Arnold, A.E., J. Miadlikowska, K.L. Higgins, S.D. Sarvate, P. Gugger, A. Way, V. Hofstetter, F. Kauff, and  F. Lutzoni. 2008. Hyperdiverse fungal endophytes and endolichenic fungi elucidate the evolution of major ecological modes in the Ascomycota. Systematic Biology, in press.

Rojas, E.I., E.A. Herre, L.C. Mejía, A.E. Arnold, P. Chaverri, and G.J. Samuels. Endomelanconium endophyticum, a new Botryosphaeria leaf endophyte from Panama. Mycologia, in revision.

Jiménez-Romero, C., E. Ortega-Barria, A.E. Arnold, and L. Cubilla-Rios. 2008. Activity against Plasmodium falciparum of lactones isolated from the endophytic fungus Xylaria sp. Pharmaceutical Biology, in press.

Arnold, A.E. Nonpathogenic, cryptic fungi shape plant communities in tropical forests. 2008. Tropical Forest Community Ecology.  (S. Schnitzer and W. Carson, eds.) Blackwell Scientific, Inc., in press.

Feldman, T.S., H. O’Brien, and A.E. Arnold. 2008. Moth dispersal of mycoparasites and endophytes associated with Claviceps paspali and the grass Paspalum (Poaceae). Microbial Ecology, early-publication copy available here: pdf

Mejía, L.C., E.I. Rojas, Z. Maynard, A.E. Arnold, S. Van Bael, G.J. Samuels, N. Robbins, and E. A. Herre. 2008. Endophytic fungi as biocontrol agents of Theobroma cacao pathogens. Biological Control, early-publication copy available here: pdf

Kluger, C., J.W. Dalling, R. E. Gallery, E. Sanchez, C. Weeks-Galindo, and A.E. Arnold. 2008. Prevalent host-generalism among fungi associated with seeds of four neotropical pioneer species. Journal of Tropical Ecology 24: 351-354. pdf

Hoffman, M. and A.E. Arnold. 2008. Geography and host identity interact to shape communities of endophytic fungi in cupressaceous trees. Mycological Research 112: 331-344. pdf

Bruns, T., A.E. Arnold, and K. Hughes. 2008. Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology. 2008. New Phytologist 177: 586-588. pdf

Kithsiri Wijeratne, E.M., P.A. Paranagama, M.T. Marron, M.K. Gunatilaka, A.E. Arnold, and A.A.L. Gunatilaka. 2008. Sesquiterpene quinines and related metabolites from Phyllosticta spinarum, a fungal strain endophytic in Platycladus orientalis in the Sonoran Desert. Journal of Natural Products 71: 218-222. pdf

Arnold, A.E. and F. Lutzoni. 2007. Diversity and host range of foliar fungal endophytes: Are tropical leaves biodiversity hotspots? Ecology 88: 541-549. pdf

Arnold, A.E. and B.M.J. Engelbrecht. 2007. Fungal endophytes nearly double minimum leaf conductance in seedlings of a tropical tree. Journal of Tropical Ecology 23: 369-372. pdf

Arnold, A.E., D.A. Henk, R.L. Eells, F. Lutzoni, and R. Vilgalys. 2007. Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99: 185-206. pdf

Arnold, A.E. 2007. Understanding the diversity of foliar fungal endophytes: progress, challenges, and frontiers. Fungal Biology Reviews 21: 51-66. pdf

Gallery, R., J.W. Dalling, and A.E. Arnold. 2007. Diversity, host affinity, and distribution of seed-infecting fungi: A case study with neotropical Cecropia. Ecology 88: 582-588. pdf

Gallery, R.E., J.W. Dalling, B. Wolfe, and A.E. Arnold. 2007. Role of seed-infecting fungi in the recruitment limitation of neotropical pioneer species. Chapter 23 in Seed dispersal: Theory and its application in a changing world. Eds. A. Dennis, R. Green, E. Schupp and D. Westcott. CABI Press. pp. 479-498. Reprint available on request.

Tsai, Y.J., K. Maloney, and A.E. Arnold. 2007. Abiotic and biotic factors influencing the distribution of Pyrgulopsis thompsoni, the Huachuca springsnail. Journal of Aquatic Ecology 22: 213-218. pdf

Agrawal, A.A., D.A. Ackerly, F. Adler, A.E. Arnold, C. Cáceres, D.F. Doak, E. Post, P. Hudson, J. Maron, K.A. Mooney, M. Power, D. Schemske, J.J. Stachowicz, S.Y. Strauss, M.G. Turner, and E. Werner. 2007. Filling key gaps in population and community ecology. Frontiers in Ecology and the Environment 5: 145-152. pdf; web panels here.

