Table 2 Significant LRTs for a subset of sites having experienced a shift in the intensity of selection pressure at the origin of the great apes (H4)
Gene2δlPqpSHIFTωBGωFG
LRT-3: M2a-rel vs. model C
 RORA47.027.04e-121.55E-100.110.263.40
 RARG15.886.76e-050.00070.900.000.08
 ESRRB11.890.00060.00410.270.110.44
 NR2C19.520.00200.01120.380.230.91
 ESRRA6.660.00980.04330.750.000.08
 PGR5.670.01730.06330.710.050.18
 NR5A24.590.03210.09460.300.210.00
 NR4A34.470.03440.09460.190.390.10
 THRA4.020.04490.10980.0251.910.00
LRT-4: M3(k = 2) vs. model D(k = 2)
 RORA47.027.04e-121.69e-100.110.263.40
 RARG15.886.76e-050.00080.900.000.08
 ESRRB11.890.00060.00450.280.110.44
 NR2C19.590.00200.01170.810.030.28
 ESRRA5.860.01550.06900.750.000.08
 PGR5.670.01730.06900.710.050.18
 NR5A24.570.03250.09670.280.230.00
 NR4A34.470.03440.09670.190.390.10
 NR1H24.380.03630.09670.890.020.00
 NR3C24.190.04070.09760.880.040.12
  • 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 1. The null model for all LRTs assumes homogenous selection pressure for all branches (ωBG = ωFG). LRT-4 and LRT-5 have d.f. = 1. 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. pSHIFT is the fraction of sites subject to a shift in selection pressure.