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Publications

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Author Title Type [ Year(Asc)]
2017
Edwards EJ, Chatelet DS, Chen B-C, Ong JYao, Tagane S, Kanemitsu H, Tagawa K, Teramoto K, Park B, Chung K-F et al..  2017.  Convergence, consilience, and the evolution of temperate deciduous forests. The American Naturalist. 190:S87–S104. (1.37 MB)
Edwards EJ, Chatelet DS, Spriggs EL, Johnson ES, Schlutius CV, Donoghue MJ.  2017.  Correlation, causation, and the evolution of leaf teeth: a reply to Givnish and Kriebel. American Journal of Botany. 104(4):509-515. (1.17 MB)
Forrestel EJ, Donoghue MJ, Edwards EJ, Jetz W, Toit JCO du, Smith MD.  2017.  Different clades and traits yield similar grassland functional responses. Proceedings of the National Academy of Sciences United States of America. 114(4):705–710. (1.55 MB)
Faith DP, Magallón S, Hendry AP, Donoghue MJ.  2017.  Future benefits from contemporary evosystem services: a response to Rudman et al.. Trends in Ecology & Evolution. 32(10):717-719. (431.28 KB)
Baker TR, R Pennington T, Dexter KG, Fine PVA, Fortune-Hopkins H, Honorio EN, Huamantupa-Chuquimaco I, Klitgård BB, Lewis GP, de Lima HC et al..  2017.  Maximising synergy among tropical plant systematists, ecologists, and evolutionary biologists. Trends in Ecology & Evolution.  (1.44 MB)
Eaton DA, Spriggs EL, Park B, Donoghue MJ.  2017.  Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants. Systematic Biology. 66(3):399-412. (914.13 KB)
Federman S, Sinnott-Armstrong M, Baden AL, Chapman CA, Daly DC, Richard AR, Valenta K, Donoghue MJ.  2017.  The paucity of frugivores in Madagascar may not be due to unpredictable temperatures or fruit resources. PLoS ONE. 12(1):e0168943. (1.23 MB)
Kim S-T, Donoghue MJ, Sultan SE.  2017.  On the resurrection of Persicaria puratinorum (Polygonaceae). Phytotaxa. 308(1):20-36. (2.06 MB)
2016
Barish S, Arakaki M, Edwards EJ, Donoghue MJ, Clement WL.  2016.  Characterization of 16 microsatellite markers for the Oreinotinus clade of Viburnum (Adoxaceae). Applications in Plant Sciences. 4(12):1600103. (514.1 KB)
Friedman WE, Dosmann MS, Boland TM, Boufford DE, Donoghue MJ, Gapinski A, Hufford L, Meyer PW, Pfister DH.  2016.  Developing an exemplary collection: A vision for the next century at the Arnold Arboretum of Harvard University. Arnoldia. 73:2-18. (2.51 MB)
Scoffoni C, Chatelet DS, Pasquet-Kok J, Rawls M, Donoghue MJ, Edwards EJ, Sack L.  2016.  Hydraulic basis for the evolution of photosynthetic productivity. Nature Plants. 2(6) (1.34 MB)
Federman S, Dornburg A, Daly DC, Downie A, Perry GH, Yoder AD, Sargis EJ, Richard AF, Donoghue MJ, Baden AL.  2016.  Implications of lemuriform extinctions for the Malagasy flora. Proceedings of the National Academy of Sciences of the United States of America.  (1.04 MB)
Judd WS, Nickrent DL, Robertson KR, J. Abbott R, Carlsward BS, Schuster TM, Campbell CS, Neubig KM, Zona S, Donoghue MJ et al..  2016.  Photo Gallery of Vascular Plants.
Judd WS, Campbell CS, Kellogg EA, Stevens PF, Donoghue MJ.  2016.  Plant Systematics: A Phylogenetic Approach.
Edwards EJ, Spriggs EL, Chatelet DS, Donoghue MJ.  2016.  Unpacking a century-old mystery: Winter buds and the latitudinal gradient in leaf form. American Journal of Botany. 103(6):975–978. (900.1 KB)
2015
Federman S, Dornburg A, Downie A, Richard AF, Daly DC, Donoghue MJ.  2015.  The biogeographic origin of a radiation of trees in Madagascar: Implications for the assembly of a tropical forest biome. BMC Evolutionary Biology. 15:216. (1.76 MB) (1.85 MB)
Donoghue MJ, Sanderson MJ.  2015.  Confluence, synnovation, and depauperons in plant diversification. New Phytologist. 207(2):260-274. (3.21 MB)
Edwards EJ, de Vos J, Donoghue MJ.  2015.  Doubtful pathways to cold tolerance in plants. Nature. 521:E5-E6. (167.91 KB)
Forrestel EJ, Donoghue MJ, Smith MD.  2015.  Functional differences between dominant grasses drive divergent responses to large herbivore loss in mesic savanna grasslands of North America and South Africa. Journal of Ecology. 103:714-724. (487.97 KB) (2.15 MB)
Beaulieu JM, O'Meara BC, Crane P, Donoghue MJ.  2015.  Heterogeneous rates of molecular evolution and diversification could explain the Triassic age estimate for angiosperms. Systematic Biology. 64(5):869-878. (1 MB)
Leslie AB, Beaulieu JM, Crane PR, Knopf P, Donoghue MJ.  2015.  Integration and macroevolutionary patterns in the pollination biology of conifers. Evolution. 69(6):1573-83. (576.18 KB) (1.37 MB)
