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Selected Contributed Papers/Abstracts
"Hybridization and isolation in Viburnum in Chiapas, Mexico," AIBS/ASPT (1978: Bot. Soc. Amer. Misc. Publ. 156:70)

"Growth patterns in Viburnum (Caprifoliaceae) and their taxonomic significance," AIBS/ASPT (1979: Bot. Soc. Amer. Misc. Publ. 157:54)

"The cladistic relationships of Viburnum--equivocal outgroups and a robust hypothesis," AIBS/ASPT (1981: Bot. Soc. Amer. Misc. Publ. 160:67-68)

"A revised form of outgroup analysis with applications to systematic entomology," Entomological Society of America (1982, with W. Maddison , D. Maddison)

"Outgroup analysis and global parsimony," Hennig Society (1982, with W. Maddison, D. Maddison)

"Pollen diversity in the Caprifoliaceae sensu lato and the evolution of the exine in Viburnum," AIBS/ASPT (1983: Amer. Jour. Bot. 70:111)

"Reticulation and hierarchy in phylogenetic systematics," AIBS/ASPT (1983, with A. Wyss, K. de Queiroz, M. Norell, Amer. Jour. Bot. 70:135)

"A method for coding partially ordered multistate characters for cladistic analysis: examples from a phylogenetic study of seed plants," AIBS/ASPT (1985, with J. Doyle, Amer. Jour. Bot. 72:950)

"Leaf morphology and evolution in the genus Viburnum," AIBS/ASPT (1986, with G. Levin, Amer. Jour. Bot. 73:760)

"Cladistic analysis and the species problem," Hennig Society (1986, with K. de Queiroz)

"Morphometric analysis of endocarp shape in Viburnum," AIBS/ASPT (1988, with R. Strauss, Amer. Jour. Bot. 75(6):170)

"Development of the ovary in Viburnum," AIBS/ASPT (1988, with W. Friedman, Amer. Jour. Bot. 75(6):27)

"Patterns of homoplasy in the evolution of Viburnum fruits," AIBS/ASPT (1988: Amer. Jour. Bot. 75(6):170)

"A reconsideration of seed plant and angiosperm phylogeny," AIBS/ASPT (1990, with J. Doyle)

"Are temperate-tropical family pairs sister groups?" AIBS/ASPT (1991, with R. Sanders and W. Judd)

"The decay index as a measure of relative robustness within a cladogram," Hennig Society (1991, with B. Mishler, V. Albert)

“Walter Zimmermann and the development of phylogenetic thought," International Society, History, Biology, Social Studies of Biology (1993, with J. Kadereit)

"Do outgroup nucleotide sequences differ from random sequences in rooting angiosperm trees," Society of Systematic Biologists (1993, with D. Maddison)

"Phylogenetic analysis of Viburnum based on chloroplast DNA restriction-site data," AIBS/ASPT (1993, with K. Sytsma, Amer. Jour. Bot. 80(6):146)

"Phylogenetic analysis of Viburnum based on ribosomal DNA sequences from the internal transcribed spacer regions," AIBS/ASPT (1993, with B. Baldwin, Amer. Jour. Bot. 80(6):145)

"Evolutionary diversity of polypore fungi: a molecular phylogenetic perspective," Botanical Society of America (1995, with D. Hibbett, Amer. Jour. Bot. 82(6):78)

"Is Potentilla monophyletic?," AIBS/ASPT (1995, with T. Eriksson, Amer. Jour. Bot. 82(6):128)

"Phylogenetic analyses of Sambucus and Adoxa," AIBS/ASPT (1995, with T. Eriksson, Amer. Jour. Bot. 82(6):128)

"A renalysis of the large rbcL dataset," AIBS/ASPT (1995, with K. Rice, R. Olmstead, Amer. Jour. Bot. 82(6):157)

"Fossil mushrooms in amber and the evolution of homobasidiomycetes," AIBS/MSA (1996, with D. Hibbett, Amer. Jour. Bot. 83(6):105)

"Simulations of the impact of classification systems on diversity patterns," GSA, Salt Lake City (1997, with C. Maley and H. Robeck)

"Phylogeny and biogeography of Triosteum," AIBS/ASPT (1998, with K. Gould)

"Phylogeny and biogeography of Hamamelis," AIBS/ASPT (1998, with J. Li) (BSA/ASPT, 2000: China, Dipsacales, phylocode)

“Phylogeny of Valerianaceae,” AIBS/ASPT (2002, with C. Bell)

“Viburnum phylogeny,” AIBS/ASPT (2002, with R. Winkworth)

“Evolution of reproductive traits in Dipsacales,” AIBS/ASPT (2002)

“Character evolution in Dipsacales,” SSE/SSB (2003)

“Character evolution and biogeography in Viburnum,” BSA/ASPT (2003)

“Historical biogeography of Viburnum” (w. R. Winkworth) BSA/ASPT (2004)

“Supertree of Dipsacales” (w. Brian Moore) BSA/ASPT (2004)

“CYC evolution in Dipsacales” (w. D. Howarth) BSA/ASPT (2004)

“Basal cactus phylogeny” (w. E. Edwards) BSA/ASPT (2004)
Invited Departmental Seminars
American Museum of Natural History (1993)

Amherst College (1989)

Arizona State University (1987, 2004)

Beijing Botanical Institute (1995)

Brown University (1993)

California Institute of Technology (1994, 2010)

Cornell University (1988, 1990)

Duke University (1990, 1999, 2005 “Superspeaker”)

Field Museum of Natural History (2004)

Florida International University (1998)

Florida State University (2001)

Harvard University (1984, 1989, 1993, 1995, 1999, 2009, 2011)

