Areas of Research

Phylogenetic systematics and molecular evolution in fungi

Professional Experience / Employment History

Duke University

Professor of Biology, Biology, 2000 - present

Professor of Botany, Botany, 1999 - 2000

Adjunct Professor, Microbiology, 1999 - present

Member, Duke University Mycology Research Unit (DUMRU), , 1999 - present

Associate Professor of Botany, Botany, 1993 - 1999

Member, Duke University Program in Genetics, , 1988 - present

Member, Duke University Program in Cell and Molecular Biology, , 1988 - present

Assistant Professor of Botany, Botany, 1986 - 1993

U.S.D.A.

Postdoctoral Associate, Systematic Mycology Laboratory, December, 1985 - August, 1986

A. Rossman, supervisor

Visiting Positions

Scientist, CSIRO Forestry Division, 1995

Awards, Honors, and Distinctions

see cv, December, 2007
New York State Regents Scholarship, 1975-1978
AAAS Fellow
Mid-Career Fellowship, Mycological Society of America
Alexopolous Award, Mycological Society of America
Outstanding dissertation award, College of Arts and Sciences, Virginia Tech
Gertrude S. Burlingham Fellowship, New York Botanical Garden

Conferences Organized

Symposium Organizer, International Mycological Congress, 1994, 1998, 2002

Symposium Organizer, XVI International Botanical Congress, 1999

Professional Service

DGS

Director of Graduate Studies, Department of Botany, 1995 - 1998

PreMajor Advisor

Pre-Major Advising Center, 1996 - 1998

Dept Committee

Biology Dept Graduate Affairs Committee, 2000 - 2005

(Faculty) Performance Review Committee, 2003 - 2006

Biology Department Curriculum Committee, 2006 - present

Graduate Advisory Committee, 2004

Chair, Tenure Review Committee for F. Lutzoni, December 2004

Tenure/Appt committee for Tom Mitchell Olds, January 2004

Plant evolutionary biologist search, Botany Department, 1998 - 1999

Department Chair search, Dept. of Microbiology, Duke Medical Center, 1993 - 1994

Plant Systematics Search Committee, Botany Department, 1988 - 1989, 1994-1995

A&S Council

Arts and Science Council, 1997 - 2000

Univ Committee

University Program in Genetics and Genomics Executive Committee, 2003 - present

Executive Committee, University Program in Genetics and Genomics, 1993 - present

Steering Committee, Duke University Institute for Genome Sciences and Policy, 2000 - 2003

Library Director Search Committee, September, 1993 - October, 1993

NSF Reviews And Panels

NSF Systematic Biology Panel, 1991-1993, 1995-1998

NSF Microbial Interactions and Processes, December 2004

NSF Biotic Surveys ans Inventories Program, 2003

NSF Microbial Ecology, 2002
   also Microbial Biology Postdocs

Univ Services

Faculty Mentor, Howard Hughes Fellowship Program, 1991 - present

Duke Young Scholars Program in Sciences and Mathematics, Summer Program 1989

Dept Services

D.U.F.C.A.S.Botany Department Representative, 1988 - 1990

Editorial Boards

Associate Editor, Intern. J. Plant Sciences, 1997 - 2005

Associate Editor, Mycological Research, 1999 - 2003

Associate Editor, Mycologia, 1993 - 1998

Assistant Editor, Systematic Biology, 1994 - 1996

Grant Panels

U.S.D.A. Forest Biology Panel, 1989

Service to the Community

Faculty Mentor, Carolinas-Ohio Science Education Network (COSEN), 1991 - present

Academic Mentor, North Carolina School of Science and Mathematics, Mentorship Program, 1989 - 1990

Other

elected Vice-President, Mycological Society of America, 5 yr term, 2007

Membership in professional organization, April 2005
   Mycological Society of America, British Mycological Society, American Society of Plant Taxonomists, Botanical Society of America, Society for Systematic Biology,Society for the Study of Evolution, Society for the Study of Molecular Evolution, American Association for the Advancement of Science, Sigma Xi Scientific Research Society

Standing Committee Member, Systematics Agenda, 1991-1992, 2000

Local Arrangements Committee, Chair, Mycological Society of America Annual Meetings, UNC-Asheville, June, 2004

Councilor, Mycological Society of America, 1991 - 1993
   Program Committee 1989-1995 (also current), Endowment Committee 1989-1992, Councilor 1999-2002

