A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish

Table 2 PAML results

Region¹	n ²	c ³	Parameters in ω distribution under M2a⁴		Parameters in ω distribution under M8⁵
B30.2	38	145	ω_>1 = 2.98787	p _>1 = 0.15644	ω_>1 = 2.64795	p ₁ = 0.17627
complete 1–435			ω₁ = 1.000	p ₁ = 0.25983		p ₀ = 0.82373
			ω_<1 = 0.18514	p _<1 = 0.58373	p= 0.64985	q = 1.07859
B30.2	38	95	ω_>1 = 2.79395	p _>1 = 0.15969	ω_>1 = 2.38329	p ₁ = 0.20431
fragment 1–285			ω₁ = 1.000	p ₁ = 0.28631		p ₀ = 0.79569
			ω_<1 = 0.17036	p _<1 = 0.554	p= 0.62590	q = 1.00411
B30.2	38	50	ω_>1 = 3.28071	p _>1 = 0.09143	ω_>1 = 2.84563	p ₁ = 0.09925
fragment 286–435			ω₁ = 1.000	p ₁ = 0.28492		p ₀ = 0.90075
			ω_<1 = 0.17611	p _<1 = 0.62365	p = 0.70827	q = 1.26680
RBB	55	155	ω_>1 = 2.1211	p _>1 = 0.06286	ω_>1 = 1.58831	p ₁ = 0.07109
complete 1–465			ω₁ = 1.000	p ₁ = 0.44597		p ₀ = 0.92891
			ω_<1 = 0.11812	p _<1 = 0.49117	p= 0.47665	q = 0.86554
RBB	55	78	ω_>1 = 2.53603	p _>1 = 0.06002	ω_>1 = 1.98626	p ₁ = 0.06121
fragment			ω₁ = 1.000	p ₁ = 0.43598		p ₀ = 0.93879
1 – 234			ω_<1 = 011843	p _<1 = 0.50400	p= 0.93879	q = 1.04448
RBB	55	76	ω_>1 = 2.05674	p _>1 = 0.02961	ω_>1 = 1.49995	p ₁ = 0.02779
fragment 238–465			ω₁ = 1.000	p ₁ = 0.46960		p ₀ = 0.97221
			ω_<1 = 0.12722	p _<1 = 0.50079	p= 0.47756	q = 0.81657

¹ For sequence fragments, the numbers correspond with the position of first and last nucleotides in the alignment with excluded gaps.
² n, the number of sequences in the alignment and tree.
³ c, the number of codons.
⁴ Parameters determined under M2a with ω the ratio of non-synonymous rates (dN) and synonymous rates (dS) and p the corresponding proportion of sites for each ω-class.
⁵ Parameters determined under M8 with ω the ratio dN/dS, the corresponding proportion (p ₁ = 1-p ₀) of sites and p- and q-estimates in the β (p, q)-distribution.

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