Sebastian Duchene Garzon

Linking Branch Lengths Across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference.

David A Duchêne, K Jun Tong, Charles SP Foster, Sebastián Duchêne, Robert Lanfear, Simon YW Ho

Journal article  |  2019  |  Molecular Biology and Evolution

Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees ..

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

Eike J Steinig, Sebastian Duchene, D Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah Williamson, Angela Kearns, Richard V Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew VN O'Sullivan, Geoffrey W Coombs, Andreas Petersen, Grainne Brennan, Anna C Shore, David C Coleman, et al.

Journal article  |  2019  |  mBio

The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health ..

The molecular clock of Mycobacterium tuberculosis

Fabrizio Menardo, Sebastian Duchene, Daniela Brites, Sebastien Gagneux

Journal article  |  2019  |  PLOS Pathogens

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Mark R Davies, Liam McIntyre, Ankur Mutreja, Jake A Lacey, John A Lees, Rebecca J Towers, Sebastian Duchene, Pierre R Smeesters, Hannah R Frost, David J Price, Matthew TG Holden, Sophia David, Philip M Giffard, Kate A Worthing, Anna C Seale, James A Berkley, Simon R Harris, Tania Rivera-Hernandez, Olga Berking, Amanda J Cork, et al.

Journal article  |  2019  |  Nature Genetics

Genome Analysis of Coxsackievirus A4 Isolates From Hand, Foot, and Mouth Disease Cases in Shandong, China

Min Wang, Juan Li, Ming-Xiao Yao, Ya-Wei Zhang, Tao Hu, Michael J Carr, Sebastian Duchene, Xing-Cheng Zhang, Zhen-Jie Zhang, Hong Zhou, Yi-Gang Tong, Shu-Jun Ding, Xian-Jun Wang, Wei-Feng Shi

Journal article  |  2019  |  Frontiers in Microbiology

Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia

Francesca Di Giallonardo, Angie N Pinto, Phillip Keen, Ansari Shaik, Alex Carrera, Hanan Salem, Barbara Telfer, Craig Cooper, Karen Price, Christine Selvey, Joanne Holden, Nadine Bachmann, Frederick J Lee, Dominic E Dwyer, Sebastian Duchene, Edward C Holmes, Andrew E Grulich, Anthony D Kelleher, Rebecca Guy, Garrett Prestage, et al.

Journal article  |  2019  |  Viruses

Evolutionary stasis of viruses?

Edward C Holmes, Sebastian Duchene

Journal article  |  2019  |  Nature Reviews Microbiology

Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes

Lilly KW Yuen, Margaret Littlejohn, Sebastian Duchene, Rosalind Edwards, Sarah Bukulatjpi, Paula Binks, Kathy Jackson, Jane Davies, Joshua S Davis, Steven YC Tong, Stephen Locarnini

Journal article  |  2019  |  Molecular Biology and Evolution

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Kelly L Wyres, Ryan R Wick, Louise M Judd, Roni Froumine, Alex Tokolyi, Claire L Gorrie, Margaret MC Lam, Sebastian Duchene, Adam Jenney, Kathryn E Holt

Journal article  |  2019  |  PLOS Genetics

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert, Timothy G Vaughan, Joelle Barido-Sottani, Sebastian Duchene, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kuehnert, Nicola De Maio, Michael Matschiner, Fabio K Mendes, Nicola F Mueller, Huw A Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A Suchard, et al.

Journal article  |  2019  |  PLOS Computational Biology

Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

Edward C Holmes, Sebastian Duchene

Journal article  |  2019  |  mBio

Phylodynamic Model Adequacy Using Posterior Predictive Simulations

Sebastian Duchene, Remco Bouckaert, David A Duchene, Tanja Stadler, Alexei J Drummond

Journal article  |  2019  |  Systematic Biology

The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas

Tao Hu, Juan Li, Michael J Carr, Sebastian Duchene, Weifeng Shi

Journal article  |  2019  |  Virologica Sinica

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Se Eun Park, Thanh Pham Duy, Christine Boinett, Vanessa K Wong, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza, Vera von Kalckreuth, Justin Im, Heidi Schuett-Gerowitt, John A Crump, Robert F Breiman, Yaw Adu-Sarkodie, Ellis Owusu-Dabo, Raphael Rakotozandrindrainy, Abdramane Bassiahi Soura, Abraham Aseffa, Nagla Gasmelseed, Karen H Keddy, Juergen May, et al.