Selected Recent Invited Talks

2008 Lectures/Seminars, 15 December 2008

Lectures/Seminars, 2007

Lectures/Seminars, 2006

seminars/symposium talks, 2005

NSF Tree of Life PI's Meeting, November, 2004

MSA Annual Meeting, 2004

NC A&T, April, 2004

University of Alaska, March, 2004

NSF IRCEB meetings, Tempe, AZ, November, 2003

Departmental seminar, Wake Forest University, September, 2003

NSF Microbial Observatories Meetings, Arlington, September, 2003

American Phytopathology Society meetings, Charlotte, August, 2003

Mycological Society of America Annual Meeting, Asilomar, CA, July, 2003

NSF Deep Hypha Meetings, Chicago, IL, April, 2003

7th International Mycological Congress, Oslo, Norway, August, 2002

Ecological Society of America/NSF NEON Program, Boulder, CO, June, 2002

Departmental Seminars, Oak Ridge Laboratories, Ga. Southern Univ., 2002

Tree of Life Symposium, American Museum of Natural History, May 29-June 1, 2002

Middle Atlantic States Mycological Conference, Beltsville, MD, April, 2002

21st Fungal Genetics Conference, Asilomar, CA, 2001

2nd Cryptococcus Genomics Meeting, St. Louis, 2001

Eastern Carolina University, 2001

Middle Atlantic States Mycology Conference, Athens, GA, 2001

Mycological Society of America annnual meeting, Salt Lake City, Utah, 2001

Penn State Univ, 2001

Workshop for Fungal Genomics, Whitehead Institute, 2001

Clark University, 2000

Harvard University Herbaria, 2000

Humboldt University, Berlin, 2000

International Union of Microbiological Sciences Congress, Sydney, Australia, 1999

Mt. Lake Biological Station, Pembroke, VA, 1999

XVI International Botanical Congress, St. Louis, 1999

6th International Mycological Congress, Jerusalem, 1998

Biology and phylogeny of basidiomycetous yeasts, Vigo, Spain, 1998

British Mycological Society Autumn meeting, Kew, United Kingdom, 1998

Dept. of Biology, Virginia Tech, 1998

Dept. of Forest Mycology and Pathology, University of Uppsala, 1998

Mycological Society of America Annual Meeting, San Juan, 1998

19th Fungal Genetics Conference, Asilomar, CA, 1997

Dept. of Biology, Vanderbilt University, 1997

Dept. of Botany, University of Georgia, 1997

Dept. of Plant Biology, UC-Berkeley, 1997

Duke University Mycology Research Unit, 1997

Plant Biotechnology Seminar, Oregon State University, 1997

Dept. of Botany, Duke University, 1996

Dept. of Microbiology, Humboldt University, Berlin, 1996

Phylogeny of Life Symposium, University of Arizona, 1996

15th Annual Meeting for Microbial Systematics, Lake Kawaguchi, Japan, 1995

Australian Society for Systematic Botany, National Herbarium, Canberra, Australia, 1995

CSIRO Division of Forestry, Canberra, Australia, 1995

Dept. of Botany and Zoology, Australian National University, Canberra, Australia, 1995

Laboratory of Systematic Mycology and Lichenology, Academica Sinica, Beijing, 1995

Landcare Research, Auckland, New Zealand, 1995

Bailey Hortorium, Cornell University, 1994

Dept. of Biological Sciences, Southern Florida University, Tampa, FL, 1994

Dept. of Plant Pathology, Texas A&M University, 1994

Fifth International Mycological Symposium, Vancouver, Canada, 1994

Doctoral Theses Directed

Jason Thacker, molecular evolution of laccase genes in fungi, (2004)

Dolores Gonzalez, (2004)

Annette Golonka, ecology of nectar-inhabiting microorganisms associated with Silene, (2002)

Anne Pringle, Genetics of arbuscular mycorrhizal (AM) fungi, (2001)

Terry Henkle, Ecology and systematics of neotropical fungi, (2001)

Shian-Ren Liou, Evolutionary genetics of speciation and intersterility in Pleurotus, (2000)

Jacqui Johnson, Molecular systematics of the genus Lepiota sensu lato, (1997)

Mary Malik, The genetics and evolution of somatic self/nonself recognition in the oyster mushroom Pleurotus ostreatus, (1996)

Peggy Schultz, Community dynamics of arbuscular mycorrhizal fungi from an old field community, (1996)

Francois Lutzoni, (1995)

John Hopple, Molecular evolution and systematics of Coprinus, (1994)

David Hibbett, Molecular systematics of the genus Lentinus, (1991)