Hong Kong Chinese University (1995)

Imperial College, London (2010)

Louisiana State University (1989)

Madrid Botanical Garden, Spain (2008)

Massachusetts Institute of Technology (1996)

Miami University, Ohio (1993)

Michigan State University (1990, 1995, 1997, 2001)

National Museum of Natural History (1993, 2012)

New York Botanical Garden (2004)

Northern Illinois University (1989)

Ohio University, Athens (2000)

Princeton University (1994)

Rancho Santa Ana Botanic Garden (1986, 1994)

San Diego State University (1983, 1985, 1994, 2010)

San Francisco State University (1999)

State University of New York, Stony Brook (1989, 2003)

Stockholm University, Sweden (1999)

Trondheim University, Norway (1999)

University of Arizona (1985, 1986, 1987, 1995)

University of British Columbia (2004)

University of California, Berkeley (1982, 1991, 1999, 2009)

University of California, Davis (1983, 1984, 1998)

University of California, Irvine (1991)

University of California, Los Angeles (2010, 2012)

University of Chicago (1992)

University of Cincinnati (1993)

University of Colorado (1994)

University of Connecticut, Storrs (1989, 1995)

University of Florida (2005, 2010)

University of Illinois, Champaign (1989)

University of Kansas, Lawrence (1985, 1993)

University of Maine (1997)

University of Maryland (1993)

University of Massachusetts, Amherst (2006)

University of Michigan (1987, 1989, 1996, 2006)

University of Montreal (2011)

University of New Hampshire (1995)

University of North Dakota (2001)

University of Oklahoma (1988)

University of Sevilla, Spain (2008)

University of Texas, Austin (1985, 1993, 2004)

University of Toronto (1994)

University of Uppsala, Sweden (1992, 1999)

University of Utah (1991)

University of Washington (1987, 1991, 2002)

University of Wisconsin (1990)

Virginia Tech (2005)

Washington University, St. Louis (1991, 2004, 2006)

Yale University (1989, 1997, 2000, 2001, 2002, 2007, 2009, 2012)

Zurich Botanical Institute (1998, 2007)


Databases/Internet/Museum Contributions
TreeBASE: a relational database for exploring phylogeny (1996, with M. Sanderson, W. Piel, K. Rice, T. Eriksson, C. Henze). http://www.treebase .org

Treezilla: reanalysis of 500 rbcL sequences (1995, with K. Rice, R. Olmstead). http://herbaria.harvard.edu/~rice/treezilla

Angiosperm coordinator for the Tree of Life (1996, Maddison, D.R. and W. P. Maddison. The Tree of Life: A distributed internet project containing information about phylogeny and biodiversity). http://phylogeny.arizona.edu/tree/phylogeny.html

Phylomatic: a database for applied phylogenetics (2004, with C. Webb) http://www.phylodiversity.net/phylomatic/

“Travels in the Great Tree of Life,” An exhibition on phylogeny for the Peabody Museum, Yale University, New Haven, CT (Curator in Charge).
Field Experience
New World: Mexico, Jamaica, Costa Rica, Honduras, Guatamala, Peru, Ecuador, Colombia

Old World: China (Sichuan, Qinghai, Yunnan), Indonesia, Malaysia, Republic of Georgia, Vietnam


Publications
1. Donoghue, M.J. 1980. Flowering times in Viburnum. Arnoldia 40:2-22.

2. Donoghue, M.J. 1981. Growth patterns in woody plants with examples from the genus Viburnum. Arnoldia 41:2-23.

3. Coombs, E.A.K., M.J. Donoghue, and R.J. McGinley. 1981. Characters, computers, and cladograms: a review of the Berkeley cladistics workshop. Syst. Bot. 6:359-372.

4. Donoghue, M.J. 1982. A botanical classification. (Review of Dahlgren, R.M.T., and H.T. Clifford. 1982. The Monocotyledons. A Comparative Study. New York: Academic Press.) Science 217:1133-1134.

5. Mishler, B.D. and M.J. Donoghue. 1982. Species concepts: a case for pluralism. Syst. Zool. 31:491-503. [Reprinted in: Ereshefsky, M. (ed.). 1991. The Units of Evolution: Essays on the Nature of Species. MIT Press, Cambridge, MA.]

6. Donoghue, M.J. 1983. A preliminary analysis of phylogenetic relationships in Viburnum (Caprifoliaceae s.l.). Syst. Bot. 8:45-58.

7. Donoghue, M.J. 1983. The phylogenetic relationships of Viburnum. In Advances in Cladistics, Volume 2, pp.143-166; N.I. Platnick and V.A. Funk (eds.). New York:

Columbia Univ. Press.

8. Donoghue, M.J. 1984. Caprifoliaceae of Japan. (Review of Hara, H. 1983. A Revision of Caprifoliaceae of Japan with Reference to Allied Plants in Other Districts and to Adoxaceae. Tokyo: Academia Sci. Books.) Syst. Bot. 9:126-127.

9. Maddison, W.P., M.J. Donoghue, and D.R. Maddison. 1984. Outgroup analysis and parsimony. Syst. Zool. 33:83-103.

10. Donoghue, M.J. and P.D. Cantino. 1984. The logic and limitations of the outgroup substitution approach to cladistic analysis. Syst. Bot. 9:192-202.

11. Donoghue, M.J. 1985. Pollen diversity and exine evolution in Viburnum and the Caprifoliaceae sensu lato. Jour. Arnold Arb. 66:421-469.