Agrawal, A.A., D.A. Ackerly, F. Adler, A.E. Arnold, C. Cáceres, D.F. Doak, E. Post, P. Hudson, J. Maron, K.A. Mooney, M. Power, D. Schemske, J.J. Stachowicz, S.Y. Strauss, M.G. Turner, and E. Werner.2007. In support of observational studies (reply). (Peer-reviewed letter). Frontiers in Ecology and the Environment 5: 294-295. pdf

Higgins, K. L., Arnold, A. E., Miadlikowska, J., Sarvate, S. D., and Lutzoni, F. 2007. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Molecular Phylogenetics and Evolution 42: 543-555. pdf

Paranagama, P.A., E.M.K. Wijeratne, M.K. Gunatilaka, A.E. Arnold, and A.A.L. Gunatilaka. 2007. Bioactive and other naphthopyrans from Corynespora sp. occurring in Usnea cavernosa: first report of metabolites of an endolichenic fungus. Journal of Natural Products 70: 1700-1705. pdf

James, T. Y., F. Kauff, C. Schoch, P.B. Matheny, V. Hofstetter, C. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska, H.T. Lumbsch, A. Rauhut, V. Reeb, A.E. Arnold, A. Amtoft, J.E. Stajich, K. Hosaka, G.-H. Sung, D. Johnson, B. O’Rourke, M. Crockett, M. Binder, J.M. Curtis, J.C. Slot, Z. Wang, A.W. Wilson, A. Schüßler, J.E. Longcore, K. O’Donnell, S. Mozley-Standridge, D. Porter, P.M. Letcher, M.J. Powell, J.W. Taylor, M.M. White, G.W. Griffith, D.R. Davies, R.A. Humber, J.B. Morton, J. Sugiyama, A.Y. Rossman, J.D. Rogers, D.H. Pfister, D. Hewitt, K. Hansen, S. Hambleton, R.A. Shoemaker, J. Kohlmeyer, B. Volkmann-Kohlmeyer, R.A. Spotts, M. Serdani, P.W. Crous, K.W. Hughes, K. Matsuura, E. Langer, G. Langer, W.A. Untereiner, R. Lücking, B. Büdel, D.M. Geiser, A. Aptroot, P. Diederich, I. Schmitt, M. Schultz, R. Yahr, D. Hibbett, F. Lutzoni, D. McLaughlin, J. Spatafora, and R. Vilgalys. 2006. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443: 818-822. pdf

Spatafora, J.W., C. Schoch, D. Johnson, G-H. Sung, K. Hosaka, B. O’Rourke, M. Serdani, R. Spotts, F. Lutzoni, V. Hofstetter, E. Fraker, C. Gueidan, J. Miadlikowska, V. Reeb, M. Saunders, R. Yahr, A.E. Arnold, T. Lumbsch, and R. Lücking. 2006. A five-gene phylogenetic analysis of the Pezizomycotina. Mycologia 98: 1018-1028. pdf

Miadlikowska, J., F. Kauff, V. Hofstetter, E. Fraker, M. Grube, V. Reeb, G. Hestmark, B. Hodgkinson, M. Kukwa, M.G. Otalora, A. Rauhut, C. Scheidegger, E. Timdal, S. Stenroos, I. Brodo, D. Ertz, P. Diederich, R. Lücking, J.C. Lendemer, E. Tripp, R. Yahr, P. May, G. Perlmutter, D.M. Hillis, W.R. Buck, C. Gueidan, A.E. Arnold, C. Robertson, J. Hafellner, and F. Lutzoni. 2006. New insights from nuclear ribosomal and protein coding genes into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota). Mycologia 98: 1088-1103. pdf

Arnold, A.E. and L.C. Lewis. 2005. Evolution of fungal endophytes, and their roles against insects. Ecological and Evolutionary Advances in Insect-Fungus Associations (F. Vega and M. Blackwell, eds.).  Oxford University Press, Oxford. pp. 74-96. pdf

Lutzoni, F., F. Kauff, C. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T.Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A.E. Arnold, J. Miadlikowska, J. Spatafora, D. Johnson, S. Hambleton, M. Crockett, R. Shoemaker, G.-H. Sung, R. Lücking, T. Lumbsch, K. O’Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, K. Hosaka, Y.-W. Lim, B. Matheny, H. Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R. Yahr, and R Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and the evolution of subcellular traits. American Journal of Botany 91: 1446-1480. pdf

Arnold, A.E., L. Mejía, D. Kyllo, E. Rojas, Z. Maynard and E.A. Herre. 2003. Fungal endophytes limit pathogen damage in a tropical tree. Proceedings of the National Academy of Sciences USA 100: 15649-15654. pdf

Arnold, A.E. and E.A. Herre. 2003. Canopy cover and leaf age affect colonization by tropical fungal endophytes: Ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95: 388-398. pdf

Arnold, A.E. and N.M. Asquith. 2002. Herbivory in a fragmented tropical forest:  patterns from islands at Lago Gatún, Panamá.  Biodiversity and Conservation 11: 1663-1680. pdf

