Note: Most reprints are protected by copyright. Please ask me for permission (simon {dot} joly {at} mail {dot} mcgill {dot} ca) before downloading or printing them.
2009
S. Joly, P. A. McLenachan, and P. J. Lockhart. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist. in press. [pdf]
S. Joly, and A. Bruneau. 2009. Measuring branch support in species trees obtained by gene tree parsimony. Systematic Biology. in press. [pdf]
S. Joly, P. B. Heenan, and P. J. Lockhart. 2009. A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand. Molecular Phylogenetics and Evolution. in press. [pdf]
2008
Collins, L. J., P. J. Biggs, C. Voelckel, S. Joly. 2008. An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Informatics. 21:3-14. [pdf]
Wang, Y., S. Joly, and D. Morse. 2008. Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with stramenopile plastid genes. Journal of Molecular Evolution. 66:175-184. [pdf]
2007
Joly, S., M. I. Stevens, and B. Jansen Van Vuuren. 2007. Haplotype Networks can be Misleading in the Presence of Missing Data. Systematic Biology 56:857-862. [pdf]
Joly, S. and A. Bruneau. 2007. Delimiting species boundaries in Rosa sect. Cinnamomeae (Rosaceae) in eastern North America. Systematic Botany 32:819-836.
Bruneau, A., J. R. Starr, and S. Joly. 2007. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and appraisal of current knowledge. Systematic Botany 32:366-378. [pdf]
2006
Joly, S. and A. Bruneau. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Systematic Biology 55:623-636. [pdf]
Joly, S. 2006. Evolution des roses (Rosa:Rosaceae) indigènes de la section Cinnamomeae à l'est des Montagnes Rocheuses. Ph.D. thesis, Département de Sciences biologiques, Université de Montréal, Montréal, Canada. [pdf]
Joly, S., J. R. Starr, W. H. Lewis, and A. Bruneau. 2006. Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany 93:412-425. [pdf]
2005
Bruneau, A., S. Joly, J. R. Starr, and J.-N. Drouin. 2005. Molecular markers indicate that the narrow QuÈbec endemics Rosa rousseauiorum and Rosa williamsii are synonymous with the widespread Rosa blanda. Canadian Journal of Botany 83:386-398. [pdf]
2004
Joly, S., and A. Bruneau. 2004. Evolution of triploidy in Apios americana (Leguminosae) revealed by the genealogical analysis of the histone H3-D gene. Evolution 58:284-295. [pdf]
Joly, S., J. T. Rauscher, S. L. Sherman-Broyles, A. H. D. Brown, and J. J. Doyle. 2004. Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial Glycine allopolyploids. Molecular Biology and Evolution 21:1409-1421. [pdf]
2001
Joly, S., L. Brouillet, and A. Bruneau. 2001. Phylogenetic implications of the multiple losses of the mitochondrial coxII.i3 intron in the angiosperms. International Journal of Plant Science 162:359-373. [pdf]
