Abstract:
: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.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Duchene S,Bouckaert R,Duchene DA,Stadler T,Drummond AJdoi
10.1093/sysbio/syy048subject
Has Abstractpub_date
2019-03-01 00:00:00pages
358-364issue
2eissn
1063-5157issn
1076-836Xpii
5044211journal_volume
68pub_type
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