Michael J. Donoghue, Ph.D.
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Email: michael.donoghue@yale.edu
My research all revolves in one way or another around understanding phylogeny. My empirical work focuses primarily on plant diversity and evolution. In particular, I have long term interests in Viburnum and Dipsacales, and in the origin and early evolution of flowering plants. In collaboration with former students, postdocs, and lab visitors, I have also published molecular phylogenetic analyses of a number of other angiosperm groups. And, with former postdoc David Hibbett I have published a series of papers on the phylogeny of basidiomycetes, especially shiitake mushrooms.
I have also worked on a number of conceptual or theoretical issues. Specifically, I have been interested in the notion of species, in patterns in the distribution of homoplasy, in character evolution and comparative methods, in phylogenetic nomenclature, and in combining data from various sources. But I've published on some other conceptual issues, including methods for assessing the direction of evolution, the analysis of large data sets, and identifying shifts in diversification rate. Finally, I helped build and still coordinate the development of a relational database of phylogenetic knowledge called TreeBASE (web site).
Previous graduate students and postdocs in the lab have worked on a wide variety of projects, but again these are united by an interest in phylogeny. In general, graduate student dissertation projects have entailed working with some group of organisms (usually a plant group), but have tended to also involve some theoretical work. For example, Mike Sanderson worked on a large legume clade, Astragalus, and linked this to theoretical work on homoplasy. Likewise, George Weiblen combined empirical work on the phylogeny of figs and fig wasp with theoretical work on comparing phylogenies and on using phylogenies to understand the structure of ecological communities. To the extent that it seems reasonable, I've also tried to encourage a side project or two. For example, Rick Ree has been pursuing an interest in methods for inferring rates of character change in a phylogeny.
Several of my interests are not yet well reflected in publications. In particular, I have been doing field work in China over the last four years, especially in the eastern Himalayan region of Qinghai, Sichuan, and Yunnan. Some of the information on these trips is now in a specimen database on the web. This work connects with another major interest: the biogeography and the historical assembly of plant communities around the Northern Hemisphere.
1980-85
Donoghue, M.J. 1980. Flowering times in Viburnum. Arnoldia 40:2-22.
Donoghue, M.J. 1981. Growth patterns in woody plants with examples from the genus Viburnum. Arnoldia 41:2-23.
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.
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.
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.]
Donoghue, M.J. 1983. A preliminary analysis of phylogenetic relationships in Viburnum (Caprifoliaceae s.l.). Syst. Bot. 8:45-58.
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.
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.
Maddison, W.P., M.J. Donoghue, and D.R. Maddison. 1984. Outgroup analysis and parsimony. Syst. Zool. 33:83-103.
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.
Donoghue, M.J. 1985. Pollen diversity and exine evolution in Viburnum and the Caprifoliaceae sensu lato. Jour. Arnold Arb. 66:421-469.
Donoghue, M.J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist 88:172-181.
1986
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.
Donoghue, M.J. and W.P. Maddison. 1986. Polarity assessment in phylogenetic systematics: a response to Meacham. Taxon 35:534-538.
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.
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.
1987
Donoghue, M.J. 1987. Experiments and hypotheses in systematics. Taxon 36:584-587.
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.
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.
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.
1988
Donoghue, M.J. 1988. Viburnum. In Chihuahuan Desert Flora; M.D. Johnston (ed.) (in press).
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.
de Queiroz, K. and M.J. Donoghue. 1988. Phylogenetic systematics and the species problem. Cladistics 4:317-338.
1989
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.
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.
Donoghue, M.J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156.
Crane, P.R., M.J. Donoghue, J.A. Doyle, and E.M. Friis. 1989. Angiosperm origins. Nature 342:131.
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.
Sanderson, M.J. and M.J. Donoghue. 1989. Patterns of variation in levels of homoplasy. Evolution 43:1781-1795.
1990
de Queiroz, K. and M.J. Donoghue. 1990. Phylogenetic systematics or Nelson's version of cladistics? Cladistics 6:61-76.
Donoghue, M.J. 1990. Sociology, selection, and success: a critique of David Hull's analysis of science and systematics. Biol. Phil. 5:125-138.
de Queiroz, K. and M.J. Donoghue. 1990. Phylogenetic systematics and species revisited. Cladistics 6:83-90.
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.
1991
Donoghue, M.J. and J.A. Doyle. 1991. Angiosperm monophyly. Trends Ecol. Evol. 6:407.
Barrett, M., M.J. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486- 493.
1992
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.
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.
Donoghue, M.J. and J.W. Kaderiet. 1992. Walter Zimmerman and the growth of phylogenetic theory. Syst. Biol. 41:74-85.
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.
Doyle, J.A. and M.J. Donoghue. 1992. Fossils and seed plant phylogeny revisited. Brittonia 44:89-106.
