Journal article
The performance of the date-randomization test in phylogenetic analyses of time-structured virus data
S Duchêne, D Duchêne, EC Holmes, SYW Ho
Molecular Biology and Evolution | OXFORD UNIV PRESS | Published : 2015
Abstract
Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of ..
View full abstractGrants
Awarded by National Health and Medical Research Council Australia Fellowship
Awarded by Australian Research Council
Funding Acknowledgements
The authors thank several anonymous reviewers of previously submitted articles, who pointed out some of the potential limitations of the date-randomization test. S.D. was supported by a Francisco Jose de Caldas Scholarship from the Colombian government and by a Sydney World Scholars Award from the University of Sydney. D.D. was supported by an Australian National University HDR Merit Scholarship. E.C.H. was supported by a National Health and Medical Research Council Australia Fellowship (AF30). S.Y.W.H. was supported by the Australian Research Council (DP110100383).