Research Faculty #70
General Information
Professor at University of British Columbia since 2004 (various ranks); Head, Department of Botany (2016-2021); Associate Director, UBC Biodiversity Research Centre (2010–2013); Research Director, UBC Botanical Garden (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.
Others: Distinguished Fellow, Botanical Society of America (2019); ISI Highly Cited Researcher (2019); Associate Editor, American Journal of Botany (since 2008); Editor, Journal of Systematics and Evolution (since 2009)
Research Information
My lab group works on the evolution, phylogenetics and comparative genomics of diverse groups of land plants (embryophytes), with a particular focus on monocots, a flowering-plant clade that includes the major crop plants that sustain human civilization.
I have mentored 27 graduate students in my lab to date, and currently supervise six PhD and two MSc students. My lab group works on a broad variety of problems in plant systematics and evolution. Our work includes inference of the major details of the land-plant portion of the 'Tree of Life,' comparative genomics, and inferring the phylogeny and evolution of understudied plant lineages:
Comparative genomics of green & mycoheterotrophic plants
Ongoing work includes studies of plastid genome dissolution in mycoheterotrophic plants—plants that obtain some or all of their nutrition from fungal partners—and comparative transcriptome studies of these plants and their relatives.
Plant deep phylogeny
A major ongoing research 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, Hydatellaceae and other ANA-grade angiosperms, seed plants, monilophytes (ferns) and bryophytes (mosses and relatives).
Evolutionary biodiversity
Phylogenetics and comparative genomics of diverse plant lineages, including several crop lineages. We use phylogenies as a framework for studying evolutionary questions, such as the origin of heterostyly, and the molecular evolution of plastid genomes We also work on molecular-assisted taxonomy.
TEACHING: I have taught a range of classes in the UBC Biology teaching program, from 200- to 500-level. I currently teach "Vascular Plants" (BIOL/APBI 210) and "Phylogenetic Biology" (BIOL 417).
CURRENT STUDENTS
Wesley Gerelle (PhD). Angiosperm organellar genomes; Parasitaxus
Nathaniel Klimpert (PhD). Monocot and eudicot mycoheterotrophs
Romulo Segovia (PhD). Genomics of Andean crops—olluco and tarwi
Philippa Stone (PhD). Genomics and systematics of Triantha (Tofieldiaceae)
Izai Kikuchi (PhD). Functional and comparative genomics of mycoheterotrophs
Marielle WIlson (PhD). Mycoheterotrophic gametophytes of seed-free plants
Edward Sun (MSc). TBD
Connor Wardrop (MSc). TBD
PAST STUDENTS & POSTDOCTORAL FELLOWS:
Marybel Soto Gomez (PhD), Project Manager, Royal Botanic Garden, Kew; David Bell (PhD), Postdoctoral Fellow, Royal Botanic Garden Edinburgh; Qianshi Lin (PhD), Postdoctoral Fellow, PennState; Lis (Natalie) Garrett (MSc), Administrative Coordinator, Division of Developmental Pediatrics, UBC; Ying Chang (PhD), Assistant Professor, National University of Singapore; Vivienne Lam (PhD), Lecturer, Depts. of Botany and Zoology, UBC; Will Iles (PhD), Associate Analyst, Vancouver; Sean Montgomery (BSc Hons), EMBO Postdoctoral Fellow, Centre for Genomic Regulation, Spain; Julia Nowak (PhD), Horticultural Technician, Western University; Hayley Darby (MSc), Technology Specialist, McCoy Russell LLP; Erin Fenneman (MSc), Research Associate, Aurora Cannabis Inc.; Isabel Marques (PDF), Researcher, Instituto Superior de Agronomia, Lisbon, Diana Percy (PDF), Research Associate, Dept. of Botany, UBC; Jeff Saarela (PhD), Research Scientist and VP Research & Collections, Canadian Museum of Nature; Greg Ross (MSc), Teacher, Delta Secondary School; Hardeep Rai (PhD), Teacher, Riverview Middle School; Solveig Adair (MSc), College Professor, Coast Mountain College, British Columbia; Marc McPherson (MSc), Agronomist, Evonik Industries; Jessie Zgurski (MSc), Biology Instructor, Northwestern Polytechnic, Alberta; Melissa Piercey (MSc); SGS Forensic Laboratories; Selena Smith (BSc), Associate Professor, University of Michigan; Martina Krieger (MSc), Director of Agency and Partnership Governance at Environment and Protected Areas, Government of Alberta
Selected Publications
Chen, X., Fang, D., Xu, Y. et al. Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite–host interactions. 2023. Nature Plants (2023). https://doi.org/10.1038/s41477-023-01517-7.
Garrett, N., J. Viruel, N. Klimpert, M. Soto Gomez, V. K.-Y. Lam, V.S.F.T. Merckx, and S.W. Graham. 2023. Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales). American Journal of Botany 110: e16141.
Klimpert, N.J., J.L.S. Mayer, D.S. Sarzi, F. Prosdocimi, F. Pinheiro, and S.W. Graham. 2022. Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii. American Journal of Botany 109: 2030–2050.
Lin Q., T. W. A. Braukmann, M. Soto Gomez, J. Lischka Sampaio Mayer, F. Pinheiro, V.S.F.T. Merckx, S. Stefanović, and S.W. Graham. 2022. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny. New Phytologist 236: 1908–1921.
Lin, Q., C. Ané, T.J. Givnish and S.W. Graham. 2021. A new carnivorous plant lineage (Triantha) with a unique sticky-inflorescence trap. Proceedings of the National Academy of Sciences, USA 118: e2022724118
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.
One Thousand Plant Transcriptomes Consortium (Leebens-Mack, J.H., M.S. Barker, E.J. Carpenter, M.K. Deyholos, M.A. Gitzendanner, S.W. Graham, et al. ~195 authors). 2019. A phylogenomic view of evolutionary complexity in green plants. Nature 574, 679–685.
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: 310–323.
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
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
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. Proceedings of the National Academy of Sciences, USA 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. Proceedings of the National Academy of Sciences, USA 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.