Donoghue, M.J. 1992. Homology. In Keywords in Evolutionary Biology; pp. 170-179; E. Fox Keller and E. Lloyd (eds.). Cambridge: Harvard Univ. Press.
1993
Doyle, J.A. and M.J. Donoghue. 1993. Phylogenies and angiosperm diversification. Paleobiology 19:141-167.
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.
Barrett, M., M. J. Donoghue, and E. Sober. 1993. Crusade? A reply to Nelson. Syst. Biol. 42:216-217.
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.
1994
Judd, W.S., R.W. Sanders, and M.J. Donoghue. 1994. Angiosperm family pairs-- preliminary phylogenetic analyses. Harvard Papers in Botany 5:1-51.
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.
Sanderson, M. J. and M. J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:1590-1593.
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.
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.
Donoghue, M. J. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Missouri Bot. Gard. 81:405-418.
1995
Weller, S. G., M. J. Donoghue, and D. Charlesworth. 1995. The evolution of self- incompatibility in angiosperms: 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.
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.
Baum, D. A. and M. J. Donoghue. 1995. Choosing among alternative "phylogenetic" species concepts. Syst. Bot. 20:560-573.
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.
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.
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.
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.
Ackerly, D. D. and M. J. Donoghue. 1995. Phylogeny and ecology reconsidered. Jour. Ecology 83:730-733.
Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1995. Cretaceous mushrooms in amber. Nature 377:487.
de Queiroz, A., M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Ann. Rev. Ecol. Syst. 26:657-681.
1996
Sanderson, M. J. and M. J. Donoghue. 1996. Reconstructing shifts in diversification on phylogenetic trees. Trends Ecol. Evol. 11:15-20.
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.
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.
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.)
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.
1997
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.
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.
Hibbett, D. S., M. J. Donoghue, and P. B. Tomlinson. 1997. Is Phellinites digiustoi the oldest homobasidiomycete? Amer. Jour. Bot. 84: 1005-1011.
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.
Rice, K. A., M. J. Donoghue, and R. G. Olmstead. 1997. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46: 554-563.
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.
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.
1998
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.
Hibbett, D. S. and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90: 347-356.
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.
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.
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.
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.
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.
Ree, R. H. and M. J. Donoghue. 1998. Step matrices and the interpretation of homoplasy. Syst. Biol. 47: 582-588.
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.
1999
Li, J. and M. J. Donoghue. 1999. More molecular evidence for the interspecific relationships of Liquidambar (Hamamelidaceae). Rhodora 101: 87-91.
Wood, E. W., T. Eriksson, and M. J. Donoghue. 1999. Strategies for using herbarium materials for molecular research. In Managing the Modern Herbarium, D. Metzger (ed.) Univ. Toronto.
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.
Ree, R. H. and M. J. Donoghue. 1999. Inferring rates of change in flower symmetry in asterid angiosperms. Syst. Biol. 48 633-641.
Mathews, S. and M. J. Donoghue. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950.
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.
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.
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.
2000
Chang, B. S. and M. J. Donoghue. 2000. Recreating ancestral proteins. Trends Ecol. Evol. 15: 109-114.
Donoghue. M. J. and J. A. Doyle. 2000. Demise of the anthophyte hypothesis? Current Biology 10: R106-R109.
Weiblen, G., R. Oyama, M. J. Donoghue. 2000. Phylogenetic analysis of breeding system evolution in monocotyledons. Amer. Nat. 155: 46-58.
Donoghue, M. J. and W. S. Alverson. 2000. A new age of discovery. Ann. Missouri Bot. Gard. 87: 110-126.
Robeck, H. E., C. C. Maley, and M. J. Donoghue. 2000. Taxonomy and temporal diversity patterns. Paleobiology 26: 171-187.
Gould, K. R. and M. J. Donoghue. 2000. Phylogeny and biogeography of Triosteum (Caprifoliaceae). Harvard Papers in Botany 5: 157-166.
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.
Hibbett, D. S., L. B. Gilbert, and M. J. Donoghue. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407: 506-508.
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.
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.
Hibbett, D. S. and M. J. Donoghue. 2000. Evolution of wood decay mechanisms, mating systems, and substrate ranges in homobasidionycetes. Syst. Biol. 50: 215-242.
Donoghue, M. J. and R. H. Ree. 2000. Homoplasy, and developmental constraint: A model and an example from plants. Amer. Zool. 40: 759-769.
Mathews, S. and M. J. Donoghue. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. Journ. Plant Sci. 161: S41-S55.
2001
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.
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.
Piel, W. H., M. J. Donoghue, and M. J. Sanderson. TreeBASE: A database of phylogenetic information. Proceedings of the 2nd international workshop of species 2000 (in press).
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.
Li, J. C. C. Davis, P. Del Tredici, and M. J. Donoghue. 2001. Phylogenetic relationships of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA. Harvard Papers in Botany 6:267-274.
