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].
We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model.
That is to say, the evolutionary rate of leptin between rabbit and other selected lineages was stable and conformed to the molecular clock model.
We also estimated integration times using a computational approach based on markov-chain monte carlo simulations (MCMC) supported by a relaxed molecular clock model with dated tree nodes.
Time to the most recent common ancestor (TMRCA) was estimated using an uncorrelated lognormal relaxed molecular clock model, implemented in Beast v1.5.4 [41].
Dating the tree using a Bayesian relaxed molecular clock model in BEAST [31] resulted in the ultrametric consensus tree depicted in Figure 1.
Chi-square test was performed to estimate whether the four genes evolved according to the molecular clock model (P value>0.05).
To investigate whether rates of molecular evolution fit with a strict molecular clock model, the likelihood of the ML phylogeny was recalculated with the constraint of global molecular clock using the Rambaut parameterization for clock optimization implemented in PAUP4b10 [58].
Under this relaxed molecular clock model the proportion of times from internal nodes to the ingroup root node – the root when we exclude the outgroup and then reroot the tree – are robust to time scaling [57].
For the UK-Brazil clade the estimated time of the MRCA was 1980 1972 to 19877) under a "relaxed molecular clock" model and 1977 19699 to 1985) under a "strict clock" model.
