Joly Lab Evolution and Biodiversity

Publications

2014

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
preprint | Link to the Journal | Request a Reprint

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
Link to the Journal | Request a Reprint

Flexible methods for estimating genetic distances from nucleotide data
Simon Joly, David Bryant, Peter J. Lockhart
BioRxiv
doi:10.1101/004184
preprint | 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
Link to the Journal | Request a Reprint

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
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2013

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
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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, and Bourlaye Fofana
Scientia Horticulturae 160: 251-263
Link to the Journal | Request a Reprint

2012

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

2011

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

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

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

2010

Fast diploidization in close mesopolyploid relatives of Arabidopsis
Terezie Mandáková, Simon Joly, Martin Krzywinski, Klaus Mummenhoff, and 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, and Daniel J. Schoen
Evolution 64: 1657-1670
PDF | Link to the Journal

2009

A statistical approach for distinguishing hybridization and incomplete lineage sorting.
Simon Joly, Patricia A. McLenachan, and Peter J. Lockhart
The American Naturalist 174: e54-e70
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Measuring branch support in species trees obtained by gene tree parsimony
Simon Joly and Anne Bruneau
Systematic Biology 58: 100-113
PDF

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

2008

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

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

2007

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

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

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

2006

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

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
PDF

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

2005

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, and Josée-Nadia Drouin
Canadian Journal of Botany 83: 386-398
PDF

2004

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

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, and Jeff J. Doyle
Molecular Biology and Evolution 21: 1409-1421
PDF

2001

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