F.J.R. Taylor

F.J.R. Taylor

Professor Emeritus

Contact Information

maxt@eos.ubc.ca

Roy Turkington

Professor Emeritus

Academic History

  • B.Sc. (1972) Ulster, Coleraine; 
  • Ph.D. (1975) Univ Col lege N. Wales, Bangor
  • Post doc, University of Western Ontario, London, ON.
  • Visiting Professor, Univ College N. Wales 1985-86
  • Visiting Professor, Hebrew University Jerusalem, Israel 1992-1993
  • Visiting Professor , Akdeniz University, Antalya, Turkey 1999-2000.
  • Visiting Professor, N. Ireland Plant Breeding Station, N. Ireland 2000.
  • Visiting Professor, Kunming Inst. Botany, Kunming, China 2006-2007.
  • Visiting Professor, Instituto Multidisciplinario de Biologia Vegetal, Cordoba, Argentina 2013-2014

Selected Publications

Note that PDFs of most papers are available on Research Gate

  1. KOMATSU, Kimberly, Kimberly J. La PIERRE, Meghan L. AVOLIO, Nathan P. LEMOINE, Forest ISBELL, Emily  GRMAN, Gregory R. HOUSEMAN, Sally E. KOERNER, David S. JOHNSON, Kevin R. WILCOX,  Juha M. ALATALO, John P. ANDERSON, Rein AERTS, Sara G. BAER, Andrew H. BALDWIN,  Jonathan BATES, Carl BEIERKUHNLEIN, R. Travis BELOTE, John BLAIR, Juliette M.G. BLOOR,  Patrick J. BOHLEN, Edward W. BORK, Elizabeth H. BOUGHTON, William D. BOWMAN, Andrea  J. BRITTON, James F. CAHILL, Jr., Enrique CHANETON, Nona CHIARIELLO, Jimin CHENG, Scott  L. COLLINS, J. Hans C. CORNELISSEN, Guozhen DU, Anu ESKELINEN, Jennifer FIRN, Bryan  FOSTER, Laura GOUGH, Katherine GROSS, Lauren HALLETT, Xingguo HAN, Harry HARMENS,  Mark J. HOVENDEN, Anke JENTSCH, Christel KERN, Kari KLANDERUD, Alan K. KNAPP,  Juergen KREYLING, Wei LI, Yiqi LUO, Rebecca L. McCULLEY, Jennie R. McLAREN, J.  Patrick MEGONIGAL, Ulf MOLAU, John MORGAN, Volodya ONIPCHENKO, Steven C. PENNINGS,  Janet S. PREVÉY, Jodi PRICE, Peter REICH, Clare H. ROBINSON, F. Leland RUSSELL, Osvaldo E.  SALA, Eric SEABLOOM, Melinda D. SMITH, Nadia A. SOUDZILOVSKAIA, Lara SOUZA, Katherine  SUDING, K. Blake SUTTLE, Tony SVEJCA, David TILMAN, Pedro TOGNETTI, Roy TURKINGTON,  Shannon R. WHITE, Zhuwen XU, Laura YAHDJIAN, Qiang YU, Pengfei ZHANG, Yunhai  ZHANG. 2019. Global change effects on plant communities are magnified by time and the number of global change factors imposed. Proc Natl Acad Sci USA; first published August 19, 2019. https://doi.org/10.1073/pnas.1819027116
  2. XIA, K., TURKINGTON,R., TAN, H-Y & L. FAN. 2018. Factors limiting the recruitment of Quercus schottkyana, a dominant evergreen oak in SW China. Plant Diversity 40:277-283.  doi.org/10.1016/j.pld.2018.11.004
  3. HARROWER, W., SRIVASTAVA, D., McCALLUM, C., FRASER, L. & R. TURKINGTON. 2017. Temperate grassland songbird species accumulate incrementally along a gradient of primary productivity. PLoS1. https://doi.org/10.1371/journal.pone.0186809
  4. SINCLAIR A. R.E., PECH, R., FRYXELL, J.M., MCCANN, K., BYROM, A., SAVORY, C.J., BRASHARES, J., ARTHUR, A.D., CATLING, P.C., TRISKA, M.D., CRAIG, M.D., SINCLAIR, T.J.E., McLAREN, J.R., TURKINGTON, R., BEYERS, R. & W. HARROWER. 2017. Predicting and assessing progress in the restoration of ecosystems. Conservation Letters. June 2017; DOI: 10.1111/conl.12390
  5. XIA, K., HARROWER, W.L., TURKINGTON, R., TAN, H-Y & Z-N ZHOU. 2016. Pre-dispersal strategies by Quercus schottkyana to mitigate the effects of weevil infestation of acorns. Scentific Reports  6: 37520; doi: 10.1038/srep37520
  6. McLAREN, J.R., NOVOPLANSKY, A. & R. TURKINGTON. 2016. Few effects of plant functional group identity on ecosystem properties in an annual desert ecosystem. Plant Ecology 217:1379-1393. DOI 10.1007/s11258-016-0660-3
  7. XIA, K., HONGYU, T., TURKINGTON, R., HU, J-J. & Z-K ZHOU.2016. Desiccation and post-dispersal predation of acorns limit germination and recruitment of Quercus schottkyana, a dominant evergreen oak in SW China. Plant Ecology 217:1369-1378.
  8. HU, J-J.,LUO, C-C., TURKINGTON, R.& Z-K ZHOU. 2016. Effects of herbivores and litter on Lithocarpus hancei seed germination and seedling survival in the understorey of a high diversity forest in SW China. Plant Ecology 217:1429-1440. DOI 10.1007/s11258-016-0610-0
  9. LORTIE, C.J., FILAZZOLA, A., WELHAM, C. & R. TURKINGTON. 2016. A cost-benefit model for plant-plant interactions: a density-series tool to detect facilitation. Plant Ecology 217:1315-1329.   DOI:10.1007/s11258-016-0604-y
  10. LU, J., TURKINGTON, R. & Z-K. ZHOU. 2016. The effects of litter quantity and quality on soil nutrients and litter invertebrates in the understory of two forests in southern China.  Plant Ecology 217:1415-1426.
  11. DeSANDOLI, L., FRASER, L.F. & R. TURKINGTON. 2016. Restoration of pile burn scars in interface forest to prevent establishment and propagation of non-native invasive plants. Canadian Journal Forest Research 46: 1042-1050. DOI: 10.1139/cjfr-2016-0037.
  12. TURKINGTON, R. & W.L. HARROWER. 2016. An experimental approach to addressing ecological questions related to the conservation of plant biodiversity in China.Plant Diversity and Resources 38:2-9.
  13. FRASER,  L.H., HARROWER, W.L., GARRIS, H.W., DAVIDSON, S., HEBERT, P.D.N., HOWIE, R., MOODY, A., POLSTER, D., SCHMITZ, O.J., SINCLAIR, A.R.E., STARZOMSKI, B.M., SULLIVAN, T.P., TURKINGTON, R. & D. WILSON. 2015. A call for applying trophic structure to restoration. (Restoration Ecology) doi: 10.1111/rec.12225
  14. TURKINGTON, R., G. SHARAM & A.R.E. SINCLAIR. 2015. Biodiversity and the Dynamics of Riverine Forests in Serengeti. Pages 235-264, In Sinclair, A.R.E., Metzger, K.L., Mduma, S.A.R. & J.M. Fryxell. Serengeti IV.  Sustaining Biodiversity in a Coupled Human-Natural System. University of Chicago Press, London.
  15. XU, J., DENG, M., JIANG, X-L., WESTWOOD, M., SONG, Y-G. & R. TURKINGTON.  2015. Phylogeography of Quercus glauca (Fagaceae), a dominant tree of East Asian subtropical evergreen forests, based on three chloroplast DNA interspace sequences.  Tree Genetics & Genomes 11: 805. doi:10.1007/s11295-014-0805-2
  16. TURKINGTON, R. 2015. “John L. Harper.” In Oxford Bibliographies in Ecology. Ed. David Gibson. New York: Oxford University Press.
  17. 1 HU, J-J., XING, Y-W., TURKINGTON, R, JACQUES, F.M.B., TAO S., HUANG, Y-J., & Z-K. ZHOU. 2015. A new positive relationship between pCO2 and stomatal frequency in Quercus guyavifolia (Fagaceae): a potential proxy for palaeo-CO2 levels. Annals of Botany; doi: 10.1093/aob/mcv007
  18. TREBERG, M. & R. TURKINGTON. 2014. Species-specific responses to community density in an unproductive perennial plant community. PLoS ONE 9(7): doi:10.1371/journal.pone.0102430
  19. TURKINGTON, R., McLAREN, J.R. & M.R.T. DALE. 2014. Herbaceous community structure and function in the Kluane region. Arctic 67: Suppl. 1; 98–107.  http://dx.doi.org/10.14430/arctic4351
  20. KREBS, C.J., BOONSTRA,R. BOUTIN, S., SINCLAIR, A.R.E., SMITH, J.N.M., GILBERT, S., MARTIN, K., O’DONOGHUE & R. TURKINGTON. 2014. Trophic dynamics of the boreal forests of the Kluane region. Arctic 67: Suppl. 1; 71–81. http://dx.doi.org/10.14430/arctic4350.
  21. CARLYLE, C.N., FRASER, L.H. & R. TURKINGTON. 2014. Response of grassland biomass production to simulated climate change and clipping along an elevation gradient. Oecologia 174:1065-1073.
  22. McLAREN, J.R. & R. TURKINGTON. 2013. Boreal forest ecosystems. In S.A. Levin, ed. Encyclopedia of Biodiversity 2nd Edition. 1:626-635.Waltham, MA: Academic Press.
  23. CSERGŐ, A.M., DEMETER, L. & R. TURKINGTON. 2013. Declining diversity in abandoned grasslands of the Carpathian Mountains: do dominant species matter?PLOS ONE 8(8): e73533. doi:10.1371/journal.pone.0073533;
  24. GRAINGER, T.N. & R. TURKINGTON. 2013. Long-term nutrient enrichment differentially affects investment in sexual reproduction in four boreal forest understory species. Plant Ecology 214:1017-1026.
  25. GRAINGER, T.N. & R. TURKINGTON. 2013. Mechanisms for success after long-term nutrient enrichment in a boreal forest understory. PLOS ONE 8(4): e61229. doi: 10.1371/journal.pone0061229.
  26. 2 MacDOUGALL, A.S., McCANN, K., GELLNER, G. & R. TURKINGTON. 2013. Diversity loss with persistent human disturbance increases the vulnerability to sudden ecosystem collapse. Nature 494:86-90.
  27. FRASER, L.H., HENRY, H.A.L, CARLYLE, C.N., WHITE, S.R., BEIERKUHNLEIN, C., CAHILL JR, J.F., CASPER, B.B., CLELAND, E., COLLINS, S.L., DUKES, J.S., KNAPP, A.K., LIND, E., LONG, R., LUO, Y., REICH, P.B., SMITH, M.D., STERNBERG, M. & R. TURKINGTON. 2012. Coordinated distributed experiments: an emerging tool for testing global hypotheses in ecology and environmental science. Frontiers in Ecology and the Environment 2012; doi: 10.1890/110279 (published on-line)
  28. RAJANIEMI, T.K., GOLDBERG, D.E., TURKINGTON, R. & A.R. DYER. 2012. Local filters limit species diversity, but species pools determine composition. Perspectives in Plant Ecology, Evolution and Systematics 14:373-380.
  29. GRAINGER, T. & R. TURKINGTON. 2012. Germinability of Epilobium angustifolium seeds from plants treated annually with fertilizer for twenty-two years. Davidsonia 22:2-8
  30. SONG,Y., TURKINGTON, R. & D. ZHOU. 2012. Soil fissures help in the restoration of vegetation on secondary bare alkali-saline soil patches on the Songnen Plain, China. Journal of Soil and Water Conservation 67:24-25.
  31. KARST, J., HOEKSEMA, J.D., JONES, M.D. & R. TURKINGTON. 2011.  Parsing the roles of abiotic and biotic factors in Douglas-fir seedling growth. Pedobiologia 54: 273– 280.
  32. McLAREN, J.R. & R. TURKINGTON. 2011.  Plant identity  influences decomposition through more than one mechanism. PLOS One 6(8): e23702. doi:10.1371/journal.pone.0023702
  33. FREMLIN, K.M., McLAREN, J.R., DeSANDOLI, L. & R. TURKINGTON. 2011. Theeffects of fertilization and herbivory on the phenology of the understory vegetation of the boreal forest in north-western Canada. Arctic, Antarctic, and Alpine Research 43:389-396.
  34. McLAREN, J.R. & R. TURKINGTON. 2011.  Biomass compensation and plant responses to 7-years of plant functional group removals. Journal of  Vegetation Science 22:503–515.
  35. CARLYLE, C.N., FRASER, L.H. & R. TURKINGTON. 2011. Tracking soil temperature and moisture in a multi-factor climate experiment in temperate grassland: do climate manipulation methods produce their intended effects?  Ecosystems 14:489-502.
  36. MARSHALL, C,B., McLAREN, J.R. & R. TURKINGTON. 2011. Soil microbial communities resistant to changes in plant functional group composition. Soil Biology and Biochemistry 43:78-85.
  37. 3, 4 CARLYLE, C.N., FRASER, L.H. & R. TURKINGTON. 2010. Using three pairs of competitive indices to test for changes in plant competition along a resource and disturbance gradient. Journal of Vegetation Science 21:1025-1034.
  38. McLAREN, J.R. & R. TURKINGTON. 2010.  Plant functional group identity differentially affects leaf and root decomposition.  Global Change Biology 16:3075-3084.
  39. TREBERG, M. & R. TURKINGTON.  2010. Density dependence in an experimental boreal forest understory community. Botany 88:753-764.
  40. TREBERG, M.A. & R. TURKINGTON. 2010.  Facilitation in an unproductive boreal forest understory community.  Journal of Vegetation Science 21:761-771.
  41. McLAREN, J.R. & R. TURKINGTON. 2010. Ecosystem properties determined by plant functional group identity. Journal of Ecology 98:459-469.
  42. ZHANG, L., TURKINGTON, R. & Y. TANG.  2010. Flowering and fruiting phenology of 24 plant species on the north slope of Mt. Qomolangma (Mt. Everest). Journal of Mountain Science 7:45-54.
  43. TREBERG, M.A., EDWARDS, K. & R. TURKINGTON. 2010. Voles are attracted to fertilizer in field experiments.  Arctic, Antarctic, and Alpine Research 43:113-116.
  44. GILBERT, B., TURKINGTON, R. &  D. S. SRIVASTAVA.  2009. Dominant species and diversity: linking relative abundance to controls of species establishment. American  Naturalist 174:850-862.
  45. TURKINGTON, R.  2009. Top-down and bottom-up forces in mammalian herbivore – vegetation systems: an essay review.  Botany  87:723-739.
  46. RAJANIEMI, T.K., TURKINGTON, R., & D. GOLDBERG. 2009. Community-level consequences of species interactions in an annual plant community. Journal of Vegetation Science 20:836-846
  47. SHARAM, G.J., SINCLAIR, A.R.E. & R. TURKINGTON. 2009. Serengeti birds maintain forests by inhibiting seed predators.  Science 325 (5936) 51.
  48. SHARAM, G. & R. TURKINGTON. 2009. Secondary defense responses of white spruce (Picea glauca) to changes in herbivory and soil nutrient levels. Ecoscience 16:258-264.
  49. FRASER, L.H., GREENALL, A., CARLYLE, C., TURKINGTON, R. & C.R. FRIEDMAN. 2009. Adaptive phenotypic plasticity of Pseudoroegneria spicata: response of stomatal density, leaf area and biomass to changes in water supply and increased temperature.  Annals of Botany 103:769-775.
  50. KARST, J., JONES, M.D. & R. TURKINGTON. 2009. Ectomycorrhizal colonization and intraspecific variation in growth responses of lodgepole pine.  Plant Ecology 200:161-165.
  51. SHARAM, G.,  SINCLAIR, A.R.E. &  TURKINGTON, R. & A.L. JACOB.  2009. The savanna tree Acacia polyacantha facilitates the establishment of riparian forests in Serengeti National Park, Tanzania.  Journal of Tropical Ecology  25:31-40.
  52. NASERI, K., HESHMATI, G., MAHINI, A.S. & R. TURKINGTON. 2008. Determination of state and transition and threshold model of semi-arid grasslands using rangeland health indicators: Case study – Tandoureh area, north Khorasan. Journal of Agricultural Sciences and Natural Resources 15:26-42.
  53. TREBERG, M.A. & R. TURKINGTON. 2008. How to grow, propagate and kill some of the native plants in the Kluane region, southwestern Yukon. Davidsonia 19:42-53.
  54. SECCOMBE-HETT, P. & R. TURKINGTON. 2008. Summer diet selection of snowshoe hares: a test of nutritional hypotheses. Oikos 117:1874-1884.
  55. LORTIE, C.J. & R. TURKINGTON.  2008. Species-specific positive effects in an annual plant community. Oikos 117:1511-1521.
  56. KARST, J., MARCZAK, L., JONES, M.D. & R. TURKINGTON. 2008. The mutualism-parasitism continuum in ectomycorrhizas: a quantitative assessment using meta-analysis. Ecology 89:1032-1042.
  57. MacDOUGALL, A.S. & R. TURKINGTON. 2007. Does the type of disturbance matter for restoring disturbance-dependent savanna ecosystems? Restoration Ecology 15:263–272.
  58. MDUMA, S.A.R, SINCLAIR, A.R.E. & R. TURKINGTON. 2007.  What is the role of seasonality and synchrony in reproduction of savanna trees in Serengeti? Journal of Ecology 95:184-196.
  59. SHARAM, G.,  SINCLAIR, A.R.E. &  R. TURKINGTON.  2006. Establishment of broad-leaved thickets in Serengeti, Tanzania: the influence of fire, browsers, grass competition and elephants. Biotropica 78:599-605.
  60. MacDOUGALL, A.S. & R. TURKINGTON. 2006. Dispersal, competition, and shifting patterns of diversity in an degraded oak savanna.  Ecology 87:1831-1843.
  61. RAJANIEMI, T.K., GOLDBERG, D.E.,  TURKINGTON, R., & A.R. DYER, A.  2006. Quantitative partitioning of regional and local processes shaping regional diversity patterns.  Ecology Letters 9:121-128.
  62. MacDOUGALL, A.S, BOUCHER, J, TURKINGTON, R. & G.E. BRADFIELD. 2006. Community-level patterns of plant invasion across a broad-scale stress gradient. Journal of Vegetation Science 17:47-56.
  63. SHARAM, G. & R. TURKINGTON.  2005. Diurnal cycle of spartein production in Lupinus arcticus. Canadian Journal of Botany 83:1345-1348.
  64. MAZE, J. & R. TURKINGTON.  2005. A study on the effect of time in plants: within-group variation in morphological integration in clover (Trifolium repens L.) In different aged pastures.  SEED (Semiotics, Energy, Evolution, Development) 5:66-75.
  65. LORTIE, C.J., E. ELLIS, A. NOVOPLANSKY, & R. TURKINGTON. 2005.  Implications of seed spatial pattern and local seed density on community-level interactions.  Oikos 109:495-502.
  66. TURKINGTON, R., GOLDBERG, D.E., OLSVIG-WHITTAKER, L. & A. R. DYER. 2005. Effects of density on timing of germination and its consequences for survival and growth in two communities of annual plants.  Journal of Arid Environments 61:377-396.
  67. SHILO-VOLIN, H., NOVOPLANSKY, A, GOLDBERG D.E., & R. TURKINGTON. 2005. Density regulation in annual plant communities under different resource levels. Oikos 108:241-252.
  68. 5,6 MacDOUGALL, A.S. & R. TURKINGTON. 2005. Are invasive species the drivers or passengers of ecological change in highly disturbed plant communities? Ecology  86:42-55.
  69. TURKINGTON, R. 2004.  Some causes and consequences of the loss of biodiversity: ten years of plant ecological research in Yukon.  Davidsonia 15:47-69.
  70. MacDOUGALL, A.S., & R. TURKINGTON.  2004. Relative importance of uptake-based and tolerance-based competition in an invaded oak grassland.  Journal of Ecology 92:422-434.
  71. ARII, K. & R. TURKINGTON.  2002.  Do nutrient  availability and competition limit plant growth of  herbaceous species in the boreal forest understory? Arctic, Antarctic and Alpine Research 34:251-261.
  72. LORTIE, C.J. & R. TURKINGTON. 2002. The small-scale spatio-temporal pattern of a seed bank in the Negev Desert, Israel.  Ecoscience 9:407-413.
  73. LORTIE, C.J., & R. TURKINGTON. 2002. The facilitative effects by seeds and seedlings on emergence from the seed bank of a desert annual plant community.  Ecoscience 9: 106-111.
  74. LORTIE, C.J., & R. TURKINGTON. 2002. The effect of initial seed density on the structure of a desert annual plant community.  Journal of Ecology 90:435-445.
  75. TURKINGTON, R., JOHN, E., WATSON, S. & P. SECCOMBE-HETT. 2002. The effects of fertilization and herbivory on the herbaceous vegetation of the boreal forest in northwestern Canada: a ten-year study.  Journal of Ecology 90:325-227.
  76. WELHAM, C.V.J., TURKINGTON, R. & C. SAYRE. 2002.  Morphological development of white clover (Trifolium repens L.) in response to spatial and temporal resource heterogeneity.  Oecologia 130:231-238.
  77. ARII, K. & R. TURKINGTON.  2001. Assessing competition intensity along nutrient gradients using a simple model.  Canadian Journal of Botany 79:1486-1491.
  78. GOLDBERG, D.E., TURKINGTON, R, OLSVIG-WHITTAKER, L. & A.R. DYER. 2001.  Density-dependence in an annual plant community:  variation among life history stages.   Ecological Monographs 71:423-446.
  79. FRID, L. & R. TURKINGTON. 2001. The influence of herbivores and neighbouring plants on risk of browsing: a case study using arctic lupine (Lupinus arcticus) and arctic ground squirrels (Spermophilus parryii plesius). Canadian Journal of Zoology 79:874-800
  80. DYER, A.R., GOLDBERG, D.E., TURKINGTON, R. & C. SAYRE.  2001. Effects of growing conditions and source habitat on plant traits and functional group definition.  Functional Ecology 15:85-95.
  81. TURKINGTON, R., JOHN, E. & M. DALE.  2001. Plant dynamics in the boreal ecosystem: Herbs and grasses.  Pages 69-91, In: Krebs, C.J., Boutin, S., & Boonstra, R.  Ecosystem dynamics of the Boreal Forest: the Kluane Project.  Oxford University Press, New York.
  82. SINCLAIR, A.R.E., KREBS, C.J., BOONSTRA, R., BOUTIN, S., & R. TURKINGTON. 2001. Community and ecosystem organization.  Pages 407-436. In: Krebs, C.J., Boutin, S., & Boonstra, R.  Ecosystem dynamics of the Boreal Forest: the Kluane Project.  Oxford University Press, New York.
  83. TURKINGTON, R.  2001. Boreal Forest Ecosystems.  Pages 521-532, In: Encyclopedia of Biodiversity, Volume 1.  Levin, S. (ed.). Academic Press, San Diego.
  84. DLOTT, F. & R. TURKINGTON.  2000. Regulation of boreal forest understory vegetation: the roles of herbivores and resources.  Plant Ecology 151:239-251.
  85. MARCUVITZ, S. & R. TURKINGTON.  2000. Differential effects of light quality, provided by different grass neighbours, on the growth and morphology of Trifolium repens L. (white clover).  Oecologia 125:293-300.
  86. HICKS, S. & R. TURKINGTON. 2000. Compensatory growth of three herbaceous perennial species: the effects of clipping and nutrient availability.  Canadian Journal of Botany 78:759-767.
  87. GRAHAM, S.A. & R. TURKINGTON.  2000. Population dynamics response of Lupinus arcticus to fertilization, neighbour removal and clipping in the understory of the boreal forest.  Canadian Journal of Botany 78:753-758.
  88. SINCLAIR, A.R.E., KREBS, C.J., FRYXELL, J.M., TURKINGTON, R., BOUTIN, S., BOONSTRA, R., LUNDBERG, P., & L. OKSANEN.  2000. Testing hypotheses of trophic level interactions using experimental perturbations of a boreal forest ecosystem.  Oikos 89:313-328.
  89. TURKINGTON, R., JOHN, E., KREBS, C.J., DALE, M., NAMS, V.O., BOONSTRA, R., BOUTIN, S., MARTIN, K., SINCLAIR, A.R.E. & J.N.M. SMITH.  1998.  The effects of NPK fertilization for nine years on the vegetation of the boreal forest in northwestern Canada.  Journal of Vegetation Science, 9:333-346.
  90. HUTCHINGS, M.J., TURKINGTON, R., CAREY, P. & E. KLEIN.  1997.  Morphological plasticity in Trifolium repens: the effects of clone genotype, soil nutrient level and the genotype of conspecific neighbours.  Canadian Journal of Botany 75:1382-1393 (note).
  91. JOHN, E. & R. TURKINGTON.  1997.  A five-year study of the effects of nutrient availability and herbivory on two boreal forest herbs.  Journal of Ecology  85:419-430.
  92. TURKINGTON, R.  1996.  Intergenotypic interactions in plant mixtures.  Euphytica 92:105-119.  Keynote address, Eucarpia Cong., Finland.
  93. TURKINGTON, R., & P. JOLLIFFE.  1996.  Interference in Trifolium repens and Lolium perenne in mixtures: short‑term and long‑term relationships.  Journal of Ecology 84:563-571.
  94. MAZE, J. & R. TURKINGTON.  1996.  The influence of pasture age, plant density, and genotype on intraspecific diversity of Trifolium repens (white clover).  Canadian Journal of Botany 74:1189-1192.
  95. MEHRHOFF, L.A. & R. TURKINGTON.  1996.  Growth and survival of white clover (Trifolium repens L.) transplanted into patches of different grass species.  Canadian Journal of Botany 74:1243-1247.
  96. QI, M.Q., UPADHYAYA, M.K. & R. TURKINGTON.  1996.  Dynamics of seed bank and survivorship of meadow salsify (Tragopogon pratensis )populations   Weed Science 44:100-108.
  97. QI, M.Q., UPADHYAYA, M.K. & R. TURKINGTON.  1996.  Reproductive behavior of natural populations of meadow salsify (Tragopogon pratensis). Weed Science 44:68-73.
  98. MEHRHOFF, L.A. & R. TURKINGTON.  1995.  Resource use and coexistence:  experimental tests from a sequence of different‑aged pastures.  Evolutionary Ecology 9:617-632.
  99. JOHN, E. & R. TURKINGTON. 1995.  Herbaceous vegetation in the understorey of the boreal forest: does nutrient supply or snowshoe hare herbivory regulate species composition and abundance?  Journal of Ecology 83:581-590.
  100. HUTCHINGS, M.J. & R. TURKINGTON.  1995.  Plasticity of branching patterns in the clonal herbs Trifolium repens L. and Glechoma hederacea L..  Pages 173-186, In, Experimental and molecular approaches to plant biosystematics.  Hoch, P.C., & Stephenson, A.G. (eds).  Proc. I.O.B.P. Symp., Monographs in Systematic Botany, Missouri Botanical Garden, St. Louis, MO.
  101. FRASER, L., CHANWAY, C.P. & R. TURKINGTON.  1995. The competitive role of Gaultheria shallon on planted western hemlock and western red cedar saplings on northern Vancouver Island.  Forest Ecology and Management 75:27-39
  102. GOLDBERG, D.E., TURKINGTON, R. & L. OLSVIG-WHITTAKER.  1995.  Quantifying the community-level effects of competition.  Folio Geobot. Phytotax. 30:231-242.
  103. KREBS, C.J., BOUTIN, S., BOONSTRA, R., SINCLAIR, A.R.E., SMITH, J.N.M., DALE, M.R.T., MARTIN, K., R. TURKINGTON.  1995. Impact of food and predation on the snowshoe hare cycle.  Science. 269:1112-1115.
  104. BOUTIN, S., KREBS, C.J. (and 20 others).  1995. Population changes of the vertebrate community during a snowshoe hare cycle in Canada’s boreal forest.  Oikos 74:69-80.
  105. TURKINGTON, R., KLEIN, E. & J. MAZE.  1994  Conditioning effects by neighbours on the growth and form of Trifolium repens L.  Canadian Journal of Botany 72:783-787.
  106. READER, R.J., WILSON, S.D., BELCHER, J.W., TURKINGTON, R. (and 16 others).  1994.  Plant competition in relation to neighbor biomass:  an intercontinental study with Poa pratensis.  Ecology 75:1753-1760.
  107. TURKINGTON, R.  1994.  Effect of propagule source on competitive ability of pasture grasses; spatial dynamics of six grasses in simulated swards.  Canadian Journal of Botany 72:111-121.
  108. FRASER, L., TURKINGTON, R. & C.P. CHANWAY. 1993.  The Biology of Canadian Weeds. 102. Gaultheria shallon.  Canadian Journal of Plant Science 73:1233-1247.
  109. TURKINGTON, R., & E. KLEIN. 1993.  The influence of neighbors on node production, stolon growth and branching of Trifolium repens L. transplants in a pasture.  Canadian Journal of Botany 71:1266-1269.
  110. TURKINGTON, R., KLEIN, E. & C.P. CHANWAY. 1993.  Interactive effects of nutrients and disturbance: an experimental test of plant strategy theory.  Ecology 74: 863-878.
  111. KREBS, C.J., BOONSTRA, R., BOUTIN, S., DALE, M., HANNON, S., MARTIN, K., SINCLAIR, A.R.E., SMITH, J.N.M., & R. TURKINGTON. 1992.  What drives the snowshoe hare cycle in Canada’s Yukon?  Pages 886-896, In, McCullough, D.R. & Barrett, R.E., (eds.).  Wildlife 2001: Populations.  Elsevier, London.
  112. TURKINGTON, R. l991.  Rapid change in a patchy environment ‑ The ‘world’ from a plant’s‑eye‑view.  Pages 194‑200.  In, Evolution in a rapidly changing environment:  Global Warming (ed. R. Buddemeir).  Proc. ICSEB 90.
  113. TURKINGTON, R., SACKVILLE HAMILTON, R. & C. GLIDDON. l991.  Within‑population variation in localized and integrated responses of Trifolium repens to biotically patchy environments.  Oecologia 86:l83‑l92.
  114. TURKINGTON, R. & E. KLEIN. l991.  Integration among ramets of Trifolium repens.  Canadian Journal of Botany 69:226‑228.
  115. CHANWAY, C.P., TURKINGTON, R. & F.B. HOLL. l991.  Ecological implications of specificity between plants and rhizosphere micro‑organisms.  Advances in Ecological Research  21: 121‑169.
  116. TURKINGTON, R. & E. KLEIN. 1991.  Competitive outcome among four pasture species in sterilized and unsterilized soils.  Soil Chemistry and Biochemistry 23: 837‑843.
  117. TURKINGTON, R. & L.A. MEHRHOFF. l990.  The role of competition in structuring pasture communities.  Pages 307‑340, In, Grace, J.B. & Tilman, D., (eds.).  Perspectives on Plant Competition.  Academic Press, New York.
  118. MEHRHOFF, L.A. & R. TURKINGTON. l990.  Microevolution and site‑specific outcomes of competition among pasture plants.  Journal of Ecology 78:745‑756.
  119. CHANWAY, C.P., HOLL, F.B. & R. TURKINGTON. l990.  Specificity of association between Bacillus isolates and genotypes of Lolium perenne and Trifolium repens L.  from a grass‑legume pasture.  Canadian Journal of Botany 68: ll26‑ll30.
  120. PARISH, R. & R. TURKINGTON. l990.  The influence of dung pats and molehills on pasture composition.  Canadian Journal of Botany 68: 1698‑1705.
  121. PARISH, R. & R. TURKINGTON. l990.  The colonization of dung pats and molehills in permanent pastures.  Canadian Journal of Botany 68: 1706‑1711.
  122. THOMPSON, J.D.,  TURKINGTON, R. & F.B. HOLL. l990.  The influence of Rhizobium leguminosarum biovar trifolii on the growth and neighbour relationships of Trifolium repens and three grasses.  Canadian Journal of Botany 68: 296‑303.
  123. PARISH, R., TURKINGTON, R. & E. KLEIN. l990.  The influence of mowing, fertilization and plant removal on the botanical composition of an artificial sward.  Canadian Journal of Botany 68: l080‑l085.
  124. TURKINGTON, R. l990.  The influence of grass root systems on growth and form of Trifolium repens.  Canadian Journal of Botany  68: l034‑l038.
  125. RATCLIFFE, M.J. & R. TURKINGTON. l989.  Comparative phenology of some alpine vascular plant species on Lakeview mountain, southern British Columbia.  Canadian Field Naturalist  l03: 348‑352.
  126. CHANWAY, C.P., F.B. HOLL & R. TURKINGTON. l989.  Effect of Rhizobium leguminosarum biovar trifolii genotype on specificity between Trifolium repens and Lolium perenne.  Journal of Ecology 77: ll50‑ll60.
  127. TURKINGTON, R. 1989.  The growth, distribution and neighbour relationships of Trifolium repens in a permanent pasture.  V.  The coevolution of competitors.  Journal of Ecology 77: 717‑733.
  128. TURKINGTON, R. 1989.  The growth, distribution and neighbour relationship of Trifolium repens in a permanent pasture.  VI.  Conditioning effects by neighbours.  Journal of Ecology 77: 734‑746.
  129. SHIVJI, A. & R. TURKINGTON. l989.  The influence of Rhizobium trifolii on growth characteristics of Trifolium repens:  integration of local environments by intact clones of T. repens.  Canadian Journal of Botany 67: l080‑l084.
  130. TURKINGTON, R., HOLL, F.B., THOMPSON, J. & C.P. CHANWAY.  1988.  The influence of microorganisms, particularly Rhizobium, on plant competition in grass‑legume communities. In “Plant Population Ecology”, pp. 343‑366.  British Ecological Soc.  Symposium, Sussex.
  131. HOLL, F.B., CHANWAY, C.P., TURKINGTON, R. & R.A. RADLEY. 1988.  Response of crested wheatgrass (Agropyron cristatus L.), perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.) to inoculation with Bacillus polymyxa.  Soil Biology and Biochemistry  20: 19‑24.
  132. EVANS, R. & R. TURKINGTON.  1988.  Maintenance of morphological variation in a biotically patchy environment.  New Phytologist  109: 369‑376.
  133. THOMPSON, J. & R. TURKINGTON.  1988.  The Biology of Canadian Weeds. 82. Holcus lanatus.  Canadian Journal of Plant Science 68: 131‑147.
  134. CHANWAY, C.P., HOLL, F.B. & R. TURKINGTON.  1988.  Genotypic coadaptation in plant growth promotion of forage species by Bacillus polymyxa.  Plant and Soil 106:  281‑284.
  135. RATCLIFFE, M.J. & R. TURKINGTON.  1987.  Vegetation patterns and environment of some Alpine plant communities on Lakeview Mt., Southern British Columbia.  Canadian Journal of Botany 65: 2507‑2516.
  136. AARSSEN, L.A. & R. TURKINGTON. 1987.  Responses to defoliation in Holcus lanatus L., Lolium perenne L. and Trifolium repens L. from three different‑aged pastures.  Canadian Journal of Botany 65: 1364‑1370.
  137. JONES, D.A. & R. TURKINGTON. 1986.  Biological Flora of the British Isles: Lotus corniculatus.  Journal of Ecology 74: 1185‑1212.
  138. UPADHYAYA, M. TURKINGTON, R. & D. McILVRIDE.  1986.  The Biology of Canadian Weeds:  75. Bromus tectorum L.  Canadian Journal of Plant Science  66: 689‑709.
  139. AARSSEN, L.W. & R. TURKINGTON. 1985.  Vegetation dynamics and neighbour associations in pasture‑community evolution.  Journal of Ecology 73: 585‑603.
  140. AARSSEN, L.W. & R. TURKINGTON. 1985.  Biotic specialization between neighbouring genotypes in Lolium perenne and Trifolium repens from a permanent pasture.  Journal of Ecology 73: 605‑614.
  141. AARSSEN, L.W. & R. TURKINGTON, 1985.  Within‑species diversity in natural populations of Holcus lanatus, Lolium perenne and Trifolium repens from four different‑aged pastures.  Journal of Ecology 73: 869‑886.
  142. TURKINGTON, R. 1985.  Variation and differentiation in populations of Trifolium repens in permanent pastures.  Pages 69-82, in White, J. (ed.), Studies on Plant Demography:  A Festschrift for J.L. Harper.  Academic Press.
  143. AARSSEN, L.W. & R. TURKINGTON. 1985.  Competitive relations among species from pastures of different ages.  Canadian Journal of Botany 63: 2319‑2325.
  144. TURKINGTON, R., HARPER, J.L., AARSSEN, L.W., & P. DeJONG. 1985.  A reanalysis of interspecific association in an old pasture.  Journal of Ecology 73: 123‑131.
  145. TURKINGTON, R. & L.W. AARSSEN. 1984. Local‑scale differentiation as a result of competition.  Pages 107-127, in: Dirzo, R. & Sarukhan, J. (eds.) Perspectives in Plant Population Ecology, Sinauer Assoc.  Cambridge, Mass.
  146. TURKINGTON, R. & L.W. AARSSEN. 1983. Biological Flora of the British Isles:  Hypochoeris radicata.  Journal of Ecology 71: 999‑1022.
  147. TURKINGTON, R. 1983. Plasticity in growth and patterns of dry matter distribution of two genotypes of Trifolium repens L. grown in different environments of neighbours.  Canadian  Journal of Botany 61:2186‑2194.
  148. AARSSEN, L.W. & R. TURKINGTON. 1983. What is community evolution?  Evolutionary Theory 6:211‑217.
  149. DEJONG, P., AARSSEN, L.W. & R. TURKINGTON. 1983. The use of contact sampling in studies of association in vegetation.  Journal of Ecology 71:545‑559.
  150. TURKINGTON, R. 1983. Leaf and flower demography of Trifolium repens L. 1. Growth in mixture with grasses.  New Phytologist 93:599‑616.
  151. TURKINGTON, R. 1983. Leaf and flower demography of Trifolium repens L. 2.  Locally differentiated populations.  New Phytologist 93:617‑633.
  152. TURKINGTON, R. & J.J. BURDON. 1983. The Biology of Canadian Weeds.  57.  Trifolium repens L.  Canadian Journal of Plant Science 63:243‑266.
  153. TURKINGTON, R. & J. MAZE. 1982. Patterns of dry matter distribution in transplanted populations of Trifolium repens and its bearing on ecological interpretations.  Canadian Journal of Botany 60:2014‑2018.
  154. DEJONG, P., AARSSEN, L.W. and R. TURKINGTON. 1980.  The analysis of contact sampling data.  Oecologia. 45:322‑324.
  155. TURKINGTON, R., KENKEL, N.C. & G. FRANKO. 1980.  The Biology of Canadian Weeds.  Stellaria media (L.) Vill.  Canadian Journal of Plant Science 60:981‑992.
  156. TURKINGTON, R. & G. FRANKO. 1980.  The Biology of Canadian Weeds.  Lotus corniculatus L.  Canadian Journal of Plant Science 60:965‑979.
  157. AARSSEN, L.W., TURKINGTON, R. & P.B. CAVERS. 1979.  Neighbour relationships in grass/legume communities. II.  Temporal stability and community evolution.  Canadian Journal of Botany 57: 2695‑2703.
  158. TURKINGTON, R. & P.A. CAVERS. 1979.  Neighbour relationships in grass/legume communities. III.  Development of pattern and association in artificial communities.  Canadian Journal of Botany 57: 2704‑2710.
  159. TURKINGTON, R. 1979.  Neighbour relationships in grass/legume communities. IV.  Fine‑scale biotic differentiation.  Canadian Journal of Botany 57: 2711‑2716.
  160. TURKINGTON, R. & J.L. HARPER. 1979.  The growth, distribution and neighbour relationships of Trifolium repens in a permanent pasture. I.  Ordination, pattern and contact.  Journal of Ecology 67: 201‑218.
  161. TURKINGTON, R. & J.L. HARPER. 1979.  The growth distribution and neighbour relationships of Trifolium repens in a permanent pasture. II. Inter‑ and intra‑specific contact.  Journal of Ecology 67: 219‑230.
  162. TURKINGTON, R., CAHN, M.A., VARDY, A. & J.L. HARPER. 1979.  The growth, distribution and neighbour relationships of Trifolium repens in a permanent pasture.  III. The establishment and growth of Trifolium repens in natural and perturbed sites.  Journal of Ecology 67: 231‑243.
  163. 7 TURKINGTON, R. & J.L. HARPER. 1979.  The growth, distribution and neighbour relationships of Trifolium repens in a permanent pasture. IV. Fine‑scale biotic differentiation.  Journal of Ecology 67: 245‑254.
  164. TURKINGTON, R. & P.B. CAVERS. 1979.  The Biology of Canadian Weeds. 33.  Medicago lupulina (L.).  Canadian Journal of Plant Science 59: 99‑110.
  165. TURKINGTON, R., CAVERS, P.B. & E. REMPEL. 1978.  The Biology of Canadian Weeds.  29.  Melilotus alba Desr. and M. officinalis (L.)  Lam. Canadian Journal of Plant Science 58:  523‑537.
  166. TURKINGTON, R. & P.B. CAVERS. 1978.  Reproductive strategies and growth patterns in four legumes.  Canadian Journal of Botany 56: 413‑416.
  167. TURKINGTON, R., CAVERS, P.B. & L.W. AARSSEN. 1977.  Neighbour relationships in grass/legume communities. I. Interspecific contacts in four grassland communities near London, Ontario.  Canadian Journal of Botany 55: 2701‑2711.