Journal article  |  2018  |  Nature Communications

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Kelly Wyres, Ryan Wick, Louise Judd, Roni Froumine, Alex Tokolyi, Claire Gorrie, Margaret Lam, Sebastian Duchene, Adam Jenney, Kathryn Holt

Journal article  |  2018  |  PLoS Genetics

Klebsiella pneumoniae (Kp) has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) hea..

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

Zhemin Zhou, Inge Lundstrom, Alicia Tran-Dien, Sebastian Duchene, Nabil-Fareed Alikhan, Martin J Sergeant, Gemma Langridge, Anna K Fotakis, Satheesh Nair, Hans K Stenoien, Stian S Hamre, Sherwood Casjens, Axel Christophersen, Christopher Quince, Nicholas R Thomson, Francois-Xavier Weill, Simon YW Ho, M Thomas P Gilbert, Mark Achtman

Journal article  |  2018  |  Current Biology

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

S Pollett, MC Melendrez, Maljkovic Berry, S Duchene, H Salje, DAT Cummings, RG Jarman

Journal article  |  2018  |  Infection, Genetics and Evolution

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Margaret MC Lam, Kelly L Wyres, Sebastian Duchene, Ryan R Wick, Louise M Judd, Yunn-Hwen Gan, Chu-Han Hoh, Sophia Archuleta, James S Molton, Shirin Kalimuddin, Tse Hsien Koh, Virginie Passet, Sylvain Brisse, Kathryn E Holt

Journal article  |  2018  |  Nature Communications

PhyloMAd: efficient assessment of phylogenomic model adequacy

David A Duchene, Sebastian Duchene, Simon YW Ho

Journal article  |  2018  |  Bioinformatics

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

Sebastian Duchene, David A Duchene, Jemma L Geoghegan, Zoe A Dyson, Jane Hawkey, Kathryn E Holt

Journal article  |  2018  |  BMC Evolutionary Biology

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy

David A Duchene, Sebastian Duchene, Simon YW Ho

Journal article  |  2018  |  Genome Biology and Evolution

A comparison of methods for estimating substitution rates from ancient DNA sequence data

K Jun Tong, David A Duchene, Sebastian Duchene, Jemma L Geoghegan, Simon YW Ho

Journal article  |  2018  |  BMC Evolutionary Biology

Bayesian molecular dating: opening up the black box

Lindell Bromham, Sebastian Duchene, Xia Hua, Andrew M Ritchie, David A Duchene, Simon YW Ho

Journal article  |  2018  |  Biological Reviews

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

David A Duchene, Jason G Bragg, Sebastian Duchene, Linda E Neaves, Sally Potter, Craig Moritz, Rebecca N Johnson, Simon YW Ho, Mark DB Eldridge

Journal article  |  2018  |  Systematic Biology

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

Carl D Britto, Zoe A Dyson, Sebastian Duchene, Michael J Carter, Meeru Gurung, Dominic F Kelly, David R Murdoch, Imran Ansari, Stephen Thorson, Shrijana Shrestha, Neelam Adhikari, Gordon Dougan, Kathryn E Holt, Andrew J Pollard

Journal article  |  2018  |  PLOS Neglected Tropical Diseases

Correction: Continental synchronicity of human influenza virus epidemics despite climactic variation.

Jemma L Geoghegan, Aldo F Saavedra, Sebastián Duchêne, Sheena Sullivan, Ian Barr, Edward C Holmes

Journal article  |  2018  |  PLOS Pathogens

[This corrects the article DOI: 10.1371/journal.ppat.1006780.].

Continental synchronicity of human influenza virus epidemics despite climactic variation

Jemma L Geoghegan, Aldo F Saavedra, Sebastian Duchene, Sheena Sullivan, Ian Barr, Edward C Holmes

Journal article  |  2018  |  PLOS Pathogens

The paradox of HBV evolution as revealed from a 16th century mummy

Zoe Patterson Ross, Jennifer Klunk, Gino Fornaciari, Valentina Giuffra, Sebastian Duchene, Ana T Duggan, Debi Poinar, Mark W Douglas, John-Sebastian Eden, Edward C Holmes, Hendrik N Poinar

Journal article  |  2018  |  PLOS Pathogens

Estimating evolutionary rates in giant viruses using ancient genomes

Sebastian Duchene, Edward C Holmes

Journal article  |  2018  |  Virus Evolution

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

Sebastian Duchene, David Duchene, Jemma Geoghegan, Zoe Anne Dyson, Jane Hawkey, Kathryn Holt

Journal article  |  2017

Background: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isol..

