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These BSPs were run under the two above-mentioned molecular clock models.
Strict molecular clock models were always used under the assumption that the evolutionary rate within a clade did not vary.
Bayesian Skyline Plots (BSPs) were run under the two molecular clock models: Strict and Relaxed Uncorrelated Lognormal.
Bayesian estimates of phylogeny were obtained using BEAST v1.5.3 [47], under both strict and relaxed lognormal molecular clock models.
Given reasonable assumptions regarding viral mutation rate and generation time,[26] time since infection (time to most recent common ancestor [TMRCA]) was estimated using Bayesian molecular clock models.
For each demographic and the molecular clock models a chain lengths of 170 million were used and sampled every 1000 states.
Comparison of the strict and relaxed molecular clock models showed that the first fitted the data better than the second in all subjects.
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The tree prior was set to the Yule process and a single uncorrelated-rates relaxed molecular clock model assuming a lognormal distribution of rates (UCLD) was applied to all partitions.
Evolutionary divergence times were estimated using the relaxed molecular clock model implemented in the software Multidivtime [56], [57].
Chi-square test was performed to estimate whether the four genes evolved according to the molecular clock model (P value>0.05).
We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model.
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