Publications

Papers Published

1. WH Hartman, CJ Richardson, R Vilgalys, GL Bruland, Environmental and anthropogenic controls over bacterial communities in wetland soils., Proceedings of the National Academy of Sciences of the United States of America, United States, vol. 105 no. 46 (November, 2008), pp. 17842-7.
2. TM Porter, CW Schadt, L Rizvi, AP Martin, SK Schmidt, L Scott-Denton, R Vilgalys, JM Moncalvo, Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life., Molecular phylogenetics and evolution, United States, vol. 46 no. 2 (February, 2008), pp. 635-44.
3. DS Hibbett, M Binder, JF Bischoff, M Blackwell, PF Cannon, OE Eriksson, S Huhndorf, T James, PM Kirk, R Lücking, H Thorsten Lumbsch, F Lutzoni, PB Matheny, DJ McLaughlin, MJ Powell, S Redhead, CL Schoch, JW Spatafora, JA Stalpers, R Vilgalys, MC Aime, A Aptroot, R Bauer, D Begerow, GL Benny, LA Castlebury, PW Crous, YC Dai, W Gams, DM Geiser, GW Griffith, C Gueidan, DL Hawksworth, G Hestmark, K Hosaka, RA Humber, KD Hyde, JE Ironside, U Kõljalg, CP Kurtzman, KH Larsson, R Lichtwardt, J Longcore, J Miadlikowska, A Miller, JM Moncalvo, S Mozley-Standridge, F Oberwinkler, E Parmasto, V Reeb, JD Rogers, C Roux, L Ryvarden, JP Sampaio, A Schüssler, J Sugiyama, RG Thorn, L Tibell, WA Untereiner, C Walker, Z Wang, A Weir, M Weiss, MM White, K Winka, YJ Yao, N Zhang, A higher-level phylogenetic classification of the Fungi., Mycological research, England, vol. 111 no. Pt 5 (May, 2007), pp. 509-47.
4. Henk DA, Vilgalys R, Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium, American Journal of Botany, vol. 94 (2007), pp. 1515-1526.
5. JL Parrent, R Vilgalys, Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization., The New phytologist, England, vol. 176 no. 1 (2007), pp. 164-74.
6. PC Ceresini, HD Shew, TY James, RJ Vilgalys, MA Cubeta, Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci., BMC evolutionary biology, England, vol. 7 (2007), pp. 163.
7. TY James, F Kauff, CL Schoch, PB Matheny, V Hofstetter, CJ Cox, G Celio, C Gueidan, E Fraker, J Miadlikowska, HT Lumbsch, A Rauhut, V Reeb, AE Arnold, A Amtoft, JE Stajich, K Hosaka, GH Sung, D Johnson, B O'Rourke, M Crockett, M Binder, JM Curtis, JC Slot, Z Wang, AW Wilson, A Schüssler, JE Longcore, K O'Donnell, S Mozley-Standridge, D Porter, PM Letcher, MJ Powell, JW Taylor, MM White, GW Griffith, DR Davies, RA Humber, JB Morton, J Sugiyama, AY Rossman, JD Rogers, DH Pfister, D Hewitt, K Hansen, S Hambleton, RA Shoemaker, J Kohlmeyer, B Volkmann-Kohlmeyer, RA Spotts, M Serdani, PW Crous, KW Hughes, K Matsuura, E Langer, G Langer, WA Untereiner, R Lücking, B Büdel, DM Geiser, A Aptroot, P Diederich, I Schmitt, M Schultz, R Yahr, DS Hibbett, F Lutzoni, DJ McLaughlin, JW Spatafora, R Vilgalys, Reconstructing the early evolution of Fungi using a six-gene phylogeny., Nature, England, vol. 443 no. 7113 (October, 2006), pp. 818-22.
8. JL Parrent, WF Morris, R Vilgalys, CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities., Ecology, United States, vol. 87 no. 9 (September, 2006), pp. 2278-87.
9. D González, MA Cubeta, R Vilgalys, Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex., Molecular phylogenetics and evolution, United States, vol. 40 no. 2 (August, 2006), pp. 459-70.
10. AP Litvintseva, R Thakur, R Vilgalys, TG Mitchell, Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana., Genetics, United States, vol. 172 no. 4 (April, 2006), pp. 2223-38.
11. TY James, P Srivilai, U Kües, R Vilgalys, Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function., Genetics, United States, vol. 172 no. 3 (March, 2006), pp. 1877-91.
12. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R, Reconstructing the early evolution of Fungi using a six-gene phylogeny, Nature, vol. 443 (2006), pp. 818-822.
13. Gonzalez D, Cubeta MA, Vilgalys R, Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex, Molecular Phylogenetics and Evolution, vol. 40 (2006), pp. 459-470.
14. Yahr R, Vilgalys R, DePriest PT, Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis, New Phytologist, vol. 171 (2006), pp. 847-860.
15. Parrent, J. L., W. F. Morris., R. Vilgalys, CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities, Ecology, vol. 87 (2006), pp. 2278-2287.