1 Selected by the Chinese Academy of Sciences as “one of the 10 most impactful papers during the 12 months, July 2014 – June 2015.”

2 Selected for F1000Prime

3 The 2010 Journal of Vegetation Science Editors’ Award for an outstanding paper

4 J. Stan Rowe award of Canadian Botanical Association for best student paper

5 J. Stan Rowe award of Canadian Botanical Association for best student paper

6 Selected for F1000Prime

7 One of the top 100 most influential papers published by the British Ecological Society (1913-2012)

Kathryn Zeiler

Associate Professor of Teaching

Contact Information

zeilerk@mail.ubc.ca

Wayne Maddison

Professor Emeritus

CRC Tier 1

Academic History

  • David and Lucile Packard Fellow for Science and Engineering (1993-1998);
  • Associate and Assistant Professor, University of Arizona (1990-2003);
  • NSERC Postdoctoral Fellow, U. C. Berkeley (1988-1990);
  • PhD, Harvard University (1988);
  • BSc Zoology, University of Toronto (1980)

My Links

Contact Information

  • wayne.maddison@ubc.ca
  • 604-822-1545

Research Interests

My research arose from a fascination with the diversity of forms and behaviours of jumping spiders, which led to systematics, which led to phylogenetic theory and computer programming. My work continues to be both empirical, on spiders, and theoretical, on the use of phylogeny in evolutionary inference.

Team Members

U. Garcilazo Cruz
K. Marathe

Shawn Mansfield

Professor
Department Head of Botany

My Links

Contact Information

  • shawn.mansfield@ubc.ca
  • 604-822-0196

Reinhard Jetter

Professor

Academic History

  • Canadian Research Chair in Plants Natural Products Chemistry
  • Full Professor (Departments of Botany and Chemistry)
  • Ph.D. Botany (1993) Univ. of Kaiserslautern (Germany); 
  • Postdoctoral Fellow (1994-96) Washington State Univ.; 
  • Research Associate (1996-2002) Univ. of Wuerzburg (Germany). 
  • Dr. habil. (2000) University of Wuerzburg (Germany).

My Links

Contact Information

  • reinhard.jetter@botany.ubc.ca
  • Office: 604-822-2477
  • Office: Room 2229, Biological Sciences Building
  • Lab Phone: 604-822-8124
  • Lab: Room 2224, Biological Sciences Building

Research Interests

The plant surface – a vast stage for interactions…

  • How do plants create flexible, long-lasting, water-proof skins that grow with their organs?
  • How do plants seal their vast surface against adverse climatic conditions?
  • How do insects assess host suitability when they first land on a plant?
  • How can plants select for partner insects while excluding their unwanted competitors?
  • How do carnivorous pitcher plants catch their prey?

These are the biological questions that motivate the research in my lab. In order to answer them, we employ molecular genetic, microscopic and eco-physiological (as well as biochemical) techniques to study plant surfaces. Depending on the individual research question, we use Arabidopsis thaliana and an array of other plant species as models for our studies.

In particular, we investigate cuticular waxes, which coat most above-ground plant organs. We explore both the biological functions of these waxes and the molecular biology underlying their formation. We investigate wax functions such as their central physiological role to seal the plant tissue against water loss and their ecological function as a first line of defence against herbivores. On the other end of the spectrum of our biological interests, we investigate the molecular machinery – the genes and enzymes – plants employ to generate their wax coatings.

Team Members

http://blogs.ubc.ca/jetterlab/team/

Selected Publications

http://blogs.ubc.ca/jetterlab/publications/

Patrick Keeling

Professor
CRC Tier 1

Academic History

  • B. Sc. (1992), Genetics, University of Western Ontario, 
  • Ph.D. (1996), Biochemistry, Dalhousie University. 
  • Visiting Scientist, Plant Cell Biology Research Centre, University of Melbourne, (1996-1998), 
  • Postdoctoral Fellow, Indiana University (1998-1999).

My Links

Contact Information

  • pkeeling@mail.ubc.ca
  • Office: 604-822-4906
  • Office Room 341/Lab 385 Biodiversity Building
  • Lab Phone: 604-822-2845

Research Interests

Research in the lab is generally related to the molecular evolution and cell biology of eukaryotes, in particular the protists (i.e., eukaryotes that are not animals, fungi, or plants). Protists are mostly single celled organisms, but are many are extremely complex and sophisticated despite their small size. Protists also represent the greatest part of eukaryotic diversity, although most protists groups are very poorly studied, especially at the molecular level. We use molecular biology, microscopy, and increasingly use genome wide analyses such as EST sequencing and genome sequence surveys to study a number of questions in different lineages of protists. Much of our research focuses on cellular organelles, in particular mitochondria and plastids. These organelles originated by endosymbiosis, or the uptake and retention of a bacterium (the endosymbiont) by a eukaryote (the host). In the case of mitochondria this involved an alpha-proteobacterium and took place around the origin of eukaryotes. Plastids originated more recently from a cyanobacterium. Plastids have also spread between eukaryotic lineages by a process called secondary endosymbiosis. In this case, a plastid-bearing alga is itself taken up by another eukaryote, and its photosynthetic apparatus is retained by this new, secondary, host. Another major focus of the research is the transition of free living organisms to parasitism and how this affects their organelles and metabolism. Below are short descriptions of several projects currently underway.

For current research visit this link: http://www3.botany.ubc.ca/keeling/research.html

Team Members

For current team members visit this link: http://www3.botany.ubc.ca/keeling/people.html

Selected Publications

Husnik, F., Tashyreva, D., Boscaro, V., Georde, E. E. Lukes, J., and Keeling, P. J. 2021. Bacterial and archaeal symbioses with protists. Curr. Biol. 31, PR862-877.

Mathur, V. Wakeman, K. C., and Keeling, P. J. 2021. Parallel functional reduction in the mitochondrion of apicomplexan parasites. Curr. Biol. 31, P2920-2928.

George, E. E., Husnik, F., Tashyreva, D., Prokopchuk, G., Horak, A., Kwong, W.K., Lukes, J., Keeling, P. J. 2020. Highly-reduced genomes of protist endosymbionts show evolutionary convergence. Curr. Biol., S0960-9822, 31703-8.

Tikhonenkov D. V. , Mikhailov K. V. , Hehenberger E., Karpov S. A. , Prokina K. I. , Esaulov A. S. , Belyakova O. I. , Mazei Y. A. , Mylnikov A. P. , Aleoshin V. V. , and Keeling P. J. 2020. New Lineage of Microbial Predators Adds Complexity to Reconstructing the Evolutionary Origin of Animals. Curr. Biol., 30, 4500-4509.

Keeling, P. J. 2019. Combining morphology, behaviour, and genomics to understand the evolution and ecology of microbial eukaryotes. Phil. Trans. Roy. Soc. B., 374, 20190085.

Hehenberger, E., Gast, R. J., and Keeling, P. J. 2019. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proc. Natl. Acad. Sci., USA, 116, 17934–17942.

Keeling, P. J., and Burki, F. 2019. Progress towards the Tree of Eukaryotes. Curr. Biol., 29, R808-R817.

Mathur, V., Kolísko, M., Hehenberger, E., Irwin, N. A. T., Leander, B. S., Kristmundsson, Á. Freeman, M. A., and Keeling, P. J. 2019. Multiple Independent Origins of Apicomplexan-Like Parasites. Curr. Biol., 29, 1-6.

Gawryluk, R. M. R., Tikhonenkov, D. V., Hehenberger, E., Husnik, F., Mylnikov, A. P., and Keeling, P. J. 2019. Non-photosynthetic predators are sister to red algae. Nature, 572, 240-243.

Kwong, W. K., del Campo, J., Mathur, V., Vermeij, M. J. A., and Keeling, P. J. 2019. A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes. Nature, 568, 103-107.

For past and current publications visit this link: http://www3.botany.ubc.ca/keeling/publications.html

Mary Berbee

Professor Emeritus

Academic History

  • B.Sc. Univ. Minnesota (1979);
  • Ph.D. Univ.California, Davis (1987);
  • Postdoctoral, Univ. Tubingen, Germany (1988);
  • Postdoctoral, Univ. California, Davis (1989);
  • Postdoctoral, Univ. California, Berkeley (1990-92).

Contact Information

  • mary.berbee@botany.ubc.ca
  • Office Phone: 604-822-3780
  • Office: Rm 3209 Biological
  • Lab Phone: 604 822-2019
  • Lab: Rm 3214 Biological Sciences

Research Interests

Fungi can cause plant diseases, serve as mycorrhizal partners, and decompose litter and woody debris. Berbee lab research is directed towards understanding how fungi evolved and adapted to interdependence with land plants. Berbee lab projects, funded by the National Science and Engineering Research Council of Canadia include:

  • Analyzing evolution of the powerful cell wall degrading enzymes that fungi secrete as an adaptation to plant-based nutrition, by using genome sequencing of early-diverging fungi. This research has the potential to reveal novel enzymes for cellulose decomposition with potential for industrial applications.

• Improving estimates of geological ages of fungi by developing evolutionary trees for modern fungi using molecular phylogenetics. Fossils of known ages can then be integrated into phylogenies to date origins of fungal groups. More accurate fungal age estimates benefit the community of fungal molecular biologists by helping to put patterns of gene and genome evolution into the perspective of geological time.  

• Clarifying systematic relationships among mushroom-forming fungi that are important as saprobes or ectomycorrhizal partners of trees. We are finding and describing many new BC species. Recognition of species helps us estimate fungal geographical ranges, habitat requirements and host specificity.

Team Members

Current students

  • Faezeh Aliabadi (MSc Student)
  • Emily Trudeau (MSc Student)

Berbee lab alumni

  • Ludovic LeRenard PhD 2019, now Laboratory Research and Development Technician, Eversio Wellness, Surrey BC.
  • Anna Bazzicalupo PhD 2018, now Research Leader in Fungal Comparative Biology, Royal Botanical Gardens, Kew, UK.
  • Brandon Landry MSc 2019, now Project Manager, Molecular You, Victoria BC.
  • Jaclyn M. Dee PhD 2018, now Instructor, Department of Botany, UBC, Vancouver BC. 
  • Benjamin Auxier MSc 2017, now PhD student, Wageningen University, Netherlands.
  • Tanay Bose MSc 2013, now Postdoctoral Fellow, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa.
  • Wyth Marshall PhD 2009, now Research Scientist, BC Centre for Aquatic Health Sciences, Campbell River BC.

Community Work

Berbee lab members give talks for mushroom clubs including the Vancouver Mycological Society and lead annual mushroom forays on the UBC campus and in regional parks.

Wild mushrooms are soaring in popularity but cooking and eating wild mushrooms carries both risks and pleasures. To reduce the risks, in 2016-2018, the Berbee lab successfully competed for $99,639 funding from a Peter Wall Inst. Wall Solutions Initiative Grant to better characterize our provinces edible and poisonous mushroom species by DNA barcoding, and to make up-to-date information on our mushrooms readily available to mushroom foragers. 

Our website is https://explore.beatymuseum.ubc.ca/mushroomsup/, and the booklet we published, “Vellinga et al., 2022. Mushrooms Up! Edible and Poisonous Species of Southwest British Columbia and the Coastal Pacific Northwest. Vancouver BC: Beaty Biodiversity Museum” can be purchased at the Beaty Museum gift shop.

This project was a collaboration with mushroom clubs, the Stuntz Foundation, BC Drug and Poison information centre, UBC undergraduates, and the Beaty Biodiversity Museum.  

Selected Publications

Invited Review

Berbee, M.L., James, T.Y., Strullu-Derrien, C. 2017. Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life. Annual Review of Microbiology 71:41-60.

Selected refereed publications

Dee JM, Berbee ML. 2021. Diverse organizations of actin and nuclei underpin the evolution of indeterminate growth in Chytridiomycota and Dikarya. Botany 99(6):303-320.

Landry B, Whitton J, Bazzicalupo AL, Ceska O, Berbee ML. 2021. Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina. Plos One 16(2) e0246575.

Le Renard L, Stockey RA, Upchurch GR, Berbee ML. 2021a. Cretaceous fungal scutella from the Lower Potomac Group Zone 1: Stomatothyrium placocentrum gen. et sp. nov., a dothideomycete colonizer of conifer stomata. International Journal of Plant Sciences 182(8):712-729.

Le Renard L, Stockey RA, Upchurch GR, Berbee ML. 2021b. Bleximothyrium ostiolatum gen. et sp. nov. a unique fossil fly-speck fungus (Dothideomycetes) from the Lower Cretaceous Potomac Group, lower Zone of Virginia USA. American Journal of Botany 108(1):129-144.

Berbee ML, Strullu-Derrien C, Delaux P-M, Strother PK, Kenrick P, Selosse M-A, Taylor JW. 2020. Genomic and fossil windows into the secret lives of the most ancient fungi. Nature Reviews Microbiology 18(12):717-730.

Le Renard L, Firmino AL, Pereira OL, Stockey RA, Berbee ML. 2020a. Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils. American Journal of Botany 107(7):1021-1040.

Le Renard L, Stockey RA, Upchurch G, Berbee ML. 2020b. A new epiphyllous fly-speck fungus from the Early Cretaceous Potomac Group of Virginia (125-112 Ma): Protographum luttrellii, gen. et sp. nov. Mycologia 112(3):504-518.

