Table 4. Parameter estimates under branch-site models along particular MEF2 branch.

Branch-site models		Parameter estimates	PSS		2Δ
Foreground MEF2A Branch	Model A H0	ω0 = 0.008 P0 = 0.989 ω1 = 1.000 P1 = 0.011	Not allowed	−1689.428	0
	(ω2 = 1)	ω2a fore = 1.000 ω2a back = 0.008 P2a = 0.000
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.000
	Model A H1	ω0 = 0.008 P0 = 0.989 ω1 = 1.000 P1 = 0.011	None	−1689.428
		ω2a fore = 1.000 ω2a back = 0.008 P2a = 0.000
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.000
Foreground MEF2C Branch	Model A H0	ω0 = 0.008 P0 = 0.989 ω1 = 1.000 P1 = 0.011	Not allowed	−1689.428	0
	(ω2 = 1)	ω2a fore = 1.000 ω2a back = 0.008 P2a = 0.000
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.000
	Model A H1	ω0 = 0.008 P0 = 0.989 ω1 = 1.000 P1 = 0.011	None	−1689.428
		ω2a fore = 1.000 ω2a back = 0.008 P2a = 0.000
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.000
Foreground MEF2B Branch	Model A H0	ω0 = 0.011 P0 = 0.832 ω1 = 1.000 P1 = 0.011	Not allowed	−1686.781	3.062*
	(ω2 = 1)	ω2a fore = 1.000 ω2a back = 0.011 P2a = 0.155
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.000
	Model A H1	ω0 = 0.011 P0 = 0.871 ω1 = 1.000 P1 = 0.011	9 (0.851) 12 (0.862)	−1685.250
		ω2a fore = 8.299 ω2a back = 0.011 P2a = 0.155	14(0.795) 51(0.760)
		ω2b fore = 8.299 ω2b back = 1.000 P2b = 0.002	53(0.996**) 64(0.964*)
			73(0.647) 85(0.614)
			90(0.694)
Foreground MEF2D Branch	Model A H0	ω0 = 0.007 P0 = 0.920 ω1 = 1.000 P1 = 0.011	Not allowed	−1682.317	3.360*
	(ω2 = 1)	ω2a fore = 1.000 ω2a back = 0.007 P2a = 0.068
		ω2b fore = 1.000 ω2b back = 1.000 P2b = 0.001
	Model A H1	ω0 = 0.011 P0 = 0.944 ω1 = 1.000 P1 = 0.011	9(0.909) 50(0.963*)	−1680.637
		ω2a fore = 999.000 ω2a back = 0.011 P2a = 0.045
		ω2b fore = 999.000 ω2b back = 1.000 P2b = 0.001

Note: Model A H0 is specified using fixed ω ₂ = 1. The p-value of Model A H0 versus Model A H1 for the MEF2B and MEF2D branches is 0.040 and 0.033, respectively, which are considered to be statistically significant.