Research Topics
| Michael J DonoghueSummaryAffiliation: Yale University Country: USA Publications
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Detail Information
Publications
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approachesStephen A Smith
National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA
BMC Evol Biol 9:37. 2009..Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare...- Colloquium paper: a phylogenetic perspective on the distribution of plant diversityMichael J Donoghue
Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, PO Box 208106, New Haven, CT 06520 8106, USA
Proc Natl Acad Sci U S A 105:11549-55. 2008..These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity... 
Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales)Stephen A Smith
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Syst Biol 59:322-41. 2010..These results suggest a possible model for the origin of the Madrean-Tethyan disjunction pattern...- Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia)Margaret E K Evans
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
Am Nat 173:225-40. 2009..Our data are also consistent with Axelrod's hypothesis that the spread of arid conditions in western North America stimulated diversification of arid-adapted lineages... - Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera)Margaret E K Evans
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
New Phytol 191:555-63. 2011..We discuss possible explanations for this pattern and possible implications with respect to anthropogenic climate change... - Rates of molecular evolution are linked to life history in flowering plantsStephen A Smith
Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
Science 322:86-9. 2008.... 
Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forestCampbell O Webb
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
Ecology 87:S123-31. 2006....- Hemisphere-scale differences in conifer evolutionary dynamicsAndrew B Leslie
School of Forestry and Environmental Studies, Yale University, New Haven, CT 06511, USA
Proc Natl Acad Sci U S A 109:16217-21. 2012.... - Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovationsBrian R Moore
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
Am Nat 170:S28-55. 2007.... - Diversification of CYCLOIDEA-like genes in Dipsacaceae (Dipsacales): implications for the evolution of capitulum inflorescencesSara E Carlson
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
BMC Evol Biol 11:325. 2011.... - Bioactive endophytes warrant intensified exploration and conservationStephen A Smith
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
PLoS ONE 3:e3052. 2008..Here we provide direct evidence from bioassays of endophytes isolated from tropical plants and bioinformatic analyses that novel biology will indeed yield novel chemistry of potential value... - Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSIRichard C Winkworth
Department of Ecology and Evolutionary Biology, Yale University, P O Box 208105, New Haven, CT 06520 8105, USA
Mol Phylogenet Evol 33:109-26. 2004..The presence of additional copies appears to be correlated with polyploidy in these clades. Placement of the homoeologues in our gene trees suggests the possibility of a hybrid origin for these polyploids... - Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)Eugenia Y Y Lo
Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06520, USA
Mol Phylogenet Evol 63:230-43. 2012..At least five major, early Old World-New World disjunctions were detected and these vicariance events are generally most consistent with movement through the Beringia... - Patterns in the assembly of temperate forests around the Northern HemisphereMichael J Donoghue
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Philos Trans R Soc Lond B Biol Sci 359:1633-44. 2004..Fortunately, many more plant groups show relevant disjunction patterns and could soon be added to such analyses... - A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of GondwanaJeremy M Beaulieu
Department of Ecology and Evolutionary Biology, Yale University, P, O, Box 208106, New Haven, CT 06520 8106, USA
BMC Evol Biol 13:80. 2013.... - Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiospermsWendy L Clement
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
BMC Evol Biol 12:73. 2012..For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS)... - Allopolyploid speciation in Persicaria (Polygonaceae): insights from a low-copy nuclear regionSang Tae Kim
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
Proc Natl Acad Sci U S A 105:12370-5. 2008..Hybridization events fostered by human introductions may be fueling the production of new species that have the potential to become aggressive weeds... - Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selectionRichard C Winkworth
Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA
Mol Phylogenet Evol 46:830-43. 2008..We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas... - Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrappingBrian R Moore
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
Syst Biol 55:662-76. 2006..These methods have been implemented in the freely available program, tREeBOOT... - Pereskia and the origin of the cactus life-formErika J Edwards
Department of Ecology and Evolutionary Biology and the Peabody Museum of Natural History, Yale University, P O Box 208105, New Haven, Connecticut 06511, USA
Am Nat 167:777-93. 2006..We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti... - Phylogenetic analysis of the "ECE" (CYC/TB1) clade reveals duplications predating the core eudicotsDianella G Howarth
Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520-8106, USA
Proc Natl Acad Sci U S A 103:9101-6. 2006..DipsCYC3B is expressed in flower and petal primordia, possibly most strongly in the ventral petal... - Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae)Sang Tae Kim
Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, Connecticut 06520 8106 USA
Am J Bot 95:1122-35. 2008..Repeated allotetraploidy (as distinct from radiation at the tetraploid level) now appears to be the key mechanism governing the diversification of this taxonomically challenging group... - The root of the angiosperms revisitedMichael J Zanis
School of Biological Sciences, Washington State University, Pullman, WA 99164 4236, USA
Proc Natl Acad Sci U S A 99:6848-53. 2002..Although we cannot conclusively choose between Amborella vs. Amborella + Nymphaeales as sister to all other angiosperms, most analyses favor the former rooting... - Recreating a functional ancestral archosaur visual pigmentBelinda S W Chang
Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, NY 10021, USA
Mol Biol Evol 19:1483-9. 2002..Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods... - Adaptive evolution in the photosensory domain of phytochrome A in early angiospermsSarah Mathews
Division of Biological Sciences, University of Missouri, USA
Mol Biol Evol 20:1087-97. 2003..The episode of selection occurred very early in the history of flowering plants, suggesting that innovation in phyA may have given the first angiosperms some adaptive advantage... - The small-world dynamics of tree networks and data mining in phyloinformaticsWilliam H Piel
Institute of Evolutionary and Ecological Sciences, Kaiserstraat 63, Leiden University 2311 GP Leiden, The Netherlands
Bioinformatics 19:1162-8. 2003..Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies... - Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forestsCharles C Davis
Department of Ecology and Evolutionary Biology, University of Michigan Herbarium, Ann Arbor, Michigan 48108 2287, USA
Am Nat 165:E36-65. 2005..This case illustrates that dated phylogenies can provide an important new source of evidence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial... - A likelihood framework for inferring the evolution of geographic range on phylogenetic treesRichard H Ree
Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA
Evolution 59:2299-311. 2005.... - The relevance of phylogeny to studies of global changeErika J Edwards
Geography Department and the Institute for Computational Earth System Science, University of California, Santa Barbara, CA 93106, USA
Trends Ecol Evol 22:243-9. 2007..We outline how phylogenetics can guide better taxon sampling of key physiological traits, and discuss how the emerging field of phyloinformatics presents a promising new framework for scaling from organism physiology to global processes... - Laurasian migration explains Gondwanan disjunctions: evidence from MalpighiaceaeCharles C Davis
Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 99:6833-7. 2002..This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions...