Bayesian estimation of past population dynamics in BEAST 1.10 using the Skygrid coalescent model

Molecular Biology and Evolution
Verity Hill, Guy Baele

Abstract

Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a non-parametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo, this coalescent model is often estimated in conjunction with a molecular clock model to produce time-stamped phylogenetic trees. We here provide a practical guide to using BEAST and its accompanying applications for the purpose of drawing inference under these models. We focus on best practices, potential pitfalls and recommendations that can be generalized to other software packages for Bayesian inference. This protocol shows how to use TempEst, BEAUti and BEAST 1.10 (http://beast.community/), LogCombiner as well as Tracer in a complete workflow.

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Citations

Feb 28, 2020·Viruses·Andrei A DeviatkinAlexander N Lukashev
Jul 6, 2020·The Lancet Infectious Diseases·Reina S SikkemaMarion P G Koopmans
Jan 27, 2021·Emerging Infectious Diseases·François-Xavier BriandBéatrice Grasland
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Feb 3, 2021·Molecular Biology and Evolution·Simon DellicourPhilippe Lemey
May 20, 2021·Molecular Biology and Evolution·Stilianos LoucaMatthew W Pennell
Jul 13, 2021·Frontiers in Veterinary Science·Alba Frias-De-DiegoElisa Crisci
Jul 10, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Dongchang HeXiufan Liu
Jul 25, 2021·Science·Moritz U G KraemerOliver G Pybus
Aug 26, 2021·Genome Biology and Evolution·Ahmed M Moustafa, Paul J Planet

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Software Mentioned

BEAST GUI
TREE
BEAUti
LogCombiner
Skygrid
Bayesian Evolutionary Analysis by Sampling Trees ( BEAST )
Skygrid Analysis
IQ
TempEst
BEAST

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