Evolution of plant reproductive systems

Adjunct professor
Department of biological sciences - University of Montreal

Botanist and researcher
Montreal Botanical Garden


Our laboratory aims at understanding biodiversity by studying plant evolution. Our research involves field work, molecular biology, and uses analytic and modelling approaches. We use tools from phylogenetics, population genetics, quantitative genetics and bioinformatics to understand the evolutionary processes that were involved in shaping the diversity of plants.

The main subjects studied in the laboratory are the evolution of reproductive systems, speciation, hybridization, plant genetics, and polyploidy.

Keywords: Evolution • Coevolution • Genomics • Plant mating systems • Pollination • Urbanization • Systematics


Ph.D. students
Jérôme Burkiewicz
Marion Leménager

M.Sc. students
Carolina Vergolino

  • Joly, S., F. Lambert, H. Alexandre, J. Clavel, É. Léveillé-Bourret et J.L. Clark. 2018. Greater pollination generalization is not associated with reduced constraints on corolla shape in Antillean plants. Evolution, 72 (2): 244-260.
  • Gonzalez, E., F.E. Pitre, A.P. Pagé, J. Marleau, W.G. Nissim, M. St-Arnaud, M. Labrecque, S. Joly, E. Yergeau et N.J.B. Brereton. 2018. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. Microbiome, 6 (1): 53.
  • Salminen, T.A., D.M. Eklund, V. Joly, K. Blomqvist, D.P. Matton et J. Edqvist. 2018. Deciphering the evolution and development of the cuticle by studying lipid transfer proteins in mosses and liverworts. Plants, 7 (1): 6.
  • Yergeau, E., J. Tremblay, S. Joly, M. Labrecque, C. Maynard, F.E. Pitre, M. St-Arnaud et C.W. Greer. 2018. Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome. The ISME Journal, 12: 869-884.
  • Yanitch, A., N.J. Brereton, E. Gonzalez, M. Labrecque, S. Joly et F.E. Pitre. 2017. Transcriptomic response of purple willow (Salix purpurea) to arsenic stress. Frontiers in Plant Science, 8: 1115.
  • Lambert, F., J.L. Clark et S. Joly. 2017. Species delimitation in the Caribbean Gesneria viridiflora complex (Gesneriaceae) reveals unsuspected endemism. Taxon, 66 (5): 1171-1183.
  • Joly, S., A. Archambault, S. Pellerin et A. Nault. 2017. Genetic structure of the American ginseng (Panax quinquefolius L.) in Eastern Canada using reduced-representation highthroughput sequencing. Botany, 95: 429-434.
  • Alexandre, H., J. Faure, S. Ginzbarg, J. Clark et S. Joly. 2017. Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae. Royal Society Open Science, 4 (11): 170293.
  • De Vriendt, L., M.-A. Lemay, M. Jean, S. Renaut, S. Pellerin, S. Joly, F. Belzile et M. Poulin. 2017. Population isolation shapes plant genetics, phenotype and germination in naturally patchy ecosystems. Journal of Plant Ecology, 10 (4): 649-659.
  • Lavoie, C., S. Joly, A. Bergeron, G. Guay et E. Groeneveld. 2016. Explaining naturalization and invasiveness: new insights from historical ornamental plant catalogs. Ecology and Evolution, 6 (20): 7188-7198.
  • Brereton, N.J., E. Gonzalez, J. Marleau, W. Guidi Nissim, M. Labrecque, S. Joly, et F.E. Pitre. 2016. Comparative transcriptomic approaches exploring contamination stress tolerance in Salix sp. reveal the Importance for a metaorganismal de novo assembly approach for nonmodel plants. Plant physiology, 171 (1) : 3-24.
  • Alexandre, H., J. Vrignaud, B. Mangin et S. Joly. 2015. Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae). PeerJ : 24 pages (e1063).
  • Almeida-Rodríguez, A.M., M.P. Gómes, A. Loubert-Hudon, S. Joly et M. Labrecque. 2015. Symbiotic association between Salix purpurea and Rhizophagus irregularis : modulation of plant responses under copper stress. Tree physiology, tpv119 : 14 pages.
  • Gonzalez, E., N.J. Brereton, J. Marleau, W. Guidi Nissim, M. Labrecque, F.E. Pitre et S. Joly. 2015. Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil. BMC plant biology, 15 (246) : 18 pages.
  • Joly, S., D. Bryant et P.J. Lockhart. 2015. Flexible methods for estimating genetic distances from single nucleotide polymorphisms. Methods in Ecology and Evolution, 6 : 938-948.
  • Liu, Y., V. Joly, S. Dorion, J. Rivoal, et D.P. Matton. 2015. The plant ovule secretome: a different view toward pollenpistil interactions. Journal of proteome research, 14 (11) : 4763-4775.
  • Ngo Ngwe, M.F.S., D.N. Omokolo et S. Joly. 2015. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.) : Implication for Conservation and Agricultural Practices. PloS one, 10 (12) : 13 pages (e0145364).
  • Paquette, A., S. Joly et C. Messier. 2015. Explaining forest productivity using tree functional traits and phylogenetic information : two sides of the same coin over evolutionary scale? Ecology and Evolution, 5 (9) : 1774-1783.
  • Fougere-Danezan, M., S. Joly, A. Bruneau, X.F. Gao et L.B. Zhang. 2014. Phylogeny and biogeography of wild roses with specific attention to polyploids. Annals of Botany, 115 (2): 275-291.
