In press

Studying flowers in 3D using photogrammetry
Marion Leménager, Jérôme Burkiewicz, Daniel Schoen, Simon Joly
New Phytologist
doi: 10.1111/nph.18553
pdf | Link to the journal | Supplementary Materials | Photogrammetry protocol | 3D Flower Models

Chromosome size matters: genome evolution in the cyperid clade
Tammy L Elliott, František Zedek, Russell L Barrett, Jeremy J Bruhl, Marcial Escudero, Zdenka Hroudová, Simon Joly, Isabel Larridon, Modesto Luceño, José Ignacio Márquez-Corro, Santiago Martín-Bravo, A Muthama Muasya, Petr Šmarda, William Wayt Thomas, Karen L Wilson, Petr Bureš
Annals of Botany
doi: 10.1093/aob/mcac136
Link to the journal

Three new Gesneria species (Gesneriaceae) support Parc National Pic Macaya (Haiti) as an important biodiversity hotspot
Simon Joly, François Lambert, William Cinea, John L. Clark
Systematic Botany


Heliotropism in Trillium grandiflorum provides increased reproductive success
Maryane Gradito, Catherine Fauteux, Simon Joly
Botany 100(8): 643-651
doi: 10.1139/cjb-2021-0205
pdf | Link to the journal | Supplementary material | Data

Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae)
Valérie Poulin, Delase Amesefe, Emmanuel Gonzalez, Hermine Alexandre, Simon Joly
PLOS ONE 17(7): e0267540
doi: 10.1371/journal.pone.0267540
pdf | Link to the journal | Supplementary material | Data

The level of pollination specialization affects the relationship between the shape of flowers and the bill of their hummingbird pollinators in Antillean Gesneriaceae
Julie Faure, Silvana Martén-Rodríguez, John L. Clark, Simon Joly
International Journal of Plant Sciences 183(3):193-204
doi: 10.1086/718221
pdf | Link to the journal | Supplementary material | Data

Red and yellow pigments in autumn leaves are associated with higher nitrogen resorption
Simon Joly
Journal of Evolutionary Biology 35(1):180-182
doi: 10.1111/jeb.13961
pdf | Link to the journal | Data


Repeated evolution of a reproductive polyphenism in plants is strongly associated with bilateral flower symmetry
Simon Joly, Daniel J. Schoen
Current Biology 31(7): 1515-1520
doi: 10.1016/j.cub.2021.01.009
Link to the journal | Data

Judge it by its shape: a pollinator-blind approach reveals convergence in petal shape and infers pollination modes in the genus Erythrina
Gonzalo Bilbao, Anne Bruneau, Simon Joly
American Journal of Botany 108(9): 1716-1730
doi: 10.1002/ajb2.1735
Link to the journal

Global dispersal and diversification of the genus Schoenus (Cyperaceae) from the Western Australian biodiversity hotspot
Tammy Elliott, Ruan van Mazijk, Russell L. Barrett, Jeremy J. Bruhl, Simon Joly, Ngalirendwe Muthaphuli, Karen L. Wilson, and A. Muthama Muasya
Journal of Systematics and Evolution 59(4): 791-808
doi: 10.1111/jse.12742
Link to the journal

Temperate forests dominated by arbuscular or ectomycorrhizal fungi are characterized by strong shifts from saprotrophic to mycorrhizal fungi with increasing soil depth
Alexis Carteron, Marie Beigas, Simon Joly, Benjamin L. Turner, Etienne Laliberté
Microbial Ecology 82: 377-390
doi: 10.1007/s00248-020-01540-7
pdf | Link to the journal | Data

Reversing extinction trends: New uses of (old) herbarium specimens to accelerate conservation action on threatened species
Giulia Albani Rocchetti, Chelsey Armstrong, Thomas Abeli, Simone Orsenigo, Caroline Jasper, Simon Joly, Anne Bruneau, Maria Zytaruk, Jana Vamosi
New Phytologist 230(2): 433-450
doi: 10.1111/nph.17133
pdf | Link to the journal


Pollinator performance of the pollination generalist Rhytidophyllum bicolor (Gesneriaceae) in Haiti 15 months after the Matthew hurricane
Julie Faure, Simon Joly
Selbyana 33(3): 32-42
pdf | Link to the journal

