234.
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  - Fernández-Brime, Samantha, Xavier Llimona, Katalin Molnar, Soili Stenroos, Filip Högnabba, Curtis Björk, François Lutzoni, and Ester Gaya. “Expansion of the Stictidaceae by the addition of the saxicolous lichen-forming genus Ingvariella.” Mycologia 103, no. 4 (July 2011): 755–63. https://doi.org/10.3852/10-287.
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  - Arnold, A. E., I. Carbone, F. Lutzoni, and G. May. “A multidimensional study of endophytic fungal diversity.” Ima Fungus 2, no. 1 (June 1, 2011): 2–4.
  - Miadlikowska, J., C. L. Schoch, S. A. Kageyama, K. Molnar, F. Lutzoni, and B. McCune. “Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure.” Bryologist 114, no. 2 (June 1, 2011): 392–400. https://doi.org/10.1639/0007-2745-114.2.392.
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  - Gaya, Ester, Benjamin D. Redelings, Pere Navarro-Rosinés, Xavier Llimona, Miquel De Cáceres, and François Lutzoni. “Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.” Mycologia 103, no. 2 (March 2011): 361–78. https://doi.org/10.3852/10-120.
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  - Joneson, Suzanne, Daniele Armaleo, and François Lutzoni. “Fungal and algal gene expression in early developmental stages of lichen-symbiosis.” Mycologia 103, no. 2 (March 2011): 291–306. https://doi.org/10.3852/10-064.
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  - Hestmark, Geir, Jolanta Miadlikowska, Frank Kauff, Emily Fraker, Katalin Molnar, and François Lutzoni. “Single origin and subsequent diversification of central Andean endemic Umbilicaria species.” Mycologia 103, no. 1 (January 2011): 45–56. https://doi.org/10.3852/10-012.
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  - Thüs, H., L. Muggia, S. Pérez-Ortega, S. E. Favero-Longo, S. Joneson, H. O’Brien, M. P. Nelsen, et al. “Revisiting photobiont diversity in the lichen family verrucariaceae (ascomycota).” European Journal of Phycology 46, no. 4 (January 1, 2011): 399–415. https://doi.org/10.1080/09670262.2011.629788.
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  - Crespo, A., F. Kauff, P. K. Divakar, R. del Prado, S. Pérez-Ortega, G. A. de Paz, Z. Ferencova, et al. “Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence.” Taxon 59, no. 6 (December 1, 2010): 1735–53. https://doi.org/10.1002/tax.596008.
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  - Otálora, Mónica A. G., Isabel Martínez, Heath O’Brien, M Carmen Molina, Gregorio Aragón, and François Lutzoni. “Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes).” Molecular Phylogenetics and Evolution 56, no. 3 (September 2010): 1089–95. https://doi.org/10.1016/j.ympev.2010.05.013.
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  - Otálora, Mónica A. G., Gregorio Aragón, M Carmen Molina, Isabel Martínez, and François Lutzoni. “Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota).” Mycologia 102, no. 2 (March 2010): 279–90. https://doi.org/10.3852/09-114.
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  - Prieto, María, Isabel Martínez, Gregorio Aragón, Mónica A. G. Otálora, and François Lutzoni. “Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.” Mycologia 102, no. 2 (March 2010): 291–304. https://doi.org/10.3852/09-168.
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  - U’Ren, J., F. Lutzoni, J. Miadlikowska, and A. E. Arnold. “Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.” Microbial Ecology 60 (2010): 340–53.
  - McLaughlin, David J., David S. Hibbett, François Lutzoni, Joseph W. Spatafora, and Rytas Vilgalys. “The search for the fungal tree of life.” Trends in Microbiology 17, no. 11 (November 2009): 488–97. https://doi.org/10.1016/j.tim.2009.08.001.
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  - O’Brien, Heath E., Jolanta Miadlikowska, and François Lutzoni. “Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus peltigera.” Evolution; International Journal of Organic Evolution 63, no. 8 (August 2009): 2076–86. https://doi.org/10.1111/j.1558-5646.2009.00685.x.
