Simon Joly

Adjunct Professor,
Université de Montréal

Institut de recherche en biologie végétale
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

    (Start: 2022, End: 2025)
    Evolution de la forme et de la taille des fleurs de l’impatiente du cap (Impatiens capensis) dans les environnements urbains

    Marion Leménager

    (Start: 2019)
    Evolution de la morphologie florale des Gesneriaceae Antillaises

    Maryane Gradito

    (Start: 2020)
    Heliotropism in Trillium grandiflorum provides increased reproductive success

    Previous students (since 2009)

    Hermine Alexandre

    (Start: 2012, End: 2016)
    Mating system evolution in Antillean plants Gesneria and Rhytidophyllum

    Yanitch Aymeric

    Other (co-)supervisor: Michel Labrecque, Université de Montréal
    (Start: 2011, End: 2017)
    Transcriptomique des espèces végétales utilisées en phytorémédiation de l'arsenic
    Personal page

    Julie Faure

    (Start: 2016, End: 2019)
    Etude des relations plantes-pollinisateurs et de l'évolution de la pollinisation des Gesneriaceae antillaises

    Marie Florence Sandrine Ngo Ngwe

    Other (co-)supervisor: OMOKOLO NDOUMOU, Denis
    (Start: 2011, End: 2017)
    Genetic diversity of species of yam (Dioscorea spp.) in Cameroon and searching for their ability å the microtuberization

    Gonzalo Bilbao Gómez-Martino

    (Start: 2015, End: 2020)
    Other QCBS (co-)supervisor: Anne Bruneau
    Pollinator prediction based on floral shape in the genus Erythrina (Fabaceae)

    Loudmila Jelinscaia Lagou

    (Start: 2021, End: 2024)
    Phylogenomics and Historical Biogeography of the Slipper Orchid Genus Cypripedium L. Using Target Enrichment Data

    François Lambert

    (Start: 2013, End: 2015)
    Délimitation d'espèces chez les plantes du complexe du Gesneria viridiflora dans les Antilles

    Examples of species studied

    Rosa rousseauiorum
    Rosa williamsii
    Apios americana
    Leavenworthia alabamica
    Rosa blanda
    Salix purpurea
    Rhizophagus irregularis
    Trillium grandiflorum
    Impatiens capensis


    84- Variation in flower size and shape of Impatiens capensis is correlated with urbanization in Montreal, Canada
    Journal Article
    Faure J , Volz V , Joly S ,
    2023 Ecology and Evolution (Date Added: 2023-12-17)

    83- The Contribution of the Montreal Botanical Garden to Plant Conservation
    Book Book Chapter
    Bailleul S , Cuerrier A , Joly S , Pellerin S , Labrecque M ,
    2023 Botanical Gardens and Their Role in Plant Conservation: European and American Botanical Gardens, Volume 3 (Date Added: 2023-10-16)

    81- Regional plant abundance explains patterns of host use by pollen-specialist bees in eastern North America
    Journal Article
    Smith C , Joly S , Antoine C , Hyjazie B , Forrest J R K ,
    2023 Ecology (Date Added: 2023-07-07)

    80- Three New Gesneria Species (Gesneriaceae) Support Parc National Pic Macaya (Haiti) as an Important Biodiversity Hotspot
    Journal Article
    Joly S , Lambert F , Cinea W , Clark J L ,
    2023 Systematic Botany (Date Added: 2023-05-02)

    79- Chromosome size matters: genome evolution in the cyperid clade
    Journal Article
    Elliott T L , Zedek F , Barrett R L , Bruhl J J , Escudero M , Hroudová Z , Joly S , Larridon I , Luceño M , Márquez-Corro J I , Martín-Bravo S , Muasya A M , Šmarda P , Thomas W W , Wilson K L , Bureš P ,
    2022 Annals of Botany (Date Added: 2023-05-02)

    78- Studying flowers in 3D using photogrammetry
    Journal Article
    Leménager M , Burkiewicz J , Schoen D J , Joly S ,
    2022 New Phytologist (Date Added: 2022-12-06)

    77- Heliotropism in Trillium grandiflorum provides increased reproductive success
    Journal Article
    Gradito M , Fauteux C , Joly S ,
    2022 Botany (Date Added: 2022-09-10)

    76- Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae)
    Journal Article
    Poulin V , Amesefe D , Gonzalez E , Alexandre H , Joly S ,
    2022 PLoS ONE (Date Added: 2022-08-01)