Spriggs EL, Clement WL, Sweeney PW, Madriñán S, Edwards EJ, Donoghue MJ.  2015.  Temperate radiations and dying embers of a tropical past: the diversification of Viburnum. New Phytologist. 207(2):340-354. (1.79 MB) (5.87 MB)
2014
Geeta R, Lohmann LG, Magallón S, Faith DP, Hendry AP, Crandall KA, de Meester L, Webb CO, Prieur-Richard A-H, Mimura M et al..  2014.  Biodiversity only makes sense in the light of evolution. Journal of Biosciences. 39(3):333-337. (118.49 KB)
Donoghue MJ, Edwards EJ.  2014.  Biome shifts and niche evolution in plants. Annual Review of Ecology, Evolution, and Systematics. 45:547–572. (1.46 MB)
Clement WL, Arakaki M, Sweeney PW, Edwards EJ, Donoghue MJ.  2014.  A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. American Journal of Botany. 101(6):1029-1049. (2.67 MB)
Davis CC, Schaefer H, Ruhfel BR, Donoghue MJ, Chimney E.  2014.  Climates and clades: Biased methods, biased results. arXiv:1406.5211.  (303.09 KB)
Leslie AB, Beaulieu JM, Crane PR, Donoghue MJ.  2014.  Cone size is related to branching architecture in conifers. New Phytologist. 203(4):1119-1127. (625.88 KB) (0 bytes)
Forrestel EJ, Donoghue MJ, Smith MD.  2014.  Convergent phylogenetic and functional responses to altered fire regimes in mesic savanna grasslands of North America and South Africa. New Phytologist. 203(3):1000-1011. (491.99 KB) (106.57 KB)
Donoghue MJ.  2014.  Historical Biogeography. The Princeton Guide to Evolution. :75-81. (1.05 MB)
Edwards EJ, Chatelet DS, Sack L, Donoghue MJ.  2014.  Leaf life span and the leaf economic spectrum in the context of whole plant architecture. Journal of Ecology. 102:328–336. (1.3 MB)
Davis CC, Schaefer H, Xi Z, Baum DA, Donoghue MJ, Harmon LJ.  2014.  Long-term morphological stasis maintained by a plant-pollinator mutualism. Proceedings of the National Academy of Sciences of the United States of America. 111(16):5914-5919. (2.52 MB)
2013
Chatelet DS, Clement WL, Sack L, Donoghue MJ, Edwards EJ.  2013.  The evolution of photosynthetic anatomy in Viburnum (Adoxaceae). International Journal of Plant Sciences. 174(9):1277-1291. (859.09 KB) (144.35 KB)
Leslie AB, Beaulieu JM, Crane PR, Donoghue MJ.  2013.  Explaining the distribution of breeding systems and dispersal syndromes in conifers. Proceedings of the Royal Society B: Biological Sciences. 280:20131812. (447.9 KB) (387.89 KB)
Beaulieu JM, Donoghue MJ.  2013.  Fruit evolution and diversification in campanulid angiosperms. Evolution. 67(11):3132-3144. (2.49 MB) (2.21 MB)
Diaz S, Purvis A, Cornelissen JHC, Mace GM, Donoghue MJ, Ewers RM, Jordano P, Pearse WD.  2013.  Functional traits, the phylogeny of function, and ecosystem service vulnerability. Ecology and Evolution. 3(9):2958–2975. (339.53 KB)
Stournaras KE, Lo EYY, Böhning-Gaese K, Cazetta E, Dehling DM, Schleuning M, M Stoddard C, Donoghue MJ, Prum RO, Schaefer H.  2013.  How colorful are fruits? Limited color diversity in fleshy fruits on local and global scales New Phytologist. 198:617-629. (2.82 MB)
Beaulieu JM, O’Meara BC, Donoghue MJ.  2013.  Identifying hidden rate changes in the evolution of a binary morphological character: The evolution of plant habit in campanulid angiosperms. Systematic Biology. 62(5):725-737. (2.8 MB)
Edwards EJ, Donoghue MJ.  2013.  Is it easy to move and easy to evolve? Evolutionary accessibility and adaptation Journal of Experimental Botany. 64(13):4047–4052. (542.19 KB)
de Queiroz K, Donoghue MJ.  2013.  Phylogenetic nomenclature, hierarchical information, and testability. Systematic Biology. 62:167-74. (152.45 KB)
Beaulieu JM, Tank DC, Donoghue MJ.  2013.  A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evolutionary Biology. 13:80. (3.12 MB)
2012
Clement WL, Donoghue MJ.  2012.  Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms. BMC Evolutionary Biology. 12:73. (961.78 KB)
Boyden GS, Donoghue MJ, Howarth DG.  2012.  Duplications and expression of RADIALIS-like genes in Dipsacales. International Journal of Plant Sciences. 173:971-983. (665.45 KB)
Schmerler SB, Clement WL, Beaulieu JM, Chatelet DS, Sack L, Donoghue MJ, Edwards EJ.  2012.  Evolution of leaf form correlates with tropical-temperate transitions in Viburnum (Adoxaceae). Proceedings of the Royal Society B: Biological Sciences. 279:3905-13. (650.86 KB) (627.02 KB)
Lo EYY, Donoghue MJ.  2012.  Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae). Molecular Phylogenetics and Evolution. 63:230-43. (1.93 MB) (369.23 KB)
Donoghue MJ.  2012.  Foreward. El arbol de la vida: sistemática y evolución de los seres vivos. :xiii-xv. (340.6 KB)