12. Donoghue, M.J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist 88:172-181.

13. Donoghue, M.J. 1986. Miscellaneous cladistics. (Review of Duncan, T., and T.F. Stuessy. 1984. Cladistics: Perspectives on the Reconstruction of Evolutionary History. New York: Columbia Univ. Press.) Syst. Bot. 11:496-499.

14. Donoghue, M.J. and W.P. Maddison. 1986. Polarity assessment in phylogenetic systematics: a response to Meacham. Taxon 35:534-538.

15. Doyle, J.A. and M.J. Donoghue. 1986. Relationships of angiosperms and Gnetales: a numerical cladistic analysis. In Systematic and Taxonomic Approaches in Paleobotany; B.A. Thomas and R.A. Spicer (eds.). London: Oxford Univ. Press.

16. Doyle, J.A. and M.J. Donoghue. 1986. Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Bot. Rev. 52:321-431.

17. Donoghue, M.J. 1987. Experiments and hypotheses in systematics. Taxon 36:584-587.

18. Doyle, J.A. and M.J. Donoghue. 1987. The importance of fossils in elucidating seed plant phylogeny and macroevolution. Rev. Paleobot. Palyn. 50:63-95.

19. Donoghue, M.J. 1987. South African perspectives on species: an evaluation of the recognition concept. (Review of Vrba, E. S., ed. 1985. Species and Speciation. Pretoria: Transvaal Museum.) Cladistics 3:265-274.

20. Doyle, J.A. and M.J. Donoghue. 1987. The origin of angiosperms: a cladistic approach. In The Origin of Angiosperms and Biological Consequences, pp.17-49; E.M. Friis, W.G. Chaloner, and P.R. Crane (eds.). Cambridge: Cambridge Univ. Press.

21. Donoghue, M.J. and P.D. Cantino. 1988. Paraphyly, ancestors, and the goals of taxonomy: a botanical defense of cladism. Bot. Rev. 54:107-128.

22. de Queiroz, K. and M.J. Donoghue. 1988. Phylogenetic systematics and the species problem. Cladistics 4:317-338.

23. Donoghue, M.J. and J.A. Doyle. 1989. Phylogenetic analysis of angiosperms and the relationships of Hamamelidae. In Evolution, Systematics and Fossil History of the Hamamelidae, Vol.1, pp.17-45; P. Crane and S. Blackmore (eds.). Oxford: Clarendon Press.

24. Donoghue, M.J. and J.A. Doyle. 1989. Phylogenetic studies of seed plants and angiosperms based on morphological characters. In The Hierarchy of Life, pp.181-193; B. Fernholm, K. Bremer, and H. Jornvall (eds.). Nobel Symposium 70. Amsterdam: Elsevier Publ.

25. Donoghue, M.J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156.

26. Crane, P.R., M.J. Donoghue, J.A. Doyle, and E.M. Friis. 1989. Angiosperm origins. Nature 342:131.

27. Donoghue, M.J., J.A. Doyle, J. Gauthier, A.G. Kluge, and T. Rowe. 1989. The importance of fossils in phylogeny reconstruction. Ann. Rev. Ecol. Syst. 20:431- 460.

28. Sanderson, M.J. and M.J. Donoghue. 1989. Patterns of variation in levels of homoplasy. Evolution 43:1781-1795.

29. de Queiroz, K. and M.J. Donoghue. 1990. Phylogenetic systematics or Nelson's version of cladistics? Cladistics 6:61-76.

30. Donoghue, M.J. 1990. Sociology, selection, and success: a critique of David Hull's analysis of science and systematics. Biol. Phil. 5:125-138.

31. de Queiroz, K. and M.J. Donoghue. 1990. Phylogenetic systematics and species revisited. Cladistics 6:83-90.

32. Donoghue, M.J. 1990. Why parsimony? (Review of Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Interference. Cambridge: M.I.T. Press.) Evolution 44:1121-1123.

33. Donoghue, M.J. and J.A. Doyle. 1991. Angiosperm monophyly. Trends Ecol. Evol. 6:407.

34. Barrett, M., M.J. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486-493.

35. Donoghue, M.J. and M.J. Sanderson. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. In Molecular Systematics in Plants, pp.340-368; P.S. Soltis, D.E. Soltis, and J.J. Doyle (eds.). New York: Chapman and Hall.

36. Donoghue, M.J., R.G. Olmstead, J.F. Smith, and J.D. Palmer. 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Missouri Bot. Gard. 79:333-345.

37. Donoghue, M.J. and J.W. Kaderiet. 1992. Walter Zimmerman and the growth of phylogenetic theory. Syst. Biol. 41:74-85.

38. Donoghue, M.J. and S.M. Scheiner. 1992. The evolution of endosperm: a phylogenetic account. In Ecology and Evolution of Plant Reproduction: New Approaches, pp.356-389; R. Wyatt (ed.). New York: Chapman and Hall.

39. Doyle, J.A. and M.J. Donoghue. 1992. Fossils and seed plant phylogeny revisited. Brittonia 44:89-106.

40. Donoghue, M.J. 1992. Homology. In Keywords in Evolutionary Biology; pp. 170-179; E. Fox Keller and E. Lloyd (eds.). Cambridge: Harvard Univ. Press.

41. Doyle, J.A. and M.J. Donoghue. 1993. Phylogenies and angiosperm diversification. Paleobiology 19:141-167.

42. Wojciechowski, M.F., M.J. Sanderson, B.G. Baldwin, and M.J. Donoghue. 1993. Monophyly of the aneuploid species of Astragalus: evidence from nrDNA internal transcribed spacer sequences. Amer. Jour. Bot. 80:711-722.