    Journal Article
    Faure J , Martén-Rodríguez S , Clark J L , Joly S ,
    2022 International Journal of Plant Sciences (Date Added: 2022-02-04)

    73- Judge it by its shape: a pollinator-blind approach reveals convergence in petal shape and infers pollination modes in the genus Erythrina
    Journal Article
    Bilbao G , Bruneau A , Joly S ,
    2021 American Journal of Botany (Date Added: 2021-10-20)

    72- Global dispersal and diversification of the genus Schoenus (Cyperaceae) from the Western Australian biodiversity hotspot
    Journal Article
    Elliott T L , Mazijk R , Barrett R L , Bruhl J J , Joly S , Muthaphuli N , Wilson K L , Muasya A M ,
    2021 Journal of Systematics and Evolution (Date Added: 2021-06-14)

    71- Repeated evolution of a reproductive polyphenism in plants is strongly associated with bilateral flower symmetry
    Journal Article
    Joly S , Schoen D J ,
    2021 Current Biology (Date Added: 2021-03-02)

    70- Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species
    Journal Article
    Albani Rocchetti G , Armstrong C G , Abeli T , Orsenigo S , Jasper C , Joly S , Bruneau A , Zytaruk M , Vamosi J C ,
    2020 New Phytologist (Date Added: 2021-01-26)

    69- A multi-platform package for the analysis of intra- and interspecific trait evolution
    Journal Article
    Gaboriau T , Mendes F K , Joly S , Silvestro D , Salamin N ,
    2020 Methods in Ecology and Evolution (Date Added: 2020-09-19)

    68- A four-year phytoremediation trial to decontaminate soil polluted by wood preservatives: phytoextraction of arsenic, chromium, copper, dioxins and furans
    Journal Note
    Yanitch A , Kadri H , Frenette-Dussault C , Joly S , Pitre F E , Labrecque M ,
    2020 International Journal of Phytoremediation (Date Added: 2020-07-19)

    67- Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth
    Journal Article
    Carteron A , Beigas M , Joly S , Turner B L , Laliberté E ,
    2020 Microbial Ecology (Date Added: 2020-06-27)

    66- On the importance of accounting for intraspecific genomic relatedness in multi-species studies
    Journal Article
    Joly S , Flynn D F B , Wolkovich E M ,
    2019 Methods in Ecology and Evolution (Date Added: 2019-05-22)

    65- An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)
    Journal Article
    Lee-Yaw J A , Grassa C J , Joly S , Andrew R L , Rieseberg L H ,
    2018 New Phytologist (Date Added: 2018-09-04)

    64- Trees, fungi and bacteria: Tripartite metatranscriptomics of a root microbiome responding to soil contamination
    Journal Article
    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)

    63- Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome
    Journal Article
    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)

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

    61-Fiche d’identification: Les impatientes
    Magazine Article
    Joly, S
    2017 Flore Alors! ( Date Added: 2018-05-17)

    60-Des plantes zombies
    Magazine Article
    Joly, S
    2017 Flore Alors! ( Date Added: 2018-05-17)

    59-Journal de botanique: Le lichen et le dentiste; Les cerfs ont rapetissé les trilles; Un palmier canadien; Traces millénaires en forêt amazonienne.
    Magazine Article
    Joly, S, Croisetière, M-H
    2017 Quatre-Temps ( Date Added: 2018-05-17)

    58-Journal de botanique: Vision souterraine; Coco en danger; Algues au menu; Mmmm, du vieux sirop!.
    Magazine Article
    Joly, S
    2017 Quatre-Temps ( Date Added: 2018-05-17)

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

    56- Species delimitation in the Caribbean gesneria viridiflora complex (Gesneriaceae) reveals unsuspected endemism
    Journal Article
    Lambert F , Clark J L , Joly S ,
    2017 Taxon (Date Added: 2017-11-05)

    55- Transcriptomic response of purple willow (Salix purpurea) to arsenic stress
    Journal Article
    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)

    54-Journal de botanique: Connaissez-vous FloraQuebeca?; Plus d’arbres que d’étoiles!; Changer de sexe... à 2000 ans!; La pollution pourrait-elle avoir certains avantages?
    Magazine Article
    Joly, S, Croisetière, M-H
    2016 Quatre-Temps ( Date Added: 2018-05-17)

