The evolution of nuclear auxin signalling

Table 2 Sites under PDS in the A. thaliana/P. trichocarpa Aux/IAA gene family: „Site-specific analysis".

Site-specific analyses	n	dN/dS (ω) under M0	2Δℓ M2 vs. M1 (df 2)	2Δℓ M8 vs. M7 (df 2)	Parameter estimates under M8	Positively selected sites under M2 (BEB)	Positively selected sites under M8 (BEB)
Aux/IAA
Node IAA1	9	0.112	0.00	0.00	ρ₀ = 1.000 (ρ₁ = 0.000) (ρ = 0.285) q = 1.705 ω = 2.40	None	22
Node IAA5	5	0.132	0.00	1.44	ρ₀ = 0.944 (ρ₁ = 0.056) (ρ = 0.315) q = 1.634 ω = 2.11	None	21 23 39 40 68
Node IAA7	10	0.090	0.00	4.62	ρ₀ = 0.948 (ρ₁ = 0.052) (ρ = 0.318) q = 3.848 ω = 1.00	None	16 19 40 42 49 75 80 81
Node IAA8	7	0.125	0.00	0.00	ρ₀ = 1.000 (ρ₁ = 0.000) (ρ = 0.537) q = 2.898 ω = 2.302	None	10 11 171
Node IAA10	6	0.076	0.00	0.10	ρ₀ = 0.977 (ρ₁ = 0.023) (ρ = 0.522) q = 3.630 ω = 1.000	None	124
Node IAA18	6	0.112	0.00	0.00	ρ₀ = 1.000 (ρ₁ = 0.000) (ρ = 0.505) q = 0.301 ω = 5.133	None	20 115 116
Node IAA20	5	0.155	0.74	4.54	ρ₀ = 0.898 (ρ₁ = 0.102) (ρ = 0.617) q = 4.304 ω = 1.307	43	13 43 49

Each comparison has n sequences, dN/dS is average ratio over sites under a codon model with one ω. Bold underline, PP ≥ 0.99 of being under positive selection; bold, 0.99>PP ≥ 0.95; italic, 0.95>PP ≥ 0.90; underline, 0.90>PP ≥ 0.70; normal, 0.70>PP > 0.50

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