43. Barrett, M., M. J. Donoghue, and E. Sober. 1993. Crusade? A reply to Nelson. Syst. Biol. 42:216-217.

44. Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson, J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue. 1993. The growth of phylogenetic information and the need for a phylogenetic database. Syst. Biol. 42:562-568.

45. Judd, W.S., R.W. Sanders, and M.J. Donoghue. 1994. Angiosperm family pairs-- preliminary phylogenetic analyses. Harvard Papers in Botany 5:1-51.

46. Donoghue, M. J. and M. J. Sanderson. 1994. Complexity and homology in plants. In Homology: The Hierarchical Basis of Comparative Biology; pp. 393-421; B. Hall (ed.). San Diego: Academic Press.

47. Sanderson, M. J. and M. J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:1590-1593.

48. Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields. 1994. Interoperability of biological databases: a meeting report. Syst. Biol. 42:562-568.

49. Doyle, J. A., M. J. Donoghue, and E. A. Zimmer. 1994. Integration of morphological and ribosomal RNA data on the origin of angiosperms. Ann. Missouri Bot. Gard. 81:419-450.

50. Donoghue, M. J. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Missouri Bot. Gard. 81:405-418.

51. Weller, S. G., M. J. Donoghue, and D. Charlesworth. 1995. The evolution of self- incompatibility in flowering plants: a phylogenetic approach. In Experimental

and Molecular Approaches to Plant Biosystematics; pp. 355-382; P. C. Hoch and

A. G. Stephenson (eds.). St. Louis: Missouri Bot. Gard.

52. Baldwin, B. G., M. J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell, and M. J. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82:247-277.

53. Baum, D. A. and M. J. Donoghue. 1995. Choosing among alternative "phylogenetic" species concepts. Syst. Bot. 20:560-573.

54. Campbell, C. S., M. J. Donoghue, B. G. Baldwin, and M. F. Wojciechowski. 1995. Phylogenetic relationships in Maloideae (Rosaceae): Evidence from sequences of internal transcribed spacers of nuclear ribosomal DNA and its congruence with morphology. Amer. Jour. Bot. 82:903-918.

55. Hibbett, D. S. and M. J. Donoghue. 1995. Progress toward a phylogenetic classification of the Polyporaceae through parsimony analysis of mitochondrial ribosomal DNA sequences. Can. Jour. Bot. 73:S853-S861.

56. Manchester, S. R. and M. J. Donoghue. 1995. Winged fruits of Linnaeeae (Caprifoliaceae) in the Tertiary of Western North America: Diplodipelta gen. nov. Int. Jour. Plant Sci. 156:709-722.

57. Hibbett, D. S., Y Fukumasa-Nakai, A. Tsuneda, and M. J. Donoghue. 1995. Phylogenetic diversity in shiitake inferred from ribosomal DNA sequences. Mycologia 87:618-638.

58. Ackerly, D. D. and M. J. Donoghue. 1995. Phylogeny and ecology reconsidered. Jour. Ecology 83:730-733.

59. Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1995. Cretaceous mushrooms in amber. Nature 377:487.

60. de Queiroz, A., M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Ann. Rev. Ecol. Syst. 26:657-681.

61. Sanderson, M. J. and M. J. Donoghue. 1996. Reconstructing shifts in diversification on phylogenetic trees. Trends Ecol. Evol. 11:15-20.

62. Hibbett, D. S. and M. J. Donoghue. 1996. Implications of phylogenetic studies for conservation of genetic diversity in shiitake mushrooms. Conser. Biol. 10:1321-1327.

63. Sanderson, M. J. and M. J. Donoghue. 1996. The relationship between homoplasy and confidence in a phylogenetic tree. Pp. 67-89 in Homoplasy and the Evolutionary Process, M. J. Sanderson and L. Hufford (eds.). San Diego: Academic Press.

64. Donoghue, M. J. and D. D. Ackerly. 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. Phil. Trans. Roy. Soc. 351:1241-1249. (Reprinted in: Silvertown, J., M. Franco, and J. L. Harper. 1997. Plant Life Histories: Ecology, Phylogeny and Evolution. Cambridge Univ. Press.)

65. Backlund, A. and M. J. Donoghue. 1996. Morphology and phylogeny of the order Dipsacales. In Phylogeny of the Dipsacales, A. Backlund, Doctoral Dissertation. Uppsala: Department of Systematic Botany, Uppsala Univ.

66. Campbell, C. S., M. F. Wojciechowski, B. G. Baldwin, L. A. Alice, and M. J. Donoghue. 1997. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14:81-90.

67. Donoghue, M.J. 1997. Viburnum. In A flora of the Chihuauan Desert region; M.D.

Johnston (ed.) privately published?

68. Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1997. Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of homobasidiomycetes. Amer. Jour. Bot. 84: 981-991.

69. Hibbett, D. S., M. J. Donoghue, and P. B. Tomlinson. 1997. Is Phellinites digiustoi the oldest homobasidiomycete? Amer. Jour. Bot. 84: 1005-1011.

70. Sang, T., M. J. Donoghue, and D. Zhang. 1997. Evolution of alcohol dehydrogenase genes in peonies (Paeonia): Phylogenetic relationships of putative non-hybrid species. Molec. Biol. Evol. 14:994-1007.

71. Rice, K. A., M. J. Donoghue, and R. G. Olmstead. 1997. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46: 554-563.

72. Hibbett, D. S., E. M. Pine, E. Langer, G. Langer, and M. J. Donoghue. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc. Nat. Acad. Sci. USA 94: 12002-12006.

73. Eriksson, T. and M. J. Donoghue. 1997. Phylogenetic analyses of Sambucus and Adoxa (Adoxoideae, Adoxaceae) based on nuclear ribosomal ITS sequences and preliminary morphological data. Syst. Bot. 22: 555-573.