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity

David A Duchene, Sebastian Duchene, Simon YW Ho

Journal article  |  2017  |  Molecular Biology and Evolution

The impacts of drift and selection on genomic evolution in insects

K Jun Tong, Sebastian Duchene, Nathan Lo, Simon YW Ho

Journal article  |  2017  |  PeerJ

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Laura S Weyrich, Sebastian Duchene, Julien Soubrier, Luis Arriola, Bastien Llamas, James Breen, Alan G Morris, Kurt W Alt, David Caramelli, Veit Dresely, Milly Farrell, Andrew G Farrer, Michael Francken, Neville Gully, Wolfgang Haak, Karen Hardy, Katerina Harvati, Petra Held, Edward C Holmes, John Kaidonis, et al.

Journal article  |  2017  |  Nature

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Jemma L Geoghegan, Sebastian Duchene, Edward C Holmes

Journal article  |  2017  |  PLOS Pathogens

17th Century Variola Virus Reveals the Recent History of Smallpox

Ana T Duggan, Maria F Perdomo, Dario Piombino-Mascali, Stephanie Marciniak, Debi Poinar, Matthew V Emery, Jan P Buchmann, Sebastian Duchene, Rimantas Jankauskas, Margaret Humphreys, G Brian Golding, John Southon, Alison Devault, Jean-Marie Rouillard, Jason W Sahl, Olivier Dutour, Klaus Hedman, Antti Sajantila, Geoffrey L Smith, Edward C Holmes, et al.

Journal article  |  2016  |  Current Biology

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

Cecile Troupin, Laurent Dacheux, Marion Tanguy, Claude Sabeta, Herve Blanc, Christiane Bouchier, Marco Vignuzzi, Sebastian Duchene, Edward C Holmes, Herve Bourhy

Journal article  |  2016  |  PLOS Pathogens

Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia

Wenjun Liu, Paul Pickering, Sebastian Duchene, Edward C Holmes, John G Aaskov

Journal article  |  2016  |  Emerging Infectious Diseases

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods

Sebastian Duchene, Jemma L Geoghegan, Edward C Holmes, Simon YW Ho

Journal article  |  2016  |  Bioinformatics

Genome-scale rates of evolutionary change in bacteria

Sebastian Duchene, Kathryn E Holt, Francois-Xavier Weill, Simon Le Hello, Jane Hawkey, David J Edwards, Mathieu Fourment, Edward C Holmes

Journal article  |  2016  |  Microbial Genomics

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

Jackie E Mahar, Leila Nicholson, John-Sebastian Eden, Sebastian Duchene, Peter J Kerr, Janine Duckworth, Vernon K Ward, Edward C Holmes, Tanja Strive

Journal article  |  2016  |  Journal of Virology

Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster

Emily J Remnant, Adam Williams, Chris Lumb, Ying Ting Yang, Janice Chan, Sebastian Duchene, Phillip J Daborn, Philip Batterham, Trent Perry

Journal article  |  2016  |  G3: Genes|Genomes|Genetics

Cross-validation to select Bayesian hierarchical models in phylogenetics

Sebastian Duchene, David A Duchene, Francesca Di Giallonardo, John-Sebastian Eden, Jemma L Geoghegan, Kathryn E Holt, Simon YW Ho, Edward C Holmes

Journal article  |  2016  |  BMC Evolutionary Biology

Estimating the number and assignment of clock models in analyses of multigene datasets