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  - Lutzoni, François, and Jolanta Miadlikowska. “Lichens.” Current Biology : Cb 19, no. 13 (July 2009): R502–3. https://doi.org/10.1016/j.cub.2009.04.034.
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  - Arnold, A Elizabeth, Jolanta Miadlikowska, K Lindsay Higgins, Snehal D. Sarvate, Paul Gugger, Amanda Way, Valérie Hofstetter, Frank Kauff, and François Lutzoni. “A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?” Systematic Biology 58, no. 3 (June 2009): 283–97. https://doi.org/10.1093/sysbio/syp001.
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  - Schoch, Conrad L., Gi-Ho Sung, Francesc López-Giráldez, Jeffrey P. Townsend, Jolanta Miadlikowska, Valérie Hofstetter, Barbara Robbertse, et al. “The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.” Systematic Biology 58, no. 2 (April 2009): 224–39. https://doi.org/10.1093/sysbio/syp020.
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  - Ertz, Damien, Jolanta Miadlikowska, François Lutzoni, Steven Dessein, Olivier Raspé, Nathalie Vigneron, Valérie Hofstetter, and Paul Diederich. “Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha.” Mycological Research 113, no. Pt 1 (January 2009): 141–52. https://doi.org/10.1016/j.mycres.2008.09.002.
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  - Gueidan, C., S. Savić, H. Thüs, C. Roux, C. Keller, L. Tibell, M. Prieto, et al. “Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: Recent progress and remaining challenges.” Taxon 58, no. 1 (January 1, 2009): 184–208. https://doi.org/10.1002/tax.581019.
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  - Hodkinson, B. P., and F. Lutzoni. “A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales.” Symbiosis 49, no. 3 (January 1, 2009): 163–80. https://doi.org/10.1007/s13199-009-0049-3.
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  - Joneson, S., and F. Lutzoni. “Revisiting compatibility and thigmotropism in the lichen symbiosis.” Symbiosis 47 (2009): 109–15.
  - Joneson, S., and F. Lutzoni. “Compatibility and thigmotropism in the lichen symbiosis: A reappraisal.” Symbiosis 47, no. 2 (January 1, 2009): 109–15. https://doi.org/10.1007/BF03182294.
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  - Ruibal, C., C. Gueidan, L. Selbmann, A. A. Gorbushina, P. W. Crous, J. Z. Groenewald, L. Muggia, et al. “Phylogeny of rock-inhabiting fungi related to Dothideomycetes.” Studies in Mycology 64 (January 2009): 123-133S7. https://doi.org/10.3114/sim.2009.64.06.
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  - Savić, Sanja, Leif Tibell, Cécile Gueidan, and François Lutzoni. “Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera.” Mycological Research 112, no. Pt 11 (November 2008): 1307–18. https://doi.org/10.1016/j.mycres.2008.05.002.
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  - Gaya, Ester, Pere Navarro-Rosinés, Xavier Llimona, Néstor Hladun, and François Lutzoni. “Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes).” Mycological Research 112, no. Pt 5 (May 2008): 528–46. https://doi.org/10.1016/j.mycres.2007.11.005.
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  - Amtoft, A., F. Lutzoni, and J. Miadlikowska. “Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North America.” Bryologist 111, no. 1 (March 1, 2008): 1–40. https://doi.org/10.1639/0007-2745(2008)111[1:DVITOH]2.0.CO;2.
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  - Gueidan, C., C. R. Villaseñor, G. S. de Hoog, A. A. Gorbushina, W. A. Untereiner, and F. Lutzoni. “A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages.” Studies in Mycology 61 (January 2008): 111–19. https://doi.org/10.3114/sim.2008.61.11.
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  - Gueidan, C., C. Ruibal Villasenor, S. de Hoog, A. Gorbushina, W. A. Untereiner, and F. Lutzoni. “An extremotolerant rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages.” Studies in Mycology 61 (2008): 111–19.
  - Otálora, M. A. G., I. Martínez, M. C. Molina, G. Aragón, and F. Lutzoni. “Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae, Ascomycota) in Europe.” Taxon 57, no. 3 (January 1, 2008): 907–21. https://doi.org/10.1002/tax.573019.