    53-Journal de botanique: L’arbre national du Brésil... rebaptisé ici!; Tic, tac, tournesol!; Chez les lichens, 1+2=1; Qui digère la mouche... digère le gluten!
    Magazine Article
    Joly, S, Gagnon E ,
    2016 Quatre-Temps ( Date Added: 2018-05-17)

    52-Fiche d’identification: la grande molène
    Magazine Article
    Joly S ,
    2016 Flore Alors! ( Date Added: 2018-05-17)

    51-Journal de botanique: La termite et la fée; Alerte aux vers de terre; Bilan mondial des plantes; Des bactéries foliaires qui coopèrent
    Magazine Article
    Joly, S, M-H Croisetière,
    2016 Quatre-Temps ( Date Added: 2018-05-17)

    50-Journal de botanique: Une boisson énergisante pour abeilles; Je t’attrape dans 3, 2, 1, ...; Liste mondiale des plantes: une étape franchie; Taraxacum toxique
    Magazine Article
    Joly, S, Derome, R
    2016 Quatre-temps ( Date Added: 2018-05-17)

    49-Fiche d’identification: l’épilobe à feuilles étroites
    Magazine Article
    Joly S ,
    2016 Flore Alors! ( Date Added: 2018-05-17)

    48- Population isolation shapes plant genetics, phenotype and germination in naturally patchy ecosystems
    Journal Article
    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)

    47- Comparative transcriptomic approaches exploring contamination stress tolerance in Salix sp. Reveal the importance for a metaorganismal de novo assembly approach for nonmodel plants
    Journal Article
    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)

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

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

    43- Explaining forest productivity using tree functional traits and phylogenetic information: two sides of the same coin over evolutionary scale?
    Journal Article
    Paquette, A, Joly, S, Messier, C
    2015 Ecology and Evolution (Date Added: 2016-07-06)

    42-Les plantes sont-elles mélomanes?
    Magazine Article
    Joly, S
    2015 Quatre-tempts ( Date Added: 2016-06-15)

    41-Journal de botanique: Peu de samares, beaucoup de sirop!; Attention aux coups de soleil; La création d’un châtaignier résistant au chancre; Le glas de la tordeuse des bourgeons de l’épinette; Une vision commune partagée entre Montréal et Paris
    Magazine Article
    Joly, S
    2015 Quatre-temps ( Date Added: 2016-06-15)

    40-Journal de botanique: Une plante carnivore géante découverte sur Facebook; Images inédites du Frère Marie-Victorin; Les plantes aussi ont leurs probiotiques; Fourmis à votre service
    Magazine Article
    Joly, S
    2015 Quatre-temps ( Date Added: 2016-06-15)

    39-Journal de botanique: Réunies après 60 millions d’années!; La clé de la biodiversité; La limace qui voulait être une plante; Une fleur pour Sir David Attenborough
    Magazine Article
    Joly, S
    2015 Quatre-temps ( Date Added: 2016-06-15)

    38-Journal de botanique: Colibri préféré, traitement accéléré; Des opiacés sans pavot?; Fertilisants contre symbioses; Botanique poétique
    Magazine Article
    Joly, S
    2015 Quatre-temps ( Date Added: 2016-06-15)

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

    36- Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices
    Journal Article
    Ngo Ngwe, MFS, Omokolo, DN, Joly, S
    2015 PloS one (Date Added: 2016-02-26)

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

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

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

    32-Le temps chez les plantes d’un point de vue évolutif
    Magazine Article
    Joly S ,
    2014 Quatre-temps ( Date Added: 2016-06-20)

    31- Increasing phytoremediation efficiency and reliability using novel omics approaches
    Journal Article
    Bell, TH, Joly, S, Pitre, FE, Yergeau, E
    2014 Trends in Biotechnology (Date Added: 2014-04-29)

    30- Testing Hybridization Hypotheses with Morphometry: the Case of Eastern American Arctic Species of <I>Potentilla</I> sect. <I>Niveae</I> (Rosaceae)
    Journal Article
    Léveillé-Bourret, , Bailleul, SM, Cayouette, J, Joly, S
    2014 Systematic Botany (Date Added: 2014-03-11)

    29- Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead
    Journal Article
    Joly, S, Davies, TJ, Archambault, A, Bruneau, A, Derry, A, Kembel, SW, Peres-Neto, P, Vamosi, J, Wheeler, TA
    2014 Molecular Ecology Resources (Date Added: 2014-03-04)