Auxier B, Dee J, Berbee ML, Momany M. 2019. Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs. BMC Evolutionary Biology 19(1):4.

Bazzicalupo AL, Whitton J, Berbee ML. 2019. Over the hills, but how far away? Estimates of mushroom geographic range extents. Journal of Biogeography 46(7):1547-1557.

Dee JM, Landry BR, Berbee ML. 2019. Actin guides filamentous rhizoid growth and morphogenesis in the zoosporic fungus Chytriomyces hyalinus. Mycologia 111(6):904-918.

Strullu-Derrien C, Spencer ART, Goral T, Dee J, Honegger R, Kenrick P, Longcore JE, Berbee ML. 2018. New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus. Philosophical Transactions of the Royal Society B: Biological Sciences 373(1739).

Bazzicalupo A, Berch S, Callan B, Ceska O, Kroeger P, Li R, McIntyre L, Miao V, Stanwick R, Trudell S et al. . 2017a. White paper on strategies to reduce risks and expand appreciation of foraged wild mushrooms. McIlvainea 26.

Bazzicalupo AL, Buyck B, Saar I, Vauras J, Carmean D, Berbee ML. 2017b. Troubles with mycorrhizal mushroom identification where morphological differentiation lags behind barcode sequence divergence. Taxon 66(4):791-810.

Auxier B, Bazzicalupo A, Betz E, Dee JM, Le Renard L, Roushdy MM, Schwartz C, Berbee M. 2016. No place among the living: phylogenetic considerations place the Palaeozoic fossil T. protuberans in Fungi but not in Dikarya. A comment on M. Smith (2016). Botanical Journal of the Linnean Society 182(4):723-728.

Berbee ML, Wong EYY, Tsui CKM. 2016. Phylogenetic evidence places the coralloid jelly fungus Tremellodendropsis tuberosa (Tremellodendropsidales) among early diverging Agaricomycetes. Mycological Progress 15(9):939-946.

Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A et al. . 2016a. A phylum-level classification of zygomycete fungi based on genome-scale data. Mycologia 108(5):1028-1046.

Patrick Martone

Professor

My Links:

Contact Information

  • pmartone@mail.ubc.ca
  • Office: 604-822-9338
  • Office Room 3211/Lab Room 3224 Biological Sciences Building
  • Lab: 604-822-9413

Jörg Bohlmann

Professor

Academic History

  • Distinguished University Scholar and NSERC E.W.R. Steacie Fellow
  • Member of the Royal Society of Canada (2015)
  • Research Scientist, Max Planck Institute Jena, Germany (1998-2000)
  • Feodor Lynen Postdoctoral Fellow of the Alexander von Humboldt Foundation, Washington State University, Pullman, USA (1995-1998)
  • Ph.D., Technical University Braunschweig, Germany (1995)

My Links

Contact Information

  • bohlmann@msl.ubc.ca
  • Office: 604-822-0282
  • Office: Room 321, MSL Building
  • Lab: 604 822-9673
  • Lab: Room 383, MSL Building

Research Interests

Plants are sessile organisms which have the ability to survive under constantly changing environmental conditions over lifespans of several weeks to hundreds of years. To cope with biotic or abiotic stress, plants have evolved a complex specialized metabolism which contains hundreds of thousands of unique small molecules. Many of these bioactive molecules have beneficial applications for humans.

Through genomic, proteomic, metabolomic and biochemical approaches our laboratory is exploring two aspects of plant specialized metabolism: (1) the role it plays in plant defense, and (2) how its  genes and enzymes can be prospected for metabolic engineering of high-value bioproducts. The foundation of our research program has concentrated primarily on the terpenoid pathway, including the large gene families of terpene synthases (TPS) and cytochrome  P450s, and more recently extended into phenolic pathways.

The first major stream of our research program combines forest health genomics and chemical ecology to better understand the ecological, biochemical, and molecular interactions that underlie conifer defense and resistance mechanisms against insect pests and insect-associated fungal pathogens. This research has resulted in the production of new conifer and pest genomic resources, the identification of new marker systems for tree breeding, and advanced knowledge to inform government decision making and policies in forest pest management. The long-term goal and outcome is the protection of global health of forests beginning with applications in Canada in partnership with provincial and federal government organizations.

The second major stream of our program combines an integrated –omics strategy to discover genes and enzymes involved in the biosynthesis of high-valued plant bioproducts. This research has successfully developed a gene discovery strategy for non-model species, generating transcriptome resources for many non-model species, and has produced a large portfolio of enzymes for bioproduct development. Applications are being realized in partnership with the biotech industry.

Team Members

Lab & Facility Managers

  • Carol Ritland, Project Manager
  • Sharon Jancsik, Lab Manager

Research Associates and Post-Doctoral Fellows

  • Lars Kruse
  • Michael Easson
  • Omnia Gamal
  • Tal Shalev

Graduate Students

  • Dylan Perera
  • Katie Lyle

Bioinformatician

  • Mack Yuen

Technicians

  • Sharon Jancsik

Selected Publications

Burnette TE, Haavik LJ, Whitehill JGA, Salisbury VB, Fischer JM, Madilao L, Brunsell KB, Bohlmann J. White ash trees (Fraxinus americana) originally from colder, drier areas are more susceptible to emerald ash borer (Agrilus planipennis). University of Montana STEM Oral Presentations. link: scholarworks.umt.edu/gsrc/2021/stem_oral/16

Rosana ARR, Pokorny S, Klutsch JG, barra-Romero C, Sanichar R, Engelhardt D, van Belkum MJ, Erbilgin N, Bohlmann J, Carroll AL, Vederas JC. Selection of entomopathogenic fungus Beauveria bassiana (Deuteromycotina: Hyphomycetes) for the biocontrol of Dendroctonus ponderosae(Coleoptera: Curculionidae, Scolytinae) in Western Canada. Applied Microbiology and Biotechnology. doi: 10.1007/s00253-021-11172-7

Link to the complete list of publications: Publications | Bohlmann lab (ubc.ca)

Laura Wegener Parfrey

Associate Professor
CRC Tier 2

Academic History

  • BS (2004) State University of New York at Albany
  • PhD (2011) University of Massachusetts – Amherst
  • Postdoc (2011-2013) University of Colorado – Boulder

My Links

Contact Information

  • lwparfrey@botany.ubc.ca
  • 604-827-2214
  • Ponderosa Annex- Room 216

Research Interests

Research in the Parfrey lab focuses on the microbial ecology of eukaryotic microbes (protists) and bacteria. We work primarily in two distinct ecosystems: the mammalian gut and coastal ecosystems. Our gut microbiome research combines descriptive research with manipulative experiments to ask what is the ‘normal’ community of eukaryotic microbes (aka “parasites”) residing in humans and other mammals, and what are the consequences of losing our microbial diversity?  Along coastal British Columbia we are investigating how water column and biofilm microbes colonize marine hosts (invertebrates, seaweed, and sea grass), and how these host-associated microbes impact host and ecosystem health.

Team Members

We have a fantastic group of student researchers, along with staff scientists, working on microbial ecology and evolution in the mammalian gut, on seaweed and seagrass surfaces, and in experimental systems.  

See the lab web page for more information. 

Selected Publications

Davis KM, Mazel FM, and Parfrey LW. 2021. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environmental Microbiology 12:641483

Billy V*, Lhotská Z*, Milan Jirků M, Hložková O, Frgelecová L, Parfrey LW, Jirků Pomajbíková K. 2021. Blastocystis colonization alters the gut microbiome and, in some cases, promotes faster recovery from induced colitis.  Frontiers in Microbiology. 12, 641483

Lemay MA, Chen MY, Mazel F, Hind KR, Starko S, Keeling PJ, Martone PT, Parfrey LW.  2020. A role for morphology in structuring host-associated microbiota. ISME Journal. 1-15

Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Parfrey LW. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. 2020. Environmental Microbiology Reports. doi:10.1111/1758-2229.12866

Mann AE, Mazel F, Lemay MA, Morien E, Billy V, Kowalewski M, Di Fiore A, Link A, Goldberg TL, Tecot S, Baden AL, Gomez A, Sauther ML, Cuozzo FP, Rice GAO, Dominy NJ, Stumpf R, Lewis RJ, Swedell L, Amato KR, Parfrey LW. 2020. Biodiversity of protists and nematodes in the wild non-human primate gut. ISME Journal. 14: 609–622

Loren Rieseberg

Professor
Univ. Killam Professor

Academic History

  • M.Sc. University of Tennessee 1984 
  • Ph.D. Washington State University 1987
  • Assistant Professor, Claremont Graduate School 1987-1993
  • Associate/Full/Distinguished Professor, Indiana University 1993-2006

My Links:

Contact Information

  • lriesebe@mail.ubc.ca
  • 604-827-4540
  • Office Room 204 Biodiversity Building (Lab room 350)
  • Lab Phone: 604-827-3535

Research Interests

My lab employs population genomic approaches, computational methods, and field and greenhouse studies to study plant adaptation and speciation. We are especially interested in how gene flow, both within and between species, influences these processes.  We also study factors that affect rates of gene flow, including reproductive barriers such as niche differentiation, phenological isolation, and pollen competition, as well as chromosomal inversions that impede gene flow mainly by suppressing recombination.  On a more practical level, we integrate genomic and phenotypic data with results from laboratory and greenhouse experiments to identify evolutionary changes that causally drive plant invasions, mine natural populations for agronomically useful alleles, develop pre-bred lines to deliver these alleles to plant breeders, and generate genomic tools and resources for important crops such as sunflower and Cannabis.

Team Members

http://rieseberglab.botany.ubc.ca/people/

Selected Publications

Todesco, M., G.L. Owens, N. Bercovich et al. 2020. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584:602-607.

Ostevik, K.L., Samuk, and L.H. Rieseberg. 2020. Ancestral reconstruction of karyotypes reveals an exceptional rate of nonrandom chromosomal evolution in sunflower. Genetics 214:1031-1045.

Huang, K., R.L. Andrew, G.L. Owens, K.L. Ostevik, and L.H. Rieseberg. 2020. Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype. Molecular Ecology 29:2535-2549.

Lee-Yaw, J.A., C.J. Grassa, S. Joly, R.L. Andrew, and L.H. Rieseberg. 2019. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus). New Phytologist 221:515-526.

Hübner, S. et al. 2019. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nature Plants 5:54-62.

Owens, G.L., G.J. Baute, S. Hubner, and L.H. Rieseberg. 2019. Genomic sequence and copy-number evolution during hybrid crop development in sunflowers. Evolutionary Applications, 12:54-65.

Bock, D.G., M. Kantar, C. Caseys, R. Matthey-Doret, and L.H. Rieseberg. 2018. Evolution of invasiveness by genetic accommodation. Nature Ecology and Evolution 2:991-999.

Smith C.C.R., S. Tittes, J.P. Mendieta, E. Collier-zans, H. Rowe, L.H. Rieseberg, and N.C. Kane. 2018. Genetics of alternative splicing evolution during sunflower domestication. Proceedings of the National Academy of Sciences USA 69:789-815.

Badouin, H. et al.  2017. The sunflower genome illuminates the evolutionary history of the Asterids and provides new insights into oil metabolism and flowering time. Nature 546:148-152.

Barrett, S.C.H., R.I. Colautti, K.M. Dlugosch, and L.H. Rieseberg (Eds). 2016.  Invasion Genetics: The Baker and Stebbins Legacy. Wiley-Blackwell, Oxford.

Yeaman, S. et al. 2016. Convergent local adaptation to climate in distantly related conifers. Science 353:1431-1433.

Ostevik, K.L., R.L. Andrew, S.P. Otto, and L.H. Rieseberg. 2016. Multiple reproductive barriers separate recently diverged sunflower ecotypes. Evolution Evolution 70:2322-2335.

Ortiz-Barrientos, D., Engelstädter, J., and L.H. Rieseberg. 2016. Recombination rate evolution and the origin of species. Trends in Ecology and Evolution 31:226-236

Todesco, M. et al. 2016. Hybridization and extinction. Evolutionary Applications 9:892–908.

Renaut, S., and L.H. Rieseberg. 2015. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Molecular Biology and Evolution 32:2273-2283.

Dlugosch, K.M. F.A. Cang, B.S. Barker, K. Andonian, S.M. Swope, and L.H. Rieseberg. 2015. Evolution of invasiveness through increased resource use in a vacant niche. Nature Plant, article number 15066.

Khoury, C.K. et al. 2014. The crops that feed the world: increasing homogeneity in global food supplies. Proceedings of the National Academy of Sciences USA 111:4001-4006.

Renaut, S., C.J. Grassa, S. Yeaman, B.T. Moyers, Z. Lai, N.C. Kane, J.E. Bowers, J.M. Burke, L.H. Rieseberg.  2013. Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nature Communications 4, 1827.

McCouch. S. et al. 2013. Agriculture: Feeding the future. Nature 499:23-24.

Mayrose, I., S.H. Zhan, C.J. Rothfels, K. Magnuson-Ford, M.S. Barker, L.H. Rieseberg, S.P. Otto.   2011. Recently-formed polyploids diversify more slowly than their diploid relatives. Science 333:1257.

Blackman, B.K., J.L. Strasburg, S.D. Michaels, and L.H. Rieseberg.  2010.  The role of recently derived FT paralogs in sunflower domestication. Current Biology 20:629–635.

Wood, T.E., N. Takebayashi, M.S. Barker, I. Mayrose, P.B. Greenspoon, L.H. Rieseberg. 2009. The frequency of polyploid speciation in vascular plants. PNAS 106:13875-13879. 

Rieseberg, L.H., and J.H. Willis. Plant speciation. 2007. Science 317:910-914. 

Rieseberg, L.H., T.E. Wood, and E. Baack.  2006.  The nature of plant species. Nature 440:524-527. 

Harter, A.V., K.A. Gardner, D. Falush, D.L. Lentz, R. Bye, L.H. Rieseberg. 2004.  Origin of extant domesticated sunflowers in eastern North America. Nature 430:201-205.

Rieseberg, L.H., O. Raymond, D.M. Rosenthal, Z. Lai, K. Livingstone, T. Nakazato, J.L. Durphy, A.E. Schwarzbach, L.A. Donovan, and C. Lexer. 2003. Major ecological transitions in annual sunflowers facilitated by hybridization. Science 301:1211-1216. 

Burke, J.M., and L.H. Rieseberg. 2003. The fitness effects of transgenic disease resistance in wild sunflowers. Science 300:1250.

Jonathan Davies

Professor

Academic History

  • M. Sc. (1997) University of Cape Town, South Africa
  • Ph. D. (2004) Imperial College, London, UK

My Links

Contact Information

  • 604-822-5486

Research Interests

My research lies at the interface between ecology and evolutionary biology, making use of the information contained within phylogenetic trees to provide a bridge between them. The integration of phylogenetic approaches in ecology has been transformative, and has given rise to new sub-disciplines in biodiversity science, invasion biology, climate change biology, emerging infectious disease research and community ecology.

Selected Publications

For past and current publications visit this link: https://phyloecology.ca/publications/

Davies, T. J. [2021]. Ecophylogenetics redux. Ecology Letters, doi.org/10.1111/ele.13682. 

Ssebuliba*, E., & Davies, T. J. [2021]. Assessing the phylogenetic host breadth of millet pathogens and its implication for disease spillover. Ecological Solutions and Evidence, 2(1), e12040. 

Davies, T.J., Daru, B.H., Bezeng, B.S., Charles-Dominique, T., Hempson, G.P., Kabongo, R.M., Maurin, O., Muasya, A.M., van der Bank, M. and Bond, W.J., [2020]. Savanna tree evolutionary ages inform the
reconstruction of the paleoenvironment of our hominin ancestors. Scientific Reports, 10: 12430. 

Hoveka, L.N., van der Bank, M. and Davies, T.J., [2020]. Evaluating the performance of a protected area network in South Africa and its implications for megadiverse countries. Biological Conservation, 248: 1085. 

Hoveka, L.N., van der Bank, M., Bezeng, B.S. and Davies, T.J., [2020]. Identifying biodiversity knowledge gaps for conserving South Africa’s endemic flora. Biodiversity and Conservation, 29: 2803–2819. 

Teitelbaum, C.S., Amoroso, C.R., Huang, S., Davies, T.J., Rushmore, J., Drake, J.M., Stephens, P.R., Byers, J.E., Majewska, A.A. and Nunn, C.L., [2020]. A comparison of diversity estimators applied to a database of host–parasite associations. Ecography doi.org/10.1111/ecog.05143. 

Menéndez-Guerrero, P.A., Davies, T.J. and Green, D.M., [2020]. Extinctions of Threatened Frogs may Impact Ecosystems in a Global Hotspot of Anuran Diversity. Herpetologica doi.org/10.1655/Herpetologica-D-20-00011.1. 

Elmasri, M., Farrell, M.J., Davies, T.J. and Stephens, D.A., [2020]. A hierarchical Bayesian model for predicting ecological interactions using scaled evolutionary relationships. Annals of Applied Statistics, 14: 221-240. 

Gupta, J., Ekins, P., Boileau, P., Asrar, G., Baker, E., Banuri, T., Bemigisha, J., Clark, G., Crump, J., Mayocyoc-Daguitan, F. and Davies, J., [2020]. Technical Summary-Global Environment Outlook (GEO- 6): Healthy Planet, Healthy People, Cambridge University Press. Updated April 26/2020 – Page 11/21

Morales-Castilla, I., Davies, J.T. and Rodríguez, M.Á., [2020] Historical contingency, niche conservatism and the tendency for some taxa to be more diverse towards the poles. J. Biogeography 47:783–794. 

Menéndez-Guerrero, P.A., Green, D.M. and Davies, T.J., [2020]. Climate change and the future restructuring of Neotropical anuran biodiversity. Ecography 43: 222–235. 

Carvajal-Endara, S., Hendry, A. P., Emery, N. C., Neu, C. P., Carmona, D., Gotanda, K. M., Davies, T. J., Chaves, J., Johnson, M. T. J. [2019] The ecology and evolution of seed predation by Darwin’s finches on Tribulus cistoides on the Galápagos Islands. Ecological Monographs e01392 

Pearse, W.D., Legendre, P., Peres-Neto, P.R. and Davies, T.J., [2019]. The interaction of phylogeny and community structure: Linking the community composition and trait evolution of clades. Global Ecology and Biogeography 28: 1499-1511. 

Davies, T.J., [2019]. The macroecology and macroevolution of plant species at risk. New Phytologist 222: 708–713. doi.org/10.1111/nph.15612.

Farrell, M.J. and Davies, T.J. [2019]. Disease mortality in domesticated animals is predicted by host evolutionary relationships. Proceedings of the National Academy of Sciences 201817323. 

Gupta, J., Hurley, F., Grobicki, A., Keating, T., Stoett, P., Baker, E., Guhl, A., Davies, J. and Ekins, P. [2019]. Communicating the health of the planet and its links to human health. The Lancet Planetary Health. DOI:https://doi.org/10.1016/S2542-5196(19)30040-3 

Elliott, T.L. and Davies, T.J. [2019]. Phylogenetic attributes, conservation status and geographical origin of species gained and lost over 50 years in a UNESCO Biosphere Reserve. Biodiversity and Conservation, 28(3): 711-728. 

Meineke, E.K., Classen, A.T., Sanders, N.J. and Davies, T.J., [2019]. Herbarium specimens reveal increasing herbivory over the past century. Journal of Ecology 107(1): 105-117. https://doi.org/10.1111/1365-2745.13057. 

Davies, T.J., Regetz, J. Wolkovich, E.M., McGill, B.J., [2019] Phylogenetically weighted regression: A method for modelling non-stationarity on evolutionary trees. Global Ecology and Biogeography 28(2): 275-285. DOI: 10.1111/geb.12841.

Elliott, T.L. and Davies, T.J. [2019]. A comparison of phylogenetic and species beta diversity measures describing vegetation assemblages along an elevation gradient. Journal of Vegetation Science 30(1): 98- 107. 

Pavoine, S., Bonsall, M.B., Davies, T.J., Masi, S., [2019] Mammal extinctions and the increasing isolation of humans on the tree of life. Ecology and Evolution 9(3): 914-924. 

Pearse, W.D., Morales-Castilla, I., James, L.S., Farrell, M., Boivin, F. and Davies, T.J. [2018]. Complexity is complicated and so too is comparing complexity metrics-A response to Mikula et al. [2018]. Evolution, 72(12): 2836-2838. 

Meineke, E.K., Davies, T.J., Daru, B.H., and Davis, C.C., [2018] Biological collections for understanding biodiversity in the Anthropocene. Philosophical Transactions of the Royal Society B 374(1763): 20170386.

Farrell, M.J., Govender, D., Hajibabaei, M., Berrang-Ford, L., van der Bank, M., Davies, T.J., [2018] Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach. Genome doi:10.1139/gen-2018-0064. 

Meineke, E.K. & Davies, T.J. [2018] Museum specimens provide novel insights into changing plantherbivore interactions. Philosophical Transactions of the Royal Society B. 374(1763): 20170393. 

Pearse, W.D., Barbosa, A.M., Fritz, S.A., Keith, S.A., Harmon, L.J., Harte, J., Silvestro, D., Xiao, X. and Davies, T.J., [2018] Building up biogeography: Pattern to process. Journal of Biogeography. 45: 1223- 1230. 

Meineke, E.K., Davis, C.C. and Davies, T.J., [2018]. The unrealized potential of herbaria for global change biology. Ecological Monographs 88(4): 505-525. DOI:10.1002/ecm.1307.

Tucker, C.M., Davies, T.J., Cadotte, M.W. and Pearse, W.D., [2018]. On the relationship between phylogenetic diversity and trait diversity. Ecology 99: 1473-1479. DOI:10.1002/ecy.2349. 

Rolshausen, G., Davies, T.J. and Hendry, A.P., [2018]. Evolutionary Rates Standardized for Evolutionary Space: Perspectives on Trait Evolution. Trends in Ecology & Evolution 33: 379-389. DOI:10.1016/j.tree.2018.04.001. 

Lewthwaite, J.M.M., Angert, A.L., Kembel, S.W., Goring, S.J., Davies, T.J., Mooers, A.Ø., Sperling, F.A.H., Vamosi, S.M., Vamosi, J.C. and Kerr, J.T., [2018]. Canadian butterfly climate debt is significant and correlated with range size. Ecography 41(12): 2005-2015. DOI:10.1111/ecog.03534.

Gogarten, J.F., Davies, T.J., Benjamino, J., Gogarten, J.P., Graf, J., Mielke, A., Mundry, R., Nelson, M.C.,
Wittig, R.M., Leendertz, F.H. and Calvignac-Spencer, S., [2018]. Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire. The ISME journal, p.1. 

Shooner, S., Davies, T.J., Saikia, P., Deka, J., Bharali, S., Tripathi, O.P., Singha, L., Latif Khan, M. and Dayanandan, S., [2018]. Phylogenetic diversity patterns in Himalayan forests reveal evidence for environmental filtering of distinct lineages. Ecosphere, 9(5), p.e02157. 

Pearse, W.D., Morales-Castilla, I., James, L.S., Farrell, M., Boivin, F. and Davies, T.J. [2018] Global macroevolution and macroecology of passerine song. Evolution doi.org/10.1111/evo.13450. 

Molina-Venegas, R., Moreno-Saiz, J.C., Parga, I.C., Davies, T.J., Peres-Neto, P.R. and Rodríguez, M.Á.,
2018. Assessing among-lineage variability in phylogenetic imputation of functional trait datasets. Ecography https://doi.org/10.1111/ecog.03480. 

Park, A.W., Farrell, M.J., Schmidt, J.P., Huang, S., Dallas, T.A., Pappalardo, P., Drake, J.M., Stephens, P.R.,
Poulin, R., Nunn, C.L. and Davies, T.J. [2018]. Characterizing the phylogenetic specialism–generalism spectrum of mammal parasites. Proceedings of the Royal Society, B, 285: 20172613. 

Daru, B.H., Bank, M. and Davies, T.J. [2018]. Unravelling the evolutionary origins of biogeographic
assemblages. Diversity and Distributions 24:313-324. 

Lacey Samuels

Professor
Academic Director, UBC Bioimaging Facility

Academic History

  • B.Sc. (1984), McGill Univ.;
  • Ph.D. Botany (1989) UBC;
  • Postdoctoral Fellow, (1993-95), Univ. Colorado
  • Research Associate, (1996-2000) UBC Vancouver
  • Assistant Professor (2000-2006) UBC Vancouver
  • Associate Professor (2006-2011) UBC Vancouver
  • Professor (2011-present) UBC Vancouver
  • Head of Botany Department, (2011-2016)
  • Visiting Professor, Nara Institute of Science and Technology, 2011

My Links

Contact Information

  • lsamuels@mail.ubc.ca
  • 604-822-5469
  • Office: South Wing Biosci- RM 2313/Heads office-North Wing- RM 3155
  • Lab Phone: 604-822-5223
  • 2312 Biological Sciences Building

Research Interests

The Samuels lab studies how plant cells secrete their cell walls, both the polysaccharides and specialized cell wall components such as lipids and lignin.  Our approach is to integrate cell biology with molecular biology and biochemistry to put cell wall biosynthesis and secretion into a cellular context. All plant growth, including agricultural and forestry production, is based on the organized assembly of plant cells into tissues, organs and whole plants.  The plant cell wall determines the shape of the cell and connects cells into tissues and higher order structures, thus plant growth depends on cell wall production.  In addition, terrestrial plants have evolved specialized regions of cell walls, such as the plant cuticle and lignified cell walls that are essential for water retention and water conduction, respectively. Lignified cell walls, such as those found in vascular tissues like wood, make the wall strong and waterproof.  The removal of lignin from the cellulose of the cell wall has been identified as a barrier to enzymatic degradation of cellulose feedstock for biofuels, so there is strong interest in understanding lignified secondary cell walls.

Cellulose biosynthesis in secondary cell walls.
         The formation of wood in the annual growth rings of trees is the most vivid example of how plant cells use carbon captured during photosynthesis to produce biomass that is rich in cellulose and lignin. Cellulose forms paper, textiles, building products, as well as having potential for the production of biofuels. Yoichiro Watanabe, a Botany Ph.D. candidate in my lab, co-supervised by Shawn Mansfield in the Faculty of Forestry, used live-cell imaging to quantitatively analyze cellulose synthase enzymes in developing xylem cells (Watanabe et al., Science 2015). This paper was featured in an accompanying ‘Perspectives’ article in Science. This was the first demonstration of live xylem cells actively depositing cellulose, and it has opened new areas of cellulose biosynthesis and bioenergy research.
         In collaboration with Staffan Persson’s lab at Uni. of Melbourne, Yoichiro went on to discover how cells remodel their cellulose synthesis machinery during the switch from primary cell walls during their growth phase, to secondary cell walls during xylem development (Watanabe/Schneider et al. 2018 PNAS USA). One of the most exciting aspects of this work was the opportunity to observe both primary and secondary cellulose synthase enzymes in the same place at the same time. This work was featured in a commentary “Two types of cellulose synthesis complex knit the plant cell wall together” (Haigler, 2018 PNAS USA), which states “Watanabe et al. have opened the door to many research avenues that will allow us to fully explain and beneficially manipulate the synthesis of abundant renewable biomaterials.”