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  - Gueidan, Cécile, Claude Roux, and François Lutzoni. “Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota).” Mycological Research 111, no. Pt 10 (October 2007): 1145–68. https://doi.org/10.1016/j.mycres.2007.08.010.
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  - Hofstetter, Valérie, Jolanta Miadlikowska, Frank Kauff, and François Lutzoni. “Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota).” Molecular Phylogenetics and Evolution 44, no. 1 (July 2007): 412–26. https://doi.org/10.1016/j.ympev.2006.10.016.
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  - Kauff, Frank, Cymon J. Cox, and François Lutzoni. “WASABI: an automated sequence processing system for multigene phylogenies.” Systematic Biology 56, no. 3 (June 2007): 523–31. https://doi.org/10.1080/10635150701395340.
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  - Rydholm, C., P. S. Dyer, and F. Lutzoni. “DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri.” Eukaryotic Cell 6, no. 5 (May 2007): 868–74. https://doi.org/10.1128/ec.00319-06.
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  - Litaker, R. W., M. W. Vandersea, S. R. Kibler, K. S. Reece, N. A. Stokes, F. M. Lutzoni, B. A. Yonish, M. A. West, M. N. D. Black, and P. A. Tester. “Recognizing dinoflagellate species using its rDNA sequences.” Journal of Phycology 43, no. 2 (April 1, 2007): 344–55. https://doi.org/10.1111/j.1529-8817.2007.00320.x.
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  - Arnold, A Elizabeth, Daniel A. Henk, Rebecca L. Eells, François Lutzoni, and Rytas Vilgalys. “Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR.” Mycologia 99, no. 2 (March 2007): 185–206. https://doi.org/10.3852/mycologia.99.2.185.
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  - Arnold, A Elizabeth, and F. Lutzoni. “Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?” Ecology 88, no. 3 (March 2007): 541–49. https://doi.org/10.1890/05-1459.
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  - Reeb, Valérie, Peik Haugen, Debashish Bhattacharya, and François Lutzoni. “Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease.” Journal of Molecular Evolution 64, no. 3 (March 2007): 285–98. https://doi.org/10.1007/s00239-005-0179-z.
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  - Higgins, K Lindsay, A Elizabeth Arnold, Jolanta Miadlikowska, Snehal D. Sarvate, and François Lutzoni. “Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages.” Molecular Phylogenetics and Evolution 42, no. 2 (February 2007): 543–55. https://doi.org/10.1016/j.ympev.2006.07.012.
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  - Gueidan, C., C. Roux, and F. Lutzoni. “Using a multigene analysis to assess generic delineation and character evolution in the Verrucariaceae (Verrucariales, Ascomycota).” Mycological Research 110 (2007): 1147–70.
  - Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. Eriksson, S. Huhndorf, et al. “A higher-level phylogenetic classification of the Fungi.” Mycological Research 111 (2007): 509–47.
  - Geiser, David M., Cécile Gueidan, Jolanta Miadlikowska, François Lutzoni, Frank Kauff, Valérie Hofstetter, Emily Fraker, et al. “Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.” Mycologia 98, no. 6 (November 2006): 1053–64. https://doi.org/10.3852/mycologia.98.6.1053.
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  - Miadlikowska, Jolanta, Frank Kauff, Valérie Hofstetter, Emily Fraker, Martin Grube, Josef Hafellner, Valérie Reeb, et al. “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, no. 6 (November 2006): 1088–1103. https://doi.org/10.1080/15572536.2006.11832636.
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  - Spatafora, Joseph W., Gi-Ho Sung, Desiree Johnson, Cedar Hesse, Benjamin O’Rourke, Maryna Serdani, Robert Spotts, et al. “A five-gene phylogeny of Pezizomycotina.” Mycologia 98, no. 6 (November 2006): 1018–28. https://doi.org/10.3852/mycologia.98.6.1018.
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  - Arnold, A. E., and F. Lutzoni. “From the leaf to the landscape: Endophyte diversity and interactions at small and large spatial scales.” Phytopathology 96, no. 6 (June 1, 2006): S136–37.