  • Bell, T.H., S. Joly, F.E. Pitre, E. Yergeau. 2014. Increasing phytoremediation efficiency and reliability using novel ‘omics approaches. Trends in Biotechnologies 32:271-280.
  • Joly, S., P.B. Heenan, P.J. Lockhart. 2014. Species radiation by niche shifts in New Zealand’s rockcresses (Pachycladon, Brassicaceae). Systematic Biology 63:192-202.
  • Joly, S., T.J. Davies, A. Archambault, A. Bruneau, A. Derry, S. Kembel, P. Peres-Neto, J. Vamosi, T. Wheeler. 2014. Ecology in the age of DNA barcoding: the resource, the promise, and the challenges ahead. Molecular Ecology Ressources 14:221-232.
  • Léveillé-Bourret, ƒ., S. Bailleul, J. Cayouette, S. Joly. 2014. Testing hybridization hypotheses with morphometry in eastern American Potentilla sect. Niveae (Rosaceae). Systematic Botany 39:193-204.
  • Ngo Ngwe, M.F.S., S. Joly, M. Bourge, S. Brown, D.N. Omokolo. 2014. Nuclear DNA content of four cultivated species of yams (Dioscorea spp.) from Cameroon. Journal of Plant Breeding and Genetics 2:87-95.
  • Gonzalez, E., S. Joly. 2013. Impact of RNA-seq length and paired-end information on differential gene or isoform expression. BMC Research Notes 6:503.
  • Kaushik G., J. McCallum, C. Kirby, K. Sanderson, S. Joly, A. Bruneau, B. Fofana. 2013. Genetic diversity, structure and domestication syndrome among Prince Edward Island cultivated wild rosehips. Scientiae Horticulturae 160:251-263.
  • Joly, S. 2012. JML: testing hybridization from species trees. Molecular Ecology Ressources 12: 179-184
  • Joly, S. and D. Schoen. 2011. Migration rates, frequency-dependent selection and the self-incompatibility locus in Leavenworthia (Brassicaceae). Evolution 65: 2357-2369
  • Busch, J.W., S. Joly, and D. Schoen. 2011. Demographic signatures accompanying the evolution of selfing in Leavenworthia alabamica. Molecular Biology and Evolution 28: 1717-1729
  • Yogeeswaran, K., C. Voelckel, S. Joly et P. B. Heenan. 2011. Pachycladon. Dans Wild Crop Relatives: Genomic and Breeding Resources, ed. C. Kole. Wild relatives of oilseeds. Berlin, Heidelberg: Springer Berlin Heidelberg. pp. 227-249.
  • Mandáková, T., S. Joly, M. Krzywinski, K. Mummenhoff et M.A. Lysak. 2010. Fast diploidization in close mesopolyploid relatives of Arabidopsis. The Plant Cell. 22:2277-2290.
  • Busch, J.W., S. Joly et D.J. Schoen. 2010. Does mate limitation in self-incompatible species promote the evolution of selfing? The case of Leavenworthia alabamica. Evolution 64:1657-1670.
  • Joly, S., P. A. McLenachan et P. J. Lockhart. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist. 174:e54-e70.
  • Joly, S. et A. Bruneau. 2009. Measuring branch support in species trees obtained by gene tree parsimony. Systematic biology. 58:100-113.
  • Joly, S., P. B. Heenan et P. J. Lockhart. 2009. A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand. Molecular Phylogenetics and Evolution. 51:365-372.
  • Collins, L., P. Biggs, C. Voelckel et S. Joly. 2008. An approach to transcriptome analysis of non-model organism using short-read sequences. Genome Informatics. 21:3-14.
  • Wang, Y., S. Joly et D. Morse. 2008. Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with stramenopile plastid genes. Journal of Molecular Evolution. 66:175-184.
  • Joly, S., M. I. Stevens et B. Jensen van Vuuren. 2007. Haplotype networks can be misleading in the presence of missing data. Systematic Biology. 56:857-862.
  • Joly, S. et A. Bruneau. 2007. Delimiting species boundaries in Rosa sect. Cinnamomeae (Rosaceae) in eastern North America. Systematic Botany. 32:819-836.
  • Bruneau, A., J. R. Starr et S. Joly. 2007. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and appraisal of current knowledge. Systematic Botany. 32(2):366-378.
  • Joly, S. et A. Bruneau. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Systematic Biology. 55:623-636.
  • Joly, S., J. R. Starr, W. H. Lewis et A. Bruneau. 2006. Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany. 93:412-425.
  • Bruneau, A., S. Joly, J. R. Starr et J.-N. Drouin. 2005. Molecular markers indicate that the narrow Québec endemics, Rosa rousseauiorum and R. williamsii, are synonymous with the widespread R. blanda. Canadian Journal of Botany.83:386-398.
  • Joly, S., J. T. Rauscher, S. L. Sherman-Broyles, A. H. D. Brown et J. J. Doyle. 2004. Evolution of the 18S-5.8S-26S nuclear ribosomal gene family and its expression in natural and artificial Glycine allopolyploids. Molecular Biology and Evolution. 21:1409-1421.
  • Joly, S. et A. Bruneau. 2004. Evolution of triploidy in Apios americana (Leguminosae) revealed by genealogical analysis of the histone H3-D gene. Evolution. 58:284-295.
  • Joly, S., L. Brouillet et A. Bruneau. 2001. Phylogenetic implications of the multiple losses of the mitochondrial coxII.i3 intron in the angiosperms. International Journal of Plant Science. 162:359-373.