16. James TY, Srivilai P, Kues U, Vilgalys R, Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function, Genetics, vol. 172 (2006), pp. 1877-1891.
17. Litvintseva, A. P., Thakur, R., Vilgalys, R., Mitchell, T. G., Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), Including a Unique Population in Botswana, Genetics, vol. 172 (2006), pp. 2223-2238.
18. R Yahr, R Vilgalys, PT DePriest, Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis., The New phytologist, England, vol. 171 no. 4 (2006), pp. 847-60.
19. HE O'Brien, JL Parrent, JA Jackson, JM Moncalvo, R Vilgalys, Fungal community analysis by large-scale sequencing of environmental samples., Applied and environmental microbiology, United States, vol. 71 no. 9 (September, 2005), pp. 5544-50.
20. N Fierer, JA Jackson, R Vilgalys, RB Jackson, Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays., Applied and environmental microbiology, United States, vol. 71 no. 7 (July, 2005), pp. 4117-20.
21. M Didukh, R Vilgalys, SP Wasser, OS Isikhuemhen, E Nevo, Notes on Agaricus section Duploannulati using molecular and morphological data., Mycological research, England, vol. 109 no. Pt 6 (June, 2005), pp. 729-40.
22. AP Litvintseva, L Kestenbaum, R Vilgalys, TG Mitchell, Comparative analysis of environmental and clinical populations of Cryptococcus neoformans., Journal of clinical microbiology, United States, vol. 43 no. 2 (February, 2005), pp. 556-64.
23. Litvintseva, A. P., L. Kestenbaum, R. Vilgalys, and T. G. Mitchell, Comparative analysis of environmental and clinical populations of Cryptococcus neoformans, J Clin Microbiol, vol. 43 (2005), pp. 556-64.
24. Wallenstein, M.D. and R. J. Vilgalys, Quantitative analyses of nitrogen cycling genes in soils, Pedobiologia, vol. 49 (2005), pp. 665-672.
25. Fierer, N., J. A. Jackson, R. Vilgalys, and R. B. Jackson, Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays, Appl. Env. Microbiol., vol. 71 (2005), pp. 4117-4120.
26. James, T. Y. and R. Vilgalys, Chytrid fungi as agents of amphibian decline- what can we learn from the earliest diverging fungi?, in Fungal Molecular principles of fungal pathogenesis, ASM Press. Joe Heitman, Scott Filler, and Aaron Mitchell-eds (2005).
27. S Diezmann, CJ Cox, G Schonian, R Vilgalys & TG Mitchell, Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis., J Clin Microbiol, United States, vol. 42 no. 12 (December, 2004), pp. 5624-5635.
28. R Yahr, R Vilgalys & PT Depriest, Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens., Mol Ecol, England, vol. 13 no. 11 (November, 2004), pp. 3367-3378.
29. TY James, SR Liou & R Vilgalys, The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor., Fungal Genet Biol, United States, vol. 41 no. 8 (August, 2004), pp. 813-825.
30. RE Marra, JC Huang, E Fung, K Nielsen, J Heitman, R Vilgalys & TG Mitchell, A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)., Genetics, United States, vol. 167 no. 2 (June, 2004), pp. 619-631.
31. GI Zervakis, JM Moncalvo & R Vilgalys, Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa., Microbiology, England, vol. 150 no. Pt 3 (March, 2004), pp. 715-726.
32. TY James, U Kües, SA Rehner & R Vilgalys, Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi., Fungal Genet Biol, United States, vol. 41 no. 3 (March, 2004), pp. 381-390.
33. AP Litvintseva, RE Marra, K Nielsen, J Heitman, R Vilgalys, TG Mitchell, Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa., Eukaryot Cell, United States, vol. 2 no. 6 (December, 2003), pp. 1162-8.
34. A Pringle, JM Moncalvo, R Vilgalys, Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica., Mycorrhiza, Germany, vol. 13 no. 4 (August, 2003), pp. 227-31.
35. PC Ceresini, HD Shew, RJ Vilgalys, LR Gale, MA Cubeta, Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities., Phytopathology, United States, vol. 93 no. 5 (May, 2003), pp. 610-5.
36. EA Morehouse, TY James, AR Ganley, R Vilgalys, L Berger, PJ Murphy, JE Longcore, Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone., Mol Ecol, England, vol. 12 no. 2 (February, 2003), pp. 395-403.
