Research Faculty #70

General Information

Academic History

Head of Botany (2016-2021). Research Director, UBC Botanical Garden & Centre for Plant Research (2006-2016). Assistant Professor (1999-2003), University of Alberta.  Postdoctoral Fellow (1996-1998), University of Washington. Ph.D. Botany (1997), University of Toronto. B.Sc. Genetics (1989), University of St. Andrews. He has mentored 24 graduate students (including six current).

Contact Information

Office Phone

Research Information

Research Abstract

Systematics and evolution of vascular plants, focusing on using DNA sequence data to infer relationships at deep and recent levels of seed plant, angiosperm and monocot phylogenetic history.

Research Interests

Professor Sean Graham specializes in plant biodiversity with a focus on both evolutionary and molecular approaches.  He earned his Ph.D. at the University of Toronto in 1997, and was a Research Associate at the University of Washington before joining the University of Alberta as an Assistant Professor in 1999.  In 2003, Dr. Graham was recruited to UBC as an Assistant Professor in the Faculty of Land & Food Systems and was promoted to Associate Professor with tenure in 2006.  In 2011, Dr. Graham moved to the Department of Botany in the Faculty of Science, and was promoted to Professor in 2012.  Prof. Graham has published more than 90 peer-reviewed papers in top journals including Nature and Proceedings of the National Academy of Sciences.  His research is well funded by NSERC programs, including a Discovery grant and Accelerator grant; he has been a co-PI on team CFI, RTI, and CREATE grants. He has taught a range of classes in our Biology program at the 200- to 500-levels, and SCIE 300 (Science Communications).  He has successfully mentored 15 graduate students and he currently supervises eight PhD and Masters students. Prof. Graham has served as the Research Director for the Centre for Plant Research and the Associate Director of the Biodiversity Research Centre.  He is currently an Associate Editor for  American Journal of Botany and the Journal of Systematics and Evolution

My lab group works on a broad variety of problems in plant systematics and evolution. Research goals include inference of the major details of the land-plant portion of the 'Tree of Life,' application of reliable phylogenies to evolutionary questions, and characterization of the biodiversity of understudied plant lineages

Comparative genomics of green & mycoheterotrophic plants
Ongoing work includes studies of plastid genome dissolution in the mycoheterotrophic plants (plants that obtain some or all of their nutrition from fungal partners) and comparative transcriptome studies.

Plant deep phylogeny
A major focus is to infer the broad backbone of plant phylogeny using molecular approaches, including the earliest evolutionary splits in plant phylogeny. Recent and ongoing work includes investigations of higher-order relationships of the monocots, ANA-grade angiosperms, seed plants, monilophytes (ferns) and bryophytes (mosses and relatives).

Evolutionary biodiversity
Studies of recent groups, including molecular-assisted taxonomy and phylogenetics of 'early-diverging' lineages. We also use phylogenies as a framework for studying various evolutionary questions (e.g., the origin of heterostyly).

Team Members

Natalie Garrett (MSc). Dioscoreales mycoheterotrophs

Wesley Gerelle (PhD). Angiosperm organellar genomes; Parasitaxus

Nathaniel Klimpert (PhD). Monocot and eudicot mycoheterotrophs

Romulo Segovia (PhD). Genomics of olluco

Philippa Stone (PhD).Genomics and systematics of Triantha (Tofieldiaceae)

Izai Kikuchi (PhD). Functional and comparative genomics of mycoheterotrophs

Selected Publications

Soto Gomez, M., Q. Lin, E. da Silva Leal, T. Gallaher, D. Scherbirich, C. Mennes, S. Smith, S.W. Graham. 2020. A bi-organellar phylogenomic study of Pandanales: inference of higher-order relationships and unusual rate-variation patterns. Cladistics 26:481–504.

Bell, D., Q. Lin, W.K. Gerelle, S. Joya, Y. Chang, Z.N.Taylor, C.J. Rothfels, A. Larsson, J. Carlos Villarreal, F.-W.i Li, L. Pokorny, P. Szövényi, B. Crandall-Stotler, L. DeGironimo, S.K. Floyd, D.J., Beerling, M.K. Deyholos, M. von Konrat, S. Ellis, A.J. Shaw, T. Chen, G.K.-S. Wong, D.W. Stevenson, J.D. Palmer, S. W. Graham. 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. American Journal of Botany 107: 91–115.