74. Donoghue, M. J., and S. Mathews. 1998. Duplicate genes and the root of angiosperms, with an example using phytochrome genes. Mol. Phyl. Evol. 9: 489-500.

75. Hibbett, D. S. and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90: 347-356.

76. Donoghue, M. J., R. H. Ree, and D. A. Baum. 1998. Phylogeny and the evolution of flower symmetry in the Asteridae. Trends Plant Sci. 3: 311-317.

77. Eriksson, T., M. J. Donoghue, and M. S. Hibbs. 1998. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Syst. Evol. 211: 155-179.

78. Hibbett, D. S., K. Hansen, and M. J. Donoghue. 1998. Phylogeny and biogeography of Lentinula inferred from an expanded rDNA dataset. Mycol. Res. 102: 1041-1049.

79. Ackerly, D. D. and M. J. Donoghue. 1998. Leaf size, sapling allometry, and Corner's rules: Phylogeny and correlated evolution in maples (Acer). Amer. Nat. 152: 767-791.

80. Feild, T. S., M. A. Zwieniecki, M. J. Donoghue, and N. M. Holbrook. 1998. Stomatal plugs of Drimys winteri (Winteraceae) protect leaves from mist but not drought. Proc. Nat. Acad. Sci. USA 95: 14256-14259.

81. Ree, R. H. and M. J. Donoghue. 1998. Step matrices and the interpretation of homoplasy. Syst. Biol. 47: 582-588.

82. Harrington, F. A., D. H. Pfister, D. Potter, and M. J. Donoghue. 1999. Phylogenetic studies within the Pezizales. I. 18s rRNA sequence data and classification. Mycologia 91: 41-50.

83. Li, J. and M. J. Donoghue. 1999. More molecular evidence for the interspecific relationships of Liquidambar (Hamamelidaceae). Rhodora 101: 87-91.

84. Wood, E. W., T. Eriksson, and M. J. Donoghue. 1999. Guidelines for the use of herbarium materials in molecular research. In Managing the Modern Herbarium, D. Metzger (ed.) Univ. Toronto. 265-276.

85. Donoghue, M. J. 1999. Foreword. Pp. xi-xii in Plant Systematics: A Phylogenetic Approach (W. S. Judd, C. S. Campbell, E. A. Kellogg, and P. F. Stevens). Sinauer Assoc: Sunderland, MA.

86. Ree, R. H. and M. J. Donoghue. 1999. Inferring rates of change in flower symmetry in asterid angiosperms. Syst. Biol. 48 633-641.

87. Mathews, S. and M. J. Donoghue. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950.

88. Li, J., A. L. Bogle, and M. J. Donoghue. 1999. Phylogenetic relationships in the Hamamelidoideae inferred from sequences of trn non-coding regions of chloroplast DNA. Harvard Papers in Botany 4: 343-356.

89. Cantino, P. D., H. N. Bryant, K. de Queiroz, M. J. Donoghue, T. Eriksson, D. M. Hillis, and M. S. Y. Lee. 1999. Species names in phylogenetic nomenclature. Syst. Biol. 48: 790-807.

90. Pine, E. M., D. S. Hibbett, and M. J. Donoghue. 1999. Phylogenetic relationships of cantharelloid and clavarioid homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. Mycologia 91: 944-963.

91. Chang, B. S. and M. J. Donoghue. 2000. Recreating ancestral proteins. Trends Ecol. Evol. 15: 109-114.

92. Donoghue. M. J. and J. A. Doyle. 2000. Demise of the anthophyte hypothesis? Current Biology 10: R106-R109.

93. Weiblen, G., R. Oyama, M. J. Donoghue. 2000. Phylogenetic analysis of breeding system evolution in monocotyledons. Amer. Nat. 155: 46-58.

94. Donoghue, M. J. and W. S. Alverson. 2000. A new age of discovery. Ann. Missouri Bot. Gard. 87: 110-126.

95. Robeck, H. E., C. C. Maley, and M. J. Donoghue. 2000. Taxonomy and temporal diversity patterns. Paleobiology 26: 171-187.

96. Gould, K. R. and M. J. Donoghue. 2000. Phylogeny and biogeography of Triosteum (Caprifoliaceae). Harvard Papers in Botany 5: 157-166.

97. Li, J., A. L. Bogle, A. S. Klein, and M. J. Donoghue. 2000. Phylogeny and biogeography of Hamamelis (Hamamelidaceae). Harvard Papers in Botany 5: 171-178.

98. Hibbett, D. S., L. B. Gilbert, and M. J. Donoghue. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407: 506-508.

99. Urbatsch, L. E., B. G. Baldwin, and M. J. Donoghue. 2000. Phylogeny of the coneflowers (Heliantheae: Asteraceae) based on nuclear rDNA internal transcribed spacer sequences. Syst. Bot. 25: 539-565.

100. Feild, T. S., M. A Zweinieki, T. Brodribb, M. J. Donoghue, and N. M. Holbrook. 2000. Structure and function of tracheary elements in Amborella trichopoda. Int. Jour. Plant Sci. 161: 705-712.

101. Mathews, S. and M. J. Donoghue. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. Journ. Plant Sci. 161: S41-S55.

102. Hibbett, D. S. and M. J. Donoghue. 2000. Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Syst. Biol. 50: 215-242.

103. Donoghue, M. J. and R. H. Ree. 2000. Homoplasy and developmental constraint: A model and an example from plants. Amer. Zool. 40: 759-769.