A multi-platform package for the analysis of intra- and interspecific trait evolution
Théo Gaboriau, Fabio Mendes, Simon Joly, Daniele Silvestro, Nicolas Salamin
Methods in Ecology and Evolution 11(11): 1439-1447
doi: 10.1111/2041-210X.13458
pdf | Link to the journal | R bite package

A four-year phytoremediation trial to decontaminate soil polluted by wood preservatives: phytoextraction of arsenic, chromium, copper, dioxins and furans
Aymeric Yanitch, Hafssa Kadri, Cédric Frenette-Dussault, Simon Joly, Frédéric Pitre, Michel Labrecque
International Journal of Phytoremediation 22(14): 1505-1514
doi: 10.1080/15226514.2020.1785387
Link to the journal


On the importance of accounting for intraspecific genomic relatedness in multi-species studies
Simon Joly, Dan F. B. Flynn, Elizabeth Wolkovich
Methods in Ecology and Evolution 10(7): 994-1001
doi: 10.1111/2041-210X.13184
pdf | Link to the journal | Media coverage | Supplementary Material | Data

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)
Julie A. Lee‐Yaw, Christopher J. Grassa, Simon Joly, Rose L. Andrew, Loren H. Rieseberg
New Phytologist 221: 515–526
pdf | Link to the journal


Soil contamination alters the willow root and rhizosphere metatranscriptomes and the root-rhizosphere interactome
Etienne Yergeau, Julien Tremblay, Simon Joly, Michel Labrecque, Christine Maynard, Frederic Pitre, Marc St-Arnaud, Charles Greer
ISME Journal 12: 869-884
pdf | Link to the journal

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination
Emmanuel Gonzalez, Frederic E. Pitre, Antoine Pagé, Julie Marleau, Werther Guidi Nissim, Marc St-Arnaud, Michel Labrecque, Simon Joly, Etienne Yergeau, Nicholas James Beresford Brereton
Microbiome 6:53
pdf | Link to the journal

Greater pollination generalization is not associated with reduced constraints on corolla shape in Antillean plants
Simon Joly, François Lambert, Hermine Alexandre, Julien Clavel, Étienne Léveillé-Bourret, John L. Clark
Evolution 72(2): 244-260
pdf | Link to the Journal | Supplementary Material | Interactive Figures | Data


Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae
Hermine Alexandre, Julie Faure, Steven Ginzbarg, John L. Clark, Simon Joly
Royal Society Open Science 4: 170293
pdf | Supplementary Material | Link to the Journal

Species delimitation in the Caribbean Gesneria viridiflora complex (Gesneriaceae) reveals unsuspected endemism
François Lambert, John L. Clark, Simon Joly
Taxon 66(5): 1171-1183

Population isolation shapes plant genetics, phenotype and germination in naturally patchy ecosystems
Laurent De Vriendt, Marc-André Lemay, Martine Jean, Sébastien Renaut, Stéphanie Pellerin, Simon Joly, François Belzile, Monique Poulin
Journal of Plant Ecology 10(4):649-659
pdf | Link to the Journal

Transcriptomic response of purple willow (Salix purpurea) to arsenic stress
Aymeric Yanitch, Nicholas J. Brereton, Emmanuel Gonzalez, Michel Labrecque, Simon Joly and Frederic Pitre
Frontiers in Plant Science 8:1115
pdf | Supplementary Material | Link to the Journal

Genetic structure of the American ginseng (Panax quinquefolius L.) in Eastern Canada using reduced-representation high-throughput sequencing
Simon Joly, Annie Archambault, Stéphanie Pellerin, Andrée Nault
Botany 95(4):429-434
pdf | Supplementary Material | Data | Link to the Journal


Explaining naturalization and invasiveness: new insights from historical ornamental plant catalogues
Claude Lavoie, Simon Joly, Alexandre Bergeron, Geneviève Guay and Elisabeth Groeneveld
Ecology and Evolution 6:7188-7198
pdf | Media coverage | Link to the Journal

