Schematic representation of the codon models used. (a) Models allowing dN/dS variation along lineages. Arrows indicate the questions addressed by the comparison between models (in (a), the arrows correspond to hierachical relationships). (b) Models allowing dN/dS variation along the gene. In M8A, ω follows a β distribution discretized into 10 categories of similar frequency (0 < ω1–10 < 1) and an additional category of ω is fixed at 1 (ωad = 1, accounting for neutral sites); M8 differs from M8A only by the additional category of ω which is constraint to be superior to 1 (ωad > 1), to account for sites under positive selection. (c) Phylogenetic trees harbours two clades, one for each paralog (the outgroup is not represented here). Models are either specifying identical categories of dN/dS in both clades (M3), or allowing one category to take a different value in each clade (MD).
Ho-Huu et al. BMC Evolutionary Biology 2012 12:195 doi:10.1186/1471-2148-12-195