104. Baum, D. A. and M. J. Donoghue. 2001. A likelihood framework for the phylogenetic analysis of adaptation. Pp. 24-44 in Adaptation and Optimality (S. Orzack and E. Sober, eds.) Cambridge Univ. Press, New York.

105. Li, J., D. E. Boufford, and M. J. Donoghue. 2001. Phylogenetics of Buckleya (Santalaceae) based on ITS sequences of nuclear ribosomal DNA. Rhodora 103: 137-150.

106. Davis, C. C., W. R. Anderson, and M. J. Donoghue. 2001. Phylogeny of

Malpighiaceae: Evidence from chloroplast ndhF and trnL-F nucleotide sequences.

Amer. Jour. Bot. 88: 1830-1846.

107. Li, J., C. C. Davis, P. Del Tredici, and M. J. Donoghue. 2001. Phylogeny and Biogeography of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA. Harvard Papers in Botany 6:267-274.

108. Li, J., C. C. Davis, M. J. Donoghue, S. Kelley, and P. Del Tredici. 2001. Phylogenetic relationships of Torreya (Taxaceae) inferred from sequences of the nuclear ribosomal DNA ITS region. Harvard Papers in Botany 6: 275-281.

109. Donoghue. M. J., C. D. Bell, and J. Li. 2001. Phylogenetic patterns in Northern Hemisphere plant geography. Int. J. Plant. Sci. 162: S41-S52.

110. Manos, P. S. and M. J. Donoghue. 2001. Progress in Northern Hemisphere phytogeography. Int. Jour. Plant Sci. 162: S1-S2.

111. Donoghue, M. J. 2001. A wish list for Systematic Biology. Syst. Biol. 50: 755-757.

112. Donoghue, M. J., T. Eriksson, P. A. Reeves, and R. G. Olmstead. 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany 6: 459-479.

113. Bell, C. D., E. J. Edwards, S. T. Kim, and M. J. Donoghue. 2001. Dipsacales phylogeny based on chloroplast DNA sequences. Harvard Papers in Botany 6: 481-499.

114. Davis, C. C., P. W. Fritsch, J. Li, and M. J. Donoghue. 2002. Phylogeny and biogeography of Cercis (Fabaceae): Evidence from chloroplast ndhF and nuclear ribosomal ITS sequences. Systematic Botany 27: 289-302.

115. Baum, D. A. and M. J. Donoghue. 2002. Transference of function, heterotopy, and the evolution of plant development. Pp. 52-69 in Developmental Genetics and Plant Evolution (Q. Cronk, R. Bateman, and J. Hawkins, eds.), Taylor and Francis, London.

116. Davis, C. C., C. D. Bell, S. Mathews, and M. J. Donoghue. 2002. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proc. Natl. Acad. Sci. USA 99: 6833-6837.

117. Zanis, M. J., D. E. Soltis, P. S. Soltis, S. Mathews,and M. J. Donoghue. 2002. The root of the angiosperms revisited. Proc. Natl. Acad. Sci. USA 99: 6848-6853.

118. Chang, B. S. W., K. Jonsson, M. Kazmi, M. J. Donoghue, and T. P. Sakmar. 2002 Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19: 1483-1489.

119. Donoghue, M. J. 2002. Plants. Pp. 911-918 in Encyclopedia of Evolution, Vol. 2 (M. Pagel, ed.), Oxford Univ. Press. Oxford, UK.

120. Li, J., P. Del Tredici, S. Yang, and M. J. Donoghue. 2002. Phylogenetic relationships and biogeography of Stewartia (Camellioideae, Theaceae) inferred from nuclear ribosomal DNA ITS sequences. Rhodora 104: 117-133.

121. Webb, C. O., D. D. Ackerly, M. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Ann. Rev. Ecol. Syst. 33: 475-505. (awarded the 2008 William Skinner Cooper Award of the Ecological Society of America)

122. Judd, W. S., C. S. Campbell, E. A. Kellogg, P. F. Stevens, and M. J. Donoghue. 2002. Plant Systematics: A Phylogenetic Approach. 2nd Edition. Sinauer Assoc., Sunderland, MA.

123. Judd, W. S., D. Nickrent, K. Robertson, C. S. Campbell, E. A. Kellogg, P. F. Stevens, and M. J. Donoghue. 2002. A Photo Gallery of Vascular Plants. A companion to Plant Systematics: A Phylogenetic Approach. 2nd Edition. Sinauer Assoc., Sunderland, MA.

124. Piel, W. H., M. J. Donoghue, and M. J. Sanderson. 2002. TreeBASE: a database of phylogenetic knowledge. Pp. 41-47 in: J. Shimura, K. Wilson, and D. Gordon, eds. The interoperable "Catalog of Life.” Research Report, National Institute for Environmental Studies No. 171, Tsukuba, Japan.

125. Eriksson, T., M. S. Hibbs, A. D. Yoder, C. Delwiche, and M. J. Donoghue, 2003. The phylogeny of Rosoideae (Rosaceae) enhanced by combining sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA with the trnL/F region of chloroplast DNA. Int. Jour. Plant Sci. 164: 197-211.

126. Mathews, S., J. G. Burleigh, and M. J. Donoghue. 2003. Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol. Biol. Evol. 20: 1087-1097.

127. Donoghue, M. J. and B. R. Moore. 2003. Toward an integrative historical biogeography. Integrative and Comparative Biology 43: 261-270.

128. Piel, W. H., M. J. Sanderson, and M. J. Donoghue. 2003. The small-world dynamics of tree networks and data mining in phyloinformatics. Bioinformatics 19: 1162-1168.

