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...
- Life history influences rates of climatic niche evolution in flowering plants
Stephen A Smith
National Evolutionary Synthesis Center, 2024 W Main Street A200, Durham, NC 27705, USA
Proc Biol Sci 276:4345-52. 2009
..The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets...
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...
- An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
Stephen A Smith
National Evolutionary Synthesis Center, Durham, NC 27705, USA
Proc Natl Acad Sci U S A 107:5897-902. 2010
..g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences...
- The origins of C4 grasslands: integrating evolutionary and ecosystem science
Erika J Edwards
Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
Science 328:587-91. 2010
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- 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...
- Patterns in the assembly of temperate forests around the Northern Hemisphere
Michael 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...
- Understanding angiosperm diversification using small and large phylogenetic trees
Stephen A Smith
Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
Am J Bot 98:404-14. 2011
..Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation...
- Resolving the evolutionary relationships of molluscs with phylogenomic tools
Stephen A Smith
Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
Nature 480:364-7. 2011
..This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy...
- Rates of molecular evolution are linked to life history in flowering plants
Stephen 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
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- Phylogenetic analyses reveal the shady history of C4 grasses
Erika J Edwards
Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
Proc Natl Acad Sci U S A 107:2532-7. 2010
..Furthermore, we argue that the evolution of cold tolerance in certain C(3) lineages is an overlooked innovation that has profoundly influenced the patterning of grassland communities across the globe...
- Bioactive endophytes warrant intensified exploration and conservation
Stephen 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...
- Phyutility: a phyloinformatics tool for trees, alignments and molecular data
Stephen A Smith
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
Bioinformatics 24:715-6. 2008
..AVAILABILITY: Phyutility, including source code, documentation, examples, and executables, is available at http://code.google.com/p/phyutility...
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...