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  - Rydholm, Carla, George Szakacs, and François Lutzoni. “Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species.” Eukaryotic Cell 5, no. 4 (April 2006): 650–57. https://doi.org/10.1128/ec.5.4.650-657.2006.
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  - Fernández, Fernando A., Andrew N. Miller, Sabine M. Huhndorf, François M. Lutzoni, and Stefan Zoller. “Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa.” Mycologia 98, no. 1 (January 2006): 121–30. https://doi.org/10.3852/mycologia.98.1.121.
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  - Geiser, D. M., J. Gueidan Miadlikowska, F. Kauff, V. Hofstetter, E. Fraker, C. L. Schoch, L. Tibell, W. A. Untereiner, A. Aptroot, and F. Lutzoni. “Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.” Mycologia 98 (2006): 1055–66.
  - James, T. Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. J. Cox, G. Celio, et al. “Reconstructing the early evolution of the Fungi using a six-gene phylogeny.” Nature 443 (2006): 818–22.
  - Miadlikowska, J., F. Kauff, V. Hofstetter, E. Fraker, M. Grube, J. Hafellner, V. Reeb, et al. “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 (2006): 1090–1103.
  - Spatafora, J. W., G. H. Sung, D. Johnson, B. O’Rourke, M. Serdani, R. Spotts, F. Lutzoni, et al. “A five-gene phylogeny of Pezizomycotina.” Mycologia 98 (2006): 1020–30.
  - Bhattacharya, Debashish, Valérie Reeb, Dawn M. Simon, and François Lutzoni. “Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA.” Bmc Evolutionary Biology 5 (November 21, 2005): 68. https://doi.org/10.1186/1471-2148-5-68.
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  - O’Brien, H. E., J. Miadlikowska, and F. Lutzoni. “Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera.” European Journal of Phycology 40, no. 4 (November 1, 2005): 363–78. https://doi.org/10.1080/09670260500342647.
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  - Paoletti, Mathieu, Carla Rydholm, Elke U. Schwier, Michael J. Anderson, George Szakacs, François Lutzoni, Jean-Paul Debeaupuis, Jean-Paul Latgé, David W. Denning, and Paul S. Dyer. “Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus.” Current Biology : Cb 15, no. 13 (July 2005): 1242–48. https://doi.org/10.1016/j.cub.2005.05.045.
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  - Lutzoni, I. “Erratum: (American Journal of Botany (October 2004) 91:10 (1450)).” American Journal of Botany 92, no. 1 (January 1, 2005).
  - Lutzoni, François, Frank Kauff, Cymon J. Cox, David McLaughlin, Gail Celio, Bryn Dentinger, Mahajabeen Padamsee, et al. “Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.” American Journal of Botany 91, no. 10 (October 2004): 1446–80. https://doi.org/10.3732/ajb.91.10.1446.
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  - Reeb, Valérie, François Lutzoni, and Claude Roux. “Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.” Molecular Phylogenetics and Evolution 32, no. 3 (September 2004): 1036–60. https://doi.org/10.1016/j.ympev.2004.04.012.
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  - Miadlikowska, Jolanta, and François Lutzoni. “Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits.” American Journal of Botany 91, no. 3 (March 2004): 449–64. https://doi.org/10.3732/ajb.91.3.449.
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  - Haugen, P., V. Reeb, F. Lutzoni, and D. Bhattacharya. “The evolution of homing endonuclease genes and group I introns in nuclear rDNA.” Molecular Biology and Evolution 21 (2004): 105–16.
  - Haugen, Peik, Valérie Reeb, François Lutzoni, and Debashish Bhattacharya. “The evolution of homing endonuclease genes and group I introns in nuclear rDNA.” Molecular Biology and Evolution 21, no. 1 (January 2004): 129–40. https://doi.org/10.1093/molbev/msh005.
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  - Zoller, Stefan, and François Lutzoni. “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, no. 3 (December 2003): 629–40. https://doi.org/10.1016/s1055-7903(03)00215-x.
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  - Miadlikowska, Jolanta, François Lutzoni, Trevor Goward, Stefan Zoller, and David Posada. “New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex.” Mycologia 95, no. 6 (November 2003): 1181–1203. https://doi.org/10.1080/15572536.2004.11833027.