Comparative transcriptomic approaches exploring contamination stress tolerance in Salix sp. reveal the importance for a metaorganismal de novo assembly approach for nonmodel plants
Nicholas J. B. Brereton, Emmanuel Gonzalez, Julie Marleau, Werther Guidi Nissim, Michel Labrecque, Simon Joly and Frederic E. Pitre
Plant Physiology 171:3-24
pdf | Link to the Journal

Symbiotic association between Salix purpurea and Rhizophagus irregularis: modulation of plant responses under copper stress
Adriana M. Almeida-Rodriguez, Marcelo P. Gómez, Audrey Loubert-Hudon, Simon Joly, Michel Labrecque
Tree Physiology36:407-420
pdf | Link to the Journal


Evolution and phylogenetic diversity of yam species (Dioscorea spp.): implication for conservation and agricultural practices
Marie Florence Sandrine Ngo Ngwe, Denis Ndoumou Omokolo, Simon Joly
PLoS ONE 10(12): e0145364
pdf | Link to the Journal

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil
Emmanuel Gonzalez, Nicholas Brereton, Julie Marleau, Wherther Guidi, Michel Labrecque, Frederic Pitre, Simon Joly
BMC Plant Biology 15:246
pdf | data | Link to the Journal

Flexible methods for estimating genetic distances from nucleotide data
Simon Joly, David Bryant, Peter J. Lockhart
Methods in Ecology and Evolution 6:938-948
pdf | Supplementary Material | data | software | Link to the Journal

Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae)
Hermine Alexandre, Justine Vrignaud, Brigitte Mangin, Simon Joly
PeerJ 3:e1028
pdf | Supplementary Material | data | Link to the journal

Functional traits related to forest productivity and phylogenetic information: two sides of the same coin over evolutionary scale
Alain Paquette, Simon Joly, Christian Messier
Ecology and Evolution 5(9):1774-1783
pdf | Supplementary Material | Link to the Journal

Phylogeny and biogeography of wild roses with specific attention to polyploids
M Fougère-Danezan, S Joly, A Bruneau, XF Gao, LB Zhang
Annals of Botany 115:275-291
pdf | Link to the Journal


Species Radiation by Niche Shifts in New Zealand’s Rockcresses (Pachycladon, Brassicaceae)
Simon Joly, Peter B. Heenan, Peter J. Lockhart
Systematic Biology 63(2):192-202
pdf | data | Link to the Journal

Increasing phytoremediation efficiency and reliability using novel ‘omics approaches
Terrence H. Bell, Simon Joly, Frédéric E. Pitre, Etienne Yergeau
Trends in Biotechnology 32(5):271-280
pdf | Link to the Journal

Ecology in the age of DNA barcoding: the resource, the promise, and the challenges ahead
Simon Joly, T. Jonathan Davies, Annie Archambault, Anne Bruneau, Alison Derry, Steven Kembel, Pedro Peres-Neto, Jana Vamosi, Terry Wheeler
Molecular Ecology Resources 14:221-232
pdf | Link to the Journal

Testing Hybridization Hypotheses with Morphometry: the Case of Eastern American Arctic Species of Potentilla sect. Niveae (Rosaceae)
Étienne Léveillé-Bourret, Stéphane M. Bailleul, Jacques Cayouette, Simon Joly
Systematic Botany 39(1):193-204

Nuclear DNA content analysis of four cultivated species of yams (Dioscorea spp.) from Cameroon
Marie Florence Sandrine Ngo Ngwe, Simon Joly, M Bourge, Spencer Brown, Denis N Omokolo
Journal of Plant Breeding and Genetics 2 (2), 87-95


Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
Emmanuel Gonzalez, Simon Joly
BMC Research Notes 6:503
pdf | Link to the Journal

Structuration of the genetic and metabolite diversity among Prince Edward Island cultivated wild rose ecotypes
Kaushik Ghose, Jason McCallum, Sherry Fillmore, Chris Kirby, Kevin Sanderson, Simon Joly, Anne Bruneau, Bourlaye Fofana
Scientia Horticulturae 160: 251-263
pdf | Link to the Journal


JML: testing hybridization from species trees
Simon Joly
Molecular Ecology Ressources 12: 179-184
pdf | Supplementary Material | Data | software | Link to the Journal