    28-Perspectives génétiques sur la conservation du ginseng à cinq folioles dans le sud québécois
    Joly, P
    2013 Jour de la terre-Québec ( Date Added: 2016-06-20)

    27-Programmes de rétablissement du carex faux-lupulina et de la carmantine d’Amérique
    Pellerin, J
    2013 Jour de la terre-Québec et aux Laboratoires Klorane ( Date Added: 2016-06-20)

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

    25- Species Radiation by Niche Shifts in New Zealand's Rockcresses (Pachycladon, Brassicaceae)
    Journal Article
    Joly, S, Heenan, PB, Lockhart, PJ
    2013 Systematic Biology (Date Added: 2013-12-19)

    24- Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
    Journal Article
    González, E, Joly, S
    2013 BMC Research Notes (Date Added: 2013-12-12)

    23- Structuration of the genetic and metabolite diversity among Prince Edward Island cultivated wild rose ecotypes
    Journal Article
    Ghose, K, McCallum, J, Fillmore, S, Kirby, C, Sanderson, K, Joly, S, Bruneau, A, Fofana, B
    2013 Scientia Horticulturae (Date Added: 2013-07-29)

    22- Demographic Signatures Accompanying the Evolution of Selfing in Leavenworthia Alabamica
    Journal Article
    Busch, JW, Joly, S, Schoen, DJ
    2011 Molecular Biology and Evolution (Date Added: 2012-04-26)

    21- Migration rates, frequency-dependant selection and the self-incompatibiliy locus in Leavenworthia (Brassicaceae)
    Journal Article
    Joly, S, Schoen, DJ
    2011 Evolution (Date Added: 2012-04-26)

    20- JML: testing hybridization from species trees
    Journal Article
    Joly, S
    2011 Molecular Ecology Resources (Date Added: 2011-09-25)

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

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

    17- Erratum: A statistical approach for distinguishing hybridization and incomplete lineage sorting (American Naturalist 174 (E54-E70))
    Journal Article
    Joly, S, Pfeil, BE, Oxelman, B, McLenachan, PA, Lockhart, PJ
    2010 American Naturalist (Date Added: 2011-04-15)

    16- Does mate limitation in self-incompatible species promote the evolution of selfing? the case of Leavenworthia alabamica
    Journal Article
    Busch, JW, Joly, S, Schoen, DJ
    2010 Evolution (Date Added: 2011-04-15)

    15- A statistical approach for distinguishing hybridization and incomplete lineage sorting
    Journal Article
    Joly, S, McLenachan, PA, Lockhart, PJ
    2009 American Naturalist (Date Added: 2011-04-15)

    14- A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand
    Journal Article
    Joly, S, Heenan, PB, Lockhart, PJ
    2009 Molecular Phylogenetics and Evolution (Date Added: 2011-04-15)

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

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

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

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

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

    8- Haplotype networks can be misleading in the presence of missing data.
    Journal Article
    Joly, S, Stevens, MI, van Vuuren, BJ
    2007 Systematic biology (Date Added: 2011-04-15)

    7- Polyploid and hybrid evolution in roses east of the Rocky Mountains
    Journal Article
    Joly, S, Starr, JR, Lewis, WH, Bruneau, A
    2006 American Journal of Botany (Date Added: 2011-04-15)

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

    4- Evolution of triploidy in Apios americana (Leguminosae) revealed by genealogical analysis of the histone H3-D gene
    Journal Article
    Joly, S, Bruneau, A
    2004 Evolution (Date Added: 2011-04-15)

    3- Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial glycine allopolyploids
    Journal Article
    Joly, S, Rauscher, JT, Sherman-Broyles, SL, Brown, AHD, Doyle, JJ
    2004 Molecular Biology and Evolution (Date Added: 2011-04-15)

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

    1- Genetic structure of the American ginseng (_Panax quinquefolius_L.) in Eastern Canada using reduced-representation high-throughput sequencing
    Journal Article
    Joly, S, Archambault, A, Pellerin, S, Nault, A
    Botany (Date Added: 2021-01-14)

    In the media

    La nature prend et redonne

    6 reasons to go to Montreal's Great Gardening Weekend
    (Marchenkova, Darya) 2018-05-24

    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