People Connected to the Hibbett Lab
Brandon Matheny
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| Brandon Matheny, Worcester, Massachusetts |
Brandon & Tim James, MSA meeting, Asheville, NC, 2004 |
Bio: Brandon received a PhD in 2003 from the University of Washington with Drs. Joe Ammirati and Ben Hall. At Clark University Brandon worked on the Assembling the Fungal Tree of Life (AFTOL) project. Brandon will continue to reconstruct the basidiomycete portion of the tree of life as a Co-PI for the phylogenomic proposal “AFTOL2.”
Research interests: Brandon's PhD thesis concerned the taxonomy, phylogeny, and biogeography of the Inocybaceae, a family of ectomycorrhizal mushrooms. During this work, Brandon was the first to employ RNA polymerase II gene sequences for molecular systematics of basidiomycetes. Brandon further developed these and other markers during the AFTOL project, which involved multi-gene phylogenies across the entire spectrum of basidiomycetes. One of the major results of the AFTOL project was the identification of at least five major lineages of Basidiomycota, up from the three that were previously known. Brandon also produced considerable progress in our understanding of evolutionary relationships among the Agaricales, the largest clade of mushroom-forming fungi. During “AFTOL2” Brandon will be responsible for screening up to 75 different genes for 25 exemplars of the Agaricomycotina with the expectation of applying a subset of these genes for phylogenetic reconstruction. Brandon continues taxonomic work in the Agaricales. Since 2003 he has described 15 species and 2 genera of fungi (Auritella, Cleistocybe) as new to science.
Publications (updated February 2008):
Padamsee, M., Matheny, P. B., Dentinger, B. T. M., and McLaughlin, D. J. (2008). The mushroom family Psathyrellaceae: Evidence for large-scale polyphyly of the genus Psathyrella. Molecular Phylogenetics and Evolution 46: 415-429. pdf
Matheny, P. B., Vellinga, E. C., Bougher, N. L., Ceska, O., Moreau, P. A., Neves, M. A., and Ammirati, J. F. (2007). Taxonomy of displaced species of Tubaria. Mycologia 99: 569-585. pdf
Ammirati, J. F., Parker, A. D., and Matheny, P. B. (2007). Cleistocybe, a new genus of Agaricales. Mycoscience 48: 282-289. pdf
Ge, Z. W., Yangl, Z. L., Zhang, P., Matheny, P. B., and Hibbett, D. S. (2007). Flammulina species from China inferred by morphological and molecular data. Fungal Diversity: in press.
Slot, J. C., Hallstrom, K. N., Matheny, P. B., and Hibbett, D. S. (2007). Diversification of NRT2 and the origin of its fungal homolog. Molecular Biology and Evolution 24(8): 1731-1743. pdf
Hibbett, D. S., Binder, M., Bischoff, J. F., Blackwell, M., Cannon, P. F., Eriksson, O. E., Huhndorf, S., James, T., Kirk, P. M., Lücking R., Lumbsch, H. T., Lutzoni, F., Matheny, P. B., McLaughlin, D. J., Powell, M. J., Redhead, S., Schoch, C. L., Spatafora, J. W., Stalpers, J. A., Vilgalys, R., Aime, M. C., Aptroot, A., Bauer, R., Begerow, D., Benny, G. L., Castlebury, L. A., Crous, P. W., Dai. Y. C., Gams, W., Geiser, D. M., Griffith, G. W., Gueidan, C., Hawksworth, D. L., Hestmark, G., Hosaka, K., Humber, R. A., Hyde, K. D., Ironside, J. E., Kõljalg, U., Jyrtznabm C. P., Larsson, K. H., Lichtwardt, R., Longcore, J., Miadlikowska, J., Miller, A., Moncalvo, J. M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J. D., Roux, C., Ryvarden, L., Sampaio, J. P., Schüßler, A., Sugiyama, J., Thorn, R. G., Tibell, L., Untereiner, W. A., Walker, C., Wang, Z., Weir, A., Weiß, M., White, M. M., Winka, K., Yao, Y. J., and Zhang, N. (2007). A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547. pdf
Arun Kumar, T. K., Celio, G. J., Matheny, P. B., McLaughlin, D. J., Hibbett, D. S., and Manimohan, P. (2007). Phylogenetic relationships of Auriculoscypha based on ultrastructural and molecular studies. Mycological Research 111: 268-274. pdf
Matheny, P. B., Wang Z., Binder M., Curtis, J. M., Lim, Y. W., Nilsson, H. R., Hughes, K. W., Hofstetter, V., Ammirati, J. F., Schoch, C., Langer, E., Langer, G., McLaughlin, D. J., Wilson, A. W., Frøslev, T., Ge, Z. W., Kerrigan, R. W., Slot, J. C., Yang, Z. L., Baroni, T. J., Fischer, M., Hosaka, K., Matsuura, K., Seidl, M. T., Vauras, J., and Hibbett, D. S. (2007). Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics and Evolution 43: 430-451. pdf
Matheny, P. B., Gossmann, J. A., Zalar, P., Arun Kumar, T. K., and Hibbett, D. S. (2006). Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Canadian Journal of Botany 84: 1794-1805. pdf
Matheny, P. B., Curtis, J. M., Hoffstetter, V., Aime, M. C., Moncalvo, J. M., Ge, Z. W., Yang, Z. L., Slot, J. C., Ammirati, J. F., Baroni, T. J., Bougher, N. L., Hughes, K. W., Lodge, D. J., Kerrigan, R. W., Seidl, M. T., Aanen, D. K., DeNitis, M., Daniele, G. M., Desjardin, D. E., Kropp, B. R., Norvell, L. L., Parker, A., Vellinga, E. C., Vilgalys, R., and Hibbett, D. S. (2006). Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98(6): 982-995. pdf