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  - Søchting, Ulrik, and François Lutzoni. “Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae).” Mycological Research 107, no. Pt 11 (November 2003): 1266–76. https://doi.org/10.1017/s0953756203008529.
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  - Gaya, Ester, François Lutzoni, Stefan Zoller, and Pere Navarro-Rosinés. “Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota).” American Journal of Botany 90, no. 7 (July 2003): 1095–1103. https://doi.org/10.3732/ajb.90.7.1095.
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  - Alfaro, Michael E., Stefan Zoller, and François Lutzoni. “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, no. 2 (February 2003): 255–66. https://doi.org/10.1093/molbev/msg028.
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  - McDonald, T., J. Miadlikowska, and F. Lutzoni. “The lichen genus Sticta in the Great Smoky Mountains: A phylogenetic study of morphological, chemical, and molecular data.” Bryologist 106, no. 1 (January 1, 2003): 61–79. https://doi.org/10.1639/0007-2745(2003)106[0061:TLGSIT]2.0.CO;2.
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  - Kauff, Frank, and François Lutzoni. “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, no. 1 (October 2002): 138–56. https://doi.org/10.1016/s1055-7903(02)00214-2.
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  - Barker, F Keith, and François M. Lutzoni. “The utility of the incongruence length difference test.” Systematic Biology 51, no. 4 (August 2002): 625–37. https://doi.org/10.1080/10635150290102302.
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  - Redhead, S. A., F. Lutzoni, J. M. Moncalvo, and R. Vilgalys. “Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics).” Mycotaxon 83 (July 1, 2002): 19–57.
  - Miadlikowska, J., B. McCune, and F. Lutzoni. “Pseudocyphellaria perpetua, a new lichen from western North America.” Bryologist 105, no. 1 (January 1, 2002): 1–10. https://doi.org/10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2.
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  - O’Donnell, K., F. M. Lutzoni, T. J. Ward, and G. L. Benny. “Erratum: Evolutionary relationships among mucoralean fungi (zygomycota): Evidence for family polyphyly on a large scale (Mycologia (2001) 93:2).” Mycologia 93, no. 4 (January 1, 2002): 814. https://doi.org/10.1080/00275514.2001.12063214.
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  - Redhead, S. A., J. M. Moncalvo, R. Vilgalys, and F. Lutzoni. “Phylogeny of agarics: Partial systematics solutions for bryophilous omphalinoid agarics outside of the Agaricales (euagarics).” Mycotaxon 82 (2002): 151–68.
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  - Alfaro, M. E., S. Zoller, and F. Lutzoni. “Comparative performance of the bootstrap and Bayesian MCMC sampling in assessing phylogenetic confidence: a simulation study.” American Zoologist 41, no. 6 (December 2001): 1379–1379.
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  - Lutzoni, F., M. Pagel, and V. Reeb. “Major fungal lineages are derived from lichen symbiotic ancestors.” Nature 411, no. 6840 (June 2001): 937–40. https://doi.org/10.1038/35082053.
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  - O’Donnell, K., F. M. Lutzoni, T. J. Ward, and G. L. Benny. “Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale.” Mycologia 93, no. 2 (January 1, 2001): 286–96. https://doi.org/10.2307/3761650.
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  - Bhattacharya, D., F. Lutzoni, V. Reeb, D. Simon, J. Nason, and F. Fernandez. “Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes.” Molecular Biology and Evolution 17, no. 12 (December 2000): 1971–84. https://doi.org/10.1093/oxfordjournals.molbev.a026298.
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  - Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. “Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.” Systematic Biology 49, no. 4 (December 2000): 628–51. https://doi.org/10.1080/106351500750049743.
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  - Wu, Q. X., G. M. Mueller, F. M. Lutzoni, Y. Q. Huang, and S. Y. Guo. “Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA ITS sequences.” Molecular Phylogenetics and Evolution 17, no. 1 (October 2000): 37–47. https://doi.org/10.1006/mpev.2000.0812.
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  - Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. “Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.” Systematic Biology 49, no. 2 (June 2000): 278–305. https://doi.org/10.1093/sysbio/49.2.278.
