Phylodynamic Model Adequacy Using Posterior Predictive Simulations.
Journal
Systematic biology
ISSN: 1076-836X
Titre abrégé: Syst Biol
Pays: England
ID NLM: 9302532
Informations de publication
Date de publication:
01 03 2019
01 03 2019
Historique:
received:
25
02
2018
accepted:
15
06
2018
pubmed:
27
6
2018
medline:
9
4
2019
entrez:
27
6
2018
Statut:
ppublish
Résumé
Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy, a package for the popular BEAST2 software that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analyzing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data were best described by the birth-death susceptible-infected-recovered model.
Identifiants
pubmed: 29945220
pii: 5044211
doi: 10.1093/sysbio/syy048
pmc: PMC6368481
doi:
Banques de données
Dryad
['10.5061/dryad.65p331m']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
358-364Références
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