129. Li, J., D. Zhang, and M. J. Donoghue. 2003. Phylogeny and biogeography of Chamaecyparis (Cupressaceae) inferred from DNA sequences of the nuclear ribosomal ITS region. Rhodora 105: 106-117.

130. Nakhleh, L., D. Miranker, F. Barbancon, W. Piel, and M. Donoghue. 2003. Requirements of phylogenetic databases. In Proc. 3rd IEEE Symp. on Bioinformatics and Bioengineering (BIBE’03): 141-148.

131. Donoghue, M. J., C. D. Bell, and R. C. Winkworth. 2003. The evolution of reproductive characters in Dipsacales. Int. Jour. Plant Sci. 164: S453-S464.

132. Bell, C. B. and M. J. Donoghue. 2003. Phylogeny of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences. Organisms, Evolution, and Diversity 3: 227-237.

133. Feild, T. S., N. C. Arens, J. A. Doyle, T. E. Dawson, and M. J. Donoghue. 2004. Dark and disturbed: a new image of early angiosperm ecology. Paleobiology 30: 82-107.

134. Schultheis, L. M. and M. J. Donoghue. 2004. Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia). Syst. Bot. 29: 77-96.

135. Donoghue, M. J., B. G. Baldwin, J. Li, and R. C. Winkworth. 2004. Viburnum phylogeny based on the chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Syst. Bot. 29: 188-198.

136. Cracraft, J. and M. J. Donoghue (eds.). 2004. Assembling the Tree of Life. Oxford University Press, New York.

137. Donoghue, M. J. and J. Cracraft. 2004. Charting the Tree of Life. Pp. 1-4 in Cracraft, J. and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford University Press, New York.

138. Donoghue, M. J. 2004. Immeasurable Progress on the Tree of Life. Pp. 548-552 in Cracraft, J. and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford University Press, New York.

139. Cracraft, J. and M. J. Donoghue. 2004. Assembling the Tree of Life: Where We Stand at the Beginning of the 21st Century. Pp. 553-561 in Cracraft, J. and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford University Press, New York.

140. Moore, B. R., K. M. A. Chan, and M. J. Donoghue. 2004. Detecting diversification rate variation in supertrees. Pp. 487-533 in O. Bininda-Emonds, ed. Phylogenetic supertrees: Combining information to reveal the tree of life. Kluwer Academic, New York.

141. Donoghue, M. J. and J. A. Gauthier. 2004. Implementing the PhyloCode. Trends Ecol. Evol. 19: 281-282.

142. Winkworth R. C. and M. J. Donoghue. 2004. Viburnum phylogeny: Evidence from the duplicated nuclear gene GBSSI. Mol. Phyl. Evol. 33: 109-126.

143. Donoghue, M. J. and S. A. Smith. 2004. Patterns in the assembly of temperate forests around the Northern Hemisphere. Phil. Trans. Roy. Soc. London B 359: 1633-1644.

144. Wiens, J. J. and M. J. Donoghue. 2004. Historical biogeography, ecology, and species richness. Trends Ecol. Evol. 19: 639-644.

145. Webb, C. O. and M. J. Donoghue. 2004. Phylomatic: tree retrieval for applied phylogenetics. Molecular Ecology Notes 5: 181-183.

146. Bell, C. D. and M. J. Donoghue. 2005. Dating the diversification of Dipsacales: comparing models, genes, and evolutionary implications. Amer. Jour. Bot. 92: 284-296.

147. Clark, L. G. and M. J. Donoghue. 2005. John H. Beaman - Recipient of the 2004 Asa Gray Award. Syst. Bot. 1-6.

148. Davis, C. C., C. O. Webb, K. J. Wurdack, C. A. Jaramillo, and M. J. Donoghue. 2005. Explosive radiation of Malpighiales suggests a mid-Cretaceous origin of rain forests. Amer. Nat. E36-E65.

149. Donoghue, M. J. 2005. Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31(2): 77-93.

150. Winkworth, R.C., and M. J. Donoghue. 2005. Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography. Amer. Jour. Bot. 92: 653-666.

151. Bell, C. D. and M. J. Donoghue. 2005. Phylogeny and biogeography of the Valerianaceae (Dipsacales) with special reference to the South American valerians. Organisms, Evolution, and Diversity 5: 147-159.

152. Howarth, D. G. and M. J. Donoghue. 2005. Duplications in the CYC-like genes of Dipsacales correlate with floral form. Int. J. Plant Sci. 166: 357-370.

153. Edwards, E. J. and M. J. Donoghue. 2005. Basal cactus phylogeny: Implications of Pereskia paraphyly for the transition to the cactus life form. Amer. Jour. Bot. 92: 1177-1188.

154. Ree, H. R., B. R. Moore, C. Webb, and M. J. Donoghue. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59: 2299-2311.

155. Donoghue, M. J. 2005. Comparisons, phylogeny, and teaching evolution. Pp. 69-77 in Cracraft, J. and R. Bybee (eds.). Evolutionary science and society: educating a new generation. Proceedings of the BSCS, AIBS Symposium. American Institute of Biological Sciences and BSCS, Colorado Springs, CO.

156. Donoghue, M. J. and M. Smith. 2005. Biodiversity inventory: Reflections on preparedness and efficiency. Pp. 79-86 in Biodiversity: Science and Governance (J-P Le Duc, ed.); Paris, France.

157. Webb, C. O., G. S. Gilbert, and M. J. Donoghue. 2006. Phylodiversity dependent seedling mortality, size structure, and disease in a Bornean rain forest. Ecology 87: S123-S131.

158. Edwards, E. J. and M. J. Donoghue. 2006. Origin of the cactus life form. American Naturalist 167: 777-793.

159. Moore, B, R., S. A. Smith, and M. J. Donoghue. 2006. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Syst. Biol. 55: 662-676.

