Skip to Main Content
Mobile Menu

James Smith, Ph.D.

Professor, Director of Snake River Plains Herbarium, and Interim PhD EEB Graduate Program Coordinator
Year arrived at BSU: 1992

Mailing Address:
Department of Biology
Boise State University
Boise, ID 83725-1515

Office Location: Science Building, Room 207
Office Number: 208-426-3551
Office Fax: 208-426-4267

E-Mail Address:


BOT 305 Systematic Botany
BIOL 401 Organic Evolution
BIOL 517 Species and Speciation
BIOL 597 Special Topics: Population Genetics
BIOL 597 Special Topics: Introduction to Bioinformatics


Evolution of Floral Symmetry in Gesneriaceae: Recent work on Antirrhinum and relatives have identified genes important in the control of floral symmetry, cycloidea and dichotoma. Homologs of cycloidea have been identified in Gesneriaceae known as GCYC. Although most Gesneriaceae have flowers with bilateral symmetry a few genera have full or partial radial symmetry (in the latter the corollas are radially symmetric or nearly radially symmetric, but stamen abortion results in 4 instead of 5 stamens). Investigations at the DNA sequence level of GCYC in Gesneriaceae with have not revealed any obvious mutations that may disrupt function of this gene in plants with radially symmetric flowers. Likewise rates of mutation at the DNA level and synonymous to nonsynonymous substitution rates are not significantly different for species with radial or bilateral symmetry. The control of symmetry for these plants must lie in other regulatory genes and investigations at the mRNA level are beginning.

Paradrymonia maculata V--French Guiana. Toward the inselberg
Pagothyra maculata from Les Nouragues, French Guiana.  Photo by Chris Davidson

Phylogenetics of tribe Episcieae (Gesneriaceae):  The latest study represents and expansion of earlier studies on this tribe that used only a few genes and sampled only a few species for each genus. We sampled more widely from larger genera,  sampled some of the more disparate morphological species in each genus and using more sequence data to more strongly support intergeneric relationships.  As a result, four new generic names were published to reflect the monophyly in this clade.

Episcia xantha for JFS 2012 100 dpi
Line drawing of Chrisopheria xantha, one of the newly described genera in Episcieae.  Drawing by Alexa DiNicola.

Phylogenetics within Columnea (Gesneriaceae): Columnea is the largest genus within Neotropical Gesneriaceae and all previous attempts to resolve relationships within this genus have been poorly resolved or poorly supported. I have sampled many low copy nuclear genes in an attempt to identify a combination of sequences that will resolve and provide support for relationships within this genus. Currently, in collaborations with John L. Clark of the University of Alabama and Marisol Amaya-Marquez of Universidad Nacional de Colombia we are  sampling nearly 40-50% of described species to test the current sectional classification within this clade.  Results indicate that no previous subgeneric classification has reflected monophyletic groups and we are in the process of analyzing the data to resolve where new sectional delimitations can be made.

JS 10771 Columnea filipes-7
Columnea filipes from Cerro del Ingles, Colombia. Photo by Oscar Marin-Gomez.

For more information on the Gesneriaceae, see the Tree of Life pages.

JS 10806 Columnea lacinisepalata-7-2
Columnea laciniata, photo from the type collection made at Cerro del Ingles, Colombia. Photo by Oscar Marin-Gomez.

Phylogenetics of Piperaceae: I have been conducting research on the phylogenetics of Piperaceae in collaboration with Dr. Chris Davidson of the Idaho Botanical Research Foundation of Boise, Idaho. Our ultimate goal is to work on the phylogenetics of the family worldwide, but we are currently focusing our efforts on two clades that have been identified as a monophyletic group by both our studies and previous investigations. These are subgenera Enckea and Arctottonia. We are also sampling from several different genes, including low copy nuclear genes. The latter project is also in collaboration with Dr. Allan Bornstein of Southeast Missouri State University, Cape Girardeau, MO.

JS 10857 or 10859 Piper-3
Piper from Colombia. Photo by Oscar Marin-Gomez.


J. F. Smith, M. Amaya-Marquez, O. H. Marin-Gomez, and J. L. Clark. 2013. Four new species of Columnea (Gesneriaceae) with primary distributions in Colombia. submitted to Journal of the Botanical Research Institute of Texas. 7: 667-679.

Smith, J. F., M. T. Ooi, L. Schulte, M. Amaya-Marquez, and J. L. Clark. 2013. Searching for monophyly in the subgeneric classification systems of Columnea (Gesneriaceae). Selbyana 31: 126-142.

Ning, A.-L., J. Wang, J. F. Smith, and M. Kang. 2013. Primulina qingyuanensis sp. nov. (Gesneriaceae) from limestone areas in Guangdon, China. Phytotaxa 137: 48-52.

