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

Peer-reviewed articles

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


Powell, A. F., J. Zhang, D. A. Hauser, J. Vilela, A. Hu, D. J. Gates*, L. A. Mueller, F. Li, S. R. Strickler, & S. D. Smith. 2022. Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae. The Plant Genome, in press. Link 

Wheeler, L. C.+, J. F. Walker, J. Ng, R. Deanna+, A. Dunbar-Wallis*, A. Backes*, P. H. Pezzi*, M. V. Palchetti, A. Monaghan, L. B. Freitas, G. E. Barboza, E. Moyroud & S. D. Smith. 2022. Transcription factors evolve faster than their targets in the anthocyanin pathway. Molecular Biology and Evolution 39: msac044. Link.

Sinnott-Armstrong, M. A., R. Deanna, C. Pretz, S. Liu, J. Harris, A. Dunbar-Wallis, S. D. Smith, & L. C. Wheeler. 2022. How to approach the study of syndromes in macroevolution and ecology. Ecology and Evolution 12: e8583.


Pretz, C.*, & S. D. Smith. 2021. Intraspecific breakdown of self-incompatibility in Physalis acutifolia (Solanaceae). AOB Plants 14 plab080. Link 

Smith, S. D. & B. K. Blackman. 2021. From deep roots to new blooms: The ever‐growing field of evo–devo across land plant. Evolution & Development 23: 119-122. Link, Reprint Request

Liu, S. & S. D. Smith. 2021. Phylogeny and biogeography of South American marsh pitcher plant genus Heliamphora (Sarraceniaceae) endemic to the Guiana Highlands. Molecular Phylogenetics and Evolution 154: 106961. Link, Reprint Request


Wheeler, L. C.+, B. A. Wing & S. D. Smith. 2020. Structure and contingency determine mutational hotspots for flower color evolution. Evolution Letters Link

Smith, S. D., M. W. Pennell, C. W. Dunn & S. V. Edwards. 2020. Phylogenetics is the new genetics (for most of biodiversity). Trends in Ecology and Evolution 35: 415-425. Link, Reprint Request


Larter, M.+, A. Dunbar-Wallis, A. E. Berardi+ & S. D. Smith. 2019. Developmental control of convergent floral pigmentation across evolutionary timescales. Developmental Dynamics 248: 1091-1100. Link, Reprint Request

Dupin, J.* & S. D. Smith. 2019. Integrating historical biogeography and environmental niche evolution to understand the geographical distribution of Datureae (Solanaceae). American Journal of Botany 106: 1-12. Link, Reprint Request

Wheeler, L. C.+ & S. D. Smith. Computational modeling of anthocyanin pathway evolution: biases, hotspots and trade-offs. Integrative and Comparative Biology 59: 585-598. Link, Preprint on bioarxiv

Deanna, R.+, M. Larter+, G. E. Barboza & S.D. Smith. 2019. Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae). American Journal of Botany 106: 270-279. Link, Reprint Request

Smith, S. D., R. Angelovici, K. Heyduk, H. A. Maeda, G. D. Moghe, J. C. Pires, J. R. Widhalm, & J. H. Wisecaver. 2019. The renaissance of comparative biochemistry. American Journal of Botany 106: 3-13. Link, Reprint Request


Ng, J.+ & S. D. Smith. 2018. Why are red flowers so rare? Testing the macroevolutionary causes of tippiness. Journal of Evolutionary Biology 31: 1863-1875. LinkReprint Request

Deanna, R.+, S. D. Smith, T. Särkinen & F. Chiarini. 2018. Patterns of chromosomal evolution in the florally diverse Andean clade Iochrominae (Solanaceae). Perspectives in Plant Ecology, Evolution and Systematics 35: 31-43. Link, PreprintReprint Request

Ng, J.+, L. B. Freitas & S. D. Smith. 2018. Stepwise evolution of floral pigmentation predicted by biochemical pathway structure. Evolution 72: 2792-2802. Link, Reprint Request

Larter, M.+, A. Dunbar-Wallis, A. E. Berardi+ & S. D. Smith. 2018. Convergent evolution at the pathway level: predictable regulatory changes during flower color transitions. Molecular Biology and Evolution 35: 2159-2169. Link, PreprintReprint Request

Dupin, J.* & S. D. Smith. 2018. Phylogenetics of Datureae (Solanaceae), including description of the new genus Trompettia and re-circumscription of the tribe. Taxon, 67: 359-375. Link Email for reprint

Gates, D. J.*, D. Pilson & S. D. Smith. 2018. Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae). Molecular Phylogenetics and Evolution 123: 26-34. Link

Smith, S. D., & R. Kriebel. 2018. Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae). Evolution 72: 688-697. Link Commentary by Dodsworth et al.