2. Lignin biosynthesis in secondary cell walls.
         In addition to cellulose, lignin represents a significant (15-30%) component of the secondary cell wall mass of woody tissues. While lignin is important to plants’ physiology by making the walls in the vascular system strong and waterproof, it makes break-down of plant biomass for renewable energy more difficult. Lignin forms when precursors called monolignols are crosslinked in the cell wall. Xylem vessels continue to lignify after they undergo programmed cell death, suggesting surrounding cells contribute monolignols for lignification. This “good neighbour” model was the subject of Rebecca Smith’s Ph.D. dissertation. We used a targeted gene knock-down to decrease monolignol biosynthesis only in lignifying cells (R. Smith and M. Schuetz et al., 2013 Plant Cell). Surprisingly, we found whether a lignifying cell had good neighbours or not depended on the context. In vascular bundles, good neighbours played an important role but in supportive fibers outside the vascular bundles, there were no good neighbours. By specifically manipulating lignin production in different cell populations, we could reduce or modify the lignin content of plants without affecting yield or vascular function (SmithPhD et al., 2015, 2017 Plant Physiol.). The finding that different populations of vessels and fibers cells have different mechanisms for wall lignification has interesting impacts for biotechnology, as it identifies different lignin pools that can be manipulated independently. Previous attempts to manipulate lignin for bioenergy crops used constitutive promoters that would alter lignin in all cell types, which has negative consequences for plant defense responses and growth. Here, we produced plants with improved release of cell wall sugars (saccharification) for biofuel production, yet the plants had normal vascular integrity, and biomass (Smith et al., 2017 Plant Physiol.). 
         Once monolignols are secreted into the secondary cell wall, they must be oxidized by enzymes called laccases and peroxidases, producing monolignol radicals that spontaneously cross-link into the lignin polymer. It is clear that lignin deposition is precisely spatially controlled in plant cell walls, and we discovered that specific laccases in Arabidopsis were responsible for directing lignin deposition (Schuetz et al., 2014 Plant Physiol.; Chou/Schuetz et al., 2018, J. Exp. Bot.). The impact of this work was to demonstrate that it is the activating oxidases, not the cell wall environment or other factors, that controls the spatial distribution of lignin in cell walls. 

     
3. Characterization of glandular trichomes of cannabis.
The flowers of Cannabis sativa L. (cannabis) are used medicinally and recreationally by humans because they contain specialized cannabinoid metabolites. The metabolites are produced in hairs (glandular trichomes) on the flower.  Early studies of cannabis had described three types of glandular trichomes (bulbous, sessile, and stalked), but their properties and relative contributions to producing metabolites were not known. We are studying the stalked glandular trichomes that dominate the cannabis flower. The cannabis stalked glandular trichomes have a large ‘head’ on a multicellular stalk. With advanced microscopy techniques, we can probe the interior of the stalked trichome head, demonstrating a proliferation of secretory cells and an extracellular storage cavity full of blue autofluorescent metabolites. This correlated with high cannabinoid content and enrichment of monoterpenes. By isolating glandular trichomes, we studied which genes are expressed during metabolite production. In addition to validating the proposed cannabinoid biosynthetic pathway, this transcriptomic data identified two new monoterpene synthases, and a suite of highly-expressed genes whose functions are presently unknown. Discovery of the unique properties of cannabis stalked trichomes, and the highly-expressed genes within them, is critical information for molecular breeding, targeted engineering, and optimized harvest and processing of this important plant.


4. Discovery of ATP-binding cassette (ABC) transporters in plant cell wall lipid export.
All land plants’ aerial surfaces are coated with a lipid-rich waxy cuticle. The plant cuticle plays critical roles in plant ecophysiology by sealing the plant surface to prevent water loss. My research group was the first to discover that ABC transporters are required for lipid export from the epidermal cells to the plant cuticle (Pighin et al. 2004 Science). In collaboration with Carl Douglas, I co-supervised T. Quilichini, who extended this work by demonstrating that an ABC transporter is required for pollen cell walls formation in developing anthers (Quilichini. et al., 2010 Plant Physiol; Quilichini. et al., 2014 Plant Cell). This work used two-photon imaging of intrinsic fluorescence in anthers and cryo-fixation of anthers for electron microscopy (Quilichini et al., 2015 Annals of Botany). These ABC transporter studies are important because they demonstrated novel mechanisms of lipid transport to the cell wall.

Team Members

Mendel Perkins, Ph.D. candidate
Sam Livingston, Ph.D. candidate
Jan Xue, M.Sc. student
Kenzie Arnott, M.Sc. student
Samuel King, Honours student

Community Work

Academic Director of the UBC Bioimaging Facility (BIF) (www.bioimaging.ubc.ca).

In 2019-2020, this campus-wide Facility served 201 graduate student, post-doc, undergraduate, and faculty researchers from 108 research groups at UBC (87 groups), as well as other universities and institutions (8 groups) and industry clients (13 groups).  A total of 180 UBC researchers (17 PIs, 49 Postdoctoral fellows, 72 PhD student, 15 Masters student, 14 undergrads, 8 staff, 5 visiting scientists) came from across 22 Departments in 8 Faculties.

BIF provides both service and training in confocal microscopy, scanning electron microscopy, transmission electron microscopy, electron tomography, cryo-fixation of cells, and cryo-TEM.

Selected Publications

Hoffmann*, N., King, S.#, Samuels, A.L., McFarlane*, H.M. (2021) Subcellular coordination of plant cell wall synthesis. Developmental Cell 56: 1-16. (#Honours Biology student; *previous Samuels lab graduate students, now Ph.D. candidate and Assistant Professor at University of Toronto) (invited review)

Perkins, M.L, Schuetz, M., Unda, F., Smith R.A., Sibout, R., Hoffman, N., Wong, D.C.J., Castellarin, S.D., Mansfield, S.D., Samuels, L. (2020) Dwarfism of high-monolignol Arabidopsis plants is rescued by ectopic LACCASE overexpression. Plant Direct 4: e00265.

Hoffmann, N., Benske, A., Betz, H., Schuetz, M., Samuels, A.L. (2020) Laccases and peroxidases co-localize in lignified secondary cell walls throughout stem development. Plant Physiology DOI: https://doi.org/10.1104/pp.20.00473

Sutthinon, P., Samuels, L.,  and Meesawat, U. (2019) Pollen development in male sterile mangosteen (Garcinia mangostana L.) and male fertile seashore mangosteen (Garcinia celebica L.). Protoplasma 256:1545–1556.

Wang, S., Yamaguchi, M., Grienenberger, E., Martone, P.T., Samuels, A.L., Mansfield, S.D. (2019) The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence secondary cell wall deposition and provide mechanical support to Arabidopsis stems. The Plant Journal. https://doi.org/10.1111/tpj.14541

Meents, M., Motani, S., Mansfield, S.D., Samuels, L. (2019)  Organization of Xylan Production in the Golgi During Secondary Cell Wall Biosynthesis. Plant Physiology. 181: 527–546. (Featured cover article)

Livingston, S., Quilichini, T., Booth, J., Wong, D., Rensing, K., Laflamme-Yonkman, J., Castellarin, S., Bohlmann, J., Page, J., Samuels, L. (2019) Cannabis glandular trichomes alter morphology and metabolite content during flower maturation. The Plant Journal. 101: 37-56 (Featured cover article)

Perkins, M., Smith, R., Samuels, L. (2019) The Transport of Monomers during Lignification in Plants: Anything Goes but How? (invited review) Current Opinion in Plant Biotechnology, DOI: 10.1016/j.copbio.2018.09.011.

Watanabe, Y., Schneider, R., Barkwill, S., Gonzales-Vigil, E., Hill, J.L., Samuels†, A.L., Persson†, S., Mansfield†, S.D. (2018) Cellulose Synthase Complexes Display Distinct Dynamic Behaviors during Xylem Transdifferentiation. Proceedings of the National Academy of Sciences USA 115: E6366-E6374. (†=co-corresponding authors).

Chou, E., Schuetz, M., Sibout, R., Hoffman, N., Watanabe, Y., Samuels, L. (2018) Distribution, Mobility and Anchoring of Lignin-Related Oxidative Enzymes in Arabidopsis Secondary Cell Walls. Journal of Experimental Botany 69: 1849-1859.

Meents, M., Watanabe, Y., Samuels, L. (2018) The Cell Biology of Secondary Cell Wall Biosynthesis (invited review). Annals of Botany 121:1107–1125.

Smith, R.A., Schuetz, M., Karlen, S.D., Bird, D.A., Tokunaga, N., Sato, Y., Mansfield, S.D., Ralph, J., and A.L. Samuels (2017) Defining the Diverse Cell Populations Contributing to Lignification in Arabidopsis thaliana Stems. Plant Physiology 174: 1028-1036.

McFarlane H.E., Lee E.K., van Bezouwen L.S, Ross B., Rosado A., Samuels A.L. (2017) Multiscale Structural Analysis of Plant ER-PM Contact Sites. Plant and Cell Physiology 58: 478-484.

Smith, R.A., Gonzales-Vigil, E., Karlen, S., Park, J-Y., Lu, F., Wilkerson, C., Samuels, L., Ralph, J., Mansfield, S.D. (2015) Engineering Monolignol p-Coumarate Conjugates into Poplar and Arabidopsis Lignins. Plant Physiology 169: 2992-3001.

Watanabe, Y., Meents, M.J., McDonnell, L.M., Barkwill, S., Sampathkumar, A., Cartwright, H.N., Demura, T., Ehrhardt, D.W., Samuels, L. †, S. D. Mansfield† (†=co-corresponding authors).  (2015) Visualization of cellulose synthases in Arabidopsis secondary cell walls. Science 350: 198-203.

Quilichini, T.D., Samuels, A.L., and Douglas, C.J. ABCG26-Mediated Polyketide Trafficking and Hydroxycinnamoyl Spermidines Contribute to Pollen Wall Exine Formation in Arabidopsis. Plant Cell doi: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​114.​130484 The Plant Cell November 2014 tpc.114.13048

Schuetz, M., Benske, A., Smith, R.E., Watanabe, Y., Tobimatsu, Y., Ralph, J., Demura, T., Ellis, B., Samuels, A.L. (2014) Laccases direct lignification in the discrete secondary cell wall domains of protoxylem.  Plant Physiology. First Published on August 25, 2014; doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​114.​245597

McFarlane, H.E., Watanabe, Y.,  Yang, W., Huang, Y., Ohlrogge, J., and Samuels, A.L. (2014) Golgi- and Trans-Golgi Network-Mediated Vesicle Trafficking Is Required for Wax Secretion from Epidermis. Plant Physiology 164: 1250-1260.

Quilichini T.D., Douglas C.J., and Samuels A.L. (2014) New views of tapetum ultrastructure and pollen exine development in Arabidopsis thaliana. Annals of Botany, doi: 10.1093/aob/mcu042

Smith, R.A., Schuetz, M., Roach, M., Mansfield, S.D., Ellis B.E., Samuels, L. (2013) Neighboring parenchyma cells can contribute to Arabidopsis xylem lignification, while lignification of interfascicular fibers is cell autonomous. Plant Cell 25: 3988-99.

McFarlane, H.E., Watanabe, Y., Carruthers, K., Lesvesque-Tremblay, G., Haughn, G.W., Gendre, D., Bhalerao, R.P., Samuels, A.L. (2013) The echidna mutant demonstrates that pectic polysaccharides and proteins require distinct post-Golgi vesicle traffic machinery. Plant & Cell Physiology 54: 1867-1880.

Kaneda, M. Schuetz, B.S.P. Lin, C. Chanis, B. Hamberger, T.L. Western, J. Ehlting, A.L. Samuels (2011) ABC transporters coordinately expressed during lignification of Arabidopsis stems include a set of ABCB’s associated with auxin transport.  Journal of Experimental Botany 62: 2063-2077.

McFarlane, H.E., Shin, J.J., Bird, D.A., and Samuels, A.L. 2010. Arabidopsis ABCG transporters, which are required for export of diverse cuticular lipids, dimerize in different combinations. Plant Cell 22: 3066-3075. [view abstract]

Quilichini, T.D., Friedmann, M.C., Samuels, A.L., and Douglas, C.J. 2010. ATP-binding cassette transporter G26 (ABCG26) is required for male fertility and pollen exine formation in Arabidopsis. Plant Physiology 154: 678-690.[view abstract]

M. Kaneda, K.H. Rensing, J.C.T. Wong, B. Banno, S.D. Mansfield, A.L. Samuels. (2008) Tracking Monolignols During Wood Development in Pinus contorta var. latifolia. Plant Physiology First published on June 11, 2008; 10.1104/pp.108.121533.

Samuels A.L., L. Kunst, R. Jetter (2008) Sealing plant surfaces: cuticular wax formation by epidermal cells. Annual Review of Plant Biology. Vol. 59: 683-70. [view full text]

Naomi Fast

Associate Professor

Academic History

  • B.Sc. (1995) University of British Columbia;
  • Ph.D. (1999) Dalhousie University, Halifax, NS;
  • NSERC/CIHR/MSFHR Postdoctoral Fellow (1999-2003) University of British Columbia

Contact Information:

  • 604-822-1630

Research Interests

Our research strives to understand genome evolution in single-celled eukaryotes, focusing on changes in genome size. As genomes are reduced in size, there are likely to be changes in the amounts of non-coding material. Of particular interest is the retention, reduction and/or removal of introns. Introns interrupt genes, and are removed from mRNA by a large macromolecular protein and RNA complex called the spliceosome. In metazoans, where genomes tend to be quite large, introns can be quite long (sometimes several kb), and the spliceosome is extremely large with over a hundred proteins. In contrast, the yeast Saccharomyces possesses a much smaller genome and has relatively few introns that tend to be short. The yeast spliceosome is also predicted to be smaller, with only ~80 proteins. A lineage of lesser-studied eukaryotes, the microsporidia, are distantly related to fungi and possess genomes that are very tiny; at the extreme, smaller than many bacterial genomes. Using microsporidia as a model system, we are examining the effects of genome reduction on the evolution of introns and the spliceosomal machinery.

​

Microsporidia are a large group of intracellular parasites. Outside of host cells they exist as highly resistant spores, which possess organelles almost entirely relegated to their amazing process of infection. The most prominent of these is the polar filament that is wrapped around the spore contents. With the appropriate environmental triggers, the filament is rapidly everted, breaking through the spore wall and forming a projectile tube that can pierce a nearby cell, much like a harpoon. The infective spore contents can then pass through the tube and are injected into the host cell. The parasite grows and divides within the host’s cytoplasm, eventually producing more spores and killing the host cell.

​

Using molecular techniques, our research strives to address genome evolution in these unusual eukaryotes. Currently we are focusing on three general areas of research: (1) A molecular examination of intron positions and lengths among microsporidia possessing a range of genome sizes.
(2) A largely bioinformatic assessment of the differing spliceosomal components among microsporidia, with comparisons to more distantly related fungi.
(3) Small-scale molecular sequence surveys of microsporidia possessing different genome sizes. ​

Team Members

Cameron Grisdale, PhD student
Alex Ardila-Garcia, PhD student

Selected Publications

Lee, R.C.H., S.W. Roy and N.M. Fast. 2010. Constrained intron structures in a microsporidian. Mol. Biol. Evol. (in press; doi: 10.1093/molbev/msq087)

Gill, E.E., R.C.H. Lee, N. Corradi, C.J. Grisdale, V.O. Limpright, P.J. Keeling and N.M. Fast. 2010. Splicing and transcription differ between spore and intracellular life stages in the parasitic microsporidia. Mol. Biol. Evol. 27:1579-1584.

Gill, E.E., J.J. Becnel and N.M. Fast. 2008. ESTs from the microsporidian Edhazardia aedis. BMC Genomics 9:296.

Williams*, B.A.P., R.C.H. Lee*, J.J. Becnel, L.M. Weiss, N.M. Fast and P.J. Keeling. 2008. Genome reduction and expansion in microsporidia. BMC Genomics 9:200.

Lee, R.C.H., B.A.P. Williams, A.M.V. Brown, M.L. Adamson, P.J. Keeling and N.M. Fast. 2008. Alpha and beta tubulin phylogenies suggest a close relationship between the microsporidia Brachiola algerae and Antonospora locustae. J. Eukaryot. Microbiol. 55:388-392.

Gill, E.E and N.M. Fast. 2007. Stripped down DNA repair in a highly reduced parasite. BMC Mol. Biol. 8:24 (p.1-14)

Gill, E.E. and N.M. Fast. 2006. Assessing the microsporidia-fungi relationship: combined phylogenetic analysis of eight genes. Gene 375:103-109.

Williams, B.A.P., C.H. Slamovits, N.J. Patron, N.M. Fast, and P.J. Keeling. 2005. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc. Natl. Acad. Sci. USA 102:10936-10941.

Keeling, P.J., B.A.P. Williams, J. Law, N.M. Fast, and C.H. Slamovits. 2005. Comparative genomics of microsporidia. Folia Parasitol .52:8-14.

Keeling, P J., J.M. Archibald, N.M. Fast, and J.D. Palmer. 2004. The evolution of modern eukaryotic phytoplankton.Science , 306:2191.

Slamovits, C., N.M. Fast, J.S. Law, and P.J. Keeling. 2004. Genome compaction and stability in microsporidian intracellular parasites. Curr. Biol. 14:891-896.

Philippe Tortell

Professor

Academic History

  • B.Sc. McGill (1994) M.A. Princeton University (1997); 
  • Ph.D. Princeton University (2001)

Contact Information

  • ptortell@eos.ubc.ca
  • 604-822-4728
  • ESB-room 2065
  • Lab Phone: 604-822-6088

Research Interests

I am a sea-going oceanographer with broad interests in marine biogeochemical cycles.  Current work in my research group focuses on understanding the biological, chemical and physical factors regulating oceanic primary productivity and the concentration of climate active gases including carbon dioxide (CO2), dimethylsulfide (DMS), methane (CH4) and nitrous oxide (N2O).  My group has made significant contributions to the development and implementation of new measurement techniques based on sea-going mass spectrometry, optical measurements and tracer-based rate incubation experiments.    Our Research includes controlled laboratory studies and extensive field campaigns to a number of ocean regions.  Current field areas of interest include the Subarctic Pacific Ocean, Canadian Arctic Archipelago and a variety of coastal Antarctic systems.

Team Members

Ana Franco, Post-Doctoral Fellow
Sacchidanandan Pillai, PhD
Brandon McNabb, M.Sc.
Yayla Sezginer, Ph.D.
Katarina Schuler, Ph.D.

Robert W. Izett and Philippe Tortell. ΔO2/N2′ as a tracer of mixed layer net community production: Theoretical considerations and proof-of-concept. 2021.  Limnology and Oceanography Methods, http://doi.org/10.1002/lom3.10440

Nina Schuback and Philippe D. Tortell.  2019. Diurnal regulation of photosynthetic light absorption, electron transport and carbon fixation in two contrasting oceanic environments.  Biogeosciences, 16, 1381–1399. https://doi.org/10.5194/bg-16-1381-2019

WJ Burt, Z. Chen, T Westberry, M Behrenfeld, J Graff, B Jones, and PD Tortell. 2018. Carbon to Chlorophyll ratios and net primary productivity of Subarctic Pacific surface waters derived from autonomous shipboard sensors.  Global Biogeochemical Cycles, Volume: 32   Issue: 2   Pages: 267-288, doi.org/10.1002/2017GB005783.

Izett R., C. Manning, R. Hamme and PD Tortell.  2018. Refined estimates of net community production in the Subarctic Northeast Pacific derived from ΔO2/Ar measurements with N2O-based corrections for vertical mixing.  Global Biogeochemical Cycles. doi:10.1002/2017GB005792

Fenwick, L. and P. Tortell.  2018.  Methane and nitrous oxide distributions in coastal and open waters of the Northeast Subarctic Pacific during 2015-2016.  Marine Chemistry, volume 200 (20) Pages 45-56

Hoppe, C, Schuback, N, Seminuik D., Giesbrecht K., Mol J., Thomas H., Maldonado M., Rost B., Tortell P. Compensation of Ocean Acidification effects in Arctic phytoplankton assemblages.  2018. Nature Climate Change, 8, 529–533

Sean Graham

Professor

Academic History

  • 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)

My Links

Contact Information

  • 604-822-4816
  • swgraham@mail.ubc.ca
  • UBC Biodiversity Research Centre

Research Interests

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).

Team Members

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.

Xin Li

Professor
Tier 1 Canada Research Chair in plant immunity and Sclerotinia biology

Academic History

  • BSc. Genetics and Genetic Engineering, Fudan University (1989)
  • Ph.D. Plant Pathology, Oklahoma State Univ., (1995)
  • Postdoctoral Fellow, Duke Univ., (1996-1999) 
  • Scientist, Maxygen. Inc. (1999-2001)

Contact Information

  • xinli@msl.ubc.ca
  • 604-822-3155
  • Office Room 317/Lab Room 377 MSL
  • Lab Phone: 604-822-3205

Research Interests

​The long-term goal of our research program is to understand the molecular mechanisms of plant innate immunity. We study plant defense against pathogen infection in the context of gene regulation, protein-protein interaction and signal transduction using the model organism Arabidopsis thaliana. Our program aims to discover new regulatory components of plant disease resistance and to elucidate the biochemical functions of a number of regulators we have already identified. Understanding the innate ability of plants to defend themselves against pathogen infection promises to revolutionize disease control practices in our fields using environmentally friendly strategies.

A model depicting the involvement of the MOS proteins in R protein-mediated defense signaling pathways in Arabidopsis, using SNC1 as an example of the journey of TIR-NB-LRR proteins. 1. At the chromosomal level, MOS1, ATXR7, and MOS9 up-regulate the transcription of SNC1 through chromatin remodeling. 2. MOS2, MOS4, and MOS12 are required for proper splicing of the transcripts of SNC1. 3. The Nup107-160 complex and MOS11 have key roles in the export of total mRNA (including mature mRNA of SNC1), which is required for effective defense. 4. MOS5 is an E1 ubiquitin-activating enzyme, an essential component of the ubiquitination cascade, required for the regulation of defense signaling components. As an example, the SCFCPR1 E3 ubiquitin ligase complex targets SNC1 for degradation, which prevents autoimmunity caused by overaccumulation of R proteins. MOS8 positively regulates plant defense, possibly through prenylation, which affects the targeting of defense regulators. 5. MOS6 and MOS7 are involved in the nucleocytoplasmic shuttling of defense signaling molecules such as SNC1, EDS1, and NPR1. As with RPS4, EDS1 is probably required for the nuclear localization and activation of SNC1 upon recognition of its corresponding effector (Bhattacharjee et al. 2011; Heidrich et al. 2011). MOS14 is required for the nuclear import of splicing factors, which may affect defense regulator RNA processing. 6. MOS10 activates the SNC1-mediated defense through transcriptional repression of negative regulators of defense such as DND1 and DND2.

Team Members

 If you are interested in pursuing a PhD degree in plant immunity and/or Sclerotinia biology, please contact Dr. Xin Li (xinli@msl.ubc.ca).

Postdoctoral Fellow:
Dr. Tongjun Sun (2018- )
Dr. Zhongshou Wu (2020- )

Ph.D. Students:
Paul Kapos (2014- )
Kevin Ao (2017- )
Rowan van Wersch (2016- )
Yan Xu (2017- )
 Karen Thulasi Devendrakumar (2017- )
Lei Tian (2019- )

MSc Students:
Nanbing Zhang (2018- )
Solveig van Wersch (2018- )
Xueru Liu (2020- )

Lab Alumni:
Dr. Marcel Wiermer, Ph.D (2005)
Dr. Sandra Goritschnig, Ph.D. (2006) 
Dr. Hugo Germain, Ph.D. Plant Science (2007)
Dr. Kristoffer Palma, Ph.D. Genetics  (2007)
Dr. Jacqueline Monaghan, Ph.D  (2010)
Patrick Gannon, MSc, Botany (2011)
Dr. Tabea Weihmann, Ph.D (2011)
Virginia Woloshen, MSc, Botany (2012)
Dr. Yuti Cheng, Ph.D (2013)
Dr. Yan Huang, Ph.D (2013)
Chipan Zhu, MSc, Botany (2014)
Dr. Fang Xu, Ph.D (2014)
Dr. Kaeli Johnson, Ph.D (2016)
Dr. Oliver Xiaoou Dong, Ph.D (2016)
Dr. Shuai Huang, Ph.D (2016)
Dr. Meixuezi Tong, Ph.D (2016)
Dr. Charles Copeland, PhD (2018)
Dr. Jianhua Huang, PhD (2019)
Dr. Zhongshou Wu (2015- 2020)
Dr. Wanwan Liang (2015-2020)

Selected Publications

Zhang, Y., Goritschnig, S., Dong, X., and Li, X. 2003. A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in the snc1 mutant. Plant Cell 15 (11): 2636-46.

Zhang Y. and Li X. 2005. A putative Nucleoporin 96, is required for both basal defense and constitutive resistance responses mediated by snc1. Plant Cell 17: 1306-16.

Palma K, Zhang Y, and Li X. 2005. An Importin alpha homolog, MOS6, plays an important role in plant innate immunity. Current Biology 15(12):1129-35.

Zhang Y.,Cheng, Y.T., Bi, D., Palma K., and Li, X. 2005. MOS2, a protein containing G-patch and KOW motifs, is essential for innate immunity in Arabidopsis thaliana. Current Biology 15(21):1936-42.

Goritschnig S, Zhang Y, and Li, X. 2007. The ubiquitin pathway is required for innate immunity in Arabidopsis. Plant Journal 49(3):540-51. 

Palma K., Zhao Q., Cheng Y.T., Bi D., Monaghan J., Cheng W., Zhang Y., and Li X. 2007. Regulation of plant innate immunity by three proteins in a complex conserved across the plant and animal Kingdoms. Genes & Development 15; 21(12):1484-93.

Monaghan J., Xu F., Zhao Q., Palma K., Chen S., Zhang Y. and Li X. 2009. Two Prp19-like U-box proteins in the MOS4-Associated Complex play redundant roles in plant innate immunity. PLoS Pathogens, Jul;5(7):e1000526.

Cheng Y.T., Germain H., Wiermer M., Bi D., Garcia A.V., Wirthmueller L., Despres C., Parker JE, Zhang Y., and Li X. 2009. MOS7 is required for plant innate immunity and nuclear accumulation of defense regulators. Plant Cell 21(8): 2503-16.

Germain H., Qu N., Cheng Y.T., Lee E.K., Huang H., Dong O.X., Gannon P., Huang S., Ding P., Li Y., Sack F., Zhang Y., and Li X. 2010. MOS11: a new component in the mRNA export pathway. PLoS Genetics 6 (12) e1001250.

Bi D, Johnson KC, Zhu Z, Huang Y, Chen F, Zhang Y, Li X. 2011. Mutations in an Atypical TIR-NB-LRR-LIM Resistance Protein Confer Autoimmunity. Front Plant Sci. 2:71. doi: 10.3389/fpls.2011.00071.

Cheng Y.T., Li Y., Huang S., Huang Y., Dong X., Zhang Y. and Li X. 2011. Stability of plant immune-receptor resistance proteins is controlled by SKP1-CULLIN1-F-box (SCF)-mediated protein degradation. PNAS 108(35):14694-9.

Xu F., Xu S., Wiermer M., Zhang Y. and Li X. 2012. The cyclin L homolog MOS12 and the MOS4-associated complex are required for proper splicing of plant resistance genes. Plant Journal, 70(6):916-28.

Cheng Y.T. and Li X. 2012. Ubiquitination in NB-LRR-mediated immunity. Current Opinion in Plant Biology 15(4):392-99.

