BMC Ecology and Evolution

Table 2 The effects of codon usage bias on LRTs (n = 29)

From: Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family

		Model
		F equal	F3×4	F codon
Estimates under model A		p₀ = 0.427, p₁ = 0.241 (p₂ + p₃) = 0.330 ω₂ = 11.182	p₀ = 0.452, p₁ = 0.170 (p₂ + p₃) = 0.376 ω₂ = 999	p₀ = 0.469, p₁ = 0.157 (p₂ + p₃) = 0.372 ω₂ = 999
Estimates under M1a		p₀ = 0.627, p₁ = 0.372 ω₀ = 0.193	p₀ = 0.711, p₁ = 0.288 ω₀ = 0.126	p₀ = 0.730, p₁ = 0.269 ω₀ = 0.113
Estimates under model A (ω₂ = 1)		p₀ = 0.437, p₁ = 0.259 (p₂ + p₃) = 0.302 ω₀ = 0.187	p₀ = 0.480, p₁ = 0.189 (p₂ + p₃) = 0.329 ω₀ = 0.121	p₀ = 0.505, p₁ = 0.178 (p₂ + p₃) = 0.316 ω₀ = 0.107
2Δl	Test 1:	35.44	53.78	54.38
	Test 2:	19.98	28.22	27.89

Note: Branch-site model A was compared to site model M1a and model A with ω₂ fixed to 1 for test 1 and 2, respectively. All tests are significant at 1%; with df = 2 and df = 1 for tests 1 and 2, respectively.

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