. 2016 Apr 11;203(2):905–922. doi: 10.1534/genetics.115.183889

Table 1. Significant LRTs for a subset of sites having experienced an episodic alteration of selection pressure.

Gene	2δl	P	q	*p_i*	*ω_i*
H₁: Great Ape
*LRT-1: model A (ω_FG = 1) vs.* model A (ω_FG > 1)**
None	N.A.	N.A.	N.A.	N.A.	N.A.
*LRT-2: M3(k = 2) vs.* model B**
NR0B2	7.07	0.0292	0.7012	P_FG(a+b) = (0.35 + 0.65)	ω_FG = 0.0
				p₁ = 0.00	ω₁ = 0.59
				p₀ = 0.00	ω₀ = 0.05
H₂: Human–Chimpanzee
*LRT-1: model A (ω_FG = 1) vs.* model A (ω_FG > 1)**
None	N.A.	N.A.	N.A.	N.A.	N.A.
*LRT-2: M3(k = 2) vs.* model B**
None	N.A.	N.A.	N.A.	N.A.	N.A.
H₃: Human
*LRT-1: model A (ω_FG = 1) vs.* model A (ω_FG > 1)**
NR1D1	10.27	0.0013	0.0650	P_FG(a+b) = 0.002	ω_FG = 99
				p₁ = 0.05	[ω₁ = 1]
				p₀ = 0.95	ω₀ = 0.04
*LRT-2: M3 (k = 2) vs.* model B**
NR1D1	15.25	0.0005	0.0234	P_FG(a+b) = 0.01	ω_FG = 99
				P₁ = 0.05	ω₁ = 0.86
				p₀ = 0.94	ω₀ = 0.04
PPARG	9.71	0.0077	0.1867	P_FG(a+b) = 0.01	ω_FG = 35
				p₁ = 0.11	ω₁ = 0.46
				p₀ = 0.88	ω₀ = 0.0
NR2C1	8.70	0.0129	0.2063	P_FG(a+b) = (0.24 + 0.76)	ω_FG = 99
				p₁ = 0.00	ω₁ = 0.33
				p₀ = 0.00	ω₀ = 0.02
PGR	7.67	0.0215	0.2586	P_FG(a+b) = (0.12+0.05)	ω_FG = 6.23
				p₁ = 0.24	ω₁ = 0.58
				p₀ = 0.59	ω₀ = 0.05

Genes having a q-value of <0.05 are shown in boldface type. The foreground (FG) branches are fully specified for each hypothesis in Figure 2. The null model for all LRTs assumes homogenous selection pressure for all branches (ω_BG = ω_FG). LRT-1 has d.f. = 1. LRT-2 has d.f. = 2. The q-value is the expected proportion of false discoveries expected if the single-test P-value is used as the boundary to control the FDR. The parameter P_FG(a+b) represents the proportion of sites subject to a change in selection intensity.