The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

Table 2 Parameter estimates and likelihood scores for branch-site model, model B.

Model	P	L	Estimates of parameters	Positively selected sites
MPO Model B	5	-33655.0405	p₀ = 0.4975, p₁ = 0.4553, (p₂ = 0.0246, p₃ = 0.0225) Background: ω₀ = 0.0458, ω₁ = 0.3307, ω₂ = 0.0458, ω₃ = 0.3307 Foreground: ω₀ = 0.0458, ω₁ = 0.3307, ω₂ = 251.6783, ω₃ = 251.6783	Foreground: NEB 19 > 0.50 2 > 0.95 1 > 0.99
EPO Model B	5	-33647.5634	p₀ = 0.4967 p₁ = 0.4469, (p₂ = 0.0297, p₃ = 0.0267) Background: ω₀ = 0.0464, ω₁ = 0.3322, ω₂ = 0.0464, ω₃ = 0.3322 Foreground: ω₀ = 0.0464, ω₁ = 0.3322, ω₂ = 774.6323, ω₃ = 774.6323	Foreground: NEB 28 > 0.50 6 > 0.95 4 > 0.99
LPO Model B	5	-33627.3508	p₀ = 0.4431, p₁ = 0.3884, (p₂ = 0.0898, p₃ = 0.0787) Background: ω₀ = 0.0470, ω₁ = 0.3414, ω₂ = 0.0470, ω₃ = 0.3414 Foreground: ω₀ = 0.0470, ω₁ = 0.3414, ω₂ = 82.8559, ω₃ = 82.8559	Foreground: NEB 96 > 0.50 18 > 0.95 11 > 0.99
TPO Model B	5	-33639.5793	p₀ = 0.4358, p₁ = 0.3690, (p₂ = 0.1057, p₃ = 0.0895) Background: ω₀ = 0.0479, ω₁ = 0.3468, ω₂ = 0.0479, ω₃ = 0.3468 Foreground: ω₀ = 0.0479, ω₁ = 0.3468, ω₂ = 999.0000, ω₃ = 999.0000	Foreground: NEB 82 > 0.50 8 > 0.95

Model B allows each foreground lineage to be tested independently of all other lineages, hence the four clusters (MPO, EPO, LPO, TPO – each in turn treated as foreground), and estimates 5 parameters (P) in total. p₀, p₁, p₂ and p₃ are proportions of sites in the dataset with the corresponding ω value, i.e, ω₀, ω₁, ω₂ and ω₃ for the foreground and the background lineages independently. The final column gives the estimated number of sites with posterior probabilities of greater than 0.50 of belonging to the positively selected category. Note: NEB: Naïve Empirical Bayes analysis.

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