Parameter estimates and Log-likelihood values under models of variable ω ratios among branches and sites.

Comparisons across neutral and selective models of codon replacements were done with the set of concatenated genes encoding ribosomal proteins in lophotrochozoans using different foreground internal branch/lineages as a target for assessing codon classes (n_codon = 5965, ns = 9) with the following Best user tree: (((((Alvine,Paralv),(Capite,Areni)),(Helobd,Lumbri)),(Crasso,Argope)),Strong); Positive sites retained with BEB p-value>0.95. ‘Poly’ corresponds to the branch leading to Polychaeta (branch #D) and ‘Alvi’ to the branch leading to Alvinellidae (branch #C). Model parameters: κ = transition/transversion kappa ratio, ω = dN/dS ratio estimated for either the tree or specific foreground branches, K = number of ω categories, p = proportion of sites in each ω category, df = degrees of freedom.