Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST

Author:

Dellicour Simon12ORCID,Gill Mandev S2,Faria Nuno R345,Rambaut Andrew6,Pybus Oliver G4,Suchard Marc A789,Lemey Philippe2

Affiliation:

1. Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium

2. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium

3. MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom

4. Department of Zoology, University of Oxford, Oxford, United Kingdom

5. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil

6. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

7. Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA

8. Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA

9. Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA

Abstract

Abstract Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.

Funder

European Union’s Horizon 2020 Project MOOD

Wellcome Trust

Royal Society Sir Henry Dale Fellowship

Medical Research Council-São Paulo Research Foundation

European Research Council

European Union’s Horizon 2020 Research and Innovation Program

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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