Johnson K.C., Dong O.X., Huang Y., Li X. 2013. A Rolling Stone Gathers No Moss, but Resistant Plants Must Gather Their MOSes. Cold Spring Harb Symp Quant Biol. Feb 21.10.1101/sqb.2013.77.014738

Huang Y., Chen X., Liu Y., Rothe C., Copeland C., McFarlane H.E., Huang S., Lipka V., Wiermer M. and Li X. 2013. Mitochondrial AtPAM16 is required for plant survival and negative regulation of plant immunity. Nature Communications, 4:2558. doi: 10.1038/ncomms3558.

Huang Y., Minaker S., Roth C., Hieter P., Lipka V., Wiermer M. and Li X. 2014. An E4 ligase facilitates polyubiquitination of plant immune receptor resistance proteins. Plant Cell 26(1):485-96.

Huang S., Monaghan J., Zhong X., Lin L., Sun T., Dong O.X. and Li X. 2014. HSP90s are required for NLR immune receptor accumulation in Arabidopsis. Plant Journal 79(3):427-39.

Xu F., Kapos P., Cheng Y.T., Li M., Zhang Y. and Li X. 2014. NLR-Associating Transcription Factor bHLH84 and Its Paralogs Function Redundantly in Plant Immunity. PLoS Pathog. 10(8):e1004312. doi: 10.1371/journal.ppat.1004312.

Xu F., Cheng Y.T., Kapos P., Huang Y. and Li X. 2014. P-Loop-Dependent NLR SNC1 Can Oligomerize and Activate Immunity in the Nucleus. Mol Plant 7(12) 1801-1804.

Xu F., Zhu C., Cevik V., Johnson K., Liu Y., Sohn K., Jones J.D., Holub E.B. and Li X. 2015. Autoimmunity conferred by chs3-2D relies on CSA1, its adjacent TNL-encoding neighbour. Sci Rep. 5:8792. doi: 10.1038/srep08792.

Li X., Kapos P. and Zhang Y.. NLRs in plants. 2015. Curr Opin Immunol. 32C:114-121. doi: 10.1016/j.coi.2015.01.014.

Xu F., Huang Y., Li L., Gannon P., Linster E., Huber M., Kapos P., Bienvenut W., Polevoda B., Meinnel T., Hell R., Giglione C., Zhang Y., Wirtz M., Chen S. and Li X. 2015. Two N-Terminal Acetyltransferases Antagonistically Regulate the Stability of a Nod-Like Receptor in Arabidopsis. Plant Cell 27(5):1547-62.

Huang S., Chen X., Zhong X., Li M., Ao K., Huang J. and Li X. 2016. Two redundant plant TRAF proteins participate in NLR immune receptor turnover. Cell Host & Microbe 19(2):204-15.

Li X. and Zhang Y. Suppressor Screens in Arabidopsis. Methods Mol Biol. 2016;1363:1-8. doi: 10.1007/978-1-4939-3115-6_1.

Dong O.X., Tong M., Bonardi V., Kasmi F.E., Woloshen V., Wünsch L.K., Dangl J.L. and Li X. TNL-mediated immunity in Arabidopsis requires complex transcriptional regulation of the redundant ADR1 gene family. New Phytologist 210(3):960-973.

Johnson K.C.M., Yu Y., Gao L., Eng R.C., Wasteneys G.O., Chen X. and Li X. 2016. A partial loss-of-function mutation in an Arabidopsis RNA polymerase III subunit leads to pleiotropic defects. Journal of Experimental Botany 67(8):2219-30.

Copeland C., Woloshen V., Huang Y. and Li X. 2016. AtCDC48A is involved in the turnover of an NLR immune receptor. Plant J. 2016 Jun 24. doi: 10.1111/tpj.13251. [Epub ahead of print]

 Huang S., Balgi A., Pan Y., Li M., Zhang X., Du L., Zhou M., Roberge M. and Li X. 2016. Identification of methylosome components as negative regulators of plant immunity using chemical genetics. Mol Plant. 9(12):1620-1633.

Johnson KC, Zhao J, Wu Z, Roth C, Lipka V, Wiermer M, and Li X. 2017. The putative kinase substrate MUSE7 negatively impacts the accumulation of NLR proteins. Plant J. 89(6):1174-1183.

Wu Z., Huang S., Zhang X., Wu D., Xia S. and Li X. 2017. Regulation of plant immune receptor accumulation through translational repression by a glycine-tyrosine-phenylalanine (GYF) domain protein. eLife2017 Mar 31;6. pii: e23684

Tong M, Kotur T, Liang W, Vogelmann K, Kleine T, Leister D, Brieske C, Yang S, Lüdke D, Wiermer M, Zhang Y, Li X, Hoth S. 2017. E3 ligase SAUL1 serves as a positive regulator of PAMP-triggered immunity and its homeostasis is monitored by immune receptor SOC3. New Phytol. 215(4):1516-1532.

Ding Y, Sun T, Ao K, Peng Y, Zhang Y, Li X, Zhang Y. 2018. Opposite Roles of Salicylic Acid Receptors NPR1 and NPR3/NPR4 in Transcriptional Regulation of Plant Immunity. Cell. 2018 Apr 11. pii: S0092-8674(18)30376-3. doi: 10.1016/j.Cell.2018.

Dong OX, Ao K, Xu F, Johnson KCM, Wu Y, Li L, Xia S, Liu Y, Huang Y, Rodriguez E, Chen X, Chen S, Zhang Y, Petersen M, and Li X. 2018. Individual components of paired typical NLR immune receptors are regulated by distinct E3 ligases. Nature Plants, doi: 10.1038/s41477-018-0216-8.

Liang W, van Wersch S, Tong M, and Li X. 2019. TIR-NB-LRR immune receptor SOC3 pairs with truncated TIR-NB protein CHS1 or TN2 to monitor the homeostasis of E3 ligase SAUL1. New Phytol.  221(4):2054-2066. doi: 10.1111/nph.15534.

Huang J, Sun Y, Orduna AR, Jetter R, and Li X. 2019. The Mediator kinase module serves as a positive regulator of salicylic acid accumulation and systemic acquired resistance. Plant J. 98(5):842-852.

Wu Z, Li M, Dong OX, Xia S, Liang W, Bao Y, Wasteneys G, and Li X. 2019. Differential regulation of TNL-mediated immune signaling by redundant helper CNLs. New Phytol. 222(2):938-953. doi: 10.1111/nph.15665.

Zhang Y and Li X. 2019. Salicylic acid: biosynthesis, perception, and contributions to plant immunity. Curr Opin Plant Biol. 50:29-36. doi: 10.1016/j.pbi.2019.02.004.

van Wersch S and Li X. Stronger When Together: Clustering of Plant NLR Disease resistance Genes. Trends in Plant Sci. 2019 Aug;24(8):688-699. doi: 10.1016/j.tplants.2019.05.005. Epub 2019 Jun 29.

Sun T, Huang J, Xu Y, Verma V, Jing J, Sun Y, Orduna AR, Tian H, Huang X, Xia S, Schafer L, Jetter R, Zhang Y and Li X. 2019. Redundant CAMTA transcription factors negatively regulate the biosynthesis of salicylic acid and N-hydroxypipecolic acid by modulating the expression of SARD1 and CBP60g. Molecular Plant Nov 13. pii: S1674-2052(19)30364-8. doi: 10.1016/j.molp.2019.10.016. [Epub ahead of print]

Wu Z., Tong M., Tian L., Zhu C., Liu X., Zhang Y. and  Li X. 2020. Plant E3 Ligases SNIPER1 and SNIPER2 Broadly Regulate the Homeostasis of Sensor NLR Immune Receptors. EMBO Journal Jun 18;e104915. doi: 10.15252/embj.2020104915. Online ahead of print.

Liang W, Tong M, Li X. SUSA2 is an F-box protein required for autoimmunity mediated by paired NLRs SOC3-CHS1 and SOC3-TN2. Nature Communications 2020 Oct 15;11(1):5190. doi: 10.1038/s41467-020-19033-z.

Li X, Zhang Y.A structural view of salicylic acid perception. Nature Plants. 2020 Oct;6(10):1197-1198. doi: 10.1038/s41477-020-0741-0.

Tian L and Li X. Enzyme formation by immune receptors. Science, 04 Dec 2020: Vol. 370, Issue 6521, pp. 1163-1164. DOI: 10.1126/science.abf2833

Tian, H., Chen, S., Wu, Z., Ao, K., Yaghmaiean, H., Sun, T., Huang, W., Xu, F., Zhang, Y., Wang, S., Li, X.**, and Zhang, Y.** (2021). Activation of TIR signalling boosts pattern-triggered immunity. Nature, https://doi.org/10.1038/s41586-021-03987-1.

Liang Song

Assistant Professor

Academic History

  • BSc., Fudan University
  • Ph.D., Pennsylvania State University
  • Postdoctoral fellow, Salk Institute for Biological Studies 

Contact Information

  • liang.song@botany.ubc.ca
  • 604-827-2720
  • Office: 2231 Biological Sciences Building
  • Lab: 2234 Biological Sciences Building

Research Interests

1. Abscisic acid-regulated gene expression networks

Animals often employ a fight-or-flight strategy when facing challenges. By contrast, plants handle challenges on site through many molecular, morphological, and physiological solutions. The plant hormone abscisic acid (ABA) is a nexus molecule of stress responses and plant development. Without proper ABA responses, plants would make unwise decisions such as germinating prematurely or failing to preserve water and other resources during a drought. The ABA responses are orchestrated through the expression of thousands of genes and the regulation of these gene products. Our lab studies ABA-regulated gene expression, and the specific regulation in different tissues or under various stresses.  

2. Environmental and genetic control of seed development

Grains and oilseeds are essential to humans. Seeds are also mini time machines that may outlive many generations of people. Several key stages of seed development, including storage reserve deposition, desiccation, and dormancy, are related to ABA. We study the environmental and genetic control of seed development, and use this model to understand how ABA shapes distinct and complex biological processes. 

Team Members

summer hiking and dinner (2019)​

new year BBQ (2020)​

summer hiking after vaccination (2021)

self portraits of graduate students (2021 winter)

Current members

graduate students:  
Milad Alizadeh, Ph.D. student (technician 2018 – 2019; UBC 4 YF awardee 2019 – )
Ryan Hoy, M.Sc. student (technician 2019 – 2020; BC Graduate Scholarship awardee 2020 – 2021)
Renwei Zheng, M.Sc. student (2021- )
Gloria Bailan Lu, M.Sc. student (WLIUR awardee, 2019; volunteer 2019 & 2020; SURE awardee 2020; BIOL448 directed studies student 2021 W2; 2021- )
Dongeun Go, M.Sc student (2021- )

undergraduate students: 

Kristen Tien (2022- )
Yasmine Tremblay (2022- )
Helena Zhou (2021- )
Ghazaleh Shoaib (volunteer 2021 – ; BIOL448 directed studies 2022)

Alumni: 

Rebecca Ching-Chia Yu (NSERC USRA awardee 2019; volunteer 2019 – 2020; Work-Learn 2021)
Emma Laqua (Co-op student / volunteer, 2020 – 2021)
Katherine Feng (NSERC USRA awardee, 2021)
Parmida Nafezi (BIOL448 directed studies student 2019 W1 & 2020 W1; volunteer 2020)
Ivan Bao, undergradate (engineering student; gadget builder, 2019)
Chanwoo Ho, undergraduate (volunteer, 2019) ​

Selected Publications

underline: trainee authors from our group

*: corresponding author

2021

Alizadeh M., Hoy R., Lu B., Song L.* (2021) Team effort: combinatorial control of seed maturation by transcription factors. Curr. Opin. Plant Biol 63, 102091

2019

Salehin M., Li  B.,  Tang M., Katz E., Song L., Ecker J.R., Kliebenstein D., Estelle M.* (2019) Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nat. Comm. 10:4021

Argueso C.T., Assmann S.M.*, Birnbaum K.D., Chen S., Dinneny J.R., Doherty C.J., Eveland A.L., Friesner J., Greenlee V.R., Law J.A., Marshall-Colón A., Mason G.A., O’Lexy R., Peck S.C., Schmitz R.J., Song L., Stern D., Varagona M.J., Walley J.W., Williams C.M. (2019) Directions for Research and Training in Plant Omics: Big Questions and Big Data. Plant Direct 3, e00133

Full Publication List in Google Scholar. 

Sean Michaletz

Assistant Professor

My Links

Contact Information

  • sean.michaletz@ubc.ca
  • 604-822-2141
  • Ponderosa Annex- Room 205

Research Interests

We are interested in the physical processes linking environmental variation to plant physiology, and how this “scales up” to influence higher-level patterns and processes.  To investigate these topics, we use interdisciplinary approaches that draw upon fields such as physics, chemistry, engineering, and geoscience.  Our work often involves development of mechanistic theory and models, which are parameterized, tested, and refined using data from the laboratory and the field.  We also focus on long-term monitoring of climate, ecophysiology, and vegetation dynamics in our growing network of Forest MacroSystems sites located around the world.  You can find out more about our research on ResearchGate.

Team Members

Nicole Bison
Marcella Cross
Josef Garen
Raquel Partelli Feltrin
Milos Simovic
Yi He (visiting MSc student)

Brian Leander

Professor

My Links

Contact Information

  • bleander@mail.ubc.ca
  • Office: 604-822-2474
  • Office Location: Biodiversity Research Centre, Room 339
  • Lab: 604-822-4892
  • Lab Location: Biodiversity Research Centre, Room 340 (computer lab) & Room 370 (wet lab)

Research Interests

Our research concentrates on the discovery and characterization of marine organismal diversity and comparative studies of novel morphological systems in predatory eukaryotes (i.e., marine zoology & protistology).

We are fundamentally interested in the diversity and evolution of organisms, particularly traits associated with feeding, locomotion and symbiotic interactions. By addressing specific hypotheses about trait evolution using comparative molecular methods, we study the innovations and transformations associated with broad patterns of organismal diversity (e.g., convergent evolution over vast phylogenetic distances).

This exploratory approach is motivated by the thrill of discovery, the beautiful and the bizarre, and the yearning to build a more comprehensive framework for understanding the interrelationships of life on Earth. The marine lineages we work on tend to be drop-dead gorgeous and reflect spectacular morphological diversity, such as meiofaunal & planktonic animals, euglenozoans, dinoflagellates, cercozoans & marine gregarine apicomplexans.

Abel Rosado

Associate Professor

Academic History

  • 1999.   BSc.   Chemistry                            University of Malaga
  • 2006.   PhD.  Molecular Biology                University of Malaga
  • 2006-2011.    Postdoctoral Fellow             UC-Riverside
  • 2012-2014.    Postdoctoral Fellow             University of Malaga

Contact Information

  • abel.rosado@botany.ubc.ca
  • 604-827-1662
  • Office: room 2315, Biosciences Building
  • Lab: room 2234, Biosciences Building

Research Interests

Out of over a quarter of a million plant species, each of which contains complex and dynamic chemical make over, a mere fraction of one percent (1%) has been adequately investigated by western science. Yet, the human experimentation and exploration of plant medicines among Indigenous populations over millennia has created an extended catalog of approximately 20000 plant species with health benefits that represents the main source of medicine for most of the World.

My laboratory is part of a cross-disciplinary research cluster encompassing Anthropology, Ethnobiology, plant and food sciences, analytical chemistry, and clinical nutrition working in collaboration with private companies and First Nation knowledge keepers in the characterization of traditional berries native to the Pacific Northwest, and their potential use as natural sources of phenolic compounds to control blood glucose levels in people living with prediabetes.

Team Memebers

Miriam Fenniri – PhD. Candidate
Elizabeth Orhuamen – MSc. Candidate
Christopher Cote – MSc. Candidate
Christiaan Spangenberger – MSc. Candidate

Selected Publications

Previous Research in Cell Biology:

2022.Bayer E, Brandizzi F, Jaillais Y, Botella MA, Wang P, Rosado A. Plant Membrane Contact Sites – Questions from the membrane interface. Plant Cell.

2022. Kang BH, Anderson CT , Arimura S, Bayer EM, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM , Chapman KD, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Wang P and Zolman BK. A Glossary of Plant Cell Structures: current insights and future questions. Plant Cell. 34:10-52

2021. Ruiz-López N, Perez-Sancho J, Esteban del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, and Botella MA. The Endoplasmic Reticulum-Plasma Membrane Contact Site Synaptotagmins Maintain Diacylglycerol Homeostasis during Abiotic Stress. Plant Cell. 33: 2431-2453.

2021. Rosado A and Bayer EM. Geometry and cellular function of organelle membrane interfaces. Plant Physiology185: 650–662.

2020.Zaman MF, Nenadic A, Radojičić A, Rosado A, and Beh CT. Sticking with it: ER-PM membrane contact sites as a coordinating nexus for regulating lipids and proteins at the cell cortex. Frontiers in Cell and Developmental Biology. 8:675

2020. Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella MA, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves-Azevedo A, Rosado A. Rare Earth Elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes. Journal of Experimental Botany. 71: 3986-3998. 

2019. Song CZ, Rosado A, Zhang Z, Castellarin SD. ABA alleviates uptake and accumulation of zinc in roots and shoots of grapevines by inducing expression of ZIP and detoxification-related genes. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.00872.

2019. Lee E, Vanneste S, Perez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. Ionic stress enhances ER-PM connectivity via phosphoinositide – associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Science USA. 116: 1420-1429.

2017. Bayer EM, Sparkes I, Vanneste S, Rosado A.From shaping organelles to signalling platforms: the emerging functions of plant ER-PM contact sites.Current Opinion in Plant Biology. 40: 89-96.

2017. McFarlane HE, Lee E, van Bezouwen LS, Ross B, Rosado A, Samuels AL. Multiscale structural analysis of plant ER-PM contact sites. Plant Cell Physiology. 58: 478-484.

2016. Perez-Sancho J, Tilsner J, Samuels AL, Botella MA, Bayer EM, Rosado A. Stitching organelles: Organization and function of specialized membrane contact sites in plants. Trends in Cell Biology. 26: 705-717.

2016. Tilsner J, Nicolas W, Rosado A, Bayer EM. Staying tight: plasmodesmal membrane contact sites and the control of cell-to-cell connectivity in plants. Annual Reviews in Plant Biology. 67: 337-364.

2016. Perez-Sancho J, Schapire AL, Botella MA, Rosado A. Analysis of protein-lipid interactions using purified C2 domains. Methods in Molecular Biology. 1363:175-187.

2015. Perez-Sancho J, Vanneste S, Lee E, McFarlane H, Esteban Del Valle A, Valpuesta V, Friml J, Botella MA, Rosado A. The Arabidopsis SYT1 is enriched in ER-PM contact sites and confers cellular resistance to mechanical stresses. Plant Physiology. 168: 132-143.

Curtis Suttle

Professor

Academic History

  • B.Sc., Ph.D., UBC; 
  • Coastal Marine Scholar SUNY StonyBrook 1987-88; 
  • Assist/Assoc Professor, Univ. Texas at Austin 1988-96.

My Links

Contact Information

  • csuttle@eos.ubc.ca
  • 604-822-8610
  • Office: Rm 346/Lab Rm 386 Beaty Biodiversity Centre
  • Lab Phone: 604-827-5715

Research Interests

There has been increasing interest in the biology and ecology of viruses and other pathogens that infect microalgae. Viruses that infect bacteria and phytoplankton play a key role in the dynamics of organisms and nutrients in marine and freshwater ecosystems, and consequently also affect nutrient and energy cycling. A primary research focus of my laboratory is to understand the biology and ecology of viruses that infect microalgae and cyanobacteria. Research interests include 1) discerning the effect of viruses on primary productivity and phytoplankton population dynamics; 2) isolating and characterizing novel viruses from marine environments; 3) developing molecular approaches for enumerating and identifying viruses; 4) determining the temporal and spatial distribution of specific viruses; 5) identifying mechanisms regulating viral abundance in nature; and 6) understanding the biology of these viruses and the infection process and exploring the molecular evolution and genetic diversity of viruses in nature.

As part of these studies, we have isolated viruses that infect ecologically important phytoplankton and cyanobacteria including toxic bloom formers. We have developed PCR primers specific for the DNA polymerase genes of viruses that infect microalgae. These primers have been used to amplify DNA from a number of different viruses infecting marine phytoplankton, as well as from natural virus communities. Sequence analysis indicates that these viruses belong to a single family, and are most closely related to herpes viruses. These viruses can occur in seawater at concentrations > 105 ml-1. Viruses that infect cyanobacteria occur at even higher concentrations, and 106 infectious units ml-1, can be found in some coastal waters. Our research will continue to investigate the role of viruses in aquatic ecosystems.

Team Members

Amy Chan – Research Scientist
Kevin Xu Zhong – Research Associate
Maria Cortazar- Post-doctoral Associate
Jan Finke – Post-doctoral Associate
Graduate Students
Anwar Al-Qattan PhD Oceanography aqattan@eoas.ubc.ca
Tianyi Chang PhD Oceanography tchang@eoas.ubc.ca
Qi Yang PhD Oceanography qyang@eoas.ubc.ca

Select Publications

Past and current publications can be found at: https://scholar.google.com/citations?user=Oaop7AQAAAAJ&hl=en

Geoffrey Wasteneys

Professor
CRC Tier 1

Academic History

  • Canada Research Chair in Plant Cell Biology and Professor; 
  • B.Sc. Biology (1983), Carleton; 
  • Ph.D. Plant Cell Biology (1989) Australian National Univ (ANU); 
  • National Research Fellow (1988-91) ANU; 
  • Humboldt Fellow (1992-1993), Univ. Heidelberg; 
  • Queen Elizabeth II Fellow (1992-1998), ANU; 
  • Fellow/Senior Fellow (1996-2004), ANU.

My Links

Contact Information

  • geoff.wasteneys@botany.ubc.ca
  • Office: 604-822-4664
  • Office: Room 2319 Biological Sciences Bldg
  • Lab: 604-822-3480
  • Lab: Room 2322 & 2312 Biological Sciences Bldg

Research Interests

1) The control of microtubule dynamics by microtubule-associated proteins.
2) Microtubule polymer activities and the spatial organization of cortical microtubule arrays.
3) The function of cortical microtubule arrays in the mechanical properties of cellulosic cell walls.

Team Memebers

Laryssa Halat, PhD Candidate
Meng Li, PhD Candidate
Aida Rakei, PhD Candidate
Jayamini Jayawardhane, PhD Candidate
Sean Ritter, PhD Candidate
Breanne Bali, MSc Candidate
Donglei Li, MSc Candidate
Chak-Chung (Tommy) Kuo, undergraduate researcher

Selected Publications

For all past and current publications visit: https://wasteneyslab.wixsite.com/ubcwasteneys/publications

Marcus Woodley, Adam Mulvihill, Miki Fujita, Geoffrey Wasteneys (2018) Exploring microtubule-dependent cellulose-synthase-complex movement with high precision particle tracking. Plants 7, 53, doi:10.3390/plants7030053

Ruan Y, Halat L, Khan D, Jancowski S, Ambrose C, Belmonte M, Wasteneys GO. (2018) The microtubule-associated protein CLASP sustains cell proliferation through a brassinosteroid signalling negative feedback loop.Current Biology, 28, 2818-2829 DOI:https://doi.org/10.1016/j.cub.2018.06.048

Zhonshou Wu, Meng Li, Oliver Xiaoou Dong, Shitou Xia, Wanwan Liang, Yongkang Bao, Geoffrey Wasteneys, Xin Li (2018) Differential regulation of TNL-mediated immune signaling by redundant helper CNLs. New Phytologist 222, 938-953. Article DOI: 10.1111/nph.15665

Arun Sampathkumar, Alexis Peaucelle, Miki Fujita, Christoph Schuster, Staffan Persson, Geoffrey O. Wasteneys and Elliot M. Meyerowitz (2019). Primary wall cellulose synthase regulates shoot apical meristem mechanics and growth. Development 146 (10) pii: dev179036. doi: 10.1242/dev.179036.

Patrick Martone, Kyra Janot, Miki Fujita, Geoffrey Wasteneys, Katia Ruel, Jean-Paul Joseleau, Jose Estevez (2019) Cellulose-rich secondary walls in wave-swept red macroalgae fortify flexible tissues. Planta 250 (6): 1867-1879. doi: 10.1007/s00425-019-03269-1. Sep 3.

Wasteneys GO (2019) Plant Cell Biology: Shifting CORDs to Fine-Tune Phragmoplast Microtubule Turnover. Current Biology 29, R1235-1238, https://doi.org/10.1016/j.cub.2019.10.006.

Halat L, Gyte K, Wasteneys GO (2020) The Microtubule-Associated Protein CLASP is translationally regulated in light-dependent root apical meristem growth. Plant Physiol. 184, 2154-2167. https://doi.org/10.1104/pp.20.00474

Michelle Tseng

Assistant Professor

Contact Information

  • tsengm@mail.ubc.ca
  • Office Phone: 604-827-4077
  • Office: Room 110, Biodiversity Research Centre
  • Lab: BRC 280

My Links:
https://www.bugsandplankton.com/

Research Interests

Plankton & Freshwater Ecosystems

  • Nutrient availability in warming waters;
  • Microplastics, warming, and aquatic ecosystem heath;
  • Responses of phytoplankton to warming waters

Insect Communities

  • Effects of warming on insect populations and communities
  • Mosquito ecology & evolution;
  • Using urban green spaces for insect conservation and pest reduction
  • Citizen science & insect conservation
  • Plastic-eating insects 

Team Members

  • Alexandre Beauchemin – SURE student
  • Sophia Fan – MSc Student
  • Natasha Klasios  – PhD Student
  • Oliver McDermott – Work learn / Undergrad research assistant
  • Savi Raghuraman – Honours thesis student / Undergrad research assistant
  • Markus Thormeyer – PhD Student

Selected Publications

Google Scholar Profile: link
* denotes undergraduate coauthors, please email for pdf requests

  • Tseng, M and 27 coauthors*. 2022. Effects of temperature on monarch caterpillar colour variation in nature. Insect Conservation and Diversity.  (BIOL411 class project) journal link
  • Büyükyilmaz, E*. and M. Tseng. 2022. Developmental temperature predicts body size, flight, and pollen load in a widespread butterfly. Ecological Entomology. 47:872-882 (Undergraduate Honours Thesis)
  • Tseng, M., C. M. Di Filippo, M. Fung*, J.O. Kim*, I.P. Forster, and Y. Zhou*. 2021 Cascading effects of warming in a freshwater community. Functional Ecology. DOI: 10.1111/1365-2435.13752.
  • Bartlett, B., J. Fortin, M. B. Kantar, M. Tseng, and Z. Mehrabi. 2021. Digital technology helps remove gender bias in academia. Scientometrics. https://doi.org/10.1007/s11192-021-03911-4​.
  • El-Sabaawi, R., M.B. Kantar, T. Moore, J.H. Pantel, M. Tseng, J. Ware. 2020. The EEB POC Project. Limnology and Oceanography Bulletin 29(3) 97-99
  • Tseng, M., R. El-Sabaawi, M. B. Kantar, J. H. Pantel, D. S. Srivastava, and J. Ware. 2020. Strategies and support for Black, Indigenous, and people of colour in ecology and evolutionary biology. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-020-1252-0
  • ​Tseng, M., E. Yangel*, and A. Zhou*. 2019. Herbivory alters thermal responses of algae. Journal of Plankton Research. 41(5): 641-649
  • Tseng, M., J. Bernhardt, and A. Chila*. 2019. Species interactions mediate thermal evolution. Evolutionary Applications 
  • ​Tseng, M. and S. Soleimani Pari*. 2019. Body size explains interspecific variation in latitude-size relationships in geographically widespread beetle species.  Ecological Entomology. 44: 151-156. DOI: 10.1111/een.12684. *Biol448 paper, undergraduate co-author.
  • ​Tseng, M., K. M. Kaur*, S. Soleimani Pari*, K. Sarai, D. Chan, C.H. Yao, P. Porto, A. Toor, H.S. Toor, and K. Fograscher. 2018. Decreases in beetle body size linked to climate change and warming temperatures. Journal of Animal Ecology.  DOI: 10.1111/1365-2656.12789 *co-second author, (all co-authors were UBC undergrads). Press coverage of this paper:  Quirks and Quarks; Science; CBC; Phys.org
  • Tseng M., and M. I. O’Connor.  2015. Predators modify the evolutionary response of prey to temperature change. Biology Letters. 11: 20150798. (sup mat), Press: UBC news, Global BC

Jeannette Whitton

Associate Professor

Academic History

  • B. Sc. (1988), Environmental Biology, McGill 
  • Ph.D. (1994) University of Connecticut
  • Postdoctoral, Indiana (1994-1997).