Aime, M. C., Matheny, P. B., Henk, D. A., Frieders, E. M., Nilsson, R. H., Piepenbring, M., McLaughlin, D. J., Szabo, L. J., Begerow, D., Sampaio, J. P., Bauer, R., Weiß, M., Oberwinkler, F., and Hibbett, D. S. (2006). An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98(6): 896-905. pdf
Moncalvo, J. M., Nilsson, R. H., Koster, B., Dunham, S. M., Bernauer, T., Matheny, P. B., McLenon, T., Margaritescu, S., Weiß, M., Garnica, S., Danell, E., Langer, G., Langer, E., Larsson, E., and Larsson, K. H. (2006). The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. Mycologia 98(6): 937-948. pdf
James, T. Y., Kauff, F., Schoch, C., Matheny, P. B., Hofstetter, V., Cox, C., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H. T., Rauhut, A., Reeb, V., Arnold, A. E., Amtoft, A., Stajich, J. E., Hosaka, K., Sung, G. H., Johnson, D., O'Rourke, B., Crockett, M., Binder, M., Curtis, J. M., Slot, J. C., Wang, Z., Wilson, A. W., Schüßler, A., Longcore, J. E., O'Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P. M., Powell, M. J., Taylor, J. W., White, M. M., Griffith, G. W., Davies, D. R., Humber, R. A., Morton, J. B., Sugiyama, J., Rossman, A. Y., Rogers, J. D., Pfister, D. H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R. A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R. A., Serdani, M., Crous, P. W., Hughes, K. W., Matsuura, K., Langer, E., Langer, G., Untereiner, W. A., Lücking, R., Büdel, B., Geiser, D. M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R.,Hibbett, D., Lutzoni, F., McLaughlin, D., Spatafora, J., and Vilgalys, R. (2006). Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822. pdf
Also see accompanying News and Views piece by Tom Bruns (PDF).
Matheny, P. B. and Ammirati, J. F. (2006). Cortinarius lucorum (Fr.) Karst., a Populus associate from North America. Pacific Northwest Fungi 1(4): 1-10. http://pnwfungi.org.
Matheny, P. B. and Bougher, N. L. (2006). The new genus Auritella from Africa and Australia (Inocybaceae, Agaricales): molecular systematics, taxonomy and historical biogeography. Mycological Progress. pdf
Frøslev, T. G., Matheny, P. B., and Hibbett, D. S. (2005). Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies. Molecular Phylogenetics and Evolution 37: 602-618. pdf
Yang, Z. L., Matheny, P. B., Ge, Z. W., and Hibbett, D. S. (2005). New Asian species of the genus Anamika (euagarics, hebelomatoid clade) based on morphology and ribosomal DNA sequences. Mycological Research 109: 1259-1267. pdf
Matheny, P. B. and Bougher, N. L. (2005). A new violet species of Inocybe (Agaricales) from urban and rural landscapes in Western Australia. Australasian Mycologist: 24: 7-12. pdf
Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett DS, James T, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold EA, Spatafora J, Sung G-H, Hambleton S, Miadlikowska J, Lücking R, Shoemaker R, O'Donnell K, Binder M, Crockett M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Johnson D, Lim Y-W, Lumbsch T, Matheny PB, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R. (2004). Where are we in assembling the fungal tree of life, classifying the fungi, and understanding the evolution of their subcellular traits? American Journal of Botany 91: 1446-1480.
Matheny, P. B. (2005). Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe, Agaricales). Molecular Phylogenetics and Evolution in press. pdf
Matheny, P. B. and Watling, R. (2004). A new and unusual species of Inocybe (Inosperma clade) from tropical Africa. Mycotaxon 89: 497-503.
Kropp, B. R. and Matheny, P. B. (2004). Basidiospore homoplasy and variation in the Inocybe chelanensis group in North America. Mycologia 96: 295-309. pdf
Matheny, P. B. and Ammirati, J. F. (2003). Inocybe angustispora, I. taedophila, and Cortinarius aureifolius: an unusual inocyboid Cortinarius. Mycotaxon 88: 401-407.
Matheny, P. B., Aime, M. C., and Henkel, T. W. (2003). New species of Inocybe from Dicymbe forests of Guyana. Mycological Research 107(4): 495-505.
Matheny, P. B., Liu, Y. J., Ammirati, J. F., and Hall, B. D. (2002). Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). American Journal of Botany 89(4): 688-698. pdf
Matheny, P. B. and Kropp, B. R. (2001) A revision of the Inocybe lanuginosa group and allied species in North America. Sydowia 53(1): 93-139.
Alignments, Data Sets and XML Files
Kropp, B. R., Matheny, P. B., Nanagyulyan, S. G., and Sirunyan A. L. Phylogenetic taxonomy of the Inocybe splendens group and the evolution of supersection “Marginatae” (Unpublished). Alignment of rpb1, rpb1-introns2-3, rpb2, and nLSU-rRNA. Dataset here
Matheny, P.B., Aime, M.C., Bougher, N.L., Buyck, B., Desjardin, D.E., Horak,
E., Kropp, B.R., Lodge, D.J., Trappe, J.M., and Hibbett, D.S. Out of the
paleotropics? Historical biogeographic patterns in the cosmopolitan
ectomycorrhizal mushroom family Inocybaceae (Unpublished).
Inocybaceae XML file
Inocybaceae alignment
Primary calibration file
Primary calibration XML file
Inocybaceae ancestral area and
ancestral plant host MacClade file