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dc.contributor.authorDuchene, S
dc.contributor.authorDuchene, DA
dc.contributor.authorGeoghegan, JL
dc.contributor.authorDyson, ZA
dc.contributor.authorHawkey, J
dc.contributor.authorHolt, KE
dc.date.accessioned2020-12-17T04:34:23Z
dc.date.available2020-12-17T04:34:23Z
dc.date.issued2018-06-19
dc.identifierpii: 10.1186/s12862-018-1210-5
dc.identifier.citationDuchene, S., Duchene, D. A., Geoghegan, J. L., Dyson, Z. A., Hawkey, J. & Holt, K. E. (2018). Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC EVOLUTIONARY BIOLOGY, 18 (1), https://doi.org/10.1186/s12862-018-1210-5.
dc.identifier.issn1471-2148
dc.identifier.urihttp://hdl.handle.net/11343/255366
dc.description.abstractBACKGROUND: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale. RESULTS: We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart. CONCLUSIONS: Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates.
dc.languageEnglish
dc.publisherBMC
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleInferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
dc.typeJournal Article
dc.identifier.doi10.1186/s12862-018-1210-5
melbourne.affiliation.departmentBiochemistry and Molecular Biology
melbourne.affiliation.departmentMicrobiology and Immunology
melbourne.source.titleBMC Evolutionary Biology
melbourne.source.volume18
melbourne.source.issue1
melbourne.identifier.nhmrc1061409
dc.rights.licenseCC BY
melbourne.elementsid1336414
melbourne.contributor.authorDuchene Garzon, Sebastian
melbourne.contributor.authorDyson, Zoe
melbourne.contributor.authorHawkey, Jane
melbourne.contributor.authorHolt, Kathryn
dc.identifier.eissn1471-2148
melbourne.identifier.fundernameidNHMRC, 1061409
melbourne.accessrightsOpen Access


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