Leslie AB, Beaulieu JM, Rai HS, Crane PR, Donoghue MJ, Mathews S.  2012.  Hemisphere-scale differences in conifer evolutionary dynamics. Proceedings of the National Academy of Sciences of the United States of America. 109:16217-21. (320.82 KB) (1.12 MB)
Carlson SE, Linder HP, Donoghue MJ.  2012.  The historical biogeography of Scabiosa (Dipsacaceae): Implications for Old World plant disjunctions. Journal of Biogeography. 39:1086-1100. (3.83 MB) (93.35 KB)
Wheeler QD, Knapp S, Stevenson DW, Stevenson J., Blum SD, Boom BM, Borisy GG, Buizer JL, De Carvalho MR, Cibrian A et al..  2012.  Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and Biodiversity. 10:1-20. (329.21 KB)
Weber MG, Clement WL, Donoghue MJ, Agrawal AA.  2012.  Phylogenetic and experimental tests of interactions among mutualistic plant defense traits in Viburnum (Adoxaceae). The American Naturalist. 180:450-63. (844.48 KB)
Beaulieu JM, Ree RH, Cavender-Bares J, Weiblen GD, Donoghue MJ.  2012.  Synthesizing phylogenetic knowledge for ecological research. Ecology. 93:S4-S13. (293.04 KB)
2011
Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS et al..  2011.  Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany. 98:704-30. (1.22 MB) (203 KB) (9.35 MB)
Donoghue MJ.  2011.  Bipolar biogeography. Proceedings of the National Academy of Sciences of the United States of America. 108:6341-2. (602.37 KB)
Clement WL, Donoghue MJ.  2011.  Dissolution of Viburnum Section Megalotinus (Adoxaceae) of Southeast Asia and its implications for morphological evolution and biogeography. International Journal of Plant Sciences. 172:559-573. (1.02 MB)
Howarth DG, Martins T, Chimney E, Donoghue MJ.  2011.  Diversification of CYCLOIDEA expression in the evolution of bilateral flower symmetry in Caprifoliaceae and Lonicera (Dipsacales). Annals of Botany. 107:1521-32. (931.89 KB)
Carlson SE, Howarth DG, Donoghue MJ.  2011.  Diversification of CYCLOIDEA-like genes in Dipsacaceae (Dipsacales): Implications for the evolution of capitulum inflorescences. BMC Evolutionary Biology. 11:325. (641.32 KB) (79.98 KB)
Desurmont GA, Donoghue MJ, Clement WL, Agrawal AA.  2011.  Evolutionary history predicts plant defense against an invasive pest. Proceedings of the National Academy of Sciences of the United States of America. 108:7070-4. (445.05 KB)
Evans MEK, Hearn DJ, Theiss KE, Cranston KA, Holsinger KE, Donoghue MJ.  2011.  Extreme environments select for reproductive assurance: Evidence from evening primroses (Oenothera). New Phytologist. 191:555-63. (396.53 KB) (48.76 KB)
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A et al..  2011.  The iPlant Collaborative: Cyberinfrastructure for plant biology. Frontiers In Plant Science. 2:34. (1.19 MB)
Greenberg AK, Donoghue MJ.  2011.  Molecular systematics and character evolution in Caryophyllaceae. Taxon. 60:1637-1652. (4.06 MB)
de Queiroz K, Donoghue MJ.  2011.  Phylogenetic nomenclature, three-taxon statements, and unnecessary name changes. Systematic Biology. 60(6):887-892. (132.03 KB)
Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ.  2011.  Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany. 98:404-14. (608.42 KB) (4.37 MB)
2010
Davis CC, Edwards EJ, Donoghue MJ.  2010.  A clade's-eye view of global climate change. Evolution since Darwin: The First 150 Years. :623-627. (476.14 KB)
Smith SA, Donoghue MJ.  2010.  Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales). Systematic Biology. 59:322-41. (1.77 MB) (169.61 KB)
Hendry AP, Lohmann LG, Conti E, Cracraft J, Crandall KA, Faith DP, Häuser C, Joly CA, Kogure K, Larigauderie A et al..  2010.  Evolutionary biology in biodiversity science, conservation and policy: A call to action. Evolution. 64:1517-1528. (776.53 KB)
Faith DP, Magallón S, Hendry AP, Conti E, Yahara T, Donoghue MJ.  2010.  Evosystem services: An evolutionary perspective on the links between biodiversity and human well-being. Current Opinion in Environmental Sustainability. 2:66-74. (241.45 KB)
Donoghue MJ, Pickering J.  2010.  Experiencing green pigeons. The Art of Ecology: Writings of G. Evelyn Hutchinson. :243-251. (1.47 MB)
Yahara T, Donoghue MJ, Zardoya R, Faith DP, Cracraft J.  2010.  Genetic diversity assessments in the century of genome science. Current Opinion In Environmental Sustainability. 2:43-49. (160.79 KB)
Tank DC, Donoghue MJ.  2010.  Phylogeny and phylogenetic nomenclature of the Campanulidae based on an expanded sample of genes and taxa. Systematic Botany. 35:425-441. (596.64 KB)