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  - Miadlikowska, J., and F. Lutzoni. “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, no. 6 (January 1, 2000): 925–58. https://doi.org/10.1086/317568.
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  - Zoller, S., F. Lutzoni, and C. Scheidegger. “Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation.” Molecular Ecology 8, no. 12 (December 1999): 2049–59. https://doi.org/10.1046/j.1365-294x.1999.00820.x.
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  - Lutzoni, F., and F. K. Barker. “Sampling confidence envelopes of phylogenetic trees for combinability testing: a reply to Rodrigo.” Systematic Biology 48, no. 3 (September 1999): 596–603. https://doi.org/10.1080/106351599260166.
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  - Fernández, F. A., F. M. Lutzoni, and S. M. Huhndorf. “Teleomorph-anamorph connections: The new pyrenomycetous genus Carpoligna and its Pleurothecium anamorph.” Mycologia 91, no. 2 (January 1, 1999): 251–62. https://doi.org/10.2307/3761370.
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  - Zoller, S., F. Lutzoni, and C. Scheidegger. “Genetic variability within and among populations of the threatened foliose lichen Lobaria pulmonaria (L.).” Molecular Ecology 8 (1999): 2049–60.
  - Lutzoni, F., and M. Pagel. “Accelerated evolution as a consequence of transitions to mutualism.” Proceedings of the National Academy of Sciences of the United States of America 94, no. 21 (October 1997): 11422–27. https://doi.org/10.1073/pnas.94.21.11422.
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  - Lutzoni, F. M. “Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets.” Systematic Biology 46, no. 3 (September 1997): 373–406. https://doi.org/10.1093/sysbio/46.3.373.
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  - Lutzoni, F. M., and I. M. Brodo. “A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized ascomycotina).” Systematic Botany 20, no. 3 (January 1, 1995): 224–58. https://doi.org/10.2307/2419494.
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  - Lutzoni, F., and R. Vilgalys. “Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichenized fungi.” Special Issue of Cryptogamic Botany 5 (1995): 82–97.
  - Lutzoni, F., and R. Vilgalys. “ntegration of morphological and molecular datasets in estimating fungal phylogenies.” Canadian Journal of Botany 73(Suppl. 1) (1995): S649–59.
  - Lutzoni, F. M. “Ionaspis alba (Ascomycotina, Hymeneliaceae), a new lichen species from eastern North America.” Bryologist 97, no. 4 (January 1, 1994): 393–95. https://doi.org/10.2307/3243904.
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  - Lutzoni, F. M., and I. M. Brodo. “Proposal to conserve the name Gyalecta suaveolens Fr. (lichenized Ascomycota) with a conserved type.” Taxon 43, no. 4 (January 1, 1994): 657–59. https://doi.org/10.2307/1223556.
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  - Grandtner, M. M., and F. Lutzoni. “References on the vegetation of Québec.” Excerpta Botanica Sec. B. Bd 29, no. 1 (1991): 1–24.
  - Sirois, L., F. Lutzoni, and M. M. Grandtner. “Les lichens sur serpentine et amphibolite du plateau du mont Albert, Gaspésie, Québec.” Canadian Journal of Botany 66 (1988): 851–62.
  - Sirois, L., F. Lutzoni, and M. M. Grandtner. “Lichens on serpentine and amphibolite on the plateau of Mt. Albert, Gaspesie, Quebec.” Canadian Journal of Botany 66, no. 5 (January 1, 1988): 851–62. https://doi.org/10.1139/b88-124.
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- Conference Papers
  - Magain, N., J. Miadlikowska, B. Goffinet, E. Sérusiaux, and F. Lutzoni. “Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota).” In Systematic Biology, 66:74–99, 2017. https://doi.org/10.1093/sysbio/syw065.
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  - Lutzoni, François, and Rytas Vilgalys. “Integration of morphological and molecular data sets in estimating fungal phytogenies.” In Canadian Journal of Botany, 73:649–59. Canadian Science Publishing, 1995. https://doi.org/10.1139/b95-307.
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- Unknown. GenomeLIFE article written about the Lutzoni Lab. 2010 2010
- Unknown. ScienceNews article written about the Lutzoni Lab. 2009 2009
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