Contact Information

  • jeannette.whitton@botany.ubc.ca
  • Office Phone: 604-822-8863
  • Office: office Room 221/Lab Room 363 Biodiversity Building (Mailing
  • Lab Phone: 604-822-8864

My Links

http://whittonlab.weebly.com

Research Interests

I am a plant evolutionary biologist with interests that span the areas of population genetics, phylogenetics and speciation. For me, questions surrounding the nature of plant species are boundlessly interesting – How do populations of a species, scattered across hundreds or thousands of kilometers, maintain their genetic and evolutionary integrity? How do factors such as changes in chromosome numbers and breeding system influence the ecological and genetic interactions of populations that differ in these traits? How does natural selection influence the divergence of populations and groups of populations when gene flow still occurs between diverging units? These are just a few of the questions that fuel my research interests.

Research in my lab takes a variety of approaches from comparative to experimental, from the level of populations, through the study of whole genera. I believe that taking a broad approach and using multiple study systems is both satisfying for my students and me, and allows for broader insights into the evolutionary process. Finding common threads and points of difference in the stories of diversification of multiple groups reminds us that understanding evolution involves both the search for generalities and an appreciation of individual stories.

Polyploidy and Apomixis in Crepis and Townsendia

My research group studies multiple systems in the sunflower family (Asteraceae). Each system possesses some shared and some unique characteristics that allow us to undertake complementary studies of specific processes. In particular, the family holds many examples of polyploid asexual (agamic) complexes, and numerous edaphic specialists that are a key focus of my research program.

Townsendia, a Rocky Mountain Agamic Complex

Townsendia is a Rocky Mountain genus of roughly 30 taxa in the Astereae. The 1957 monograph of the genus by John Beaman described the group’s diversity, characterizing ploidy and breeding system variation and laying the foundation for further studies. The genus is highly charismatic (cutest plants ever!), including a number of diminutive forms that are easily overlooked, along with some more conspicuous members. Two features of the complex are of special interest to our research. First, Townsendia includes at least 13 species with both diploid sexual and polyploidy asexual populations. Our research has focused on understanding the origins of asexual polyploids, so far focusing mostly on one species, Townsendia hookeri.

Former graduate student Stacey Thompson focused on, Townsendia hookeri. This species includes sexual diploid and asexual polyploid populations. This species ranges from the foothills of Colorado, northward to Jasper NP in Alberta. Disjunct northern populations also occur in the Yukon and Alaska. Sexual diploids are restricted to unglaciated regions of Colorado and adjacent Wyoming, or the Yukon. Only polyploid asexuals occupy previously glaciated regions. Stacey’s work showed that polyploids originated at least four times in this system, and also characterized ploidy levels and reproductive mode in a large number of populations, from Colorado to Yukon (Thompson and Whitton 2006). Stacey also characterized breeding patterns and patterns of diversity in Yukon populations, which include sexuality and apomixis (Thompson et al. 2008).

A key focus of ongoing research on T. hookeri will be to understand what governs this distribution. Are asexuals successful in previously glaciated areas because they are better colonizers (it only takes one seed to establish an asexual population), or do diploids and polyploids differ in ecological traits? Whatever we learn from T. hookeri serve as a point of comparison for other species in the genus. If we find that multiple sexual/ asexual groups are governed by the same factors, this will suggest that these factors are generally important.

Current graduate student Chris Lee is examining patterns of relationship in the genus as a whole. We are especially interested in using niche modeling approaches, together with phylogenetic hypotheses, to test ideas about patterns of speciation. We want to know what role ecological divergence has played in the diversification of species in this group, and also in governing the distribution of sexuals and asexuals, as noted above.

The North American Crepis Agamic Complex

The situation in this second agamic complex is probably even more complicated than that in Townsendia, for two reasons: First, the polyploids of Townsendia are triploid or tetraploid, while those in Crepis can go higher, perhaps to decaploids (with 10 sets of chromosomes). Second, many of the polyploids in Crepis look like hybrids, combining features of at least two diploids. The existence of so many hybrid types, propagated by asexual reproduction, has produced a bewildering array of morphological types in nature.

As with Townsendia, we are using previous studies to help inform our approach. E.B. Babcock and G. L. Stebbins first documented patterns of variation in this complex, in their 1938 monograph. While that work was often cited, this group of plants was largely untouched until the early 1990s. I studied the group as part of my Ph. D. thesis, despite being warned against it by G. L. Stebbins himself, in his response to a letter I wrote asking for suggestions (interestingly, one of the groups he thought would be more promising was Townsendia – it only took me 10 years to heed his advice). In most ways, his concerns were well founded. While I learned that the group was at least as challenging as Stebbins and Babcock had thought, the tools available at the time of my Ph. D. limited sampling depth, and did not provide any shortcuts to estimating ploidy. So that chapter of my thesis sat on a shelf, but did not gather dust. We have tried to ask some questions, for example in a 2008 paper examining the relationships and breeding patterns of two sets of populations (Whitton et al. 2008), but the big breakthroughs in our understanding are coming through the work of Ph. D. student Chris Sears. Chris has been able to sample many populations (more than 80) and characterize ploidy using flow cytometry, a technique that estimates DNA content of cells. This means that we can now examine complex relationships while knowing the ploidy of each individual under study. For a group in which ploidy variation is well known, this is an essential step in understanding the role that ploidy and breeding system shifts have played in these groups. Chris nearing the completion of his thesis, and will have more to say about this fascinating system soon.

Broader Context of Apomixis Research
Fewer than 1% of plant species are apomictic, but nonetheless, what we learn studying these systems has potential relevance for the other 99% of species. One interesting observation is that Crepis populations very often include more than one species. For the cases that we understand well, it seem that these species can coexist in part because they are asexual – they do not appear to share gene flow, and thus distinct types can be maintained in one place. This suggests that it is interference through breeding, and not ecological interactions (such as competition) that limit coexistence.

In addition, while apomixis is relatively uncommon, polyploidy is a pervasive feature of flowering plants. Studying asexual polyploids can provide broader insights into the role of multiple polyploid origins on patterns of diversification.

Evolution and Ecology of Invasive Plants

In addition to working on these systems, I am part of a research collaboration led by Loren Rieseberg, with Keith Adams and Sally Otto that aims to look for the genetic traits that may enhance a species’ ability to become invasive. This project involves comparisons of invasive and native populations of 5 species in the sunflower family.

M. Sc. Student Jamie Leathem is studying plant invasion in Yukon. While more southern regions have a relatively long history of plant invasions, the spread of invasive in Yukon is more recent. Jamie is documenting this phenomenon and looking for traits that correlate with high local densities. Identification of such traits may aid in predicting invasions and managing or mitigating the spread of invasives.

Team Members

Graduate Students
Chris Sears, Ph. D. Candidate
Chris Lee, Ph. D. Candidate
Jamie Leathem, M. Sc. Student (co-supervised with Mark Vellend)

Undergraduates (Summer 2010)
Ryan Godfrey
Kate McGrath

Selected Publications

A. Ø. Mooers, D.F. Doak, C.S. Findlay, D.M. Green, C. Grouios, L.L. Manne, A. Rashvand, M.A. Rudd, and J. Whitton. 2010. Science, policy and species at risk in Canada. Bioscience (in press)

Leander, C.A. and J. Whitton. 2010. Bling my research! A mock grant panel activity illustrating the importance of basic research. American Biology Teacher 72(5): 308-310.

Whitton J, K.M. Dlugosch and C.J. Sears. 2008. Molecular and morphological evidence for and against gene flow in sympatric apomicts of the North American Crepis agamic complex (Asteraceae). Botany 86(8): 877-885. (Invited contribution to the special issue: Plant systematics at the species level)

Whitton, J. C. J. Sears, E. J. Baack, and S. P. Otto. 2008. The dynamic nature of apomixis in the angiosperms. International Journal of Plant Sciences 169: 169-182. (Invited contribution to the special issue: Major Evolutionary Transitions in Flowering Plant Reproduction)

Thompson, S. L., G. Choe, K. Ritland and J. Whitton. 2008. Cryptic sex within male sterile polyploid populations of the Easter daisy, Townsendia hookeri. International Journal of Plant Sciences 169: 183-193. (Invited contribution to the special issue: Major Evolutionary Transitions in Flowering Plant Reproduction)

Saarela, J. M., L. Lipsen, C. M. Sayre, and J. Whitton. 2007. Vascular plant type specimens in the University of British Columbia Herbarium (UBC). Journal of the Botanical Research Institute of Texas. 1: 437-448.

Thompson, S. L., and J. Whitton. 2006. Patterns of recurrent evolution and geographic parthenogenesis within apomictic Easter daisies (Townsendia hookeri). Molecular Ecology 15:3389-3400.

Ryall, K., J. Whitton, W. Schofield, S. Ellis and A. J. Shaw. 2005. Molecular phylogenetic study of interspecific variation in the moss Isothecium (Brachytheciaceae). Systematic Botany 30(2): 242-247.

Rajakaruna, N. M. Y. Siddiqi, J. Whitton, B. A. Bohm and A. D. M. Glass. Differential response to Na+/K+ and Ca2+/ Mg2+ in two edaphic races of the Lasthenia californica (Asteraceae) complex: A case for parallel evolution of physiological traits. New Phytologist 157: 93-103..

Rundle, H. D., F. Breden, C. Griswold, A. Ø. Mooers, R. A. Vos and J. Whitton. 2001. Hybridization without guilt: gene flow and the biological species concept. J. Evol. Biol. 14(6): 868-869.

Otto, S. P. and J. Whitton. 2000. Incidence and patterns of polyploidy. Invited review. Annual Review of Genetics 34: 401-437.

Rieseberg, L. H., J. Whitton, and K. Gardner. 1999. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152: 713-727.

Whitton, J., D. E. Wolf, D. M. Arias, A. A. Snow, and L. H. Rieseberg. 1997. The persistence of cultivar alleles in wild populations of sunflowers five generations after hybridization. Theoretical and Applied Genetics 95: 33-40.

Yuelin Zhang

Professor

Academic History

  • Full Professor (Departments of Botany, UBC)
  • B.Sc. Genetics (1989), Fudan Univ.;
  • Ph.D. Biochemistry and Molecular Biology (1995), Oklahoma State Univ.;
  • Postdoctoral Fellow (1995-98) University of North Carolina, Chapel Hill;                  
  • Postdoctoral Fellow (1998-99) Duke University;                       
  • Assistant and Associate Investigator (2005-2011), NIBS, Beijing

Contact Information

  • yuelin.zhang@ubc.ca
  • Office Phone: 604-827-3794
  • Office: Room 2207 Biological Sciences Building
  • Lab Phone: 604-827-0076
  • Lab: Room 2214 Biological Sciences Building

Research Interests

Sensing and defending against microbial infections is essential to the survival of multicellular organisms. Recognition of PAMPs (pathogen-associated molecular patterns) or effector proteins from pathogens by plant immune receptors leads to activation of downstream signaling cascades and plant resistance to pathogens at the infection site. Activation of local defense further induces a secondary immune response in the distal parts of plants termed systemic acquired resistance (SAR). Our research is focused on the following two areas.

1. Signal Transduction Pathways downstream of Plant Immune Receptors
In plants, there are three main classes of immune receptors. The largest class encodes intracellular NB-LRR type Resistance (R) proteins. The other two classes belong to the transmembrane receptor-like kinase (RLK) and receptor-like protein (RLP) families. We have obtained a series of mutants such as snc2-1D, snc4-1D, bir1-1, and mkk1 mkk2 that constitutively activate immunity mediated by these three classes of immune receptors. To identify components downstream of the receptors, suppressor screens have been performed in these mutant backgrounds. Cloning the suppressor genes and analyzing biochemical functions of proteins encoded by them will help us build the signal transduction network of plant immunity.

2. Systemic Acquired Resistance
Genetic analysis of SAR has been hampered by lack of good assays for studying SAR in Arabidopsis. We developed an SAR assay in which we inoculated the local leaves with the bacterial pathogen P.s.m. ES4326 and assayed the distal leaves for induced resistance against the virulent oomycete pathogen H. a. Noco2. This new assay is sensitive and reproducible and it can be used to screen a large number of plants. Using this high-throughput assay, we have carried out both forward and reverse genetic screens to look for mutants with defects in SAR. Identification and characterization of genes required for SAR will help us better understand the underlining mechanisms of SAR.

Selected Publications

Tian, H., Chen, S., Wu, Z., Ao, K., Yaghmaiean, H., Sun, T., Huang, W., Xu, F., Zhang, Y., Wang, S., Li, X.**, and Zhang, Y.** (2021). Activation of TIR signaling boosts pattern-triggered immunity. Nature, https://doi.org/10.1038/s41586-021-03987-1.

Peng, Y., Yang, J., Li, X. and Zhang, Y. (2021) Salicylic acid: Biosynthesis and Signaling. Annual Review in Plant Biology, 72:761-791.

Mohnike, L., Rekhter, D., Huang, W., Feussner, K., Tian, H., Herrfurth, C., Zhang, Y.*(* Co-corresponding author) and Feussner, I*. (2021) The glycosyltransferase UGT76B1 modulates N-hydroxy-pipecolic acid homeostasis and plant Immunity. Plant Cell, 33(3), 735-749.

Liu, Y., Sun, T., Sun, Y., Zhang, Y., Radojičić, A., Ding, Y., Tian, H., Huang, X., Lan, J., Chen, S. and Orduna, A.R., Zhang, K., Jetter, R., Li, X. and Zhang, Y. (2020) Diverse Roles of the Salicylic Acid Receptors NPR1 and NPR3/NPR4 in Plant Immunity. Plant Cell, 32(12), 4002-4016.

Sun, T. and Zhang, Y.(2020) Short and long-distance signaling in plant defense. Plant Journal, https://doi.org/10.1111/tpj.15068.

Liu, Y., Zhong, X., Zhang, Z., Lan, J., Huang, X., Tian, H., Li, X. and Zhang, Y. * (2020) Receptor-like kinases MDS1 and MDS2 promote SUMM2-mediated immunity. Journal of Integrative Plant Biology, 63 (2):277-282.

Zhou, J.* and Zhang, Y.* (* Co-corresponding author) (2020) Plant immunity: danger perception and signaling. Cell, 181(5): 978-989.

Nitta, Y., Qiu, Y., Yaghmaiean, H., Zhang, Q., Huang, J., Adams, K. and Zhang, Y. (2020) MEKK2 inhibits activation of MAP kinases in Arabidopsis. Plant Journal, 103(2):705-714.

Huang, W., Wang, Y., Li, X. and Zhang, Y. (2020) Biosynthesis and regulation of salicylic acid and N-hydroxypipecolic acid in plant immunity. Molecular Plant, 13 (1): 31-41.

Sun, T., Huang, J., Xu, Y., Verma, V., Jing, B., Sun, Y., Ordunac, A., Tian, H., Huang, X., Xia, S., Schaferc, L., Jetter, R., Zhang, Y.* (* Co-corresponding author) and Li, X.* (2019) Redundant CAMTA transcription factors negatively regulate the biosynthesis of salicylic acid and N-hydroxypipecolic acid by modulating the expression of SARD1 and CBP60g. Molecular Plant, 13: 144-156.

Rekhter, D., Lüdke, D., Ding, Y., Feussner, K., Zienkiewicz, K., Lipka, V., Wiermer, M.*, Zhang, Y.* (* Co-corresponding author) and Feussner, I*. (2019) Isochorismate-derived biosynthesis of the plant stress hormone salicylic acid. Science, 365, 498-502.

Zhang, Y. and Li, X. (2019) Salicylic acid: Biosynthesis, perception and contributions to plant immunity. Current Opinion in Plant Biology, 50:1-8.

Lian, K., Gao, F., Sun, T., Wersch, R., Ao, K., Kong, Q., Nitta, Y., Wu, W., Krysan, P., and Zhang, Y. 2018. Arabidopsis MKK6 functions in two parallel MAP kinase cascades in immune signaling. Plant Physiology, 178, 1284-1295.

Ding, Y., Sun, T., Ao, K., Peng, Y., Zhang, Y., Li, X. and Zhang, Y. 2018. Opposite roles of salicylic acid receptors NPR1 and NPR3/NPR4 in transcriptional regulation of plant immunity. Cell, 173, 1454–1467.

Sun, T., Nitta, Y., Zhang, Q., Wu, D., Tian, H., Lee, J.S. and Zhang, Y. 2018. Antagonistic interactions between two MAP kinase cascades in plant development and immune signaling. EMBO Reports, e45324.

Sun, T., Busta, L., Zhang, Q., Ding, P., Jetter, R. and Zhang, Y.  2018. TGACG-BINDING FACTOR 1 (TGA1) and TGA4 regulate salicylic acid and pipecolic acid biosynthesis by modulating the expression of SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1) and CALMODULIN-BINDING PROTEIN 60g (CBP60g). New Phytologist, 217: 344–354. doi:10.1111/nph.14780.

Ma C., Liu Y., Bai B., Han Z, Tang J., Zhang H., Yaghmaiean H., Zhang Y. (Co-corresponding author) and Chai J. 2017. Structural basis for BIR1-mediated negative regulation of plant immunity. Cell Research, 27, 1521–1524.

Ding, P., Rekhter, D., Ding, Y., Feussner, K., Busta, L., Haroth, S., Xu, S., Li, X., Jetter, R., Feussner, I. and Zhang, Y. 2016. Characterization of a pipecolic pcid biosynthesis pathway required for systemic acquired resistance. Plant Cell, 28: 2603–2615.

Zhang Z., Liu Y., Huang H., Gao M., Wu D., Kong Q. and Zhang Y. 2016. Sensing the disruption of a MAP kinase cascade by an NLR protein through a MAP kinase substrate. EMBO Reports, pii: e201642704.

Liu, Y., Huang, X., Li, M., He, P. and Zhang, Y. 2016. Loss-of-function of Arabidopsis receptor-like kinase BIR1 activates cell death and defense responses mediated by BAK1 and SOBIR1. New Phytologist, doi: 10.1111/nph.14072. [Epub ahead of print].

Kong, Q., Sun, T., Qu, N., Ma, J., Li, M., Cheng, Y.-t., Zhang, Q., Wu, D., Zhang, Z. and Zhang, Y. 2016. Two redundant receptor-like cytoplasmic kinases function downstream of pattern recognition receptors to regulate activation of SA biosynthesis in Arabidopsis. Plant Physiology, 171(2): 1344-1354.

Liang, X., Ding, P., Lian, K., Wang, J., Ma, M., Li, L., Li, L., Li, M., Zhang, X., Chen, S., Zhang, Y. (Co-corresponding author) and Zhou, J. 2016. Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor. eLife 5, e13568.

Sun T., Zhang Y., Li Y., Zhang Q., Ding Y. and Zhang, Y. 2015. ChIP-seq analysis reveals broad roles of SARD1 and CBP60g in regulating plant immunity. Nature Communications, 6:10159.

Li, X., Kapos, P. and Zhang, Y. (2015). NLRs in plants. Current Opinion in Immunology, 32, 114-121.

Sun, T., Zhang, Q., Gao, M. and Zhang, Y. 2014. Regulation of SOBIR1 accumulation and activation of defense responses in bir1-1 by specific components of ER quality control. Plant Journal, 77(5):748-56.

Zhang, Z., Liu, Y., Ding, P., Li, Y., Kong, Q. and Zhang, Y.2014. Splicing of Receptor-like kinase-encoding SNC4 and CERK1 is regulated by two conserved splicing factors that are required for plant immunity. Molecular Plant, 7(12):1766-75.

Liu, J., Ding, P., Sun, T., Nitta, Y., Dong, O., Huang, X., Yang, W., Li, X., Botella, J. and Zhang, Y. 2013. Heterotrimeric G proteins serve as a converging point in plant defense signaling activated by multiple receptor-like kinases. Plant Physiology, 161(4), 2146-2158.

Zhang Z., Wu Y., Gao M., Zhang J., Kong Q., Liu Y., Ba H., Zhou J.M. and Zhang Y.  2012. Disruption of a PAMP-induced MAP Kinase Cascade Activates Plant Immunity Mediated by an NB-LRR Protein. Cell Host & Microbe,11(3):253-63.

Kong, Q., Qu, N., Gao, M., Zhang, Z., Ding, X., Yang, F., Li, Y., Dong, X., Chen, S., Li, X., and Zhang, Y. 2012. The MEKK1-MKK1/MKK2-MPK4 kinase cascade negatively regulates immunity mediated by a MAP kinase kinase kinase. Plant Cell, 24(5):2225-36.

Yang, Y., Zhang, Y., Ding, P., Johnson, K., Li, X., and Zhang Y. 2012. The ankyrin-repeat transmembrane protein BDA1 functions downstream of the receptor-like protein SNC2 to regulate plant immunity. Plant Physiology, 159(4):1857-65.

Xu, S., Zhang, Z., Jing, B., Gannon, P., Ding, J., Xu, F., Li, X. and Zhang, Y. 2011. Transportin-SR is required for proper splicing of resistance genes and plant immunity.  PLoS Genetics, 7(6): e1002159.

Jing, B., Xu, S., Xu, M., Li, Y., Li, S., Ding, J. and Zhang, Y. 2011. Brush and Spray: A high throughput systemic acquired resistance assay suitable for large-scale genetic screening. Plant Physiology, 157(3):973-80.

Germain, H., Qu, N., Cheng, Y.T., Lee, E.K., Huang, H., Dong, O.X., Gannon, P., Huang, S., Ding, P., Li, Y., Sack, F. and Zhang, Y. (co-corresponding), and Li X. 2010. MOS11: a new component in the mRNA export pathway. PLoS Genetics, 6(12): e1001250.

Zhang, Y., Xu, S., Ding, P., Wang, D., Cheng, Y., He, J., Gao, M., Xu, F., Li, Y., Zhu, Z., Li, X., and Zhang, Y. 2010. Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors. PNAS (track II).107(42):18220-18225.

Li, Y., Li, S., Bi, D., Cheng, Y., Li, X. and Zhang, Y. 2010. SRFR1 negatively regulates plant NB-LRR Resistance protein accumulation to prevent autoimmunity. PLoS Pathogens, 6 (9), e1001111.

Zhang, Y., Yang, Y., Fang, B., Gannon, P., Ding, P., Li, X., and Zhang, Y. 2010. snc2-1D activates receptor like protein-mediated immunity transduced through WRKY70. Plant Cell, 22(9):3153-3163.

Zhu, Z., Xu, F., Zhang, Y., Cheng, Y., Wiermer, M., Li, X., and Zhang, Y. 2010. Arabidopsis Resistance protein SNC1 activates immune responses through association with a transcriptional co-repressor. PNAS (track II). 107(31):13960-13965.

Bi, D., Cheng, Y., Li, X., and Zhang, Y. 2010. Activation of plant immune responses by a gain-of-function mutation in an atypical receptor-like kinase. Plant Physiology, 153(4):1771-1779.

Li, Y., Tessaro, M., Li, X., and Zhang, Y. 2010. Regulation of the expression of plant Resistance gene SNC1 by a Protein with a Conserved BAT2 Domain. Plant Physiology, 153(3):1425-1434.

Gao, M., Wang, X., Wang, D., Xu, F., Ding, X., Zhang, Z., Bi, D., Cheng, Y.T., Chen, S., Li, X., and Zhang, Y. 2009. Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis. Cell Host & Microbe 6:34-44.

Gao, M., Liu, J., Bi, D., Zhang, Z., Cheng, F., Chen, S., and Zhang, Y. 2008. MEKK1, MKK1/MKK2 and MPK4 function together in a mitogen-activated protein kinase cascade to regulate innate immunity in plants. Cell Research 18:1190-1198. (Cover story)

Uncertainty in the research process is a source of excitement for Yujun Peng, Dewar Cooper Fellowship recipient

Yujun Peng, a member of Dr. Yuelin Zhang’s lab group, was recently awarded the Dewar Cooper doctoral fellowship for her work on the salicylic acid hormone signaling pathway. Her lab group focuses on how plant immune responses are regulated against the pathogen invasion, and early studies show that salicylic acid plays an essential role in plant immunity. 

“Recent research has uncovered the receptor of salicylic acid in plants,” said Peng, “But there are still a lot of mysteries about this pathway. We don’t know how the signal is transduced downstream and we don’t know how salicylic acid regulates its receptors.”

Peng expressed her appreciation for receiving the Dewar Cooper fellowship and the funding that came along with it. As much as she enjoyed being a TA, the fellowship’s guaranteed funding meant that she could focus on her research.

Below, Peng talks about her journey as a scientist – from her early interest in biology to her current challenges, passions and aspirations.

How did you end up working on plant immunity? 

I did my undergrad and Master’s degree in China, but not in the area of plant immunity. I was focusing on plant development, on a hormone called brassinosteroid. At that time I visited the countryside and learned that fruit trees in the area were being destroyed by pesticide-resistant insects. The experience got me thinking that I could switch my future research to plant immunity. 

What key experiences drew you to botany? 

My undergraduate university provided us with a lot of opportunities to have a close look at what scientists do; we had a lot of chances to get into the lab. We also had anatomy and physiology courses where you’re really touching animals and learning the structural components of life, from the simplest to most complex. When I was in my second year, we went to and stayed at a nature reserve, which provided us with a clear look at what nature is, how the ecosystem of the reserve works and opportunities to learn about the various species in that location. 

Those experiences convinced me to stick with biology. I wanted to work in a lab, so I rotated in three research settings. First, I worked in a group studying protein structures. Second, because my parents wanted me to do something related to the medical field, where they thought it would be easier for me to find a job, I visited a group based in a hospital studying the dengue virus. Then I worked in a lab in the cancer research center of our university studying nasopharyngeal carcinoma. I learned that the environment wasn’t the right fit for me.

I think it is very important for new students to know not just think about what it might be like to be in a lab; instead, you should go to the lab and talk to the people there. Due to my experiences, I was able to identify what was most important to me. What I wanted was an environment where people can discuss their research, learn a lot of things from other people and expand their own views. 

Later, I took a course about plant physiology and this raised my interest in plant research, and I applied to work in a plant physiology lab. There, the lab’s PI was a great fit for me, and I stayed in this lab as I started my Master’s degree. 

When I was choosing my PhD program, I had the same mindset of searching for a program that matched my interest. I was really impressed with the first conversation I had with my current adviser, and this is why I chose to come to UBC Botany.

I feel like a lot of parents, when they’re giving advice to their kids, they care a lot about whether their kids’ career paths are stable and how much they can earn. But I’ve learned that it’s also really important to consider choosing something you’re interested in doing. If I choose something I’m not interested in, I won’t be very happy in the future.

