Simon Joly
Adjunct Professor,Université de Montréal
Institut de recherche en biologie végétale
E-mail: simon.joly@umontreal.ca
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EducationResearchSimon 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 honoursQCBS students Jérôme BurkiewiczPh.D.  Marion LeménagerPh.D.  Maryane GraditoB.Sc. Previous students (since 2009) Tammy ElliottPostdoctoral fellow  Hermine AlexandrePh.D.  Yanitch AymericPh.D.  Julie FaurePh.D.  Marie Florence Sandrine Ngo NgwePh.D.  Gonzalo Bilbao Gómez-MartinoNA Loudmila Jelinscaia LagouM.Sc.  François LambertM.Sc. Involvement within the QCBS
Examples of species studiedPachycladon Brassicaceae Leavenworthia Rosaceae Rosa rousseauiorum Rosa williamsii Apios americana Leguminosae Arabidopsis Leavenworthia alabamica Rosa blanda Rhytidophyllum Gesneriaceae Colibri Salix purpurea Rhizophagus irregularis Salix Helianthus Gesneria Panax Schoenus Cyperaceae Erythrina Trillium grandiflorum Impatiens capensis Publications87- Latitudinal gradients in seed predation persist in urbanized environments Journal Article Hargreaves A L , Ensing J , Rahn O , Oliveira F M P , Burkiewicz J , Lafond J , Haeussler S , Byerley-Best M B , Lazda K , Slinn H L , Martin E , Carlson M L , Sformo T L , Dawson-Glass E , Chiuffo M C , Vargas-Rodriguez Y L , GarcÃa-Jiménez C I , Gomes I J M T , Klemet-N’Guessan S , Paolucci L , Joly S , Mehltreter K , Muñoz J , Buono C , Brodie J F , Rodriguez-Campbell A , Veen T , Freeman B G , Lee-Yaw J A , Muñoz J C , Paquette A , Butler J , Suaréz E , 2024 Nature Ecology and Evolution (Date Added: 2024-09-11) 86- Phenology varies with phylogeny but not by trophic level with climate change Journal Article Loughnan D , Joly S , Legault G , Kharouba H M , Betancourt M , Wolkovich E M , 2024 Nature Ecology and Evolution (Date Added: 2024-09-10) 85- Herbarium collections remain essential in the age of community science Journal Article Eckert I , Bruneau A , Metsger D A , Joly S , Dickinson T A , Pollock L J , 2024 Nature Communications (Date Added: 2024-09-07) 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) 82- Erratum: Three new species of Gesneria (Gesneriaceae) Systematic Botany 48(1): 34–43 (2023) DOI: 10.1600/036364423X16758873924081) Journal Erratum , 2023 Systematic Botany (Date Added: 2023-07-25) 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 , MartÃn-Bravo S , Muasya A M , Å marda P , Thomas W W , Wilson K L , BureÅ¡ 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) 75- THE LEVEL OF POLLINATION SPECIALIZATION AFFECTS THE RELATIONSHIP BETWEEN THE SHAPE OF FLOWERS AND THE BILLS OF THEIR HUMMINGBIRD POLLINATORS IN ANTILLEAN GESNERIACEAE Journal Article Faure J , Martén-RodrÃguez S , Clark J L , Joly S , 2022 International Journal of Plant Sciences (Date Added: 2022-02-04) 74- Red and yellow pigments in autumn leaves are associated with higher nitrogen resorption: A comment on Peña-Novas and Marchetti 2021 (https://doi.org/10.1111/jeb.13903) Journal Note Joly S , 2022 Journal of Evolutionary Biology (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, Ã, 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) 44- Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae) Journal Article Alexandre, H, Vrignaud, J, Mangin, B, Joly, S 2015 PeerJ (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, Ã, 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 Report 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 Report 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) 19-Pachycladon 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) 6- Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: An example from Rosa in North America. Journal Article Joly, S, Bruneau, A 2006 Systematic biology (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 mediaLa nature prend et redonne 2019-02-20 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 |