Sebastian Duchene, Charles SP Foster, Simon YW Ho

Journal article  |  2016  |  Bioinformatics

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales

Sebastian Duchene, Francesca Di Giallonardo, Edward C Holmes

Journal article  |  2016  |  Molecular Biology and Evolution

Time-dependent estimates of molecular evolutionary rates: evidence and causes

Simon YW Ho, Sebastian Duchene, Martyna Molak, Beth Shapiro

Journal article  |  2015  |  Molecular Ecology

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

David A Duchene, Sebastian Duchene, Edward C Holmes, Simon YW Ho

Journal article  |  2015  |  Molecular Biology and Evolution

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods

Sebastian Duchene, Robert Lanfear

Journal article  |  2015  |  Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A Morin, Kim M Parsons, Frederick I Archer, Maria C Avila-Arcos, Lance G Barrett-Lennard, Luciano Dalla Rosa, Sebastian Duchene, John W Durban, Graeme M Ellis, Steven H Ferguson, John K Ford, Michael J Ford, Cristina Garilao, M Thomas P Gilbert, Kristin Kaschner, Craig O Matkin, Stephen D Petersen, Kelly M Robertson, Ingrid N Visser, Paul R Wade, et al.

Journal article  |  2015  |  Molecular Ecology

Comment on "Phylogenomics resolves the timing and pattern of insect evolution"

K Jun Tong, Sebastian Duchene, Simon YW Ho, Nathan Lo

Journal article  |  2015  |  Science

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

Simon YW Ho, Sebastian Duchene, David Duchene

Journal article  |  2015  |  Molecular Ecology Resources

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

Sebastian Duchene, David Duchene, Edward C Holmes, Simon YW Ho

Journal article  |  2015  |  Molecular Biology and Evolution

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

David Duchene, Sebastian Duchene, Simon YW Ho

Journal article  |  2015  |  Molecular Ecology Resources

Mammalian genome evolution is governed by multiple pacemakers

Sebastian Duchene, Simon YW Ho

Journal article  |  2015  |  Bioinformatics

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes

Susana Caballero, Sebastian Duchene, Manuel F Garavito, Beth Slikas, C Scott Baker

Journal article  |  2015  |  PLOS ONE

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models

Sebastian Duchene, Simon YW Ho, Edward C Holmes

Journal article  |  2015  |  BMC Evolutionary Biology

Molecular-clock methods for estimating evolutionary rates and timescales

Simon YW Ho, Sebastian Duchene

Journal article  |  2014  |  Molecular Ecology

The impact of calibration and clock-model choice on molecular estimates of divergence times

Sebastian Duchene, Robert Lanfear, Simon YW Ho

Journal article  |  2014  |  Molecular Phylogenetics and Evolution

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data

Sebastian Duchene, Simon YW Ho

Journal article  |  2014  |  Molecular Phylogenetics and Evolution

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

Sebastian Duchene, Edward C Holmes, Simon YW Ho

Journal article  |  2014  |  Proceedings of the Royal Society B: Biological Sciences

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

Sebastian Duchene, Martyna Molak, Simon YW Ho

Journal article  |  2014  |  Bioinformatics

The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus

Ryosuke Yasaka, Huy D Nguyen, Simon YW Ho, Sebastian Duchene, Savas Korkmaz, Nikolaos Katis, Hideki Takahashi, Adrian J Gibbs, Kazusato Ohshima

Journal article  |  2014  |  PLoS ONE

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago

Huy D Nguyen, Yasuhiro Tomitaka, Simon YW Ho, Sebastian Duchene, Heinrich-Josef Vetten, Dietrich Lesemann, John A Walsh, Adrian J Gibbs, Kazusato Ohshima

Journal article  |  2013  |  PLoS ONE

Phylogeography and Sex-Biased Dispersal across Riverine Manatee Populations (Trichechus inunguis and Trichechus manatus) in South America

Paula Satizabal, Antonio A Mignucci-Giannoni, Sebastian Duchene, Dalila Caicedo-Herrera, Carlos M Perea-Sicchar, Carmen R Garcia-Davila, Fernando Trujillo, Susana J Caballero

Journal article  |  2012  |  PLoS ONE

Marine turtle mitogenome phylogenetics and evolution

Sebastian Duchene, Amy Frey, Alonzo Alfaro-Nunez, Peter H Dutton, M Thomas P Gilbert, Phillip A Morin

Journal article  |  2012  |  Molecular Phylogenetics and Evolution

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

S Caballero, V Islas-Villanueva, G Tezanos-Pinto, S Duchene, A Delgado-Estrella, R Sanchez-Okrucky, AA Mignucci-Giannoni

Journal article  |  2012  |  Animal Conservation

Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation

Sebastian Duchene, Frederick I Archer, Julia Vilstrup, Susana Caballero, Phillip A Morin

Journal article  |  2011  |  PLoS ONE