Simon Joly

Adjunct Professor,
Université de Montréal

Institut de recherche en biologie végétale
Bureau C-317
4101 Sherbrooke Est
Montréal, QC H1X 2B2
Tel: 514.872.0344
Institution page
Personal page

  • Ph.D. Université de Montréal, 2006
  • B. Sc. Université de Montréal, 2000

  • Research
    Simon Joly’s laboratory aims at understanding biodiversity by studying plant evolution. Their research involves field work, molecular biology, and uses analytic and modelling approaches. They 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.

    Prizes and honours
  • Médaille d'or du Gouverneur Général du Canada (2006)
  • Prix E.A. Porsild (2006)
  • Prix Lionnel Cinq-Mars (2002)

  • QCBS students
    Jérôme Burkiewicz, B.Sc.
    (Start: 2017)

    Thesis title: Variation florale entre populations de l'impatiente du cap : un cas de sélection imposée par les pollinisateurs ?
    Tammy Elliott, Postdoctoral fellow
    (Start: 2017, End: 2019)

    Other (co-)supervisor: Dr. Muthama Muasya
    Thesis title: Speciation and genome sizes in Schoenus (tribe Schoeneae)
    Link to thesis (pdf)
    Personal page
    Gonzalo Bilbao Gómez-Martino, Ph.D.
    (Start: 2015, End: 2020)

    Other QCBS (co-)supervisor: Anne Bruneau
    Thesis title: The evolution of pollination systems in the genus Erythrina (Fabaceae)
    Julie Faure, Ph.D.
    (Start: 2016, End: 2019)

    Thesis title: Etude des relations plantes-pollinisateurs et de l'évolution de la pollinisation des Gesneriaceae antillaises
    Valérie Poulin, M.Sc.
    (Start: 2017)
    Thesis title: The search for genes that determine the shape of flowers in Gesneriaceae.
    Previous students (since 2009)
    Hermine Alexandre, Ph.D.
    (Start: 2012, End: 2016)
    Thesis title: Mating system evolution in Antillean plants Gesneria and Rhytidophyllum
    Yanitch Aymeric, Ph.D.
    (Start: 2011, End: 2017)

    Other (co-)supervisor: Michel Labrecque, Université de Montréal
    Thesis title: Transcriptomique des espèces végétales utilisées en phytorémédiation de l'arsenic
    Personal page
    Marie Florence Sandrine Ngo Ngwe, Ph.D.
    (Start: 2011, End: 2017)

    Other (co-)supervisor: OMOKOLO NDOUMOU, Denis
    Thesis title: Genetic diversity of species of yam (Dioscorea spp.) in Cameroon and searching for their ability å the microtuberization
    François Lambert, M.Sc.
    (Start: 2013, End: 2015)

    Thesis title: Délimitation d'espèces chez les plantes du complexe du Gesneria viridiflora dans les Antilles
    45- Trees, fungi and bacteria: Tripartite metatranscriptomics of a root microbiome responding to soil contamination
    Gonzalez E., Pitre F.E., Pagé A.P., Marleau J., Guidi Nissim W., St-Arnaud M., Labrecque M., Joly S., Yergeau E., Brereton N.J.B.
    2018 Microbiome (Date Added: 2018-04-04)

    44- Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome
    Yergeau E., Tremblay J., Joly S., Labrecque M., Maynard C., Pitre F.E., St-Arnaud M., Greer C.W.
    2018 ISME Journal (Date Added: 2018-03-30)

    43- Greater pollination generalization is not associated with reduced constraints on corolla shape in Antillean plants
    Joly S., Lambert F., Alexandre H., Clavel J., Léveillé-Bourret
    2018 Evolution (Date Added: 2018-01-21)

    42- Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae
    Alexandre H., Faure J., Ginzbarg S., Clark J., Joly S.
    2017 Royal Society Open Science (Date Added: 2017-11-15)

    40- Transcriptomic response of purple willow (Salix purpurea) to arsenic stress
    Yanitch A., Brereton N.J.B., Gonzalez E., Labrecque M., Joly S., Pitre F.E.
    2017 Frontiers in Plant Science (Date Added: 2017-08-08)

