Lengths of these three classes of branches average 5.2, 19.5, and 29.7 MY respectively; this variation is significant (Kruskal-Wallis test, 2 df, p = 0.0012).
Three main classes of branches in the GO tree are biological processes, molecular functions and cellular components [ 33].
The evolutionary model we evaluated assumed two classes of branches with different ω values: Duplication branches (resulting from a duplication event labeled on the OG's phylogenetic tree) and speciation branches (the remaining branches, i.e., those resulting from speciation events).
The statistical significance of the ω differences between the two classes of branches was obtained by comparing the fit of the BM with that of a null model (M0), in which all lineages have the same ω, using the likelihood-ratio test (LRT).
Above conclusion fits for a class of branches, composed of actuated pendulum and passive two-force bar, such as RUS, RUU and RRS branches (U stands for the universal joint).
Such unbalanced samples may require the introduction of a third λ parameter class of branches to accommodate (i) over-sampled within-species branches, (ii) within-species branches and (iii) among-species branches.
The second alternative model ("local selection") omits the class of branch-specific neutral evolution of the "local relaxation" model and replaces it by two additional classes in which sites are under positive selection (with ω2 > 1) on the tested branch es) but are either under purifying selection (with ω0 < 1) or evolve neutrally (with ω1 = 1) on the rest of tree.
We discern three classes of long branch effects.
These two classes of terminal branch substitutions were then used to infer patterns of substitution specific to the saltans and willistoni groups, respectively.
In cereal species, such as rice, maize, barley and wheat, there are three classes of starch branching enzymes (SBE I, SBE IIa and SBE IIb).