Gaskin, J. F., M. Schwarzländer, C. L. Kinter, J. F. Smith and S. J. Novak, . Propagule pressure, genetic structure and geographic origins of Chondrilla juncea (Asteraceae): An invader on three continents. American Journal of Botany 100: 1871-1882.

J. F. Smith and J. L. Clark. 2013. Molecular phylogenetic analyses reveal undiscovered monospecific genera in Episcieae (Gesneriaceae). Systematic Botany 38: 451-463.

Ning, Z.-L., G.-F. Li, J. Wang, J. F. Smith, H. Rasolonjatove, and M. Kang. 2013. Primulina huaijiensis (Gesneriaceae) a new species from Guangdon, China. Acta Botanica Fennici 50: 119-122.

Clay, D. L., D. C. Tank, S. J. Novak, M. D. Serpe, and J. F. Smith. 2012. Homoploid hybrid speciation in a rare endemic Castilleja from Idaho (Castilleja christii, Orobanchaceae). American Journal of Botany 99: 1976-1990.

Amaya M., M. and J. F. Smith. 2012. Columnea paraguensis (Gesneriaceae) a remarkable and rare new species from Colombia. Rev. Acad. Colomb. Cienc. 36: 137-140.

Clark, J. L., M. M. Funke, A. M. Duffy, and J. F. Smith. 2012. Phylogeny of a Neotropical clade in the Gesneriaceae: More tales of convergent evolution International Journal of Plant Sciences. 173: 894-916. Featured on cover.

Schubert, H. K., A. J. Bornstein, M. S. Taylor, and J. F. Smith. 2012. A Systematic Revision of the Genus Manekia (Piperaceae). Systematic Botany 37: 587-598. Featured on cover.

Carlson, K. M., D. H. Mansfield, and J. F. Smith. 2011. A new variety of Lomatium ravenii (Apiaceae) from the northern Great Basin and adjacent Owyhee region. Aliso 29(2):105-114.

Symmank, L., M.-S. Samain, J. F. Smith, G. Pino, A. Stoll, P. Goetghebur, C. Neinhuis, and S. Wanke. 2011. The extraordinary journey of Peperomia subgenus Tildenia (Piperaceae): insights into diversification and colonization patterns from its cradle in Peru to the Tans-Mexican volcanic belt. Journal of Biogeography. 38: 2337-2349.

Clark, J. L. and J. F. Smith. 2011. Columnea pygmaea, a new small-flowered species from Ecuador. Journal of the Botanical Research Institute of Texas 5: 87-95.

Carlson, K. M, D. H. Mansfield, and J. F. Smith. 2011. A New Species in the Lomatium foeniculaceum (Apiaceae) Clade Revealed Through Combined Morphometric and Phylogenetic Analyses. Systematic Botany 36: 495-507. Featured on cover.

Woo, V. L., Smith, J. F., M. M. Funke, P. J. Lockhart, and P. J. Garnock-Jones. 2011. Phylogenetic relationships in Coronanthereae (Gesneriaceae) reveal multiple introductions from South America into the Pacific. International Journal of Plant Sciences 172: 434-457.

Wang, Y.-Z., R.-B. Mao, Y. Li, J.-M. Li, Y. Dong, Z.-Y. Li, and J. F. Smith.. 2011. Phylogenetic reconstruction of Chirita and allies (Gesneriaceae) with taxonomic treatments. Journal of Systematics and Evolution.49: 50-64.

Smith, J. F., D. N. Perkins, C. Bjork, and G. Glenne. 2010. AFLP analyses reveal species boundaries within Pyrrocoma (Asteraceae). Madroño. 57: 95-105.

Smith, J. F. , A. J. Stillman, S. R. Larson. C. M. Culumber, I. C. Robertson , and S. J. Novak. 2009. Phylogenetic relationships among Lepidium papilliferum (L. Henderson) A. Nels & J. F. Macbr., L. montanum Nutt., and L. davisii Rollins (Brassicaceae). Journal of the Torrey Botanical Club 136: 149-163.


As director of the Snake River Plains Herbarium at Boise State University (SRP), I have seen the collection grow from a small teaching collection of ~6,000 specimens to a research and reference collection of ~50,000 specimens. The collection focuses primarily on plants of southwest Idaho, but we continue to add plants from throughout Idaho and surrounding states. The collection continues to expand through collections of faculty and students as well as an active exchange program. For information about exchange contact Dr. James Smith,

C. christii
Castilleja christii from Mt. Harrison, site of the first Idaho Botanical Foray.

The first Idaho Botanical Foray was held in 2008, click here for a summary of that foray and updates on future forays and workshops.

Foray 1try
Group photo from the third Idaho Botanical Foray in 2010, hosted by College of Idaho.