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We derive the distribution of ages of nodes in the tree under a birth–death-sequential-sampling (BDSS) model and use it as the prior for divergence times in the dating analysis.
We implement the prior in the MCMCtree program in the PAML package for divergence dating.
We examined the impact of tree topology on time estimates and suggest that multifurcating consensus trees should be avoided in dating analysis.
We found posterior time estimates for old nodes to be sensitive to the priors on times and rates and suggest that previous Bayesian dating studies may have produced overconfident estimates.
This is the case with viral gene sequences and also in a few ancient DNA studies (Drummond et al. The different sample dates allow evolutionary changes to be calibrated to generate estimates of absolute rates and times.
The Bayesian Markov chain Monte Carlo (MCMC) program multidivtime (Thorne et al.
We require the user to specify a diffuse prior on the root age.
While conditioning on the number of sampled tips may be too diffuse and misleading, running the risk that the posterior time estimates are unduely influenced by the prior without the user’s knowledge.
To restore access and understand how to better interact with our site to avoid this in the future, please have your system administrator contact [email protected]) appears to be the first to implement such models for non-contemporary sequences although this option has rarely been used.Currently, BEAST (Drummond and Rambaut 2007) appears to be the only program being used for dating viral divergences.The term lineage here can mean a viral sequence in analysis of viral data with sample dates (as in this artcile) or a species in analysis of species phylogenies.A birth may correspond to a viral transmission or a speciation event, and a death may correspond to the host becoming noninfectious or to a species extinction.