Migration rates, frequency-dependent selection and the self-incompatibility locus in Leavenworthia (Brassicaceae)
Simon Joly, Daniel J. Schoen
Evolution 65: 2357-2369
pdf | Supplementary Material | Link to the Journal

Demographic signatures accompanying the evolution of selfing in Leavenworthia alabamica
Jeremiah W. Busch, Simon Joly, Daniel J. Schoen
Molecular Biology and Evolution 28: 1717-1729
pdf | Supplementary Material | Link to the Journal

Krithika Yogeeswaran, Claudia Voelckel, Simon Joly, Peter B. Heenan
Dans Wild Crop Relatives: Genomic and Breeding Resources, ed. Chittaranjan Kole.
Springer, Berlin. pp. 227-249


Fast diploidization in close mesopolyploid relatives of Arabidopsis
Terezie Mandáková, Simon Joly, Martin Krzywinski, Klaus Mummenhoff, Martin A. Lysak
The Plant Cell 22: 2277-2290
pdf | Supplementary Material | Link to the Journal

Does mate limitation in self-incompatible species promote the evolution of selfing? The case of Leavenworthia alabamica
Jeremiah W. Busch, Simon Joly, Daniel J. Schoen
Evolution 64: 1657-1670
pdf | Link to the Journal


A statistical approach for distinguishing hybridization and incomplete lineage sorting.
Simon Joly, Patricia A. McLenachan, Peter J. Lockhart
The American Naturalist 174: e54-e70
pdf | Correction

Measuring branch support in species trees obtained by gene tree parsimony
Simon Joly, Anne Bruneau
Systematic Biology 58: 100-113

A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand
Simon Joly, Peter B. Heenan, Peter J. Lockhart Molecular Phylogenetics and Evolution 51:365-372.
pdf | Supplementary Material


An approach to transcriptome analysis of non-model organisms using short-read sequences.
Lesley J. Collins, Patrick J. Biggs, Claudia Voelckel, Simon Joly
Genome Informatics 21: 3-14

Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with stramenopile plastid genes
Yunling Wang, Simon Joly, David Morse
Journal of Molecular Evolution 66: 175-184


Haplotype Networks can be Misleading in the Presence of Missing Data
Simon Joly, Mark I. Stevens, Bettine Jansen Van Vuuren
Systematic Biology 56:857-862.

Delimiting species boundaries in Rosa sect. Cinnamomeae (Rosaceae) in eastern North America
Simon Joly, Anne Bruneau
Systematic Botany 32: 819-836

Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and appraisal of current knowledge
Anne Bruneau, Julian R. Starr, Simon Joly
Systematic Botany 32:366-378.


Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America
Simon Joly, Anne Bruneau
Systematic Biology 55: 623-636

Evolution des roses (Rosa:Rosaceae) indigènes de la section Cinnamomeae à l'est des Montagnes Rocheuses
Simon Joly
Thèse de doctorat, Département de Sciences biologiques, Université de Montréal, Montréal, Canada

Polyploid and hybrid evolution in roses east of the Rocky Mountains
Simon Joly, Julian R. Starr, Walter H. Lewis, Anne Bruneau
American Journal of Botany 93: 412-425


Molecular markers indicate that the narrow Québec endemics Rosa rousseauiorum and Rosa williamsii are synonymous with the widespread Rosa blanda
Anne Bruneau, Simon Joly, Julian R. Starr, Josée-Nadia Drouin
Canadian Journal of Botany 83: 386-398


Evolution of triploidy in Apios americana (Leguminosae) revealed by the genealogical analysis of the histone H3-D gene
Simon Joly, Anne Bruneau
Evolution 58: 284-295

Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial Glycine allopolyploids
Simon Joly, Jason T. Rauscher, Susan L. Sherman-Broyles, A. H. D. Brown, Jeff J. Doyle
Molecular Biology and Evolution 21: 1409-1421


Phylogenetic implications of the multiple losses of the mitochondrial coxII.i3 intron in the angiosperms
Simon Joly, Luc Brouillet, Anne Bruneau
International Journal of Plant Science 162: 359-373