The definition of key terms often differs between different branches and traditions of engineering.
In contrast to many models, we assume that the molecular clock might differ between different branches.
Likelihood ratio tests were then used to identify cases in which these rates differed across different branches of a species tree; we identified possible targets of lineage-specific selection by locating elevated rates of evolution in protein-coding or regulatory regions that occurred only on specific branches of the tree.
The NMD pathway can be activated via different branches that differ in their dependence on the NMD factors UPF2, UPF3b, and EJC components (Chan et al., 2007; Gehring et al., 2005; Ivanov et al., 2008); however, they all require UPF1 to activate NMD.
These contrasts were estimated for each variable using the three kinds of trees differing in branch length (see above).
When one of eight synthetic hydrocarbons (differing in branch position, chain length, or both) was added to this filter paper, the ants started to be aggressive.
Although differing in branching order, TConsensus and TOptimal had similar overall tree lengths; as a result, the same priors were applied to both topologies in the program Multidivtime: rtrate = rtratesd = 0.012, and brownmean = brownmeansd = 0.01.
Second, post-burnin trees, sampled each 250 generations, were obtained using MrBayes and filtered with PAUP to obtain a sample of 1,105 trees differing in branch length but containing the consensus topology.
A likelihood ratio test (LRT) was used to compare various hypothesis models in which ω values are expected to differ among branches, in comparison to a null hypothesis in which all the branches have similar ω.