Smith SA, Beaulieu JM, Donoghue MJ.  2010.  An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 107:5897-902. (1.12 MB) (559.71 KB)
2009
Moore BR, Donoghue MJ.  2009.  A Bayesian approach for evaluating the impact of historical events on rates of diversification. Proceedings of the National Academy of Sciences of the United States of America. 106:4307-4312. (712.77 KB) (461.17 KB)
Donoghue MJ, Yahara T, Conti E, Cracraft J, Crandall KA, Faith DP, Häuser C, Hendry AP, Joly CA, Kogure K et al..  2009.  bioGENESIS: Providing an Evolutionary Framework for Biodiversity Science. :52pp. (4.9 MB)
Evans MEK, Smith SA, Flynn RS, Donoghue MJ.  2009.  Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, Sections Anogra and Kleinia). The American Naturalist. 173:225-240. (821.7 KB)
Howarth DG, Donoghue MJ.  2009.  Duplications and expression of DIVARICATA-like genes in Dipsacales. Molecular Biology and Evolution. 26:1245-1258. (390.88 KB)
Cellinese N, Smith SA, Edwards EJ, Kim S-T, Haberle RC, Avramakis M, Donoghue MJ.  2009.  Historical biogeography of the endemic Campanulaceae of Crete. Journal of Biogeography. 36:1253-1269. (677.51 KB)
Smith SA, Beaulieu JM, Donoghue MJ.  2009.  Mega-phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches. BMC Evolutionary Biology. 9:37. (4.05 MB) (64.35 KB)
Carlson SE, Mayer V, Donoghue MJ.  2009.  Phylogenetic relationships, taxonomy, and morphological evolution in Dipsacaceae (Dipsacales) inferred by DNA sequence data. Taxon. 58:1075-1091. (824 KB)
2008
Kim S-T, Sultan SE, Donoghue MJ.  2008.  Allopolyploid speciation in Persicaria (Polygonaceae): Insights from a low-copy nuclear region. Proceedings of the National Academy of Sciences of the United States of America. 105:12370-5. (1.26 MB)
Smith SA, Tank DC, Boulanger L-A, Bascom-Slack CA, Eisenman K, Kingery D, Babbs B, Fenn K, Greene JS, Hann BD et al..  2008.  Bioactive endophytes warrant intensified exploration and conservation. PLoS ONE. 3:1-4. (170.1 KB)
Donoghue MJ.  2008.  Colloquium paper: A phylogenetic perspective on the distribution of plant diversity. Proceedings of the National Academy of Sciences of the United States of America. 105 Suppl 1:11549-55. (339.83 KB)
Jacobs B, Donoghue MJ, Bouman F, Huysmans S, Smets E.  2008.  Evolution and phylogenetic importance of endocarp and seed characters in Viburnum (Adoxaceae). International Journal of Plant Sciences. 169:409-431. (1.72 MB)
Kim S-T, Donoghue MJ.  2008.  Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). American Journal of Botany. 95:1122-1135. (1.37 MB) (117.07 KB)
Winkworth RC, Bell CD, Donoghue MJ.  2008.  Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection. Molecular Phylogenetics and Evolution. 46:830-843. (232.4 KB)
Kim S-T, Donoghue MJ.  2008.  Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae). Systematic Botany. 33:77-86. (508.3 KB)
Theis N, Donoghue MJ, Li J.  2008.  Phylogenetics of the Caprifolieae and Lonicera (Dipsacales) based on nuclear and chloroplast DNA sequences. Systematic Botany. 33:776-783. (352.72 KB)
Havill NP, Campbell CS, Vining TF, LePage B, Donoghue MJ.  2008.  Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Systematic Biology. 33:478-489. (565.04 KB)
Smith SA, Donoghue MJ.  2008.  Rates of molecular evolution are linked to life history in flowering plants. Science. 322:86-89. (733.97 KB) (1.71 MB)
Winkworth RC, Lundberg J, Donoghue MJ.  2008.  Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales. Taxon. 57:53-65. (567.89 KB)
Hong DY, Chen ZD, Qiu Y-L, Donoghue MJ.  2008.  Tracing patterns of evolution through the tree of life: Introduction. Journal of Systematics and Evolution. 46:237-238. (118.66 KB)
2007
Yahara T, Donoghue MJ.  2007.  bioGENESIS – a new DIVERSITAS Core Project is launched. DWIPA Newsletter. 21:1-2.
Moore BR, Donoghue MJ.  2007.  Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. The American Naturalist. 170 Suppl 2:S28-55. (1.19 MB)
Korner C, Donoghue MJ, Fabbro T, Häuser C, Nogues-Bravo D, Arroyo MTKalin, Soberon J, Speers L, Spehn EM, Sun H et al..  2007.  The Kazbegi Research Agenda of GMBA-DIVERSITAS: For creative use of mountain biodiversity databases. Mountain Research and Development. 27:276-281. (387.54 KB)
Judd WS, Nickrent D, Robertson K, Campbell CS, Kellogg EA, Donoghue MJ.  2007.  Photo Gallery of Vascular Plants. A Companion to Plant Systematics: A Phylogenetic Approach.
Judd WS, Campbell CS, Kellogg EA, Stevens PF, Donoghue MJ.  2007.  Plant Systematics: A Phylogenetic Approach.
