I started my PhD at the MEEP lab in early 2012 under the supervision of Dr Simon Ho and Prof. Eddie Holmes (arriving late 2012). I am investigating the factors that govern evolutionary rate variation in RNA and DNA viruses, focussing on time-dependent rates and the timescale of viral evolution.
Before coming to Sydney, I completed my M.Sc. and B.Sc. at Universidad de los Andes (Bogotá, Colombia) and collaborated with the Southwest Fisheries Science Center (La Jolla, California, USA) on phylogenetic analyses of mitochondrial genomes of cetacans and sea turtles.
My main interests include phylogenetics, molecular clocks (and molecular evolution in general), computational statistics, and data analysis with R. I have written a few basic scripts for phylogenetic utilities in R, available here.
|Present||Ph.D., University of Sydney
Supervisor: Simon Ho
|2011||M.Sc., Universidad de los Andes (Colombia)
Thesis: Mitogenome phylogenetics: The impact of using single regions and partitioning schemes on topology, substitution rate, and divergence time estimation
Supervisors: Susana Caballero & Phillip Morin
|2007||B.Sc., Universidad de los Andes (Colombia)
Thesis: The oscillating connectivity hypothesis: Phylogeographic patterns and an ancient Amazon lagoon
Supervisor: Susana Caballero
Nguyen HD, Tomitaka Y, Ho SYW, Duchêne S, Vetten H-J, Lesemann D, Walsh JA, Gibbs AJ, & Ohshima K (in press)
Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago. PLOS ONE.
Satizábal P, Mignucci-Giannoni AA, Duchêne S, Caicedo-Herrera D, Perea-Sicchar CM, et al. (2012) Phylogeography and sex-biased dispersal across riverine manatee populations (Trichechus inunguis and Trichechus manatus) in South America. PLOS ONE 7: e52468.
Duchêne S, Frey A, Alvaro-Núñez A, Dutton PH, gilbert MTP, Morin PA (2012) Marine turtle mitogenome phylogenetics and evolution. Molecular Phylogenetics and Evolution, 65: 241-250.
Duchêne S, Archer FI, Vilstrup J, Caballero S, & Morin PA (2011) Mitogenome phylogenetics: The impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLOS ONE, 6: e27138.
Caballero S, Islas-Villanueva V, Tezanos-Pinto G, Duchêne S, Delgado-Estrella A, Sanchez-Okrucky R, & Mignucci-Giannoni AA (2011) Phylogeography, genetic diversity and population structure of common bottlenose dolphins in the Wider Caribbean inferred from analyses of mitochondrial DNA control region sequences and microsatellite loci: conservation and management implications. Animal Conservation, 1496-1795.
Understanding evolutionary rate variation in viruses
Phylomania Conference. Hobart, Australia. Nov 2012.
Understanding evolutionary rate variation in viruses (poster)
Genetics Society of Australasia Conference. Melbourne, Australia. Jul 2012.
Introduction to bioinformatic tools for evolutionary analyses of molecular data
Universidad Javeriana. Bogota, Colombia. Jun 2012.
Mitogenome phylogenetics: variation in topologies, date estimation, and mutation rates among analysis partitions
Conference on the Biology of Marine Mammals. Tampa, USA. Nov 2011.