Sokoloff, D.D., I. Marques, T.D. Macfarlane, M.V. Remizowa, V.K.Y. Lam, J. Pellicer, O. Hidalgo, P.J. Rudall, S.W. Graham. 2019. Cryptic species in an ancient flowering-plant lineage (Hydatellaceae, Nymphaeales) revealed by molecular and micromorphological data sets. Taxon 68: 1-19.

Soto Gomez, M., L. Pokorny, M.B. Kantar, F. Forest, I.J. Leitch, B. Gravendeel, P. Wilkin, S.W. Graham, J. Viruel. 2019. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae).  Applications in Plant Sciences 7: e11254.

Lam, V.K.Y., H. Darby, V.S.F.T. Merckx, G. Lim, T. Yukawa, K.M. Neubig, J.R. Abbott, G.E. Beatty, J. Provan, M. Soto Gomez, S.W. Graham. 2018. Phylogenomic inference in extremis: a case study with mycoheterotroph plastomes. American Journal of Botany 105: 480-494.

Graham, S.W., V.K.Y. Lam, V.S.F.T. Merckx. 2017. Plastomes on the edge: The evolutionary breakdown of mycoheterotroph plastid genomes. New Phytologist 214: 48–55.

Marques, I., S.A. Montgomery, M.S. Barker, T.D. Macfarlane, J.G. Conran, P. Catalán, L.H. Rieseberg, P.J. Rudall, S.W. Graham. 2016. Transcriptome‐derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytologist 210:310-32.

Ross, T.G., C.F. Barrett, M. Soto Gomez, V.K.Y. Lam, C.L. Henriquez, D.H. Les, J.I Davis, A. Cuenca, G. Petersen, O. Seberg, M. Thadeo, T.J. Givnish, J. Conran, D.W. Stevenson, S.W. Graham. 2016. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics  32:160-178

Lam, V.K.Y., V.S.F.T. Merckx, S.W. Graham. 2016. A few-gene plastid phylogenetic framework for mycoheterotrophic monocots. American Journal of Botany 103:692-708.

Lam, V.K.Y., M. Soto Gomez, S.W. Graham. 2015. The highly reduced plastome of mycoheterotrophic Sciaphila (Triuridaceae) is colinear with its green relatives and is under strong purifying selection. Genome Biology and Evolution 8:2220-2236

Iles, W.J.D, S.S. Smith, M.A. Gandolfo and S.W. Graham. 2015. Monocot fossils suitable for molecular dating analyses. Botanical Journal of the Linnean Society. 178:346-374

Percy, D.M., G.W. Argus, Q.C. Cronk, A.J. Fazekas, P.R. Kesanakurti, K.S. Burgess, B.C. Husband, S.G. Newmaster, S.C.H. Barrett and S.W. Graham 2014. Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Molecular Ecology 19:4737-4756

Chang, Y. and S.W. Graham. 2014. Patterns of clade support across the major lineages of moss phylogeny. Cladistics 30:590-606

Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M.S. Barker, J.G. Burleigh, M.A. Gitzendanner, B.R. Ruhfel, E. Wafula, J.P. Der, S.W. Graham, et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. PNAS 111:E4859–E4868.

Hollingsworth, P.M., L.L. Forrest, J.L. Spouge, M. Hajibabaei, S. Ratnasingham, M. van der Bank, M.W. Chase, R.S. Cowan, D.L. Erickson, A.J. Fazekas, S.W. Graham, et al. 2009. A DNA barcode for land plants. PNAS 106:12794-12797.

Saarela J.M., H.S. Rai, J.A. Doyle, P.K. Endress, S. Mathews, A.D. Marchant, B.G. Briggs and S.W. Graham. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446:312-315.

Graham S.W., J.M. Zgurski, M.A. McPherson, D.M. Cherniawsky, J.M. Saarela, E.F.C. Horne,S.Y. Smith, W.A. Wong, H.E. O’Brien, V.L. Biron, J.C. Pires, R.G. Olmstead, M.W. Chase and H.S. Rai. 2006. Robust inference of monocot deep phylogeny using an expanded multigene plastid data set. In J.T. Columbus, E.A. Friar, J.M. Porter, L.M. Prince and M.G. Simpson [eds.], Monocots: comparative biology and evolution (excluding Poales). Rancho Santa Ana Botanic Garden, Claremont, California, USA, pages 3–21.