    39- Population isolation shapes plant genetics, phenotype and germination in naturally patchy ecosystems
    De Vriendt, L., Lemay, M.-A., Jean, M., Renaut, S., Pellerin, S., Joly, S., Belzile, F., Poulin, M.
    2016 Journal of Plant Ecology (Date Added: 2017-07-31)

    38- Comparative transcriptomic approaches exploring contamination stress tolerance in Salix sp. Reveal the importance for a metaorganismal de novo assembly approach for nonmodel plants
    Brereton N.J.B., Gonzalez E., Marleau J., Nissim W.G., Labrecque M., Joly S., Pitre F.E.
    2016 Plant Physiology (Date Added: 2017-02-15)

    37- Explaining naturalization and invasiveness: new insights from historical ornamental plant catalogs
    Lavoie, C., Joly, S., Bergeron, A., Guay, G., Groeneveld, E.
    2016 Ecology and Evolution (Date Added: 2016-11-29)

    36- Symbiotic association between Salix purpurea L. and Rhizophagus irregularis: modulation of plant responses under copper stress
    Almeida-Rodriguez, A.M., Gomes, M.P., Loubert-Hudon, A., Joly, S., Labrecque, M.
    2016 Tree Physiology (Date Added: 2016-07-06)

    33- Nuclear DNA content of four cultivated species of yams (Dioscorea spp.) from Cameroon.
    Ngo Ngwe, M.F.S., Joly, S., Bourge, M., Brown, S., Omokolo, D.N.
    2015 Journal of Plant Breeding and Genetics (Date Added: 2016-06-15)

    32- Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices
    Ngo Ngwe, M.F.S., Omokolo, D.N., Joly, S.
    2015 PloS one (Date Added: 2016-02-26)

    31- Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil
    Gonzalez, E., Brereton, N.J.B., Marleau, J., Guidi Nissim, W., Labrecque, M., Pitre, F.E., Joly, S.
    2015 BMC Plant Biology (Date Added: 2015-11-16)

    30- Flexible methods for estimating genetic distances from single nucleotide polymorphisms
    Joly, S., Bryant, D., Lockhart, P.J., Bunce, M.
    2015 Methods in Ecology and Evolution (Date Added: 2015-08-26)

    29- Phylogeny and biogeography of wild roses with specific attention to polyploids
    Fougere-Danezan, M., Joly, S., Bruneau, A., Gao, X.-F., Zhang, L.-B.
    2015 Annals of Botany (Date Added: 2015-02-27)

    28- Increasing phytoremediation efficiency and reliability using novel omics approaches
    Bell, T.H., Joly, S., Pitre, F.E., Yergeau, E.
    2014 Trends in Biotechnology (Date Added: 2014-04-29)

    27- Testing Hybridization Hypotheses with Morphometry: the Case of Eastern American Arctic Species of <I>Potentilla</I> sect. <I>Niveae</I> (Rosaceae)
    Léveillé-Bourret, Étienne, Bailleul, Stéphane M., Cayouette, Jacques, Joly, Simon
    2014 Systematic Botany (Date Added: 2014-03-11)

    26- Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead
    Joly, Simon, Davies, T. Jonathan, Archambault, Annie, Bruneau, Anne, Derry, Alison, Kembel, Steven W., Peres-Neto, Pedro, Vamosi, Jana, Wheeler, Terry A.
    2014 Molecular Ecology Resources (Date Added: 2014-03-04)

    25-Des codes à barre pour toutes les espèces vasculaires québécoises!
    Léveillé-Bourret É., Joly S.
    2013 Flora Québéca ( Date Added: 2016-06-15)

    24- Species Radiation by Niche Shifts in New Zealand's Rockcresses (Pachycladon, Brassicaceae)
    Joly, Simon, Heenan, Peter B., Lockhart, Peter J.
    2013 Systematic Biology (Date Added: 2013-12-19)

    23- Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
    González, Emmanuel, Joly, Simon
    2013 BMC Research Notes (Date Added: 2013-12-12)

    22- Structuration of the genetic and metabolite diversity among Prince Edward Island cultivated wild rose ecotypes
    Ghose, Kaushik, McCallum, Jason, Fillmore, Sherry, Kirby, Chris, Sanderson, Kevin, Joly, Simon, Bruneau, Anne, Fofana, Bourlaye
    2013 Scientia Horticulturae (Date Added: 2013-07-29)

