Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

(2020) Philippe Lemey et al.   Nature Communications

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages — Application to rabies virus spread in Iran

(2019) Simon Dellicour et al.   MOLECULAR ECOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

(2017) Simon Dellicour et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demographic inference under a spatially continuous coalescent model

(2016) T A Joseph et al.   HEREDITY

Demographic inference under the coalescent in a spatial continuum

(2016) Stéphane Guindon et al.   THEORETICAL POPULATION BIOLOGY

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Coalescent simulation in continuous space: Algorithms for large neighbourhood size

(2014) J. Kelleher et al.   THEORETICAL POPULATION BIOLOGY

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Coalescent simulation in continuous space

(2013) Jerome Kelleher et al.   BIOINFORMATICS

Bayesian Analysis of Biogeography when the Number of Areas is Large

(2013) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

A New Model for Evolution in a Spatial Continuum

(2012) Nick Barton et al.   ELECTRONIC JOURNAL OF PROBABILITY

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Origins and Expansion of the Indo-European Language Family

(2012) R. Bouckaert et al.   SCIENCE

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

(2011) Ceiridwen J. Edwards et al.   CURRENT BIOLOGY

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

(2011) Nuno R. Faria et al.   INFECTION GENETICS AND EVOLUTION

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY

(2010) Nicholas H. Barton et al.   EVOLUTION

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape

(2008) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY