In press

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

Symbiotic association between Salix purpurea and Rhizophagus irregularis: modulation of plant responses under copper stress
Adriana Almeida-Rodriguez, Marcelo Gómez, Audrey Loubert-Hudon, Simon Joly, Michel Labrecque
Tree Physiology


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
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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
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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