37. JM Moncalvo, R Vilgalys, SA Redhead, JE Johnson, TY James, M Catherine Aime, V Hofstetter, SJ Verduin, E Larsson, TJ Baroni, R Greg Thorn, S Jacobsson, H Clémençon, OK Miller, One hundred and seventeen clades of euagarics., Mol Phylogenet Evol, United States, vol. 23 no. 3 (June, 2002), pp. 357-400.
38. J Xu, G Luo, RJ Vilgalys, ME Brandt, TG Mitchell, Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD., Microbiology, England, vol. 148 no. Pt 1 (January, 2002), pp. 203-12.
39. A Forche, J Xu, R Vilgalys & TG Mitchell, Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers., Fungal Genet Biol, United States, vol. 31 no. 3 (December, 2001), pp. 189-203.
40. U Kües, TY James, R Vilgalys & MP Challen, The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic homobasidiomycete Coprinus bilanatus., Curr Genet, United States, vol. 39 no. 1 (February, 2001), pp. 16-24.
41. TY James & R Vilgalys, Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling., Mol Ecol, England, vol. 10 no. 2 (February, 2001), pp. 471-479.
42. J Xu, C Onyewu, HJ Yoell, RY Ali, RJ Vilgalys, TG Mitchell, Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans., Antimicrob Agents Chemother, United States, vol. 45 no. 2 (February, 2001), pp. 420-7.
43. TY James, JM Moncalvo, S Li, R Vilgalys, Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune., Genetics, United States, vol. 157 no. 1 (January, 2001), pp. 149-61.
44. J Xu, R Vilgalys, TG Mitchell, Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans., Mol Ecol, ENGLAND, vol. 9 no. 10 (October, 2000), pp. 1471-1481.
45. JM Moncalvo, FM Lutzoni, SA Rehner, J Johnson, R Vilgalys, Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences., Syst Biol, England, vol. 49 no. 2 (June, 2000), pp. 278-305.
46. G Schönian, A Forche, HJ Tietz, M Müller, Y Gräser, R Vilgalys, TG Mitchell, W Presber, [Genetic structure of geographically different populations of candida albicans], Mycoses, Germany, vol. 43 Suppl 2 (2000), pp. 51-6.
47. JG McEwen, JW Taylor, D Carter, J Xu, MS Felipe, R Vilgalys, TG Mitchell, T Kasuga, T White, T Bui, CM Soares, Molecular typing of pathogenic fungi., Med Mycol, England, vol. 38 Suppl 1 (2000), pp. 189-97.
48. AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, United States, vol. 99 no. 2 , pp. 185-206.
49. PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys, DS Hibbett, Major clades of Agaricales: a multilocus phylogenetic overview., Mycologia, United States, vol. 98 no. 6 , pp. 982-95.
50. JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiss, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson, R Vilgalys, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods., Mycologia, United States, vol. 98 no. 6 , pp. 937-48.
51. TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith, R Vilgalys, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)., Mycologia, United States, vol. 98 no. 6 , pp. 860-71.
52. AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, United States, vol. 99 no. 2 , pp. 185-206.
53. PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys, DS Hibbett, Major clades of Agaricales: a multilocus phylogenetic overview., Mycologia, United States, vol. 98 no. 6 , pp. 982-95.
54. JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiss, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson, R Vilgalys, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods., Mycologia, United States, vol. 98 no. 6 , pp. 937-48.
55. TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith, R Vilgalys, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)., Mycologia, United States, vol. 98 no. 6 , pp. 860-71.

Book Chapters

1. Idnurm, A., T. Y. James, and R. Vilgalys, Sex in the rest: mysterious mating in the Chytridiomycota and Zygomycota, in Sex in fungi: molecular determination and evolutionary implications, edited by Joe Heitman, Jim Kronstad, John Taylor, and Lorna Casselton eds (2007), ASM Press, Washington, D.C..
2. James, T. Y. and R. Vilgalys, Amphibian chytridiomycosis as an emerging infectious disease of wildlife: what can we learn from the earliest diverging fungi?, in Molecular principles of fungal pathogenesis, edited by J. Heitman, S.G. Filler, J.E. Edwards, Jr, and A.P. Mitchell (2006), ASM Press, Washington, D.C..