The Angola strain is suggested to represent the most ancestral branch.
In general, more clade models were significant than ancestral branch models, even where these corresponded to the same taxa.
The matrix W is given by the inverse of B whose matrix element Bij is the common ancestral branch length of the i-th and j-th species.
The only case that differed was the comparison between the one-ratio model and the two-ratio model in which the Yangochiroptera (YAN) ancestral branch was the foreground.
We first modeled a strong instantaneous acceleration as an analogue to what is inferred by FIR to have occurred ancestral branch leading to Laurasiatheria.
Four "genes", psaC, rbcL, rpl6, and PS13, have significantly lower ω1 than ω0 (stronger purifying selection in the ancestral branch of Poaceae than in other branches).
Megabats have a greater reliance on vision compared to microbats, thus we tested for selective pressures on the common ancestral branch for megabats (marked m in Figure 5).
The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution.
We found that only when the ancestral branch of the NWM lineage was considered as the foreground branch, the branch-site model exhibits a better fit to the data (p = 0.003, χ2-test), and shows the signal of positive selection on the ancestral branch of NWM Tetherin (Table 1).
Assuming Bonferroni's correction, only the common ancestral branch for the modern human, Neanderthal and mtAncestor-1 lineages indicates the significantly lower dN/dS ratio than the background dN/dS.
When we applied the branch-site-specific (Bayes empirical Bayes random-effects) method to the ancestral branch subtending the LP719 allele and b-like clade, dN/dS again did not differ significantly from one (dN/dS = 1.05, P = 0.75).
