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François Lutzoni
Assistant Professor
Department of Biology
Duke University
Box 90338
Durham, North Carolina
USA 27708
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Education •
Research Interests •
Awards •
Publications
Education
DUKE UNIVERSITY, Durham, NC, USA.
Ph.D. Botany/Genetics. Sept. 1990-Dec. 1995
UNIVERSITY OF OTTAWA, Ottawa, Ontario, Canada.
M.Sc. in Biology. August 1987-May 1990
UNIVERSITÉ LAVAL, Ste-Foy, Québec, Canada.
B.Sc. in Bio-Agronomy; specialized in Plant and Soil Sciences.
August 1982-May 1987
Awards
2000. GEORGE R. COOLEY AWARD. For best contributed paper in plant systematics. Awarded by the American Society of Plant Taxonomist at the Botany 2000 meeting, Portland, Oregon. First authorship required; graduate students or those within 5 years of finishing their Ph.D. are eligible.
1996. TWELFTH ANNUAL PERRY PRIZE, DEPARTMENT OF BOTANY, DUKE UNIVERSITY. This award is given to a graduating Ph.D. student in recognition of an outstanding dissertation as determined by vote of the faculty.
1994-1995. DUKE UNIVERSITY MELLON PROGRAM IN PLANT SYSTEMATICS DISSERTATION FELLOWSHIP. Final year dissertation award.
1993. MYCOLOGICAL SOCIETY OF AMERICA GRADUATE FELLOWSHIP. Awarded annually to two promising graduate students in mycology. Applicants are evaluated on the basis of their scholastic merit, research ability, and promise shown as a mycologist.
1992. NEW ENGLAND BOTANICAL CLUB AWARD FOR THE SUPPORT OF BOTANICAL RESEARCH. Awarded to the graduate student submitting the best research proposal dealing with field studies in systematic botany, biosystematics, plant ecology, or plant conservation biology.
1989. A. J. SHARP AWARD. For the best student paper in the Bryological and Lichenological Section at the annual meeting of the Botanical Society of America. Paper presented at the AIBS congress held at the University of Toronto.
1989. LIONEL CINQ-MARS AWARD. For the best student paper presented at the annual meeting of the Canadian Botanical Association. Paper presented at the AIBS congress held at the University of Toronto.
Research Interests:
My general research interests are centered on the study of symbiosis using phylogenetics as a framework for developing specific projects. I am interested in phylogenetic studies of lichen-forming and allied fungi and their use as a model system for the study of mycobiont-photobiont symbiotic interactions and coevolution. The main goals of my phylogenetic studies are to resolve relationships among the main basal lineages of Euascomycetes (lichenized and non-lichenized) with high confidence levels, specifically to contribute toward establishing a stable supraordinal classification of the Ascomycota, reconstruct the origin of the lichen symbiosis, and identify all main lineages of ascomycetes derived from lichen ancestors. We are currently testing the hypothesis that lichenicolous fungi (fungi dwelling on or in lichens as parasites, commensals or saprobes) may be one explanation for the high rate of loss of the lichen symbiotic habit, by allowing the transformation of a fungus from a mutualistic to a parasitic state, and acting as a fungal "half-way house" that could facilitate further transitions to different substrates. We are also assessing the evolutionary and ecological roles of mutualistic associations such as lichens and endophytes in the diversification of the fungi.
I developed a model system that includes closely related symbiotic (lichenized) and non-symbiotic species of the mushroom genus Omphalina to study the evolutionary consequences (at the genotypic and phenotypic levels) of transitions to mutualism and to identify potential predispositions for successful transitions. The discovery of key innovations associated with mutualism that led to major adaptive radiations is another driving force of my research. I use phylogenetic comparative methods to test specific coevolutionary hypotheses and consequences (including shifts in rates of nucleotide substitution) associated with transitions to a mutualistic state.
Research projects in my lab also include population and phylogeographic studies of Aspergilus fumigatus; evolution, diversity and ecology of fungal endophytes; shifts in modes of reproduction in lichens; conservation genetics; evolution of group I and spliceosomal introns; evolution of algae and cyanobacteria found in lichens and their co-evolution with lichenized fungi; as well as classical systematic studies of lichen-forming fungi using an integrative approach, i.e., based on detailed morphological, anatomical, chemical (secondary compounds), biogeographical, and molecular data. My lab is also responsible for developing the bioinformatics structure for the NSF funded project "Assembling the Fungal Tree of Life" (AFTOL) and for sequencing 7 loci (= 10 kb) for 400 species of the 1,500 fungal species targeted for this project.
Because many aspects of my research rely heavily on phylogenetic trees, I am interested in theoretical aspects of phylogenetic methods that are relevant to alignments, Bayesian inference of phylogenetic confidence, congruence among data partitions, and comparative studies. We are developing new approaches that permit the integration of ambiguously aligned regions into phylogenetic analyses without violating positional homology (e.g., the program INAASE). We have also conducted an extensive series of simulations to compare the performance of bootstrapping and Bayesian Markov chain Monte Carlo sampling in assessing phylogenetic confidence. We are currently developing a new test of congruence to determine if data sets can be combined without diminishing phylogenetic accuracy, and with Mark Pagel (http://www.ams.rdg.ac.uk/zoology/pagel/) we have developed and implemented a new method to account for phylogenetic uncertainty in phylogenetic comparative studies.
Publications:
Eells, R. L., Henk, D. A., Arnold, A. E., Lutzoni, F., Vilgalys, R. 2004. Assessing diversity of foliar endophytes in a mature loblolly pine (Pinus taeda) plantation. . Microbial Ecology.
(in review).
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., Shcoch, 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 euascomycetes (Pezizomycotina, 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.
95:1181-1203 (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(1): 129-140.
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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 .
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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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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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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.
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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..
Pp. 151-164 .
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Lutzoni, F. 2002. Lichens. In: Encyclopedia of Evolution. Vol. 2M. Pagel (Ed.), Oxford University Press.
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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.
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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Downloadable data set (Stuffit file)
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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Downloadable data set (Stuffit file)
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)
Dowloadable Mac PPC version of INAASE (Stuffit file)
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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Downloadable data set (Stuffit file)
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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Downloadable data set (Stuffit file)
Kranner, I., and Lutzoni, F. 1999. Evolutionary consequences of transition to a lichen symbiotic state and physiological adaptation to oxidative damage associated with poikilohydry. In: Plant response to environmental stresses: From phytohormones to genome reorganization. H. R. Lerner (ed.).
591-628.
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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Downloadable data set (Stuffit file)
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.
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.
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.
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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