Baum, D. A. and Smith, S.D. 2012. Tree-thinking: An Introduction to Phylogenetic Biology. Roberts & Company.

Losos, J., D. A. Baum, D. Futuyma, H. Hoekstra, R. Lenski, A. Moore, D. Schluter, and M. Whitlock (eds.). 2012. The Princeton Guide to Evolution. Princeton University Press.

Correa, R., Stanga, J., Larget, B., Roznowski, A., Shu, G., Dilkes, B., and Baum, D.A. 2012. An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species. New Phytologist 193(2):494-503.

Duarte, M.C., Esteves, G.L., Salatino, M.L.F. Walsh, K.C, and Baum, D.A. 2011. Phylogenetic Analyses of Eriotheca and Related Genera (Bombacoideae, Malvaceae). Systematic Botany 36(3):690-701.

Liu, N., Sliwinski, M.K., Correa, R., and Baum, D.A. 2011. Possible contributions of TERMINAL FLOWER 1 to the evolution of rosette flowering in Leavenworthia (Brassicaceae). New Phytologist 189(2):616-628.

Koopman, M and Baum, D. A. Accepted. Isolating nuclear genes and identifying lineages without monophyly: An example of closely related species from Southern Madagascar. International Journal of Plant Sciences.

Oyama, R. K., Jones, K. N., and Baum, D. A. 2010. Sympatric sister species of Californian Antirrhinum and their transiently specialized pollinators.  American Midland Naturalist 164(2): 337-347.

Cacho, N. I. , Berry, P. E., Olson, M. E., Steinmann, V. W., and Baum, D. A.  2010. Are spurred cyathia a key innovation? Molecular systematics and trait evolution in the Slipper-Spurges (Pedilanthus clade - Euphorbia, Euphorbiaceae).  American Journal of Botany 97: 493–510.

Yue, J.-P., Sun, H., Baum, D. A., Al-Shehbaz, I. L., and Ree, R. 2009.  Molecular phylogeny of Solms-laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications.  Journal of Systematics and Evolution 47(5): 402-415.

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

Smith, J. J., Baum. D. A., and Moore A. 2009. The need for molecular genetic perspectives in evolutionary education (and vice versa).  Trends in Genetics 25: 427-429. [Forum]

Baum, D. A.  2009. Species as ranked taxa. Systematic Biology 58:74–86.

Smith S. D., Izquierado, P., and Baum, D. A. 2008. Comparative pollination biology of sympatric and allopatric Andean Iochroma (Solanaceae).  Annals of the Missouri Botanical Garden 95: 600-618.

Janka, H, von Balthazar, M., Alverson, W. S., Baum, D. A., Semir, J., and Bayer, C. 2008. Structure, development, and evolution of the androecium in Adansonieae (core Bombacoideae, Malvaceae s.l.).  Plant Systematics and Evolution 275: 69-91

Koopman, M. M. and Baum, D. A.  2008. Phylogeny and biogeography of Hibisceae (Malvaceae) on Madagascar.  Systematic Botany 33: 364-374.

Baum, D. A.  and Offner, S.  2008.  Phylogenies and tree thinking.  American Biology Teacher 70: 222-229.

Bosch. J. A., Heo, K., Sliwinski, M. K., and Baum, D. A.  2008. An exploration of LEAFY expression in independent evolutionary origins of rosette flowering in Brassicaceae.  American Journal of Botany 95:286-293.

Davis, C. C., P. Endress, and Baum, D. A. 2008.  The evolution of floral gigantism.  Current Opinions in Plant Biology 11:49-57.

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

Smith, S. D. and Baum, D. A. 2007. Systematics of Iochrominae (Solanaceae): Patterns in floral diversity and interspecific crossability. Acta Horticulturae. 745:241-254.

Sliwinski, M. K., Bosch, J. A., Yoon, H.-S., von Balthazar, M. and Baum, D. A.  2007. The role of two LEAFY paralogs from Idahoa scapigera (Brassicaceae) in the evolution of a derived plant architecture.  The Plant Journal 51:211-219 [cover].

Davis, C.C., Latvis, M., Nickrent, D. L., Wurdack, K. J., and Baum, D. A.  2007. Floral gigantism in Rafflesiaceae.  Science 315: 1812.

Baum, D. A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.

Ané, C., Larget, B., Baum, D. A., Smith, S. D., & Rokas, A. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24: 412-426 (corrigendum - 24:1575).