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.
Donoghue. M. J., C. D. Bell, and J. Li. 2001. Phylogenetic patterns in Northern Hemisphere plant geography. Int. J. Plant. Sci. 162: S41-S52.
Manos, P. S. and M. J. Donoghue. 2001. Progress in Northern Hemisphere phytogeography. Int. Jour. Plant Sci. 162: S1-S2.
Donoghue, M. J. 2001. A wish list for Systematic Biology. Syst. Biol. 50: 755-757.
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.
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.
2002
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.
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.
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.
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.
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.
Donoghue, M. J. 2002. Plants. Pp. 911-918 in Encyclopedia of Evolution, Vol. 2 (M. Pagel, ed.), Oxford Univ. Press. Oxford, UK.
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.
Webb, C. O., D. D. Ackerly, M. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Ann. Rev. Ecol. Syst. 33: 475-505.
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.
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.
2003
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.
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.
Donoghue, M. J. and B. R. Moore. 2003. Toward an integrative historical biogeography. Integrative and Comparative Biology 43: 261-270.
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.
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.
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.
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.
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.
2004
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.
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.
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.
Cracraft, J. and M. J. Donoghue (eds.). 2004. Assembling the Tree of Life. Oxford University Press, New York.
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.
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.
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.
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.
Donoghue, M. J. and J. A. Gauthier. 2004. Implementing the PhyloCode. Trends Ecol. Evol. 19: 281-282.
Winkworth R. C. and M. J. Donoghue. 2004. Viburnum phylogeny: Evidence from the duplicated nuclear gene GBSSI. Mol. Phyl. Evol. 33: 109-126.
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.
Wiens, J. J. and M. J. Donoghue. 2004. Historical biogeography, ecology, and species richness. Trends Ecol. Evol. 19: 639-644.
Webb, C. O. and M. J. Donoghue. 2004. Phylomatic: tree retrieval for applied phylogenetics. Molecular Ecology Notes.
2005
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.
Clark, L. G. and M. J. Donoghue. 2005. John H. Beaman - Recipient of the 2004 Asa Gray Award. Syst. Bot. 1-6.
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.
Donoghue, M. J. 2005. Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31(2): 77-93.
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.
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.
Chang, B. S. W. and M. J. Donoghue. Phylogenetic reconstruction of the origin of rod opsins from cone opsins. Journal of Molecular Evolution (in review).
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.
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.
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.
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.
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.
2006
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.
Donoghue, M. J. and J. Pickering. 2006. Experiencing green pigeons: G. Evelyn Hutchinson on museums and natural history collections. In press in D. Skelly, M. Smith, and D. Post, eds., Yale Univ. Press, New Haven.
Edwards, E. J. and M. J. Donoghue. 2006. Origin of the cactus life form. American Naturalist 167: 777-793.
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.
Howarth, D. G. and M. J. Donoghue. 2006. Phylogenetic analyses of the 褽CE ?(CYC/TB1) clade reveal duplications that predate the core eudicots. Proc. Nat. Acad. Sci. USA 103: 9101-9106.
Loreau, M. et al. 2006. Diversity withour representation. Nature 442: 245-246.
2007
Moore, B. R., S. A. Smith, R. H. Ree, and M. J. Donoghue. 2007. Incorporating fossil data in biogeographic inference: a likelihood approach. Ann. Missouri Bot. Gard. (in press).
Edwards, E. J., C. J. Still, and M. J. Donoghue. Another inconvenient truth? The relevance of phylogeny to studies of global climate change. Trends Ecol. Evol. (in press).
Moore, B. R. and M. J. Donoghue. 2007. Correlates of diversification in the plant clade Dipsacales: Geographical dispersal and evolutionary innovation. Amer. Nat. (in press).
Winkworth, R. C., C. D. Bell, and M. J. Donoghue. Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection. Mol. Phyl. Evol (in review).
Cantino, P. D., W. S. Judd, P. S. Soltis, D. E. Soltis, R. G. Olmstead, S. W. Graham, and M. J. Donoghue. Towards a phylogenetic nomenclature of Tracheophyta. Taxon (in review).
Lundberg, J., R. C. Winkowrth, and M. J. Donoghue. Phylogeny of the campanulid Asteridae. Int. Jour. Plant Sci. (in prep.).
Kim, S.-T. Kim and M. J. Donoghue. The placement of Eupersicaria within Persicarieae (Polygonaceae). Syst. Bot. (in prep.).
Theis, N., M. J. Donoghue, and J. Li. Phylogenetics of the Caprifolieae and Lonicera (Dipsacales) based on nuclear and chloroplast DNA sequences. Syst. Bot. (in prep.).
Havill, N. et al. Tsuga phylogeny and biogeography. AJB (in prep.).
last updated: January 2007
