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. PDF

1982

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. PDF

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.] PDF

1983

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

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. PDF

1984

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. PDF

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

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. PDF

1985

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

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

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. PDF

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

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. PDF

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. PDF

1987

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

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. PDF

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. PDF

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. PDF

1988

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. PDF

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

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. PDF

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. PDF

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

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

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. PDF

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

1990

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

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

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

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. PDF

1991

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

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

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. PDF

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. PDF

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

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. PDF

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

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

1993

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

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. PDF

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

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. PDF

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. PDF

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. PDF

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

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. PDF

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. PDF

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

1995

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. PDF

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. PDF

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

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. PDF

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. PDF

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. PDF

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. PDF

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

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

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

1996

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

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. PDF

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. PDF

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.) PDF

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. PDF

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. PDF

Donoghue, M.J. 1997. Viburnum. A flora of the Chihuahuan Desert region; M.D. Johnston (ed.) privately published. PDF

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. PDF

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

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. PDF

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

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.PDF

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. PDF

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. PDF

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

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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

1999

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. PDF

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

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

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. PDF

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

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

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. PDF

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. PDF

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. PDF

2000

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

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

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

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

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

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

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. PDF

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

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. PDF

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. PDF

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

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. PDF

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

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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

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

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

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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

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. PDF

Webb, C. O., D. D. Ackerly, M. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Ann. Rev. Ecol. Syst. 33: 475-505. PDF

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.

Judd, W. S., K. Nickrent, 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.

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. PDF

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. PDF

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. PDF

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

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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

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

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. PDF

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

Webb, C. O. and M. J. Donoghue. 2004. Phylomatic: tree retrieval for applied phylogenetics. Molecular Ecology Notes. PDF

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. PDF

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

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. PDF

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

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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. PDF

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

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. PDF

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. PDF

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

2007

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. PDF

Moore, B. R. and M. J. Donoghue. 2007. Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. Amer. Nat. 170: S29-S55. PDF

Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, P. S. Soltis, and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56(3): 822-846. PDF

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.

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

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

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.PDF

2008

Kim, S.-T. and M. J. Donoghue. 2008. Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae). Syst. Bot. 33(1): 77-86. PDF

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): 53-65. PDF

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. 46: 830-843. PDF

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. PDF

In press / in review / in preparation

Moore, B. R., S. A. Smith, R. H. Ree, and M. J. Donoghue. 2008. Incorporating fossil data in biogeographic inference: a likelihood approach. Evolution (in press).

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. (in press).

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. (in press).

Donoghue, M. J. and J. Pickering. 2008. Experiencing green pigeons: G. Evelyn Hutchinson on museums and natural history collections. in D. Skelly, M. Smith, and D. Post, eds., Yale Univ. Press, New Haven. (in press).

Donoghue, M. J., and P. D. Cantino. Campanulidae. 2008. Pp. xx-yy in K. de Queiroz, P. D. Cantino and J. Gauthier (eds.), Phylonyms: A Companion to the PhyloCode. University of California Press, Berkeley (in press).

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. Cad. Sci. USA (in press).

Cellinese, N., S. A. Smith, E. J. Edwards, S-T. Kim, M. Avramakis, and M. J. Donoghue. 2008. Historical biogeography of the endemic Campanulaceae of Crete. Jour. Biogeography (in press).

Donoghue, M. J. 2008. A phylogenetic perspective on the distribution of plant diversity. Proc. Nat. Acad. Sci. USA (in press).

Smith, S. A., D. C. Tank, L. A Boulanger, C. A. Bascom-Slack, K. Eisenmen, M. J. Donoghue, and S. A. Strobel. Bioactive endophytes support intensified exploration and conservation. PLOS Biology (in review).

Kim, S-T. and M. J. Donoghue. Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). Amer. Jour. Bot. (in review).

Dayrat, B. and M. J. Donoghue. An era of integration for biodiversity research? Science (letter in review).

Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. Climate, niche evolution, and diversification of the �bird cage� evening primroses (Oenothera sections Anogra and Kleinia). Amer. Nat. (in review).

Chang, B. S. W. and M. J. Donoghue. Phylogenetic reconstruction of the origin of rod opsins from cone opsins. Jour. Mol. Evol. (in prep.).

Moore, B. A., M. J. Donoghue, and J. Xiang. Cornus diversification. Evolution (in prep.).

Smith, S. A., R. H. Ree, and M. J. Donoghue. Accuracy of maximum-likelihood inferences of geographic range reconstructions and parameter estimates: a simulation study. Syst. Biol. (in prep.).

last updated: April 2008

publications