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dc.contributor.author
Möller, Simon
dc.contributor.author
du Plessis, Louis
dc.contributor.author
Stadler, Tanja
dc.date.accessioned
2018-04-30T14:58:41Z
dc.date.available
2018-04-27T05:13:05Z
dc.date.available
2018-04-30T14:58:41Z
dc.date.issued
2018-04
dc.identifier.issn
0027-8424
dc.identifier.issn
1091-6490
dc.identifier.other
10.1073/pnas.1713314115
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/261007
dc.identifier.doi
10.3929/ethz-b-000261007
dc.description.abstract
Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in the sampling period of sequences. In particular, clock rates of epidemic outbreaks are often estimated to be higher compared with the long-term clock rate. Purifying selection has been suggested as a biological factor that contributes to this phenomenon, since it purges slightly deleterious mutations from a population over time. However, other factors such as methodological biases may also play a role and make a biological interpretation of results difficult. In this paper, we identify methodological biases originating from the choice of tree prior, that is, the model specifying epidemiological dynamics. With a simulation study we demonstrate that a misspecification of the tree prior can upwardly bias the inferred clock rate and that the interplay of the different models involved in the inference can be complex and nonintuitive. We also show that the choice of tree prior can influence the inference of clock rate on real-world Ebola virus (EBOV) datasets. While commonly used tree priors result in very high clock-rate estimates for sequences from the initial phase of the epidemic in Sierra Leone, tree priors allowing for population structure lead to estimates agreeing with the long-term rate for EBOV.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
National Academy of Sciences
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
molecular clock
en_US
dc.subject
Bayesian phylodynamics
en_US
dc.subject
tree inference
en_US
dc.subject
phylogenetics
en_US
dc.subject
Ebola
en_US
dc.title
Impact of the tree prior on estimating clock rates during epidemic outbreaks
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
ethz.journal.title
Proceedings of the National Academy of Sciences of the United States of America
ethz.journal.volume
115
en_US
ethz.journal.issue
16
en_US
ethz.journal.abbreviated
Proc Natl Acad Sci U S A
ethz.pages.start
4200
en_US
ethz.pages.end
4205
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
New phylogenetic methods for inferring complex population dynamics
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
Washington, DC
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.grant.agreementno
335529
ethz.grant.fundername
EC
ethz.grant.funderDoi
10.13039/501100000780
ethz.grant.program
FP7
ethz.date.deposited
2018-04-27T05:13:12Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-04-30T14:58:49Z
ethz.rosetta.lastUpdated
2020-02-15T12:44:03Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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