Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?
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Accepted version
Author(s)
Parag, Kris V
Pybus, Oliver G
Wu, Chieh-Hsi
Type
Journal Article
Abstract
In Bayesian phylogenetics, the coalescent process provides an informative framework for inferring changes in the effective size of a population from a phylogeny (or tree) of sequences sampled from that population. Popular coalescent inference approaches such as the Bayesian Skyline Plot, Skyride and Skygrid all model these population size changes with a discontinuous, piecewise-constant function but then apply a smoothing prior to ensure that their posterior population size estimates transition gradually with time. These prior distributions implicitly encode extra population size information that is not available from the observed coalescent data i.e., the tree. Here we present a novel statistic, Ω, to quantify and disaggregate the relative contributions of the coalescent data and prior assumptions to the resulting posterior estimate precision. Our statistic also measures the additional mutual information introduced by such priors. Using Ω we show that, because it is surprisingly easy to over-parametrise piecewise-constant population models, common smoothing priors can lead to overconfident and potentially misleading inference, even under robust experimental designs. We propose Ω as a useful tool for detecting when effective population size estimates are overly reliant on prior assumptions and for improving quantification of the uncertainty in those estimates.
Date Issued
2021-05-13
Date Acceptance
2021-05-08
Citation
Systematic Biology, 2021, 71 (1)
ISSN
1063-5157
Publisher
Oxford University Press
Journal / Book Title
Systematic Biology
Volume
71
Issue
1
Copyright Statement
© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Sponsor
Medical Research Council (MRC)
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/33989428
PII: 6275766
Grant Number
MR/R015600/1
Subjects
coalescent processes
effective population size
information theory
phylodynamics
prior assumptions
skyline plots
Publication Status
Published online
Coverage Spatial
England
Date Publish Online
2021-05-13