Tell us about your favorite part of being a scientist.

My favorite part of science is also what I fear the most – and that is uncertainty! You may have expectations/hopes for your project, but it’s kind of a dilemma if everything happens according to what you expected. You might be as excited by the result. And if you have this expectation it means other people may think in the same way, too. Yet if you get a result that is beyond your expectations – something kind of uncertain – then you may have discovered something new! 

It can be painful to work with uncertainty. Unexpected or uncertain results mean you need to do more work to verify what you found, and there’s a high risk that you won’t be able to figure out the answer to the question you started out with. This matters a lot for PhD students, because if you can’t wrap up a project in a specific timeframe, you probably won’t be able to compile a good publication from the results, which has consequences for being hired after graduation.

I’ve had to learn that having an inconclusive result doesn’t mean that one isn’t “good enough.” There could be issues outside of one’s own control, such as with the technique or the time limits of a PhD. When choosing a new project, I try to choose something that includes the chance for exciting novelty, without being so uncertain that I won’t get any results.

Have you encountered any big challenges during your degree?

Definitely. The biggest challenge during my PhD was when I started a genetic screen looking for mutants. At first I thought I’d obtained a lot of potential mutants, but later I discovered that most of these (more than 90 per cent of them!) were contaminants. I panicked and blamed myself, thinking that I should have been more careful. I talked to my supervisor about it, and what he told me has stuck with me. He said mistakes happen, and the most important thing is that I gained a huge amount of important training by working on this forward genetic screen.

What do you like to do for fun?

I like hiking, traveling and cooking. Canada is a great place to hike! The most amazing thing is being able to birdwatch while hiking. 

Congratulations to Yujun! Check out her publications here.  

Elizabeth Mahon, Jonathan Page Fellowship awardee, finds satisfaction in scientific problem-solving

​

Elizabeth Mahon, PhD student in the lab group of Dr. Shawn Mansfield, was awarded the Jonathan Page Fellowship for her research on the biochemistry of the wood of poplar trees. The goal of her project is to engineer poplar trees for use as feedstock for renewable bioproducts like biofuels, pulp and paper.

The Jonathan Page Fellowship has allowed Mahon to enjoy doing research, including the process of problem-solving.

“Troubleshooting protocols and trying to figure out what’s working and what’s not working can lead to a lot of failure. When it does work it’s just the most satisfying and exciting feeling in the world,” said Mahon. “The fellowship is allowing me to complete the last year of my research and finish my thesis without feeling like I’m under pressure.”

Below is our conversation with Elizabeth Mahon where she discusses the details of her work, her rewarding experiences working with tricky protocols, and her thoughts on the mental burdens of graduate school.

What is the key question of your research?

Mainly, I’m interested in how we can modify the metabolism of phenolic compounds in the developing xylem of poplar trees to improve poplar as a feedstock for bioproducts like biofuels, pulp and paper.

The wood of trees is made of biopolymers, such as lignin and cellulose. I work on lignin, which is the biopolymer that makes wood strong and allows trees to stand up. I am introducing new chemicals that are normally found in grass lignin into the poplar trees using genetic engineering. This could make the lignin more easily extracted from trees for use in bioproducts. As a team, we work on trying to understand how the cell wall is assembled naturally in a growing tree, as well as how we can modify the component parts to improve the biomass’s characteristics for certain uses.

How did you end up working on poplar trees in Dr. Mansfield’s lab?

When I first started as an undergrad, I decided to just take a bunch of different general science classes to see what I was interested in. I really enjoyed genetics problem sets like the ones involving Punnett squares. Maybe I already had inclinations towards problem-solving at that point, but I think as an undergrad I was employing such a different set of skills that it wasn’t until I started doing directed studies in my third and fourth year that I got a taste for the hands-on problem-solving part of research.

I decided to do my Master’s work in the same lab where I completed my directed studies.I did my Master’s degree on pine trees; I was working at the University of Alberta within the field of forestry using genetics to better understand the defense response to mountain pine beetles. Moving into my PhD, I knew that I wanted to stay within the realm of forestry, and I really wanted to be able to work with a species that I could genetically manipulate. Poplar is a really unique tree species in that it is very amenable to genetic transformation. Poplar is also a very productive tree and grows very well in Canada.

Additionally, after my Master’s, I became more interested in population genetics and I knew I wanted to come to UBC Botany – it’s one of the biggest plant science programs in Canada! All those factors initially drew me to work with Dr. Carl Douglas, who at the time was utilizing  bioinformatics techniques to examine almost 400 different unique popular genotypes to find particular loci that contribute to wood characteristics. He unfortunately passed away the summer before I came to UBC. I really wanted to continue on with the poplar project he had started. I contacted Dr. Sean Mansfield, who specializes in genetic manipulation in the context of forestry, and he agreed to take me on as a student with the research focus I’d already chosen.

You’ve described that poplar species are attractive as model organisms for multiple reasons. Does this mean that it has been easy to work with poplar species in the lab?

In the Mansfield lab, I got lucky in that there is a really well-established protocol for genetically transforming poplar to introduce novel genes. Where things got complicated was when I started doing biochemical characterization of enzymes, which hadn’t been done in our lab frequently. To trouble-shoot the experimental protocol, I couldn’t find anything from online databases that could work with the equipment we had in the lab. Finally, I found a protocol in an actual physical book published thirty years ago which was very satisfying! Even though it took three months of work, it felt really rewarding when everything came together in the end.

Describe a key value of yours that you’ve identified from your time as a student.

One thing I’ve learned throughout my degree, which a lot of people are echoing right now, is the importance of mental health. When you’re doing your PhD, you can get so wrapped up and so focused on that one thing. Completing a graduate degree is a very challenging thing to do; it challenges you intellectually but also challenges your mental wellbeing.

Making sure that mental health is a priority is something that I take really seriously. It’s very important to me as an older student in my lab to encourage conversations around wellbeing with newer graduate students. I also extend this perspective to the undergraduates in my lab. It’s really fun to see new undergrads come into the lab and get the chance to actually apply their knowledge beyond studying for tests. Once they get their feet under them, I try to help them enjoy their experience while also learning a lot along the way.

​What has been challenging in your scientific journey?

My feeling and the feeling of a lot of students who are close to graduation is that there is simply not a lot of certainty about staying in academic careers. About 25% of the students who graduate from UBC Botany get tenure-track academic jobs. Throughout your degree you can feel as if you’re on a singular track to a position in academia, and when you get to the end you begin to realize that that career path is not as clear as it used to be historically, or as clear as what you thought initially. There can be pressure and negativity as well as reward and positivity in facing the fact that while most of your mental energy is being occupied by getting your research done and writing it up, you do have to have to consider what you’re going to do afterwards.

The mentors I’ve had at UBC Botany have been very encouraging of me exploring different career paths. I work a lot with Dr. Lacey Samuels and her lab; I appreciate that she encourages students to go down whichever path is best for them. I’ve been able to see what other students who’ve recently graduated have gone on to do, which has helped me realize that I don’t have to stay within academia. Many students have gone on to have really fascinating jobs and that relieves a lot of the pressure.

When you’re not focused on research, what do you like doing?

My partner and I both really like to swim. I was on the UBC Masters swim team for a while, but they’re not practicing regularly because of COVID. I recently started open water swimming with my partner at Kitsilano Beach in the summertime, and we both enjoy heading to the pool during the winter. ​

Quentin Cronk

Professor

My Links:

Contact Information

  • quentin.cronk@ubc.ca
  • 604-781-6740
  • Office: Rm 222, Biodiversity Research Centre
  • Lab: Rm 255, Biodiversity Research Centre

Research Interest

Our lab integrates comparative genomics, molecular developmental biology and evolutionary biology to study plant form. We are interested in the how different morphologies evolve in plants, as well as the functional significance of morphological differences between species.

Our model organisms for this include the Leguminosae (floral morphology) and black cottonwood, Populus trichocarpa (adaptive evolution of trees). Next generation sequencing of whole genomes and transcriptomes is an important part of our work.

Funding for research in our lab comes from the Discovery Grants programme of the Natural Sciences and Engineering Research Council of Canada (NSERC) and Genome Canada.

Team Members

Graduate students (PhD)

Mannfred Boehm – Hummingbird pollination
Mikko Paajanen – Asteraceae of St Helena
Yutong Zhang – Floral evolution
Seni Senjaya – Phylogeny and biology of tropical ginger genus, Alpinia

Postdoctoral Researchers

Biao Xiong – Genomics of Lauraceae

Associated researchers

Dr Diana Percy – plant insect interactions

Former Graduate students (PhD)

Julia Nowak – polarity and evolution of leaves
Xinxin Xue – molecular basis of evolutionary shifts in flower colour
Sæmundur Sveinsson – evolutionary studies in Lathyrus

Former Postdoctoral Researchers

Armando Geraldes – population genomics of black cottonwood trees (Populus trichocarpa)
Charles Hefer – bioinformatics and genomics, POPCAN project (Douglas lab)
Daisie Huang – evolutionary genomics of Salicaceae, POPCAN project
Ji Yong Yang – evolutionary population studies

Brett Couch

Associate Professor of Teaching

Academic History

B.Sc., M.Sc. and Ph.D. in Botany from the University of Toronto

Contact Information

  • brett.couch@botany.ubc.ca
  • 604-822-9650

Teaching Interests

Approach to Teaching: As an instructor in the departments of Botany and Zoology at the University of British Columbia, I am part of the large teams that teach introductory biology lectures and labs.  As well, I am responsible for second year Botany and eukaryotic microbiology labs. I have been involved in curriculum development, designing the lab for eukaryotic microbiology and writing the lab manual as well as development of activities and case studies as part of the flexible learning initiative in BIOL121.  I have published case studies through Pearson to support their texts and through the National Center for Case Study Teaching in Science.  I am currently collaborating on a project to use fine art to teach observational skills in organismal biology labs. 

Maryam Moussavi

Lecturer

Academic History

BSc (biology), MSc and PhD in Medicine from University of British Columbia

Contact Information

  • moussavi@zoology.ubc.ca
  • 604-827-3862
  • Biosciences- East Wing RM 1018

Teaching Interests

As an instructor in biology I aim to engage, intrigue, and help my students critically observe life around us. I strive to create an inclusive environment, where students feel comfortable to think out loud, engage in problem solving, and be actively involved in the process of their own learning. My hope is that my students leave my class armed with a set of tools that will help them to better evaluate biological data and to communicate their findings through logical scientific arguments. To meet these goals, I take a scholarly approach to my teaching and also utilize my own experiences (both as an educator and as a student).

The core principles that guide my teaching are: positive classroom climate, learning through active engagement, encouraging scientific communication, and maintaining a reflective practice.

Courses Taught/Teaching

  • BIOL 112- Biology of the cell 
  • BIOL 121- Genetics, Evolution and Ecology 
  • BIOL 140- Laboratory Investigations in Life Science
  • BIOL 204- Vertebrate Structure and Function
  • BIOL 200- Fundamentals of Cell Biology
  • BIOL 340- Introductory Cell Biology Laboratory
  • BIOL 341- Introductory Molecular Biology Laboratory
  • BIOL 342- Integrative Biology Laboratory

Selected Publications

Moussavi M, Tearle H, Fazli L, Bell JC, Jia W, Rennie PS. Targeting and killing of metastatic cells in the transgenic adenocarcinoma of mouse prostate model with vesicular stomatitis virus. Molecular Therapy. 2013 Apr;21(4):842-8.

Moussavi M, Moshkabadi N, Jia W, Rennie PS. Using 5’UTR derived from fibroblast growth factor and ornithine decarboxylase for targeting eIF4E in prostate cancer cells and PTEN-/- mice. Cancer Gene Therapy. 2012 Jan;19(1):19-29.

Moussavi M, Fazli L, Tearle H, Guo Y, Cox M, Bell J, Ong C, Jia W, Rennie PS. Oncolysis of Prostate Cancers Induced by Vesicular Stomatitis Virus in PTEN knockout mice. Cancer Research. 2010 Feb 15;70(4):1367-76.

Celeste Leander

Professor of Teaching

Academic History

  • Humboldt State University, BC- Zoology
  • Humboldt State University, MSc- Immunology
  • University of Georgia, PhD- Botany
  • Currently serving as Academic Director for First Year Experience

Contact Information

  • cleander@mail.ubc.ca
  • 604-827-5608

My Links

https://blogs.ubc.ca/celesteleander/

Teaching Interests

My teaching interests include First Year Transition, Collaborative Learning, and Interdisciplinary Learning. Although I am not currently teaching first year courses, I spend the bulk of the year advising, designing, and delivering training for UBC orientation programming (Jump Start and Imagine Day). Doing so provides a great opportunity to work closely with academics from other faculties where I constantly learn new approaches that I bring into my classrooms. I am also embedded in UBC Collegia as a Faculty Fellow where I experience first year students outside of the classroom and outside of Science. Doing so provides rich opportunity to gauge the first year experience on this campus. I am interested in collaborative learning processes, including complete and total examinations (as opposed to two-stage examinations.)

Courses Taught/Teaching

  • Biol 121
  • Science One
  • Biol 345
  • Biol 342

Jaclyn Dee

Lecturer

Contact Information:

deej@mail.ubc.ca

Caitlin Donnelly

Lecturer

Academic History

  • BSc in Microbiology from UBC Okanagan
  • PhD in Botany from UBC Vancouver

Contact Information

caitlin.donnelly@ubc.ca

Teaching Interests

As a Lecturer who primarily teaches first- and second-year students, one of my main goals is to inspire students to become interested in learning more about biology and its relevance to their lives.  By sparking their interest, and introducing them to a scientific way of thinking, I hope that they will start to consider the world around them in a different way, start asking questions, and gain a greater appreciation for the complexity and diversity of life.

I aim to equip my students with skills that will be useful to them, whether in their day-to-day lives, or in future scientific careers: these include collaboration, problem-solving, and scientific literacy and writing.  I believe that these skills must be as much a part of coursework as the understanding of scientific concepts and facts.  I encourage students to develop these skills through active participation in assignments, discussions, and activities that model real-world scenarios and issues that they might encounter.

Courses Taught/Teaching

  • BIOL 111 (Introduction to Modern Biology)
  • SCIE 113 (First-Year Seminar in Science), through Vantage One Science
  • I am also the course coordinator for SCIE 113 (First-Year Seminar in Science), and collaborate with many instructors and TAs from different departments in the Faculty of Science to deliver the course.

Shona Ellis

Professor of Teaching

Academic History

  • Professor of Teaching (2012), University of British Columbia
  • Senior Instructor (2007 – 2012), University of British Columbia
  • M.Sc. Plant Natural Products Chemistry (1993), University of British Columbia
  • B.Sc. Botany (1985), University of British Columbia

Contact Information

  • shona@mail.ubc.ca
  • 604-822-9728
  • Office: Room 2521 – 6270 University Blvd

My Links

Courses Taught/Teaching

  • BIOL 324 – Seed Plant Taxonomy: Course Coordinator and Lab Instructor
  • BIOL 210 – Introduction to Vascular Plants: Course Coordinator, Lecturer, Lab Instructor
  • BIOL 321- Morphology and Evolution of Bryophytes: Course Coordinator, Lecturer, Lab Instructor
  • Public Website: http://blogs.ubc.ca/biology321 
  • BIOL 343- Plants and People (summer session): Course Coordinator, Lecturer, Lab Instructor

Selected Publications

Nachonechny, J and S. M. Ellis 2012 Bryofolios: Individual and Group E-portfolio Learning Spaces for Developing Authentic Science Scholars. In D. Cambridge (Ed.), Hershey PA: Global Diffusion of E-Portfolios: IGI Global Publications 

Ryall, K., Whitton, J., Schofield,W.B., Ellis, S.M. and A.J. Shaw. 2005 Molecular Phylogenetic Study of Interspecific Variation in the Moss Isothecium (Brachytheciaceae). Systematic Botany 30: 242-247. 

Ellis, S.M., 2004 Arbor vitae: A personal, teacher’s view of tree-life on the University of British Columbia Campus Davidsonia 15:1 pages 15 – 33. 

Ellis, S.M., Schofield, W.B., Haddad, N, Stewart, N., and J.K. Webb 2002 Bryophytes of UBC Botanical Garden Davidsonia 13:3 pages 35 – 43. 

McCutcheon, A. T., Stokes, R. W., Thorson, L. M., Ellis, S. M., Hancock, R. E. W., and Towers, G. H.N. 1997 Anti-Mycobacterial screening of British Columbian medicinal plants. J. Ethnopharmacognosy 35:77-103. 

Razal, R. A., Ellis, S. M., Singh, S., Lewis, N. U., and Towers, G. H. N. 1996 Nitrogen recycling in phenylpropanoid metabolism. Phytochemistry 41: 31-35.

Ellis, S. M, Balza, F., Constabel, P., Hudson, J.B. and Towers, G. H. N. 1995 Thiarubrines: Novel Dithiacyclohexadiene Polyyne Photosensitizers from Higher Plants In: Light-Activated Pest Control. ACS Symposium Series 616, Eds. Heitz, J.R., and Downum, K.R., pp. 174-178.

Ellis, S. M., Balza, F., Constabel, P., Hudson, J.B. and Towers, G. H. N. 1995 Thiarubrines: Novel Dithiacyclohexadiene Polyyne Photosensitizers from Higher Plants In: Light-Activated Pest Control. ACS Symposium Series 616, Eds. Heitz, J.R., and Downum, K.R., pp. 174-178. 

McCutcheon, A. T., Roberts.T. E., Gibbons, E., Ellis, S. M., Babiuk, L. A., Hancock, R. E. W., and Towers, G. H.N. 1995 Antiviral screening of British Columbian medicinal plants. J. Ethnopharmacology. 49: 101-110. 

McCutcheon, A. T., Ellis, S. M., Hancock, R. E. W., and Towers, G. H.N. 1994 Antifungal screening of medicinal plants of British Columbian native peoples. J. Ethnopharmacology 44: 157-169.

Towers, G. H. N. and Ellis, S. M. 1993 Secondary Metabolism in Plant Cultures Transformed withAgrobacterium tumefaciens and A. rhizogenes. CRC In: Human Medicinal Agents from Plants ACS Symmposium Series 534, Eds A. D. Kinghorn and M. F. Balanrin, pp. 56-78.

Ellis, S. M., Balza, F., and Towers, G. H. N. 1993 A dithiacyclohexadiene polyyne alcohol from Ambrosia chamissonis. Phytochemistry: 33: 224-226.

Ellis, S. M. and Towers, G. H. N. 1993 Root cultures of Asteraceae as sources of thiarubrines and other polyyne antibiotics. In Advances in Developmental Biology and Biotechnology of Higher Plants.(W. Y Soh, J. R. Liu, and A. Komamine eds.) The Korean Society of Plant Tissue Culture, pp. 454-473.

Towers, G. H. N. and Ellis, S. M. 1993 Secondary Metabolism in Plant Cultures Transformed withAgrobacterium tumefaciens and A. rhizogenes. CRC In: Human Medicinal Agents from Plants ACS Symmposium Series 534, Eds A. D. Kinghorn and M. F. Balanrin, pp. 56-78.

McCutcheon, A. T., Ellis, S. M., Hancock, R. E. W., and Towers, G. H.N. 1992 Antibiotic screening of medicinal plants of the British Columbian native peoples. J. Ethnopharmacology. 37: 213-223.

McDougall, S., Ellis, S. M., and Taylor, I. E. P. 1988 The occurrence of polar structures in callus cultures from mature lodgepole pine (Pinus contorta var. latifolia). Can. J. Bot. 66: 2595-2596.

Bridgette Clarkston

Associate Professor of Teaching

Academic History

  • B.Sc. Biology, University of Victoria (2005) 
  • Ph.D. Biology, University of New Brunswick (2011)
  • Postdoctoral Fellow, Carl Wieman Science Education Initiative, University of British Columbia (2012-2013)

My Links

Twitter feed: @funnyfishes – I’m most active here for work-related social media.
My personal professional website

Contact Information

  • bridgette.clarkston@botany.ubc.ca
  • 604-822-6495
  • Office: Biological Sciences Building, room 2142

Awards

  • Faculty of Science Achievement Award for Service (2013)
  • Killam Teaching Award (2011).

Teaching Interests

In all of my UBC courses, I teach aspects of biodiversity: the sheer richness and complexity of life in all its forms, how we document and preserve records of diversity in literal “libraries of life” like the Beaty Biodiversity Museum, why we as a species rely on biodiversity for our very survival and well-being.

Measuring kelp specimens at the Beaty Biodiversity Museum for an activity about variation within species

My joy in teaching comes from seeing my students connect to nature, develop scientific literacy and feel empowered — especially in their first few semesters of university — to develop and pursue their educational goals. If I could take my ~200 first-year biology students to the Bamfield Marine Sciences Centre for their introductory biology courses, I would in a heartbeat. Since I can’t (yet), I bring nature into my students’ lives as much as possible.

Students in Bamfield working on their field-journals after a hike to Kiixiin, a 19th century Huu-ay-aht First Nations village and fortress

My general approach to teaching can be illustrated in four core practices:  

  1. Bring evidence-based teaching and authentic practices into the classroom. The evidence supporting active learning is now legion; I am a big fan of getting students active and thinking during our precious class time together.
  2. Model habits of mind and the scientific process. For me, the discipline-specific content and skills I teach in any course go hand-in-hand with teaching relevant habits of mind: e.g., perseverance, flexible thinking, metacognition, thinking independently, taking ownership of learning, and applying past knowledge to new situations.
  3. Create an inclusive classroom for all students. I am committed to creating an inclusive classroom for all my students, regardless of gender, gender identity, sexual orientation, race, ethnicity, religion, disability, age or socio-economic status. I engage with the discourse around equity, diversity and inclusion happening within and outside UBC and work to bring best practices into my classroom so that all students feel safe, included and empowered to learn.
  4. Collaborate with teaching partners to maximize learning. Undergraduate courses are often taught in isolation of subsequent courses and programmatic goals. I work closely with my teaching colleagues within and between courses and consider program-level goals when developing my courses.

Students in Biology 209: Algae, Fungi & Bryophytes playing the Got Algae? Game on the first day of the Algae course theme

Courses Taught/Teaching

Recent courses taught at UBC:

  • Biology 121: Genetics, Evolution, Ecology
  • Biology 209: Biodiversity of Algae, Fungi & Bryophytes
  • Biology 320: Survey of Algae (starting January 2021)
  • Biology 336: Fundamentals of Evolutionary Biology (2018, 2019)

Buttons made by students during a Biol 209 lab activity to combine art, science and a chance to de-stress before exams

Community Work

Selected recent community work includes:

Phycological Society of America:  Education Committee Chair (2019-current)

  • Organize workshops for the annual society meetings. Recent offerings: Traditional Uses of Seaweeds w/ Dr. Dolly Garza, Introduction to R, Introduction to Taxonomic Nomenclature.
  • Curate algae-related educational resources for the PSA website. Recent events: #TeachAlgae contest to solicit and publish 28 algae-related lessons from experienced university educators, a crowd-sourced list of algae-related resources for online teaching (over 100 resources, accessed 600+ times in summer 2020) & a match-making initiative to pair algae experts with classrooms (150 participants). 

Raincoast Education Society: Seaweeds of the West Coast 3-day field course (created 2014, 2018-current).

  • Immersive introduction to the wonderful world of seaweeds, co-taught with Dr. Katy Hind. Located in Tofino on the stunning West Coast of Vancouver Island.

Seaweed dishes cooked up during various workshops including: kelp noodles & bread, candied Egregia, Nori fries & sesame-oatmeal snaps, & Fucus stir-fry

Selected Publications

Peer-reviewed publications

Cooke, J.E, Weir, L. Clarkston, B.E. 2019. Retention following Two-Stage Collaborative Exams Depends on Timing and Student Performance. CBE—Life Sciences Education. 2019;18(2): ar12,1–ar12,8. https://www.lifescied.org/doi/full/10.1187/cbe.17-07-0137

Oehlman, N., Haeger, H., Clarkston, B.E. and Banks, J.E. 2016. Maximizing the Function of the Student ePortfolio: Demonstrating Learning in High-Impact Practices. Peer Review Summer 2016 (3) https://www.proquest.com/docview/1826255017?sourcetype=Scholarly%20Journals

Gilley, B. and Clarkston, B.E. 2014. Collaborative Testing: Evidence of Learning in a Controlled In–Class Study of Undergraduate Students. Journal of College Science Teaching 43(3): 83–91. http://bit.ly/1gtZyp4

Clarkston, B.E. and Saunders, G.W. 2013. Resolving species diversity in the red algal genus Callophyllis (Gigartinales, Florideophyceae) in Canada using an integrated taxonomic method. European Journal of Phycology 48(1): 27–46.

Clarkston, B.E. and Saunders, G.W. 2012. An examination of the red algal genus Pugetia (Kallymeniaceae, Gigartinales) with descriptions of Salishia firma gen. et comb. nov., Pugetia cryptica sp. nov., and Beringia wynnei sp. nov. Phycologia 51(1): 33–61.

Clarkston, B.E. and Saunders, G.W. 2010. A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp.nov. Botany 88(2): 119−131.

Publications for a public audience

Pacific Seaweeds: A Guide to Common Seaweeds of the West Coast

Written with my longtime mentor and kelp world expert Dr. Louis Druehl, this updated and expanded guide (to Louis’ original 2002 edition of Pacific Seaweeds) thoroughly documents every aspect of seaweed life, from species identification and seaweed biology to the essential—and often surprising—roles seaweed plays in the marine ecosystem and our everyday lives. Seaweeds are used in everything from cosmetics to sustainable biofuels, and some species, like kelp, contribute to the remediation of coastal ecosystems. Features 247 seaweed species in 121 genera, which breaks down to 40 species of greens, 119 reds, 78 browns, 5 seagrasses and 5 shore plants. Lots to explore!

A Field Guide to Seaweeds of the Pacific Northwest

The pocket-sized Field Guide to Seaweeds of the Pacifc Northwest is packed with full-colour photos and information on a select variety of the most important and interesting seaweeds commonly encountered on the West Coast. Whether you want to identify seaweeds, better understand their role in the ocean, forage for food, collect for art or you’re just plain curious as you poke around the seashore, this educational guide is your ultimate source for casual phycological fun.

You can find both publications on the Harbour Publishing Website

Preventing autoimmunity in plants

​

Article by Xin Li lab

Like animals, plants are constantly exposed to bacteria, viruses, and fungi that have the potential to cause diseases. To remain healthy plants possess a complex immune system which relies on immune receptors that are able to recognize pathogens and respond before an infection is established. If a pathogen is able to avoid detection by the immune system, the resulting plant disease can result in dramatic economic losses. An estimated 15% of potential crop output is lost to plant diseases, and periodic disease outbreaks can lead to large-scale social turmoil, such as the Irish potato famine1. Despite the importance of the plant immune system, the molecular details of immune signalling are only partially understood. Thus, the study of plant-microbe interactions is an active area of research, often involving the model plant Arabidopsis thaliana.

Plants have cell-surface receptors to detect common molecules produced by microbes, such as components of bacterial flagella and fungal cell wall polymers. However, many plant pathogens produce effector proteins that hamper this recognition. In response to this, higher plants have evolved Resistance (R) proteins that act as sensors to detect specific effectors. They may bind to effectors and recognize them directly, or they may recognize the changes that the effectors cause on other host proteins. Recognition of the effectors leads to activation of the R proteins, culminating in a defense response that effectively prevents the spread of the pathogen into healthy tissue.

