We used the branch model to identify fast-evolving genes, with the null model assuming that all branches have been evolving at the same rate and the alternative model allowing foreground branches to evolve under a different rate.
Indeed the model that allows branches to evolve under different selective pressures (M0b) better explains the evolution of the PTP gene family compared to a model with no branch specific selection (M0) (see Table 1 for comparison of models by LRT).
A major difference between them, however, is that PL assumes that rates are auto-correlated (inheritable), whereas in Bayesian relaxed clock dating each branch is allowed to evolve at its own rate.
In clade 1, several branches were shown to evolve under positive selection, with notably 35% of branches evolving under significant positive selection (ω > 1) both in the PTP Cα and Z subclades (p < <0.05 and p < 0.05, respectively) (Table 3).
M1 is a model in which all branches are assumed to evolve at different rates.
In the null model, all codons in the foreground and background branches are assumed to evolve under negative selection (ω < 1) or neutrally (ω = 1), whereas in the alternative model A, the foreground branch also includes sites evolving under positive selection (ω > 1).
A noteworthy consequence of this observation is that it is not a paradox that there is a general tendency for some branches of life to evolve, without predictable directions, toward progressively more elaborate forms (discovery of multicellularity was one of those remarkable events).
Sea biscuits and sand dollars are representatives of the order Clypeasteroida, the latest major branch of irregular echinoids to evolve.