Edwards EJ, Still CJ, Donoghue MJ.  2007.  The relevance of phylogeny to studies of global change. Trends in Ecology and Evolution. 22:243-249. (861.13 KB)
Cantino PD, Doyle JA, Graham SW, Judd WS, Olmstead RG, Soltis DE, Soltis PS, Donoghue MJ.  2007.  Towards a phylogenetic nomenclature of Tracheophyta. Taxon. 56:822-846. (887.91 KB)
Cantino PD, Doyle JA, Graham SW, Judd WS, Olmstead RG, Soltis DE, Soltis PS, Donoghue MJ.  2007.  Towards a phylogenetic nomenclature of Tracheophyta (Electronic Supplement). Taxon. 56:E1-E44. (9.73 MB)
2005
Edwards EJ, Nyffeler R, Donoghue MJ.  2005.  Basal cactus phylogeny: Implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form. American Journal of Botany. 92:1177-1188. (1.45 MB)
Donoghue MJ, Smith M.  2005.  Biodiversity Inventory: Reflections on Preparedness and Efficiency. Proceedings of the International Conference "Biodiversity: Science and Governance". :79-86. (1015.45 KB)
Bell CD, Donoghue MJ.  2005.  Dating the Dipsacales: comparing models, genes, and evolutionary implications. American Journal of Botany. 92:284-96. (116.42 KB)
Howarth DG, Donoghue MJ.  2005.  Duplications in CYC-like genes from Dipsacales correlate with floral form. International Journal of Plant Sciences. 166:357-370. (559.35 KB)
Davis CC, Webb CO, Wurdack KJ, Jaramillo CA, Donoghue MJ.  2005.  Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests. The American Naturalist. 165:E36-65. (375.24 KB)
Winkworth RC, Donoghue MJ.  2005.  Viburnum phylogeny based on combined molecular data: Implications for taxonomy and biogeography. American Journal of Botany. 92:653-666. (261.74 KB)
Clark LC, Donoghue MJ.  2005.  John H. Beaman—Recipient of the 2004 Asa Gray Award. Systematic Botany. 30:1-6. (528.56 KB)
Donoghue MJ.  2005.  Key innovations, convergence, and success: Macroevolutionary lessons from plant phylogeny. Paleobiology. 31:77-93. (1.09 MB)
Ree RH, Moore BR, Webb CO, Donoghue MJ.  2005.  A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution. 59:2299-2311. (1.37 MB)
Bell CD, Donoghue MJ.  2005.  Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians. Organisms Diversity and Evolution. 5:147-159. (351.73 KB)
Webb CO, Donoghue MJ.  2005.  Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Notes. 5:181-183. (53.77 KB)
2004
Cracraft J, Donoghue MJ.  2004.  Assembling the Tree of Life.
Cracraft J, Donoghue MJ.  2004.  Assembling the tree of life: Where we stand at the beginning of the 21st century. Assembling the Tree of Life. :553-561. (4.32 MB)
Donoghue MJ, Cracraft J.  2004.  Charting the tree of life. Assembling the Tree of Life. :1-4. (2.09 MB)
Donoghue MJ.  2004.  Comparisons, Phylogeny, and Teaching Evolution. Proceedings of the Biological Sciences Curriculum Study (BSCS), American Institute of Biological Sciences (AIBS) Symposium. :69-77. (3.03 MB)
Feild TS, Arens NC, Doyle JA, Dawson TE, Donoghue MJ.  2004.  Dark and disturbed: A new image of early angiosperm ecology. Paleobiology. 30:82-107. (500.68 KB)
Moore BR, Chan MA, Donoghue MJ.  2004.  Detecting diversification rate variation in supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. :487-533. (2.78 MB)
Wiens JJ, Donoghue MJ.  2004.  Historical biogeography, ecology and species richness. Trends in Ecology & Evolution. 19:639-644. (171.67 KB)
Donoghue MJ.  2004.  Immeasurable progress on the tree of life. Assembling the Tree of Life. :548-552. (3.33 MB)
Donoghue MJ, Gauthier JA.  2004.  Implementing the PhyloCode. Trends in Ecology & Evolution. 19:281-282. (52.48 KB)
Donoghue MJ, Baldwin BG, Li J, Winkworth RC.  2004.  Viburnum phylogeny based on the chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Systematic Botany. 29:188-198. (276.71 KB)
Winkworth RC, Donoghue MJ.  2004.  Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI. Molecular Phylogenetics and Evolution. 33:109-126. (1.06 MB)
Schultheis LM, Donoghue MJ.  2004.  Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia). Systematic Botany. 29:77-96. (563.22 KB)
Donoghue MJ, Smith SA.  2004.  Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society B: Biological Sciences. 359:1633-1644. (299.85 KB)
2003
Mathews S, Burleigh JG, Donoghue MJ.  2003.  Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Molecular Biology and Evolution. 20:1087-1097. (162.02 KB)
Donoghue MJ, Bell CD, Winkworth RC.  2003.  The evolution of reproductive characters in Dipsacales. International Journal of Plant Sciences. 164:S453-S464. (492.07 KB)
Li J, Zhang DL, Donoghue MJ.  2003.  Phylogeny and biogeography of Chamaecyparis (Cupressaceae) inferred from DNA sequences of the nuclear ribosomal ITS region. Rhodora. 105:106-117. (2.34 MB)
Bell CD, Donoghue MJ.  2003.  Phylogeny and biogeography of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences. Organisms, Diversity, and Evolution. 3:227-237. (88.32 KB)
Eriksson T, Hibbs MS, Yoder AD, Delwiche CF, Donoghue MJ.  2003.  The phylogeny of Rosoideae (Rosaceae) based on sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the trnL/F region of chloroplast DNA. International Journal of Plant Sciences. 164:197-211. (261.82 KB)
Nakhleh L, Miranker D, Barbancon F, Piel WH, Donoghue MJ.  2003.  Requirements of Phylogenetic Databases. Annual IEEE International Symposium on Bioinformation and Biomedical Engineering.  (169.42 KB)
Piel WH, Sanderson MJ, Donoghue MJ.  2003.  The small-world dynamics of tree networks and data mining in phyloinformatics. Bioinformatics. 19:1162-1168. (121.5 KB)
Donoghue MJ, Moore BR.  2003.  Toward an integrative historical biogeography. Integrative and Comparative Biology. 43:261-270. (181.06 KB)
2002
Davis CC, Bell CD, Mathews S, Donoghue MJ.  2002.  Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proceedings of the National Academy of Sciences of the United States of America. 99:6833-6837. (554.15 KB)
Judd WS, Nickrent D, Robertson K, Campbell CS, Kellogg EA, Stevens PF, Donoghue MJ.  2002.  Photo Gallery of Vascular Plants. A companion to Plant Systematics: A Phylogenetic Approach.