160. Howarth, D. G. and M. J. Donoghue. 2006. Phylogenetic analyses of the “ECE ” (CYC/TB1) clade reveal duplications that predate the core eudicots. Proc. Nat. Acad. Sci. USA 103: 9101-9106.

161. Loreau, M. et al. 2006. Diversity without representation. Nature 442: 245-246.

162. Edwards, E. J., C. J. Still, and M. J. Donoghue. 2007. The relevance of phylogeny to studies of global change. Trends Ecol. Evol. 22: 243-249.

163. Yahara, T. and M. J. Donoghue. 2007. bioGENESIS – a new DIVERSITAS Core Project is launched. DWIPA Newsletter 21: 1-2.

164. Cantino, P. D., J. A. Doyle, S. W. Graham W. S. Judd, R. G. Olmstead, P. S. Soltis, D. E. Soltis, , and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56: 822-846.

165. Cantino, P. D., J. A. Doyle, S. W. Graham W. S. Judd, R. G. Olmstead, P. S. Soltis, D. E. Soltis, , and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56: E1-E44. (Electronic Supplement)

166. Judd, W. S., C. S. Campbell, E. A. Kellogg, P. F. Stevens, and M. J. Donoghue. 2007. Plant Systematics: A Phylogenetic Approach. 3rd Edition. Sinauer Assoc., Sunderland, MA.

167. Judd, W. S., D. Nickrent, K. Robertson, C. S. Campbell, E. A. Kellogg, and M. J. Donoghue. 2007. A Photo Gallery of Vascular Plants. A companion to Plant Systematics: A Phylogenetic Approach. 3rd Edition. Sinauer Assoc., Sunderland, MA.

168. Moore, B. R. and M. J. Donoghue. 2007. Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. Amer. Nat. S28-S55.

169. Körner, C., M. Donoghue, T. Fabbro, C. Häuser, D. Noguès, M. T. Kalin Arroyo, J. Soberon, L. Speers, E. M. Spehn, H. Sun, A. Tribsch, P. Tykarski, and N. Zbinden. 2007. The Kazbegi Research Agenda of GMBA-DIVERSITAS: For creative use of mountain biodiversity databases. Mountain Research and Development 27: 276-281.

170. Winkworth, R. C., J. Lundberg, and M. J. Donoghue. 2008. Toward a resolution of campanulid phylogeny, with special reference to the placement of Dipsacales. Taxon 57: 1-13.

171. Winkworth, R. C., C. D. Bell, and M. J. Donoghue. 2008. Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection. Mol. Phyl. Evol. 46: 830-843.

172. Theis, N., M. J. Donoghue, and J. Li. 2008. Phylogenetics of the Caprifolieae and Lonicera (Dipsacales) based on nuclear and chloroplast DNA sequences. Syst. Bot. 33: 776-783.

173. Havill, N. P., C. S. Campbell, T. F. Vining, B. LePage, and M. J. Donoghue. 2008. Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Syst. Bot. 33: 478-489.

174. Kim, S.-T. and M. J. Donoghue. 2008. Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae). Syst. Bot. 33: 77-86.

175. Jacobs, B., M. J. Donoghue, F. Bouman, S. Huysmans, and E. Smets. 2008. The phylogenetic value and evolution of endocarp and seed characters within Viburnum (Adoxaceae). Int. J. Plant Sci. 169(3): 409-431.

176. Kim, S-T., S. E. Sultan, and M. J. Donoghue. 2008. Allopolyploid speciation in Persicaria (Polygonaceae): Insights from a low-copy nuclear marker. Proc. Nat. Acad. Sci. USA 105: 12370-12375.

177. Donoghue, M. J. 2008. A phylogenetic perspective on the distribution of plant diversity. Proc. Nat. Acad. Sci. USA 105 (Suppl. 1): 11549-11555.

178. Smith, S. A., D. C. Tank, L. A. Boulanger, C. A. Bascom-Slack, K. Eisenman, D. Kingery, B. Babbs, K. Fenn, J. S. Greene, B. D. Hann, J. Keehner, E. G. Kelley-Swift, V. Kembaiyan, S. J. Lee , P. Li, D. Y. Light, E. H. Lin, C. Ma, E. Moore, M. A. Schorn, D. Vekhter, P. V. Nunez, G. A. Strobel, M. J. Donoghue, S. A. Strobel. 2008. Bioactive endophytes warrant intensified exploration and conservation. PLoS ONE 3, e3052.

179. Kim, S-T. and M. J. Donoghue. 2008. Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). Amer. Jour. Bot. 95: 1122-1135.

180. Smith, S. A. and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.

181. Hong, D-Y., Z-D. Chen, Y-L. Qui, and M. J. Donoghue. 2008. Tracing patterns of evolution through the Tree of Life: Introduction. Jour. Syst. Evol. 46: 237-238.

182. Cellinese, N., S. A. Smith, E. J. Edwards, S-T. Kim, M. Avramakis, and M. J. Donoghue. 2009. Historical biogeography of the endemic Campanulaceae of Crete. Jour. Biogeography 36: 1253-1269.

183. Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, and diversification of the “bird cage” evening primroses (Oenothera sections Anogra and Kleinia). Amer. Nat. 173: 225-240. (President’s Award for Best Paper of the Year, American Society of Naturalists, 2010)

184. Carlson, S. E., V. Mayer, and M. J. Donoghue. 2009. Phylogenetic relationships, taxonomy, and morphological evolution in Dipsacaceae (Dipsacales) inferred by DNA sequence data. Taxon 58: 1075-1091

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