Baum, D. A., and S. D. Smith. 2013. Tree-Thinking: An Introduction to Phylogenetic Biology. Roberts & Co., Greenwood Village, Colorado.

Selected articles

(**undergraduate authors, *graduate students, +postdocs)

McCarthy, E. W., A. E. Berardi+, S. D. Smith, and A. Litt. 2017. Related allopolyploids display distinct floral pigment profiles and transgressive pigments. American Journal of Botany, in press. Link

*Dupin, J. , N. J. Matzke, T. Sarkinen, S. Knapp, R. G. Olmstead, L. Bohs, and S. D. Smith. 2016. Bayesian estimation of global biogeographic history of Solanaceae. Journal of Biogeography, in press.  PDF

*Gates, D. J, S. R. Strickler, L. A. Mueller, B. J. S. C. Olson, and S. D. Smith. 2016. Diversification of R2R3 MYB transcription factors in the tomato family Solanaceae. Journal of Molecular Evolution 83: 26-37. PDF

+Berardi, A. E., S. B. Hildreth, R. F. Helm, B. S. J. Winkel, and S. D. Smith. 2016. Evolutionary correlations in flavonoid production across flowers and leaves in the Iochrominae (Solanaceae). Phytochemistry 130:119-127. PDF

+Ho, W. H., and S. D. Smith. 2016. Molecular evolution of anthocyanin pigmentation genes following losses of flower color. BMC Evolutionary Biology 16: 98. Link

O’Meara, B. C., S. D. Smith, W. S. Armbruster, L. D. Harder, C. Hardy, L. C. Hileman, L. Hufford, A. Litt, S. Magallón, S. A. Smith, P. F. Stevens, C. B. Fenster, and P. K. Diggle. 2016. Non-equilibrium dynamics lead to long-term persistence of ancestral floral forms in modern angiosperms. Proceedings of the Royal Society B 283: 20152304 . Indicates co-first author PDF

+Ng, J., and S. D. Smith. 2016. How to make a red flower: the combinatorial effects of pigments. AOB Plants 8: plw013. Link

+Ng, J., and S. D. Smith. 2016. Widespread flower color convergence in Solanaceae via alternate biochemical pathways. New Phytologist 209: 407-417. PDF

Smith, S. D. 2016. Pleiotropy and the evolution of floral integration. New Phytologist 209: 80-85. PDF

Cueva-Manchego, M., S. D. Smith, and S. Leiva-Gonzáles. 2015. A new and endangered species of Iochroma (Solanaceae) from the cloud forests of central Peru and its phylogenetic position in Iochrominae. Phytotaxa 227: 147-157. PDF

Smith, S. D., and E. E. Goldberg. 2015. Tempo and mode of flower color evolution. American Journal of Botany 102: 1014-1025. PDF

**Coburn, R. C., R. H. Griffin, and S. D. Smith. 2015. Genetic basis of a rare floral mutant in an Andean species of Solanaceae. American Journal of Botany 102: 264-272. PDF

+Ng, J., and S. D. Smith. 2014. How traits shape trees: New approaches for detecting character state-dependent lineage diversification. Journal of Evolutionary Biology 27: 2035-2045. PDF

+Muchhala, N., S. Johnsen, and S. D. Smith. 2014. Competition for hummingbird pollination shapes flower color variation in Andean Solanaceae. Evolution 68: 2275-2286. PDF SI

Smith, S. D. 2014. Interpretation of phylogenetic trees. In Oxford Bibliographies in Evolutionary Biology. J. Losos, ed. Oxford University Press, New York. HTML Text

Smith, S. D. 2014. Quantifying color variation: improved formulas for calculating hue with segment classification. Applications in Plant Sciences 2: 1300088. PDF

Smith, S. D., S. Wang, and M. D. Rausher. 2013. Functional evolution of an anthocyanin pathway enzyme during a flower color transition.  Molecular Biology and Evolution 30: 602-612. PDF SI

Smith, S. D., and S. Leiva G. 2011. A new species of Iochroma (Solanaceae) from Ecuador. Novon 21: 491-495. PDF

Smith, S. D., and M. D. Rausher. 2011. Gene loss and parallel evolution contribute to species difference in flower color.  Molecular Biology and Evolution 28: 2799-2810. PDF

Rosas-Guerrero, V., M. Quesada, W. Scott Armbruster, R. Pérez-Barrales and S. D. Smith. 2011. Influence of pollination specialization and breeding system on floral integration and phenotypic variation in Ipomoea. Evolution 65: 350-364. Link [recommended by Faculty of 1000]

Smith, S. D., R. E. Miller, S. P. Otto, R. G. FitzJohn and M. D. Rausher. 2010. The effects of flower color transitions on diversification rates in morning glories (Ipomoea subg. Quamoclit, Convolvulaceae). Pp. 202-226 in M. Long, H. Gu & Z. Zhou, Darwin's Heritage Today. Higher Education Press, Beijing, China. PDF

Smith, S. D. 2010. Using phylogenetics to detect pollinator-mediated floral evolution. New Phytologist 188: 354-363. PDF

Smith, S. D., C. Ané, and D. A. Baum. 2009. Macroevolutionary tests of pollination syndromes: A reply to Fenster et al. Evolution 63: 2763-2767.  PDF Erratum

Smith, S. D., C. Ané, and D. A. Baum. 2008. The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae). Evolution 62: 793-806. PDF

Ané, C., B. Larget, D. A. Baum, S. D. Smith and A. Rokas. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24: 412-426. Link

Smith, S. D., and D. A. Baum. 2006. Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae). American Journal of Botany 93: 1140-1153. PDF

D. A. Baum, S. D. Smith and S. S. Donovan. 2005. The tree-thinking challenge. Science 310: 979-980. Link Tree-thinking quizzes! 


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