Parameter estimates and tests of selection for phylogenetic analysis of variation in the ω = dN/dS ratio in the carotenoid biosynthesis pathway.

M0 is a model that assumes a constant ω ratio for all phylogenetic branches and all codons. M1 and M2 are branch models that assume variations in the ω ratio in the phylogeny, but consider a constant ω ratio for all codons. M1 assumes an independent ω ratio for each branch. M2 assumes a specific ω1 ratio for the carrot branch, in comparison with the background ω0 ratio of the remaining branches. M1a and M2a are site models that assume different classes of codons with contrasting ω ratios, but a constant ω ratio in the phylogeny. M1a assumes two different classes of codons: codons with 0ω0p0 and other codons with ω1 = 1 at a frequency p1. M2a assumes three classes of codons: codons with 0ω0p0, ω = 1 at a frequency p1 and ω2>1 at a frequency p2. We did not detect any codons in the latter class and therefore did not display results for M2a. The likelihood (LnL) is shown for each model, with the p-value p(χ2) associated with the likelihood ratio test.*: P**: P***: P