    21- Demographic Signatures Accompanying the Evolution of Selfing in Leavenworthia Alabamica
    Busch, Jeremiah W, Joly, Simon, Schoen, Daniel J
    2011 Molecular Biology and Evolution (Date Added: 2012-04-26)

    19- JML: testing hybridization from species trees
    Joly, Simon
    2011 Molecular Ecology Resources (Date Added: 2011-09-25)

    Joly, S.
    2011 Wild crop relatives : genomic and breeding resources : cereals ( Date Added: 2011-08-26)

    17- Fast diploidization in close mesopolyploid relatives of Arabidopsis
    Mandáková, T., Joly, S., Krzywinski, M., Mummenhoff, K., Lysaka, M.A.
    2010 Plant Cell (Date Added: 2011-04-15)

    16- Erratum: A statistical approach for distinguishing hybridization and incomplete lineage sorting (American Naturalist 174 (E54-E70))
    Joly, S., Pfeil, B.E., Oxelman, B., McLenachan, P.A., Lockhart, P.J.
    2010 American Naturalist (Date Added: 2011-04-15)

    14- A statistical approach for distinguishing hybridization and incomplete lineage sorting
    Joly, S., McLenachan, P.A., Lockhart, P.J.
    2009 American Naturalist (Date Added: 2011-04-15)

    13- A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand
    Joly, S., Heenan, P.B., Lockhart, P.J.
    2009 Molecular Phylogenetics and Evolution (Date Added: 2011-04-15)

    12- Measuring branch support in species trees obtained by gene tree parsimony
    Joly, S., Bruneau, A.
    2009 Systematic Biology (Date Added: 2011-04-15)

    11- An approach to transcriptome analysis of non-model organisms using short-read sequences
    Collins, L.J., Biggs, P.J., Voelckel, C., Joly, S.
    2008 Genome informatics. International Conference on Genome Informatics (Date Added: 2011-04-15)

    10- Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with red algal plastid genes
    Wang, Y., Joly, S., Morse, D.
    2008 Journal of Molecular Evolution (Date Added: 2011-04-15)

    9- Phylogenetic relationships in the genus Rosa: New evidence from chloroplast DNA sequences and an appraisal of current knowledge
    Bruneau, A., Starr, J.R., Joly, S.
    2007 Systematic Botany (Date Added: 2011-04-15)

    8- Delimiting species boundaries in Rosa sect. Cinnamomeae (Rosaceae) in eastern North America
    Joly, S., Bruneau, A.
    2007 Systematic Botany (Date Added: 2011-04-15)

    7- Haplotype networks can be misleading in the presence of missing data.
    Joly, S., Stevens, M.I., van Vuuren, B.J.
    2007 Systematic biology (Date Added: 2011-04-15)

    6- Polyploid and hybrid evolution in roses east of the Rocky Mountains
    Joly, S., Starr, J.R., Lewis, W.H., Bruneau, A.
    2006 American Journal of Botany (Date Added: 2011-04-15)

    4- Molecular markers indicate that the narrow Québec endemics Rosa rousseauiorum and Rosa williamsii are synonymous with the widespread Rosa blanda
    Bruneau, A., Joly, S., Starr, J.R., Drouin, J.-N.
    2005 Canadian Journal of Botany (Date Added: 2011-04-15)

    2- Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial glycine allopolyploids
    Joly, S., Rauscher, J.T., Sherman-Broyles, S.L., Brown, A.H.D., Doyle, J.J.
    2004 Molecular Biology and Evolution (Date Added: 2011-04-15)

    1- Phylogenetic implications of the multiple losses of the mitochondrial coxll.i3 intron in the angiosperms
    Joly, S., Brouillet, L., Bruneau, A.
    2001 International Journal of Plant Sciences (Date Added: 2011-04-15)

    In the media
    Champignons et bactéries aident les plantes
    UdeMNouvelles (Sauvé, Mathieu-Robert) 2014-04-24

    Reproduction végétale valorisée
    Les années lumière 2012-03-25

    What part of a scented flower gives off the smell?
    Quirks & Quarks (McDonald, Bob) 2011-05-28