Sampling through time and phylodynamic inference with coalescent and birth-death models
Author(s)
Volz, EM
Frost, SDW
Type
Journal Article
Abstract
Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the birth–death-sampling model (BDM), in the context of estimating population size and birth rates in a population growing exponentially according to the birth–death branching process. For sequences sampled at a single time, we found the coalescent and the BDM gave virtually indistinguishable results in terms of the growth rates and fraction of the population sampled, even when sampling from a small population. For sequences sampled at multiple time points, we find that the birth–death model estimators are subject to large bias if the sampling process is misspecified. Since BDMs incorporate a model of the sampling process, we show how much of the statistical power of BDMs arises from the sequence of sample times and not from the genealogical tree. This motivates the development of a new coalescent estimator, which is augmented with a model of the known sampling process and is potentially more precise than the coalescent that does not use sample time information.
Date Issued
2014-10-29
Date Acceptance
2014-10-07
Citation
Journal of the Royal Society Interface, 2014, 11 (101)
ISSN
1742-5689
Publisher
The Royal Society
Journal / Book Title
Journal of the Royal Society Interface
Volume
11
Issue
101
Copyright Statement
© 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
Sponsor
Medical Research Council (MRC)
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000362679500004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
MR/K010174/1B
Subjects
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
phylodynamics
coalescent
infectious diseases
PHYLOGENETIC INFERENCE
DEMOGRAPHIC HISTORY
GENEALOGICAL TREES
SKYLINE PLOT
TRANSMISSION
HIV
NEUTRALITY
SEQUENCES
EPIDEMIC
Animals
Death
Genetics, Population
Humans
Models, Genetic
Parturition
General Science & Technology
MD Multidisciplinary
Publication Status
Published
Article Number
ARTN 20140945