Relax, keep walking - A practical guide to continuous phylogeographic Inference with BEAST

Simon Dellicour; Mandev S. Gill; Nuno R. Faria; Andrew Rambaut; Oliver G. Pybus; Marc A. Suchard; Philippe Lemey

doi:10.1093/molbev/msab031

Relax, keep walking - A practical guide to continuous phylogeographic Inference with BEAST

Simon Dellicour^*
, Mandev S. Gill
, Nuno R. Faria
, Andrew Rambaut
, Oliver G. Pybus
, Marc A. Suchard
, Philippe Lemey

^*Corresponding author for this work

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	3486-3493
Number of pages	8
Journal	Molecular Biology and Evolution
Volume	38
Issue number	8
Early online date	2 Feb 2021
DOIs	https://doi.org/10.1093/molbev/msab031
Publication status	Published - 1 Aug 2021

Keywords / Materials (for Non-textual outputs)

BEAST
continuous phylogeography
relaxed random walk
viruses

Access to Document

10.1093/molbev/msab031Licence: Creative Commons: Attribution (CC-BY)

LemeyEtalMBE2022RelaxKeepWalkingFinal published version, 4.14 MBLicence: Creative Commons: Attribution (CC-BY)

Putting genomic surveillance at the heart of viral epidemic response.
Rambaut, A. (Principal Investigator)
UK-based charities
1/08/17 → 31/07/24
Project: Research

Cite this

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title = "Relax, keep walking - A practical guide to continuous phylogeographic Inference with BEAST",

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. ",

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author = "Simon Dellicour and Gill, \{Mandev S.\} and Faria, \{Nuno R.\} and Andrew Rambaut and Pybus, \{Oliver G.\} and Suchard, \{Marc A.\} and Philippe Lemey",

note = "Funding Information: S.D. is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). S.D. and P.L. acknowledge funding from the European Union{\textquoteright}s Horizon 2020 Project MOOD (Grant Agreement No. 874850). N.R.F. is supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and by a Medical Research Council-S\textasciitilde{}ao Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0). A.R., M.A.S., and P.L. acknowledge funding from the European Research Council under the European Union{\textquoteright}s Horizon 2020 Research and Innovation Program (Grant Agreement No. 725422-ReservoirDOCS) and from the Wellcome Trust through project 206298/Z/17/Z (The Artic Network).M.A.S. acknowledges support from National Institutes of Health (Grant Nos. U19 AI135995 and R65 AI149004). P.L. acknowledges support by the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek—Vlaanderen, G066215N, G0D5117N, and G0B9317N). Publisher Copyright: {\textcopyright} 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.",

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AU - Pybus, Oliver G.

AU - Suchard, Marc A.

AU - Lemey, Philippe

N1 - Funding Information: S.D. is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). S.D. and P.L. acknowledge funding from the European Union’s Horizon 2020 Project MOOD (Grant Agreement No. 874850). N.R.F. is supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and by a Medical Research Council-S~ao Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0). A.R., M.A.S., and P.L. acknowledge funding from the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 725422-ReservoirDOCS) and from the Wellcome Trust through project 206298/Z/17/Z (The Artic Network).M.A.S. acknowledges support from National Institutes of Health (Grant Nos. U19 AI135995 and R65 AI149004). P.L. acknowledges support by the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek—Vlaanderen, G066215N, G0D5117N, and G0B9317N). Publisher Copyright: © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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N2 - 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.

AB - 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.

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KW - relaxed random walk

KW - viruses

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VL - 38

SP - 3486

EP - 3493

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 8

ER -

Relax, keep walking - A practical guide to continuous phylogeographic Inference with BEAST

Abstract

Keywords / Materials (for Non-textual outputs)

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Projects

Putting genomic surveillance at the heart of viral epidemic response.

Cite this