Li J, Del Tredici P, Yang SX, Donoghue MJ.  2002.  Phylogenetic relationships and biogeography of Stewartia (Camellioideae, Theaceae) inferred from nuclear ribosomal DNA ITS sequences. Rhodora. 104:117-133. (3.85 MB)
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ.  2002.  Phylogenies and community ecology. Annual Review of Ecology and Systematics. 33:475-505. (314.27 KB)
Davis CC, Fritsch PW, Li J, Donoghue MJ.  2002.  Phylogeny and biogeography of Cercis (Fabaceae): Evidence from chloroplast ndhF and nuclear ribosomal ITS sequences. Systematic Botany. 27:289-302. (244.67 KB)
Judd WS, Campbell CS, Kellogg EA, Stevens PF, Donoghue MJ.  2002.  Plant Systematics: A Phylogenetic Approach.  (7.27 MB)
Donoghue MJ.  2002.  Plants. Encyclopedia of Evolution. 2:911-918.
Chang BSW, Jönsson K, Kazmi MA, Donoghue MJ, Sakmar TP.  2002.  Recreating a functional ancestral archosaur visual pigment. Molecular Biology and Evolution. 19:1483-1489. (333.24 KB)
Zanis MJ, Soltis DE, Soltis PS, Mathews S, Donoghue MJ.  2002.  The root of the angiosperms revisited. Proceedings of the National Academy of Sciences of the United States of America. 99:6848-6853. (281.18 KB)
Baum DA, Donoghue MJ.  2002.  Transference of function, heterotopy, and the evolution of plant development. Developmental Genetics and Plant Evolution. :52-69. (3.26 MB)
Piel WH, Donoghue MJ, Sanderson MJ.  2002.  TreeBASE: a database of phylogenetic knowledge. The Interoperable "Catalog of Life". :41-47. (53.84 KB)
2001
Hibbett DS, Donoghue MJ.  2001.  Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in Homobasidiomycetes. Systematic Biology. 50:215-242. (487.55 KB)
Bell CD, Edwards EJ, Kim S-T, Donoghue MJ.  2001.  Dipsacales phylogeny based on chloroplast DNA sequences. Harvard Papers in Botany. 6:481-500. (567.63 KB)
Baum DA, Donoghue MJ.  2001.  A likelihood framework for the phylogenetic analysis of adaptation. Adaptation and Optimality. :24-44. (3.29 MB)
Donoghue MJ, Bell CD, Li J.  2001.  Phylogenetic patterns in Northern Hemisphere plant geography. International Journal of Plant Sciences. 162:S41-S52. (499.63 KB)
Li J, Davis CC, Donoghue MJ, Kelley S, Del Tredici P.  2001.  Phylogenetic relationships of Torreya (Taxaceae) inferred from sequences of the nuclear ribosomal DNA ITS region. Harvard Papers in Botnay. 6:275-281. (3.09 MB)
Li J, Boufford DE, Donoghue MJ.  2001.  Phylogenetics of Buckleya (Santalaceae) based on ITS sequences of nuclear ribosomal DNA. Rhodora. 103:137-150. (3.77 MB)
Li J, Davis CC, Del Tredici P, Donoghue MJ.  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. (3.27 MB)
Donoghue MJ, Eriksson T, Reeves PA, Olmstead RG.  2001.  Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany. 6:459-480. (163.06 KB)
Davis CC, Anderson WR, Donoghue MJ.  2001.  Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences. American Journal of Botany. 88:1830-1846. (920.68 KB)
Manos PS, Donoghue MJ.  2001.  Progress in Northern Hemisphere phytogeography: An introduction. International Journal of Plant Sciences. 162:S1-S2. (39.06 KB)
Donoghue MJ.  2001.  A wish list for systematic biology. Systematic Biology. 50:755-757. (69.47 KB)
2000
Mathews S, Donoghue MJ.  2000.  Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. International Journal of Plant Sciences. 161:S41-S55. (438.66 KB)
Hibbett DS, Gilbert LB, Donoghue MJ.  2000.  Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature. 407:506-508. (125.22 KB)
Donoghue MJ, Ree RH.  2000.  Homoplasy and developmental constraint: a model and an example from plants. American Zoologist. 40:759-769. (130.91 KB)
Donoghue MJ, Alverson WS.  2000.  A new age of discovery. Annals of the Missouri Botanical Garden. 87:110-126. (7.99 MB)
Weiblen GD, Oyama RK.  2000.  Phylogenetic analysis of dioecy in monocotyledons. The American Naturalist. 155:46-58. (151.44 KB)
Li J, Bogle A.L, Klein AS, Donoghue MJ.  2000.  Phylogeny and biogeography of Hamamelis (Hamamelidaceae). Harvard Papers in Botany. 5:171-178. (3.34 MB)
Gould KR, Donoghue MJ.  2000.  Phylogeny and biogeography of Triosteum (Caprifoliaceae). Harvard Papers in Botany. 5:157-166. (3.3 MB)
Urbatsch LE, Baldwin BG, Donoghue MJ.  2000.  Phylogeny of the coneflowers and relatives (Heliantheae : Asteraceae) based on nuclear rDNA internal transcribed spacer (ITS) sequences and chlorplast DNA restriction site data. Systematic Botany. 25:539-565. (450.46 KB)
Chang BSW, Donoghue MJ.  2000.  Recreating ancestral proteins. Trends in Ecology and Evolution. 15:109-114. (101.92 KB)
Donoghue MJ, Doyle JA.  2000.  Seed plant phylogeny: Demise of the anthophyte hypothesis? Current Biology. 10:R106-R109. (115.44 KB)
