. 2019 Apr 25;7:e6840. doi: 10.7717/peerj.6840

Table 2. Likelihood ratio tests of site-specific models on avian digestive enzyme genes performed in PAML (Yang, 2007).

Category	Gene	Site models	lnL^a	Pvalue^b	ω in M8	Positively selected sites^c
Carbohydrases	hepatic amy	M8	−8,835.49	0.0002^b	2.209	4(0.92) 70(0.97) 477(0.99)
	hepatic amy	M8a	−8,842.33	0.0002^b	2.209	4(0.92) 70(0.97) 477(0.99)
	pancreatic amy	M8	−9,610.63	0.0001^b	2.639	22(1.00) 23(0.97) 157(0.98) 367(0.96) 455(0.99)
	pancreatic amy	M8a	−9,617.84	0.0001^b	2.639	22(1.00) 23(0.97) 157(0.98) 367(0.96) 455(0.99)
	agl	M8	−27,765.85	0.1195	1.154	none
	agl	M8a	−27,767.07	0.1195	1.154	none
	g6pc	M8	−7,572.03	0.0852	1.550	none
	g6pc	M8a	−7,573.51	0.0852	1.550	none
	gaa i	M8	−10,960.54	0.1796	1.439	none
	gaa i	M8a	−10,961.44	0.1796	1.439	none
	gaa ii	M8	−8,355.26	0.4193	1.425	none
	gaa ii	M8a	−8,354.93	0.4193	1.425	none
	gck	M8	−4,081.65	0.9931	5.490	none
	gck	M8a	−4,081.65	0.9931	5.490	none
Lipases	cyp7a1	M8	−12,177.26	0.0010^b	1.501	3(0.98) 10(0.95) 30(0.96) 327(0.92) 392(0.97) 501(0.94)
	cyp7a1	M8a	−12,182.67	0.0010^b	1.501	3(0.98) 10(0.95) 30(0.96) 327(0.92) 392(0.97) 501(0.94)
	pnlip	M8	−15,109.12	9.14E–28^b	2.244	38(1.00) 66(1.00) 75(1.00) 76(0.95) 79(1.00) 80(1.00) 184(0.96) 250(0.91) 256(1.00) 312(1.00) 318(1.00) 340(1.00) 390(0.99) 402(0.99) 424(1.00)
	pnlip	M8a	−15,168.75	9.14E–28^b	2.244
Proteases	pgb1	M8	−10,322.64	0.0002^b	1.464	50(0.92) 133(0.96) 216(1.00) 220(0.97) 234(0.93) 248(0.91) 288(0.94) 343(0.94)
	pgb1	M8a	−10,329.80	0.0002^b	1.464
	pgb2	M8	−9,220.00	5.17E-08^b	1.731	108(0.99) 118(0.99) 197(0.95) 212(0.91) 253(1.00) 254(0.93) 261(1.00) 262(0.97) 273(0.95)
	pgb2	M8a	−9,234.82	5.17E-08^b	1.731
Chitinase	chia	M8	−5,885.92	2.58E–06^b	3.747	401(0.99) 402(1.00) 411(0.95)
Chitinase	chia	M8a	−5,896.97	2.58E–06^b	3.747	401(0.99) 402(1.00) 411(0.95)
Lysozymes	lygA	M8	−5,992.18	2.17E–05^b	1.593	11(0.99) 23(0.95) 24(0.94) 83(1.00) 131(1.00)
	lygA	M8a	−6,001.20	2.17E–05^b	1.593	11(0.99) 23(0.95) 24(0.94) 83(1.00) 131(1.00)
	lygB	M8	−4,314.25	1.98E–26^b	3.092	8(0.94) 10(1.00) 22(1.00) 33(0.99) 81(1.00) 83(1.00) 88(0.96) 91(1.00) 99(1.00) 103(0.95) 110(1.00) 128(1.00) 129(1.00) 132(0.98)
	lygB	M8a	−4,370.83	1.98E–26^b	3.092
	lygC	M8	−4,318.04	1.25E–07^b	2.606	22(1.00) 39(1.00) 128(1.00)
	lygC	M8a	−4,332.01	1.25E–07^b	2.606	22(1.00) 39(1.00) 128(1.00)
	lyz	M8	−4,100.09	0.0035^b	1.743	31(0.97) 50(0.97) 58(0.92)
	lyz	M8a	−4,104.34	0.0035^b	1.743	31(0.97) 50(0.97) 58(0.92)

Notes.

The natural logarithm of likelihood value.

P values denoted with two asterisks (**) when less than 0.01.

Positively selected sites with posterior probabilities ≥ 0.9. Posterior probability values are shown in parentheses next to site numbers, which follow chicken genes.