Moghe, G. D., & S. D. Smith. 2017. The push and pull of plant specialized metabolism underlies a long-standing, colorful mystery. New Phytologist 217: 471-473. Link

Gates, D. J.*, B. J. S. C. Olson, T. E. Clemente, and S. D. Smith. 2017. A novel R3 MYB transcriptional repressor associated with the loss of floral pigmentation in Iochroma. New Phytologist 217: 1346-1356.  PDF

Fernandez-Hilario, R., & S. D. Smith. 2017. A new species of Saracha Ruiz & Pav. (Solanaceae) from the Central Andes of Peru. Phytokeys 85: 31–43. Link

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 104: 1–10. 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 44: 887–899.  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. 2015. Pleiotropy and the evolution of floral integration. New Phytologist, in press. PDF

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

Ng, J.+, and S. D. Smith. 2015. Widespread flower color convergence in Solanaceae via alternate biochemical pathways. New Phytologist, in press. 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. Link

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


Weisrock, D. W, S. D. Smith, L. M. Chan, K. Biebouw, P. M. Kappeler, and A. D. Yoder. 2012. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Molecular Biology and Evolution 29: 1615-1630. Link


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

Johnson, M. T. J., R. G. FitzJohn, S. D. Smith, M. D. Rausher & S. P. Otto. 2011. Loss of sexual recombination and segregation is associated with increased diversification in evening primroses. Evolution 65: 3230-3430. Link

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


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

Johnson, M. T. J., S. D. Smith and M. D. Rausher. 2010. The effects of plant sex on range distributions and allocation to reproduction. New Phytologist 186: 769-779. Link


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

Johnson, M. T. J., S. D. Smith and M. D. Rausher. 2009. Plant sex and the evolution of plant defenses against herbivores. PNAS 106: 18079-18084. Link


Smith, S. D., S. J. Hall, P. R. S. Izquierdo and D. A. Baum. 2008. Comparative pollination biology of sympatric and allopatric Andean Iochroma (Solanaceae).  Annals of the Missouri Botanical Garden 95: 600-617. Link

Smith, S. D., D. A. Baum, and **V. J. Kolberg. 2008. Morphological and cytological evidence for homoploid hybridization in Iochroma (Solanaceae) Madroño 55: 280-284.

Paape, T., B. Igic, S. D. Smith, R. Olmstead, L. Bohs and J. R. Kohn. 2008. A 15-Myr-old genetic bottleneck. Molecular Biology and Evolution 25: 655-663. Link

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

Paape, T., B. Igic, S. D. Smith, R. Olmstead, L. Bohs and J. R. Kohn. 2008. A 15-million-year-old genetic bottleneck. Molecular Biology and Evolution 25: 655-663. 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. 2007. Systematics of Iochrominae (Solanaceae): Patterns in floral diversity and interspecific crossability. Acta Hort. 745: 241-254. PDF


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! 

Smith, S. D., and S. Leiva G. 2005. Recuento cromosómico y estado actual de Dunalia spathulata (R. &P.) Braun & Bouché (Solanaceae: Solaneae) endémica de Perú. Arnaldoa 12: 68-71.


D. A. Baum, S. D. Smith, A. Yen, W. S. Alverson, R. Nyffeler, B. A. Whitlock and R. L. Oldham. 2004.  Phylogenetic relationships of Malvatheca (Bombacoideae & Malvoideae; Malvaceae sensu lato) as inferred from plastid DNA sequences. American Journal of Botany 91: 1863-1871.

S. D. Smith, R. Cowan, K. B. Gregg, M.W. Chase, N. Maxted and M. F. Fay. 2004.  Genetic discontinuities among populations of Cleistes (Orchidaceae, Vanilloideae) in North America. Botanical Journal of the Linnean Society 145: 87-95.


S. D. Smith and J. E. Bond. 2003. An analysis of the secondary structure of the mitochondrial large subunit rRNA gene (16S) in spiders and its implications for phylogenetic reconstruction.  Journal of Arachnology 31: 44-54.


S. D. Smith and I. E. Peralta. 2002. Ecogeographic surveys as tools for analyzing potential reproductive isolating mechanisms: An example using Solanum juglandifolium Dunal, S. ochranthum Dunal, S. lycopersicoides Dunal and S. sitiens I. M. Johnston. Taxon 51: 341-349.

S. D. Smith and S. Knapp. 2002. The natural history of reproduction in Solanum and Lycianthes (Solanaceae) in a subtropical moist forest. Bulletin of the Natural History Museum Botany 32: 125-136.