Although plant cells must contain high enough levels of R proteins to quickly recognize invading pathogens, plants must carefully regulate the levels of these proteins in order to optimize growth, because excessive R protein accumulation may activate the defense responses even in the absence of pathogens. This is detrimental to the plant, as exemplified by the snc1 mutant of Arabidopsis identified by UBC professor Dr. Xin Li2,3. The snc1 mutant produces a form of an R protein that is more resistant to protein degradation, and therefore accumulates to higher levels in the plant.

In an attempt to search for genes which are involved in immunity, a forward genetic screen was performed looking for mutants which enhanced the autoimmune phenotype of snc1; this was named the muse (mutant, snc1-enhancing) screen4. From this screen a variety of mutants were identified, many of which play roles in R protein turnover. One of the mutants, muse6, was identified to be a subunit of an N-terminal acetyltransferase (Nat) complex5. N-terminal modification has been a long documented method of proteins regulation in plants as well as other eukaryotic organisms6.

Two recent UBC Botany graduates, Dr. Fang Xu and Dr. Yan Huang, made most of the findings in the story. This discovery led to a detailed study of the N-terminal modifications of SNC1. What was discovered is that SNC1 has a rather unusual pattern of N-terminal modification. The SNC1 protein was found to have alternative initiation, meaning that its translation can begin from either of two adjacent methionines (Met); interestingly, SNC1 appears to be differentially regulated depending on which Met is used as the start codon. If SNC1 translation begins at the first Met it is acetylated by NatA, the Nat complex of which MUSE6 is a component, whereas if it begins at the second MET it is acetylated by a different complex, NatB.

The result of this alternative acetylation has unexpected consequences on SNC1 regulation. The initial screen demonstrated that disrupting NatA caused an increased autoimmune phenotype, and this is because acetylation of the first Met of SNC1 targets the protein for degradation. Alternatively, the acetylation of the second Met by NatB was found to stabilize SNC1. This interesting combination of alterative initiation and differential acetylation has never been reported until now. This novel pattern of alternative acetylation is likely one factor allowing for careful regulation of SNC1 protein levels, and by acting at the level of translation it allows for rapid changes in protein levels during the induction of defense responses.


1. Dangl, J. L., Horvath, D. M. & Staskawicz, B. J.  Science  341, 746–751 (2013).
2. Li, X., Clarke, J. D., Zhang, Y. & Dong, X. Mol Plant Microbe Interact 14, 1131–9 (2001).
3. Zhang, Y., Goritschnig, S., Dong, X. & Li, X. Plant Cell 15, 2636–2646 (2003).
4. Huang, Y. et al. Nat. Commun. 4, 2558 (2013).
5. Xu, F. et al. Plant Cell. May 12. pii: tpc.15.00173 (2015). [Epub ahead of print]
6. Gibbs, D. J., Bacardit, J., Bachmair, A. & Holdsworth, M. J. Trends Cell Biol. 24, 603–611 (2014).

Figure 1. A nata mutant, muse6-1, identified from a genetic screen to search for enhancers of snc1.
Figure 2. A working model on the different N-terminal acetylations of SNC1. In wild type plants, SNC1 protein synthesis can be initiated at either the first or the second Met. The peptide translated from the first Met can be acetylated by NatA, which serves as a degradation signal. The peptide translated from the second Met can be acetylated by NatB, where the protein is stabilized by the modification. SNC1 protein homeostasis is maintained by the coexistence of these different protein isoforms. In nata mutants including naa15-1, aminaa15 and aminaa10 plants, almost all the SNC1 peptides are acetylated at the second Met by NatB due to the inefficiency of NatA. The stabilization by acetylation on the second Met leads to increased SNC1 accumulation, partly leading to the autoimmune phenotypes of these plants. In natb plants, as a result of inefficient acetylation of the second Met of SNC1 by NatB that stabilizes the protein, SNC1 protein levels are decreased. ​

New branch on tree of life includes ‘lions of the microbial world’

On the left is a starving provoran. On the right, it has engulfed its prey. Photo Credit: Tikhonenkov, Mikhailov, Gawryluk, Belyaev, Mathur, Karpov, Zagumyonnyi, Borodina, Prokina, Mylnikov, Aleoshin, and Keeling, Nature

There’s a new branch on the tree of life and it’s made up of predators that nibble their prey to death.

These microbial predators fall into two groups, one of which researchers have dubbed “nibblerids” because they, well, nibble chunks off their prey using tooth-like structures. The other group, nebulids, eat their prey whole. And both comprise a new ancient branch on the tree of life called “Provora,” according to a paper published today in Nature.

Microbial lions

Like lions, cheetahs, and more familiar predators, these microbes are numerically rare but important to the ecosystem, says senior author Dr. Patrick Keeling, professor in the UBC department of botany. “Imagine if you were an alien and sampled the Serengeti: you would get a lot of plants and maybe a gazelle, but no lions. But lions do matter, even if they are rare. These are lions of the microbial world.”

Using water samples from marine habitats around the world, including the coral reefs of Curaçao, sediment from the Black and Red seas, and water from the northeast Pacific and Arctic oceans, the researchers discovered new microbes. “I noticed that in some water samples there were tiny organisms with two flagella, or tails, that convulsively spun in place or swam very quickly. Thus began my hunt for these microbes,” said first author Dr. Denis Tikhonenkov, senior researcher at the Institute for Biology of Inland Waters of the Russian Academy of Sciences.

Dr. Tikhonenkov, a long-time collaborator of the UBC co-authors, noticed that in samples where these microbes were present, almost all others disappeared after one to two days. They were being eaten. Dr. Tikhonenkov fed the voracious predators with pre-grown peaceful protozoa, cultivating the organisms in order to study their DNA.

“In the taxonomy of living organisms, we often use the gene ‘18S rRNA’ to describe genetic difference. For example, humans differ from guinea pigs in this gene by only six nucleotides. We were surprised to find that these predatory microbes differ by 170 to 180 nucleotides in the 18S rRNA gene from every other living thing on Earth. It became clear that we had discovered something completely new and amazing,” Dr. Tikhonenkov said.

New branch of life

On the tree of life, the animal kingdom would be a twig growing from one of the boughs called “domains,” the highest category of life. But sitting under domains, and above kingdoms, are branches of creatures that biologists have taken to calling “supergroups.” About five to seven have been found, with the most recent in 2018 – until now.

Understanding more about these potentially undiscovered branches of life helps us understand the foundations of the living world and just how evolution works.

“Ignoring microbial ecosystems, like we often do, is like having a house that needs repair and just redecorating the kitchen, but ignoring the roof or the foundations,” said Dr. Keeling. “This is an ancient branch of the tree of life that is roughly as diverse as the animal and fungi kingdoms combined, and no one knew it was there.”

The researchers plan to sequence whole genomes of the organisms, as well as build 3D reconstructions of the cells, in order to learn about their molecular organization, structure and eating habits.

International culture

Culturing the microbial predators was no mean feat, since they require a mini-ecosystem with their food and their food’s food just to survive in the lab. A difficult process in itself, the cultures were initially grown in Canada and Russia, and both COVID and Russia’s war with Ukraine prevented Russian scientists from visiting the lab in Canada in recent years, slowing down the collaboration.

Grassroots effort champions inclusive language in science

A new grassroots effort—announced this month in Trends in Ecology and Evolution—is calling for a reevaluation of some terminology used in ecology and evolutionary biology (EEB) to make it more inclusive and precise.

The initiative, the EEB Language Project was launched by like-minded scientists across the United States and Canada, including three University of British Columbia researchers—Dr. Kaitlyn Gaynor, Dr. Alex Moore and Dr. Danielle Ignace.

“The project started as a Twitter conversation among a few people discussing potentially harmful terminology,” says Dr. Gaynor, an author on the paper who studies the impact of human activity on biodiversity.

“It was important for us to think through one tractable approach that people can take in their work at an individual level—and at varying scales within the discipline—to make thoughtful choices moving forward.”

“We reached out to different networks in ecology and evolution that were focused on increasing inclusion and equity in the field to rally support for one very specific action—revising terminology that might be harmful to certain people, particularly those from groups historically and currently excluded from science.”

The EEB Language Project will provide resources and support action to reconsider harmful terminology at the levels of individuals, institutions and broader scientific communities. This crowdsourced effort includes a repository of words that are identified by community members as harmful, with suggested alternatives, which is meant to serve as a starting point for dialogue.

Haley Branch, a PhD candidate with UBC Botany, published a complementary paper in the American Naturalist in July outlining the roots of ableism in evolutionary research and how it limits the potential of the field.

“While some of it’s about language, the bigger picture is looking at the conceptualization of our field,” says Branch. “What kinds of questions are being missed because of the narrow breadth of the field? It’s a call to broaden our understanding of the natural world and look at what kinds of questions we’ll be asking in the future.”

Terms like “fitness” are not only harmful to some people—in an ableist context—but also vague. 

“The definition is about reproductive output, which doesn’t take into account individuals that don’t produce offspring,” says Branch. “Often researchers aren’t even measuring the number of offspring. They’re looking at proxies of fitness instead, which becomes very convoluted.”

Other words like “optimization” can be misleading as it perpetuates the idea that a species is evolving towards a defined permanent optimum, when there is no true species-wide optimization. Optimum phenotypes fluctuate over time and in different environments.

Both the EEB Language Project members and Haley’s research group are quick to point out that the use of harmful language isn’t usually intentional—what is harmful to one person may not be perceived as problematic to another, and inadvertent harm can arise as a result of the inherent complexities and historical legacies of language.

Ecology and evolutionary biology both have histories rooted in eugenics, ableism and racism—beliefs that fed into harmful practices across North America and Europe and unfortunately still influence the fields today. Part of this legacy is imbedded in the disciplinary terms we use on a daily basis.

“There have been many large conversations around inclusion in the fields, and often there are no clear steps that people can take,” says Dr. Moore. “It was important for us to think through one tractable approach that people can take in their work at an individual level—and at varying scales within the discipline—to make thoughtful choices moving forward.”

“The EEB Language Project will be a living document, as particular words that are harmful and their alternatives can change over time,” says Dr. Ignace. “People can submit their suggestions online and have their voices heard. They can also get more involved as an individual, as an institution, or at the community level. The hope is that this grassroots effort brings people together.”

This parasitic plant convinces hosts to grow into its own flesh

Dr. Chen and colleagues—including University of British Columbia botanist Dr. Sean Graham—compared the genomes of Balanophora and Sapria, another extreme parasitic plant in the family Rafflesiaceae that has a very different vegetative body.

The UBC science summary: https://science.ubc.ca/news/parasitic-plant-convinces-hosts-grow-its-own-flesh

Robert J. Bandoni

Professor Emeritus Robert (Bob) Joseph Bandoni passed away peacefully on May 18, 2009 at Mountain View Manor Extended Care Unit in Ladner, B.C. Bob was born November 9, 1926 in Weeks, Nevada to Giuseppe and Albina Bandoni, and graduated from high school in Hawthorne, Nevada. He earned degrees from the University of Nevada at Reno and the University of Iowa before joining the faculty of the Department of Botany at the University of British Columbia in 1958. Following his retirement from the Botany Department in 1989. Bob maintained an active presence both within the Botany Department and in the wider mycological community. He is survived by wife Alice-Ann (Webb) of 20 years, daughter Susan (Thomas) Muench of Geneseo, New York, stepsons Danai (Angela) Bisalputra and Rabin Bisalputra, and sisters Margaret McGhie of Nevada, Evelyn Smith of Illinois, and Mary (Frank) Fahrenkopf of Virginia. Predeceased by wife Inger (Van Nostrand) of 30 years, and siblings Estelle Perry, Grace Bandoni and Alfred Bandoni.

A celebration of Bob’s life will be scheduled for September. Condolences can be expressed on line at www.deltafuneral.ca. In lieu of flowers, please send contributions to the Delta Hospital Foundation (5800 Mountain View Blvd., Delta, B.C., V4K 3V6, or www.deltahospital.com).

As a biologist, Bob was drawn to strange, diverse, and inconspicuous basidiomycete fungi. He was both a superb naturalist and an attentive scientist. By searching in places where no one else looked, he found many of the ‘duck-billed platypuses’ of the fungal world, fungi with astonishing and unexpected combinations of characters that helped reveal patterns of early fungal evolution (Bandoni and Oberwinkler 1981; Oberwinkler et al. 1990).

Bob specialized in the Tremellales, and Jack Maze recalled:

I first became aware of Bob while taking a course in Mycology at U. Wash. from Dan Stuntz. When we got to the Tremellales, Dan and one of his students, Hugh Klett, spent a great deal of time praising Bob Bandoni and the quality of his work. Thus when I arrived at UBC in 1968 I was quite excited to realize I’d get to meet Bob. I did and my first thought was, “Geez, he’s old.” Bob then was in his early 40s but I was a mere kid of 31, an age at which anyone over 35 was suspected of having ridden in on a glacier. It was always pleasant to encounter Bob. In the hall, he could extract the glumness from a typical day in academia with humor or just an irrevant comment, often in more colorful language than is commonly heard in the halls of academe. In meetings, Bob’s comments, while rare, were also a pleasure to hear, and were often useful. He usually kept his own council in meetings, aside from private remarks on various things, some of them germane to the meeting. But when necessary he had the ability to use a few pithy remarks to place a discussion in perspective, usually in the context of what was being discussed was a waste of time and, if the ideas presented were carried out, would be an even greater waste of time. These opinions were based on a combination of knowledge and experience, things at which Bob excelled. 
–Jack Maze

Shannon Berch

Associate Member

Contact Information

  • shannon.berch@gov.bc.ca
  • 250-952-4122

Research Interests

A large part of the energy that plants allocate to roots actually supports an intricate web of below ground, largely microscopic, life. In the interface between root and soil (the rhizosphere), interactions between roots, fungi, microarthropods and soil can improve or impair plant growth. Traditional commercial use of the forest of British Columbia has focused primarily on trees, especially trees of known economic value. As societal priorities have shifted and broadened to include many other forest uses and values, there has been an awakening to the diversity of life in our forests and to the impact that forest management has on other resources.

Our most important natural resource is the soil. Soil is a physical matrix, a chemical brewhouse. It is the biological community of soil about which the least is currently known because of the challenges of studying soil organisms in natural ecosystems. I am involved in the study of soil fungi and particularly mycorrhizal fungi from a variety of perspectives: the health of containerized nursery seedlings; the long-term impacts of soil compaction and organic matter removal; the ecology and management of commercially harvested wild mushrooms; the use of molecular tools to identify and detect the presence of fungal species on mycorrhizal roots (in collaboration with Mary Berbee).

Selected Publications

Berch, S.M., B. Baumbrough, J. Battigelli, P Kroeger, N. Strub, and L. de Montigny. 2001. Preliminary assessment of selected communities of soil organisms under different conifer species. B.C. Min. For., Res. Br., Victoria, BC. Research Report 20.

Berch, S.M. and A. M. Wiensczyk. 2001. Ecological description and classification of some Pine Mushroom (Tricholoma magnivelare) habitat in British Columbia. B.C. Min. For.;SIFERP. Victoria, BC; Kamloops, BC. Research Report 19.

Cade-Menun, B.J., S.M. Berch, C.M. Preston and L.M. Lavkulich. 2000a.Phosphorus forms and related soil chemistry of podzolic soils of northern Vancouver Island. I. A comparison of two forest types.Can. J. For. Res. 30: 1714-1725.

Cade-Menun, B.J., S.M. Berch, C.M. Preston and L.M. Lavkulich. 2000b. Phosphorus forms and related soil chemistry of podzolic soils of northern Vancouver Island.II. The effects of clear-cutting and burning.Can. J.For. Res. 30: 1726-1741.

Monreal, M., S.M. Berch, and M. Berbee. 1999. Molecular diversity of ericoid mycorrhizal fungi. Can. J. Bot. 77: 1580-1594.

Berch, S.M., G. Xiao, and C. Bulmer. 1999. Commercial mycorrhizal inoculants: value-added conifers for site rehabilitation or just another way to spend money? In Proceedings: 19th Annual Meeting of the Forest Nursery Association of British Columbia, September 27-30, Vancouver, B.C. Extension Services, Tree Improvement Br., Surrey.

Columbia. B.C. Min. For.;SIFERP. Victoria, BC; Kamloops, BC. Research Report 19.

Colin Bates

Adjunct Professor

My Links

  • Click here to see a CBC News story about my Masters research.
  • Click here to visit my photography website

Contact Information

  • colin.bates@botany.ubc.ca

Research Interests

I am interested in all aspects of marine ecology, but most of my work has focused on seaweeds. In particular, my research involves understanding the consequences of human-induced alterations in intertidal community structure. This work has two components: 

a) monitoring for changes in algal communities. This work is taking place in Barkley Sound & the Broughton Archipelago (British Columbia). As an continuation of my M.Sc work, I am also collaborating with Dr. Gary Saunders to maintain a long-term monitoring program in the Bay of Fundy (New Brunswick).

b) using manipulative experiments to determine the ramifications of change in seaweed communities, with specific reference to resultant change in invertebrate communities. This work takes place in Barkley Sound, and is based out of the Bamfield Marine Science Centre

Other research interests include:

1) Communication of science through video and multimedia. I teach science filmmaking workshops with Jeff Morales (National Geographic Film & Television, VONIGO Films). To learn more about this work, visit www.sciencefilm.org.

2) Measurement of biodiversity. I am particularly interested in understanding the relationships between taxonomic and functional diversity. Major questions also surround a) the benefits and consequences of sampling and analysis at various data resolutions (e.g. coarse taxonomic levels, functional groups, diversity indices, etc.) ; and b) the incorporation of taxonomic information into diversity indices. 

3) Biostatistics, with a focus on nonparametric multivariate analysis of biological community structure 

4) Understanding the relative importance of positive interactions in structuring marine biological communities.

5) Marine conservation issues. To facilitate understanding about the effects of human influence on marine intertidal communities, I organized a marine biodiversity workshop in April 2004.

Selected Publications

Bates CR, Saunders GW, & Chopin T. (2009) Historical vs. contemporary measures of seaweed biodiversity in the Bay of Fundy, New, Brunswick, Canada. Botany 87: 1066-1076.

Bates C.R. (2009) A comparison of host taxonomic relatedness and functional group affiliation as predictors of seaweed-invertebrate epifauna associations. Marine Ecology Progress Series 387: 125-136.

Bates, C.R. and R.E. DeWreede (2007) Do changes in seaweed biodiversity influence invertebrate epifauna?Journal of Experimental Marine Biology and Ecology 344: 206-214.

Bates, C.R., G. Scott, M. Tobin, and R. Thompson (2007) Weighing the costs and benefits of reduced sampling resolution in biomonitoring studies: Perspectives from the rocky intertidal. Biological Conservation 137: 617-625.

Bates CR, Chopin T, and Saunders GW (2005). Taxonomic distinctness and seaweed community responses to environmental stress in the Bay of Fundy, NB, Canada. Botanica Marina 48:231-234.

Bates, CR. (2004). An introduction to the seaweeds of British Columbia. In: Klinkenberg, Brian.(Editor) 2004. E-Flora BC: Atlas of the Plants of British Columbia [www.eflora.bc.ca]. Lab for Advanced Spatial Analysis, Department of Geography, University of British Columbia, Vancouver.

Bates CR, T Chopin, and Saunders GW (2001). Monitoring seaweed diversity in the Bay of Fundy, New Brunswick, Canada. p.163-176. In: Opportunities and challenges for protecting, restoring and enhancing coastal habitats in the Bay of Fundy. Proceedings of the 4th Bay of Fundy Science Workshop, Saint John, New Brunswick, September 19-21, 2000. Chopin T. and P.G. Wells (Eds.). Environment Canada, Atlantic Region Occasional Report No. 17, Environment Canada, Dartmouth, Nova Scotia. 237p.

Chopin T, Yarish C, Neefus C, Kraemer G, Belyea E, Carmona R, Saunders G, Bates C, Page F, & Dowd, M. (2001) Underutilized tools: seaweeds as bioremediation and diversification tools and bio-indicators for integrated aquaculture and coastal management. Journal of Phycology 37 (3), 12-12.

Submitted manuscripts

Bates CR (in review) Seaweed morphology and wave exposure interact to determine biodiversity of invertebrate epifauna.

Biology Learning Centre

Biology Learning Centre (BioSc 1114): this room is available for quiet study and is also where some BIOL course TAs/Peer Tutors hold scheduled office hours.

Meeting rooms: there are a number of meeting rooms in the North and East wings of the BioSci Building.
– Small meeting rooms (5-8 people): 1114C, 1119, 2002, 2025, and 3021.
– Larger meeting rooms (12-16 people): 1108, 1114B, and 3051.
Bookings for these rooms are reserved for Biology/Botany/Zoology internal members (e.g. faculty, staff, graduate students).

CCCM

The Canadian Center for the Culture of Microorganisms (CCCM) maintains living specimens of marine phytoplankton, freshwater microalgae and fungal isolates for research, teaching and commercial use.

Please visit the CCCM website at https://cccm.botany.ubc.ca/

Herbarium

The University of British Columbia Herbarium is the largest in Canada west of Ottawa, and is home to over half a million plant specimens from around the world. This collection is critical to the identification, monitoring, and conservation of plant biodiversity in British Columbia, and is an important resource for scientific research and education. Please visit the Herbarium website at https://beatymuseum.ubc.ca/research-2/collections/herbari

Bioimaging

The UBC Bioimaging Facility is a multi-user microscopy facility that is open to everyone and provides both training and service. The facility has been known as the most comprehensive biological imaging facility in Western Canada. We are located in beautiful Vancouver, British Columbia at the University of British Columbia.
Our facility provides researchers with top-end optical and electron microscope infrastructure for live-cell imaging, multi-photon imaging, advanced sample preparation including cryo-preparation for electron microscopy, routine SEM and TEM, Cryo-TEM, TEM tomography, and Correlative Light and Electron Microscopy (CLEM). Currently, the BIF is equipped with 4 electron microscopes (1 SEM and 3 TEMs), 2 advanced fluorescence microscopes (confocal/multi-photon, spinning disk), cryo-fixation (High pressure freezer, Vitrobot) and EM processing equipment (Microwave, critical point dryer, coaters).
The Bioimaging Facility has three technical staff who all have more than 10 years of experience providing technical knowledge and can support users from diverse research disciplines from life sciences to material sciences.

Please visit the Bioimaging Facility website at https://www.bioimaging.ubc.ca/

Image courtesy of Jordan Tam

Greenhouse

The Department of Botany maintains a greenhouse that facilitates research projects ranging from ecology and systematics to cell and developmental biology.

Contact Oscar Dorado Ruiz for more information: 604-822-9681 or oscar.dorado@botany.ubc.ca.

Janet Ruth Stein Taylor

Obituary
Janet Ruth Stein Taylor born October 10th 1930 died January 16th 2016

Janet Ruth Stein Taylor was born on October 10th 1930 and raised in Denver CO.  She graduated with a BA from University of Colorado (1951), an M.A. from Wellesley College, Wellesley (1953). Her thesis was A Comparative Study of Brachytic and Normal Zea mays. Thesis Supervisor: Dr. Rhoda Garrison. Her PhD research in Botany, from University of California, Berkeley (1957) was under the supervision of George F. Pappenfuss. Her dissertation was A Morphological and Physiological Study of Three Colonial Volvocales. In 1960 she received the “Dorbaker Award” for the best phycological paper published in North America in 1960.

Between 1957 and 1959, Janet worked as a Technician at Berkeley, and held visiting positions at the University of Minnesota Biological Station, and in the University Teachers Institute at Indiana University.  She joined the UBC Department of Botany in 1959 as an Instructor, and after 5 years on the then traditional path for young women she became an Assistant Professor. Her teaching forte was the smallish class with a strong lab requirement. Many students noted her welcoming experience in 2nd year botany as a major influence in their choice of Botany as at least a minor in the BSc programmes.  Throughout her career she was an effective mentor for undergraduate and graduate students as well as for newly appointed faculty members.  She was probably the last of the ‘put-upon’ women in the Department, and she was certainly a valuable contributor to the fall of male patronage in both the Department and the Faculty of Science at UBC.


During her career (1959-1985), her research interests were in the Freshwater and Estuarine Algae (especially) of British Columbia. She did extensive fieldwork and identification and data base preparation for what is now part of the E-Flora of BC: Electronic Atlas of Plants of British Columbia www.eflora.bc.ca. She established the algal part of the UBC Microbial Culture Collection work that may well have led to her involvement as the Organizing Editor of the 4 volume Handbook of Phycological Methods; published by Cambridge University Press between 1973 and 1986.


Janet was an active member of the scientific societies that she joined, particularly of the  Canadian Botanical Association/L’Association Botanique du Canada (Director; Editor of CBA/ABC Bulletin; Vice-President; President 1970-71)  and the Phycological Society of America (Editor of the News Bulletin and Newsletter; Editor, Journal of Phycology, 1975-1980; Treasurer from 1982-1987; and President 1965).


Over the years Janet taught in the introductory Botany course, brought freshwater algae into the Department, became a stalwart colleague who lead the much respected advising group in the Department, and eventually served as Associate Dean of Science.  She was one of the original authors of the textbook, edited by Bob Scagel, Evolutionary Survey of the Plant Kingdom, by Scagel, R.F., Bandoni, R.J., Rouse, G.E., Schofield, W.B., Stein, J.R. & Taylor, T.M. 1965 Wadsworth Press, Belmont, California.


Janet’s graduate students were a diverse and independent minded group.  The first was Joseph Gerrath (MSc 1965; PhD 1965) who studied the ecology, culture and taxonomy of Desmids.  He married Janet’s undergraduate student/technician, Jean Drewry, and they moved to the University of Guelph, where Joe pursued an academic career until retirement.  Jean did different technical and teaching jobs in Botany at Guelph and 18 years later she extended her Honours degree in freshwater phycology to a career in higher plant morphology, completed a PhD, and became a professor at the University of Northern Iowa.


Dean Blinn (PhD 1969) worked on saline environments and became a career-long faculty member at Northern Arizona University.  John Wehr moved to Durham University in the UK for a PhD (1982) and then onto Fordham University, NY, where he is a Professor and Director of the Calder Ecology Center.  John, and Robert Sheath, a former visitor with Kay Cole, edited a book on Freshwater Algae of North America: Ecology and Classification that was published in 2003.


Martin Pomeroy, Richard Nordin, Helene Contant and Robert Prange all worked in Government.  A post-doctoral husband-wife team, Davis and Diane Findley, from the U S Corps of Engineers, Mobile, AL, contributed much to our knowledge of the ecology of Skaha Lake in the BC Okanagan region during their work with Janet (1969-1971).


Carol-Ann Borden (MSc 1969) did much of the early work on the culture collection, Gary Butler (MSc 1970), Marion McCauley (MSc 1974) and Bob Prange made strong contributions and went along their chosen paths.  Robert Prange (MSc 1976) did a PhD and was last heard of in Kentville, Nova Scotia working on apples!

Janet married Roy Taylor, then Director of the UBC Botanical Garden and moved with Roy to the Chicago Garden in 1985, and then to the Rancho Santa Ana Garden in Claremont CA.  They retired to Nanaimo where both became involved in matters botanical and horticultural and were very active volunteers.

Janet was predeceased by Roy in 2013.

Janet requested no ceremony and only this ‘scientific’ obituary.

I have prepared a more complete biographical commentary in the History of 100 years of the UBC Botany Department, which should be available in a few months through the Botany Department’s web site.