Feild TS, Zweiniecki MA, Brodribb T, Jaffré T, Donoghue MJ, Holbrook NM.  2000.  Structure and function of tracheary elements in Amborella trichopoda. International Journal of Plant Sciences. 161:705-712. (760.74 KB)
Robeck HE, Maley CC, Donoghue MJ.  2000.  Taxonomy and temporal diversity patterns. Paleobiology. 26:171-187. (2.29 MB)
1999
Donoghue MJ.  1999.  Foreword. Plant Systematics: A Phylogenetic Approach. :xi-xii. (616.33 KB)
Wood EW, Eriksson T, Donoghue MJ.  1999.  Guidelines for the use of herbarium materials in molecular research. Managing the Modern Herbarium. :265-276. (2.26 MB)
Ree RH, Donoghue MJ.  1999.  Inferring rates of change in flower symmetry in asterid angiosperms. Systematic Biology. 48:633-641. (290.72 KB)
Li J, Donoghue MJ.  1999.  More molecular evidence for interspecific relationships in Liquidambar (Hamamelidaceae). Rhodora. 101:87-91. (1.05 MB)
Li J, Bogle A.L, Donoghue MJ.  1999.  Phylogenetic relationships in the Hamamelidoideae inferred from sequences of TRN non-coding regions of chloroplast DNA. Harvard Papers in Botany. 4:343-356. (5.55 MB)
Pine EM, Hibbett DS, Donoghue MJ.  1999.  Phylogenetic relationships of cantharelloid and clavarioid Homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. Mycologia. 91:944-963. (8.81 MB)
Harrington FA, Pfister DH, Potter D, Donoghue MJ.  1999.  Phylogenetic studies within the Pezizales. I. 18s rRNA sequence data and classification. Mycologia. 91:41-50. (4.77 MB)
Mathews S, Donoghue MJ.  1999.  The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science. 286:947-950. (194.16 KB)
Cantino PD, Bryant HN, de Queiroz K, Donoghue MJ, Eriksson T, Hillis DM, S Y Lee M.  1999.  Species names in phylogenetic nomenclature. Systematic Biology. 48:790-807. (207.23 KB)
1998
Donoghue MJ, Mathews S.  1998.  Duplicate genes and the root of angiosperms, with an example using phytochrome sequences. Molecular Phylogenetics and Evolution. 9:489-500. (341.94 KB)
Hibbett DS, Donoghue MJ.  1998.  Integrating phylogenetic analysis and classification in fungi. Mycologia. 90:347-356. (4.09 MB)
Ackerly DD, Donoghue MJ.  1998.  Leaf size, sapling allometry, and Corner’s rules: Phylogeny and correlated evolution in maples (Acer). The American Naturalist. 152:767-791. (475.69 KB)
Eriksson T, Donoghue MJ, Hibbs MS.  1998.  Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution. 211:155-179. (1.8 MB)
Hibbett DS, Hansen K, Donoghue MJ.  1998.  Phylogeny and biogeography of Lentinula inferred from an expanded rDNA dataset. Mycological Research. 102:1041-1049. (3.44 MB)
Donoghue MJ, Ree RH, Baum DA.  1998.  Phylogeny and the evolution of flower symmetry in the Asteridae. Trends in Plant Science. 3:311-317. (193.66 KB)
Ree RH, Donoghue MJ.  1998.  Step matrices and the interpretation of homoplasy. Systematic Biology. 47:582-588. (150.79 KB)
Feild TS, Zweiniecki MA, Donoghue MJ, Holbrook NM.  1998.  Stomatal plugs of Drimys winteri (Winteraceae) protect leaves from mist but not drought. Proceedings of the National Academy of Sciences of the United States of America. 95:14256-14259. (360.71 KB)
1997
Rice KA, Donoghue MJ, Olmstead RG.  1997.  Analyzing large data sets: rbcL 500 revisited. Systematic Biology. 46:554-563. (1.51 MB)
Sang T, Donoghue MJ, Zhang DL.  1997.  Evolution of alcohol dehydrogenase genes in peonies (Paeonia): Phylogenetic relationships of putative nonhybrid species. Molecular Biology and Evolution. 14:994-1007. (2.16 MB)
Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ.  1997.  Evolution of Gilled Mushrooms and Puffballs Inferred from Ribosomal DNA Sequences. Proceedings of the National Academy of Sciences of the United States of America. 94:12002-12006. (2.18 MB)
Hibbett DS, Grimaldi D, Donoghue MJ.  1997.  Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of Homobasidiomycetes. American Journal of Botany. 84:981-991. (2.22 MB)
Hibbett DS, Donoghue MJ, Tomlinson PB.  1997.  Is Phellinites digiustoi the oldest homobasidiomycete? American Journal of Botany. 84:1005-1011. (6.08 MB)
Donoghue MJ.  1997.  Viburnum. A Flora of the Chihuahuan Desert Region.  (605.64 KB)
Campbell CS, Wojciechowski MF, Baldwin BG, Alice LA, Donoghue MJ.  1997.  Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Molecular Biology and Evolution. 14:81-90. (1.81 MB)
Eriksson T, Donoghue MJ.  1997.  Phylogenetic relationships of Sambucus and Adoxa (Adoxoideae, Adoxaceae) based on nuclear ribosomal ITS sequences and preliminary morphological data. Systematic Botany. 22:555-573. (2.49 MB)
1996
