Table 3. Result of the branch-site model A test for the detection of positively selected sites on the ancestral branches of Old World fruit bats and New World fruit bats.

Branch-site model	np a	Parameters	LRT b	ℓ	P-value	Site with elevated omega values c
M1a(nearly Neutral)	58	P 0 = 0.906,P 1 = 0.094, ω0 = 0.038, ω1 = 1.00		-13500.24
Model A (alternative hypothesis) for Old World fruit bats	60	P 0 = 0.862, P 1 = 0.090, P 2a = 0.044, P 2b = 0.005 Background: ω0 = 0.037, ω1 = 1.00, ω2a = 0.037, ω2b = 1.00 Foreground: ω0 = 0.037, ω1 = 1.00, ω2a = 1.00,ω2b = 1.00	Test 1	-13496.27	0.019	10G, 13G, 62A, 66L, 95V, 188D, 270V, 349E, 352R, 375E, 534V, 578L, 591V
Model A (null hypothesis) for Old World fruit bats	59	P 0 = 0.862, P 1 = 0.090, P 2a = 0.044,P 2b = 0.005 Background: ω0 = 0.037, ω1 = 1.00, ω2a = 0.037, ω2b = 1.00 Foreground: ω0 = 0.037, ω1 = 1.00, ω2a = 1.00,ω2b = 1.00	Test 2	-13496.27	1	Not allowed
Model A (alternative hypothesis) for New World fruit bats	60	P 0 = 0.837, P 1 = 0.087, P 2a = 0.068,P 2b = 0.007 Background: ω0 = 0.038, ω1 = 1.000, ω2a = 0.038, ω2b = 1.00 Foreground: ω0 = 0.038, ω1 = 1.00, ω2a = 1.00,ω2b = 1.00	Test 1	-13498.58	0.191	Not allowed
Model A (null hypothesis) for New World fruit bats	59	P 0 = 0.837, P 1 = 0.087, P 2a = 0.068,P 2b = 0.007 Background: ω0 = 0.038, ω1 = 1.00, ω2a = 0.038, ω2b = 1.00 Foreground: ω0 = 0.038, ω1 = 1.00, ω2a = 1.00,ω2b = 1.00	Test 2	-13498.58	1	Not allowed

^anp, number of parameters.

^bLRT, likelihood ratio test.

^clocation of sites with elevated omega values detected by branch-site model A test refer to Homo sapiens sequence.

The sites with BEB posterior probabilities > 0.95 were highlight by underline.