Books

Baum, D. A., and S. D. Smith. 2013. . Roberts & Co., Greenwood Village, Colorado.
听

Peer-reviewed articles

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

2023

Wheeler, L. C.+, A. Dunbar-Wallis, K. Schutz*, & S. D. Smith. 2023. Evolutionary walks through flower color space driven by gene expression in Petunia and allies (Petunieae). Proceedings of the Royal Society B, in press. 听

Deanna R. +, C. Mart铆nez, S. Manchester, P. D. Wilf, A. Campos**, S. Knapp, F. E. Chiarini, G. E. Barboza, G. Bernardello, H. Sauquet, E. Dean, A. Orejuela & S. D. Smith. 2023. Fossil berries reveal global radiation of the nightshade family by the early Cenozoic. New Phytologist, in press. 听Reprint Request

Pretz, C.*, & S. D. Smith. 2023. How does a self-incompatible individual transition to self-compatibility during its lifetime?听American Journal of Botany听110: e16150.听

Dellinger, A.+, A. Hamilton*, C. Wessinger, & S. D. Smith. 2023. Opposing patterns of altitude-driven pollinator turnover in the tropical and temperate Americas.听American Naturalist, in press.听

2022

Tenhumberg, B. T., A. Dellinger+, & S. D. Smith. 2022. Modeling pollinator and non-pollinator selection on flower color variation.听Journal of Ecology听111: 746-760.听

Sinnott-Armstrong, M. A.+, Y. Ogawa, G. van de Kerkhof, S. Vignolini, & S. D. Smith. 2022. Convergent evolution of disordered lipidic structural color in the fruits of听Lantana strigocamara听(syn.听L. camara听hybrid cultivar).听New Phytologist听235: 898-906.听听

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. 听

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.听.

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: .

2021

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

Smith, S. D. & B. K. Blackman. 2021. From deep roots to new blooms: The ever鈥恎rowing field of evo鈥揹evo across land plant.听Evolution & Development 23: 119-122.听, 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.听, Reprint Request

2020

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

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听35: 415-425.听, Reprint Request

2019

Larter, M.+, A. Dunbar-Wallis, A. E. Berardi+ & S. D. Smith. 2019. Developmental control of convergent floral pigmentation across evolutionary timescales. Developmental Dynamics听248: 1091-1100.听, 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听106: 1-12.听, Reprint Request

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

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听106: 270-279.听, Reprint Request

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

2018

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

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

Ng, J.+, L. B. Freitas & S. D. Smith. 2018. Stepwise evolution of floral pigmentation predicted by biochemical pathway structure. Evolution听72: 2792-2802.听, 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听35: 2159-2169.听, ,听Reprint 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. 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听123: 26-34.

Smith, S. D., & R. Kriebel. 2018. Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae). Evolution听72: 688-697.听听

2017

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

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听217: 1346-1356. 听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鈥�43.

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听104: 1鈥�10.听

2016

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听44: 887鈥�899.听 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.听Journal of Molecular Evolution 83: 26-37.

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听16: 98.

O鈥橫eara, B. C., S. D. Smith鈥�, W. S. Armbruster, L. D. Harder, C. Hardy, L. C. Hileman, L. Hufford, A. Litt, S. Magall贸n, 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 . 鈥�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听8: plw013.

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

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

2015

Cueva-Manchego, M., S. D. Smith, and S. Leiva-Gonz谩les. 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

2014

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

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

2013

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

2012

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.

2011

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. 听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.

Rosas-Guerrero, V., M. Quesada, W. Scott Armbruster, R. P茅rez-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.

2010

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.

2009

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

2008

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). 听Annals of the Missouri听Botanical听Garden听95: 600-617.

Smith, S. D., D. A. Baum, and **V. J. Kolberg. 2008. Morphological and cytological evidence for homoploid hybridization in Iochroma (Solanaceae) 惭补诲谤辞帽辞 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听25: 655-663.

Smith, S. D., C. An茅, 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

2007

An茅, 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.

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

2006

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

2005

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

Smith, S. D., and S. Leiva G. 2005. Recuento cromos贸mico y estado actual de Dunalia spathulata (R. &P.) Braun & Bouch茅 (Solanaceae: Solaneae) end茅mica de Per煤. Arnaldoa 12: 68-71.

2004

D. A. Baum, S. D. Smith, A. Yen, W. S. Alverson, R. Nyffeler, B. A. Whitlock and R. L. Oldham. 2004.听 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.听 Genetic discontinuities among populations of Cleistes (Orchidaceae, Vanilloideae) in North America. Botanical Journal of the Linnean Society 145: 87-95.

2003

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.听 Journal of Arachnology 31: 44-54.

2002

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.

听