People

Sebastián Duchêne

Sebastian Duchene

I started my PhD at the MEEP lab in early 2012 under the supervision of A/Prof. 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.


Academic Record

Present Ph.D., University of Sydney
Supervisors: Simon Ho & Edward Holmes
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

Prizes and Awards

  • Finalist for Postgraduate Excellence Prize, University of Sydney, 2014
  • Student Talk Prize, Genetics Society of Australasia Conference, 2013
  • Francisco José de Caldas Scholarship, 2012-2015
  • University of Sydney World Scholars Award, 2012-2015

Publications

Duchêne D, Duchêne S, & Ho SYW. 2015. Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences. Molecular Ecology Resources, in press.

Ho SYW*, Duchêne S* (equal first authors), & Duchêne D. 2015. Simulating and detecting autocorrelation of molecular evolutionary rates among lineages. Molecular Ecology Resources, in press.

Ho SYW, & Duchêne S. 2014. Molecular-clock methods for estimating evolutionary rates and timescales Molecular Ecology, 23: 5947-5965.

Duchêne S, Lanfear R, & Ho SYW. 2014. The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phylogenetics and Evolution, 78: 277-289.

Duchêne S, Holmes EC, & Ho SYW. 2014. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society of London B, 281: 20140732.

Duchêne S, & Ho SYW. 2014. Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data. Molecular Phylogenetics and Evolution, 77: 65-70.

Duchêne S, Molak M, & Ho SYW. 2014. ClockstaR: Choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics, 30: 1017-1019.

Yasaka R, Nguyen HD, Ho SYW, Duchêne S, Korkmaz S, Katis N, Takahashi H, Gibbs AJ, & Ohshima K (2014) The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus. PLOS ONE, 9: e85641.

Nguyen HD, Tomitaka Y, Ho SYW, Duchêne S, Vetten H-J, Lesemann D, Walsh JA, Gibbs AJ, & Ohshima K (2013)
Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago. PLOS ONE, 8: e55336.

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-NĂșñez 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.

Presentations

Comparing pacemaker models of genome evolution in mammals
Genetics Society of Australasia Conference. Sydney, Australia. Jul 2014.

Improving molecular-clock estimation of evolutionary timescales using ClockstaR (poster)
Genetics Society of Australasia Conference. Sydney, Australia. Jul 2014.

Calibration strategies for the molecular clock
Australasian Evolution Society Conference. Geelong, Australia. Oct 2013.

Calibration strategies for the molecular clock
Australian Centre for Ancient DNA, University of Adelaide. Adelaide, Australia. Sep 2013.

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.

Workshops

Introduction to phylogenetic analysis
University of Sydney. Sydney, Australia. Jul 2014.
2 days. 42 registered participants.

Statistical computing and data analysis using R
Genetics Society of Australasia Conference. University of Sydney. Sydney, Australia. Jul 2014.
1 day. 26 registered participants.

Statistical computing and data analysis using R
University of Sydney. Sydney, Australia. Nov 2013.
1 day. 28 registered participants.

Introduction to phylogenetic analysis
University of Sydney. Sydney, Australia. Jul 2013.
2 days. 51 registered participants.


Influenza
The rate of molecular evolution