Arnold, A.E., Z. Maynard and G. Gilbert. 2001. Fungal endophytes in dicotyledonous neotropical trees:  patterns of abundance and diversity.  Mycological Research 105: 1502-1507. pdf

Arnold, A.E., Z. Maynard, G. Gilbert, P.D. Coley and T.A. Kursar. 2000. Are tropical fungal endophytes hyperdiverse?  Ecology Letters 3: 267-274. pdf

Asquith, N.M., J. Terborgh, A.E. Arnold and M. Riveros-C. 1999. The fruits the agouti ate:  Hymenaea courbaril seed fate when its disperser is absent.  Evidence from Lago Guri, Venezuela.  Journal of Tropical Ecology 15: 229-235. pdf

M. Hoffman, M. Gunatilaka, J. Ong, M. Shimabukuro, and A.E. Arnold. 2008. Molecular analysis reveals a distinctive fungal endophyte community associated with foliage of montane oaks in southeastern Arizona. Report to the Arizona Nevada Academy of Science, Journal of the Arizona Nevada Academy of Science, in press. Reprint available on request.

Bashyal, B.P., A.M. Burns, M.X. Liu, P.A. Paranagama, C.J. Seliga, T.J. Turbyville, E.M.K. Wijeratne, J. Zhan, M.K. Gunatilaka, A.E. Arnold, S.H. Faeth, L. Whitesell, and A.A.L. Gunatilaka. 2007. Discovery of small molecule bioactive agents from endophytic fungi of the Sonoran Desert. Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses. Grassland Research and Practice Series No. 13, New Zealand Grassland Association, Christchurch. pdf

Arnold, A.E. 2005. Diversity and Ecology of fungal endophytes in tropical forests. Current Trends in Mycological Research (S. Deshmukh, ed.). Oxford & IBH Publishing Co. Pvt. Ltd., New Delhi:  pp. 49-68. pdf

Van Bael, S.A., Z. Maynard, N. Robbins, J.F. Bischoff, A.E. Arnold, E. Rojas, L.C. Mejía, D.A. Kyllo, and E.A. Herre. 2005.  Emerging perspectives on the ecological roles of endophytic fungi in tropical plants. The Fungal Community: its organization and role in the ecosystem (J.F. White, Jr., J. Dighton, & P. Oudemans, eds). 3rd Edition. Marcel-Dekker, New York, NY.  Pp. TBA. Reprint available on request.

Herre, E.A., S. A. Van Bael, Z. Maynard, N. Robbins, J.  Bischoff, A. E. Arnold, E. Rojas, L. C. Mejia, R. A. Cordero, C. Woodward, and D.A.Kyllo. 2005. Tropical plants as chimera: some implications of foliar endophytic fungi for the study of host plant defense, physiology, and genetics. Biotic Interactions in the Tropics (D.F.R.P. Burslem, M.A. Pinard, & S.E. Hartley, eds.) Cambridge University Press. pp. 226-237. Reprint available on request.

Mejia, L. C., E. Rojas, Z. Maynard, A.E. Arnold, D. Kyllo, N. Robbins, and E.A. Herre. 2003. Inoculation of beneficial endophytic fungi into Theobroma cacao tissues. In Proceedings of the 14th International Cocoa Research Conference, Accra-Ghana. Reprint available on request.

Arnold, A.E.  2001.  Fungal endophytes in neotropical trees:  Abundance, diversity, and ecological interactions.  In Tropical Ecosystems: Structure, Diversity and Human Welfare (K. N. Ganeshaiah, R. Uma Shaanker, & K. S. Bawa, eds.).  Oxford & IBH Publishing Co. Pvt. Ltd., New Delhi:  pp. 739-743. pdf

Arnold, A. E., L. Mejía, E. Rojas, Z. Maynard, N. Robbins and E. A. Herre.  2001.  Organismos endofíticos:  Microorganismos en plantas.  (Endophytic organisms:  microorganisms in plants.) El Uso de Microorganismos Benéficos en la Agricultura Moderna.  Universidad E.A.R.T.H., Guácimo, Limón, Costa Rica. Reprint (in Spanish) available on request.

Arnold, A.E.  1999.  Fungal endophytes of tropical trees: methods and potential for biological control of fungal  pathogens of cocoa.  Proceedings of the Research Methodology of Biocontrol of Plant Diseases Workshop, San Jose: CATIE. Reprint available on request.

Arnold, A.E.  1999.  Sustainable cocoa: the fungal community component. American Cocoa Research Institute Features in Integrated Pest Management for Cocoa:  Online: www.oardc.ohiostate.edu/cocoa/main_ftr.htm.

Arnold, A.E.  1998.  Various entries, Encyclopaedia Britannica Online Rainforest Resources CD.

Arnold, A.E.  1993.  Flower color variation and morph-specific outcrossing in morning glories polymorphic for corolla color. Vertices (Duke University).