Hibbett DS, Donoghue MJ.  1996.  Implications of phylogenetic studies for conservation of genetic diversity in shiitake mushrooms. Conservation Biology. 10:1321-1327. (602.59 KB)
Backlund A, Donoghue MJ.  1996.  Morphology and phylogeny of the order Dipsacales. Phylogeny of the Dipsacales, A. Backlund, Doctoral Dissertation.  (23.72 MB)
Donoghue MJ, Ackerly DD.  1996.  Phylogenetic uncertainties and sensitivity analyses in comparative biology. Philosophical Transactions of the Royal Society B: Biological Sciences. 351:1241-1249. (1.71 MB)
Sanderson MJ, Donoghue MJ.  1996.  Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology and Evolution. 11:15-20. (841.14 KB)
Sanderson MJ, Donoghue MJ.  1996.  The relationship between homoplasy and confidence in a phylogenetic tree. Homoplasy: The Recurrence of Similarity in Evolution. :67-89. (5.35 MB)
1995
Baum DA, Donoghue MJ.  1995.  Choosing among alternative "phylogenetic" species concepts. Systematic Botany. 20:560-573. (1.91 MB)
Hibbett DS, Grimaldi D, Donoghue MJ.  1995.  Cretaceous mushrooms in amber. Nature. 377:487. (297.17 KB)
Weller SG, Donoghue MJ, Charlesworth D.  1995.  The evolution of self-incompatibility in flowering plants: A phylogenetic approach. Experimental and Molecular Approaches to Plant Biosystematics. :355-382. (5.54 MB)
Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ.  1995.  The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden. 82:247-277. (3.61 MB)
Hibbett DS, Fukumasanakai Y, Tsuneda A, Donoghue MJ.  1995.  Phylogenetic diversity in shiitake inferred from ribosomal DNA sequences. Mycologia. 87:618-638. (9.54 MB)
Campbell CS, Donoghue MJ, Baldwin BG, Wojciechowski MF.  1995.  Phylogenetic relationships in Maloideae (Rosaceae): Evidence from sequences of internal transcribed spacers of nuclear ribosomal DNA and its congruence with morphology. American Journal of Botany. 82:903-918. (3.17 MB)
Ackerly DD, Donoghue MJ.  1995.  Phylogeny and ecology reconsidered. Journal of Ecology. 83:730-733. (429.39 KB)
Hibbett DS, Donoghue MJ.  1995.  Progress toward a phylogenetic classification of the Polyporaceae through parsimony analysis of mitochondrial ribosomal DNA sequences. Canadian Journal of Botany-Revue Canadienne de Botanique. 73:S853-S861. (4.4 MB)
de Queiroz A, Donoghue MJ, Kim J.  1995.  Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics. 26:657-681. (1.65 MB)
Manchester SR, Donoghue MJ.  1995.  Winged fruits of Linnaeeae (Caprifoliaceae) in the Tertiary of Western North America: Diplodipelta gen. nov.. International Journal of Plant Sciences. 156:709-722. (4.62 MB)
1992
Donoghue MJ, Scheiner SM.  1992.  The evolution of endosperm: a phylogenetic account. Ecology and Evolution of Plant Reproduction: New Approaches. :356-389. (8.26 MB)
Doyle JA, Donoghue MJ.  1992.  Fossils and seed plant phylogeny reanalyzed. Brittonia. 44:89-106. (2.71 MB)
Donoghue MJ.  1992.  Homology. Keywords in Evolutionary Biology. :170-179. (2.62 MB)
Donoghue MJ, Olmstead RG, Smith JF, Palmer JD.  1992.  Phylogenetic relationships of Dipsacales based on rbcL sequences. Annals of the Missouri Botanical Garden. 79:333-345. (2.03 MB)
Donoghue MJ, Sanderson MJ.  1992.  The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Molecular Systematics of Plants. :340-368. (7.86 MB)
Donoghue MJ, Kadereit JW.  1992.  Walter Zimmerman and the growth of phylogenetic theory. Systematic Biology. 41:74-85. (1.74 MB)
1991
Barrett M, Donoghue MJ, Sober E.  1991.  Against consensus. Systematic Zoology. 40:486-493. (1.09 MB)
Donoghue MJ, Doyle JA.  1991.  Angiosperm monophyly. Trends in Ecology and Evolution. 6:407. (161.4 KB)
1989
Crane PR, Donoghue MJ, Doyle JA, Friis EMarie.  1989.  Angiosperm origins. Nature. 342:131. (144.72 KB)
Donoghue MJ, Doyle JA, Gauthier JA, Kluge AG, Rowe T.  1989.  The importance of fossils in phylogeny reconstruction. Annual Review of Ecology and Systematics. 20:431-460. (1.69 MB)
Sanderson MJ, Donoghue MJ.  1989.  Patterns of variation in levels of homoplasy. Evolution. 43:1781-1795. (2.33 MB)
Donoghue MJ, Doyle JA.  1989.  Phylogenetic analysis of angiosperms and the relationships of Hamamelidae. Evolution, Systematics, and Fossil History of the Hamamelidae. 1:17-45. (1.74 MB)
Donoghue MJ, Doyle JA.  1989.  Phylogenetic studies of seed plants and angiosperms based on morphological characters. The Hierarchy of Life: Molecules and Morphology in Phylogenetic Analysis: Proceedings from Nobel Symposium 70.  (3.19 MB)
Donoghue MJ.  1989.  Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution. 43:1137-1156. (2.99 MB)
1980
Donoghue MJ.  1980.  Flowering times in Viburnum. Arnoldia. 40(1):2-22. (4.8 MB)