Table 2.

Likelihood Ratio Test Results for the P19, Calcyon, and NEEP21 gene families. Branch numbers are as labeled in Figure 3A.

Parameter estimates and log likelihood scores Model	P19	p	l	NEEP21	p	l	Calcyon	p	l
Null Model	w = 0.039	22	−1676.77	w = 0.029	20	−2397.85	w = 0.101	20	−2263.16
Free-Ratio Model	on branch 1, w = 999.0	41	−1652.77	on branch 2, w = 999.00	37	−2390.05	on branch 6, w = 999.00	37	−2239.75
				on branch 3, w = 999.00			on branch 7, w = 999.00
				on branch 4, w = 999.00
				on branch 5, w = 23.800
	p0 = 0.97691, w0 = 0.03811	23	−1674.02	p0 = 0.99368, w0 = 0.02747	21	−2395.48	p0 = 0.92047, w0 = 0.08631	21	−2252.47
Branches-sites Null Model	p1 = 0.02309, w1 = 1.00000			p1 = 0.00632, w1 = 1.00000			p1 = 0.07953, w1 = 1.00000
Branches-sites Model	on branch 1	25	−1670.72	on branch 2			on branch 6	23	−2219.98
	p0 = 0.84028, w0 = 0.03883			p0 = 0.00000, w0 = 0.02371	23	−2394.61	p0 = 0.79419, w0 = 0.06334
	p1 = 0.00885, w1 = 1.00000			p1 = 0.00000, w1 = 1.00000			p1 = 0.03893, w1 = 1.00000
	p2a = 0.14930, w2a = 999.0000			p2a = 0.99354, w2a = 1.00000			p2a = 0.15908, w2a = 999.0000
	p2b = 0.00157, w2b = 999.0000			p2b = 0.00646, w2b = 1.00000			p2b = 0.00780, w2b = 999.0000
				on branch 3			on branch 7	23	−2251.90
				p0 = 0.51862, w0 = 0.02754	23	−2393.52	p0 = 0.48078, w0 = 0.08255
				p1 = 0.00361, w1 = 1.00000			p1 = 0.04474, w1 = 1.00000
				p2a = 0.47447, w2a = 999.0000			p2a = 0.43408, w2a = 1.00000
				p2b = 0.00330, w2b = 999.0000			p2b = 0.04040, w2b = 1.00000
				on branch 4
				p0 = 0.00000, w0 = 0.02638	23	−2394.97
				p1 = 0.00000, w1 = 1.00000
				p2a = 0.99389, w2a = 103.03332
				p2b = 0.00611, w2b = 103.03332
				on branch 5
				p0 = 99367, w0 = 0.02747	23	−2395.48
				p1 = 0.00632, w1 = 1.00000
				p2a = 0.00001, w2a = 1.00000
				p2b = 0.00000, w2b = 1.00000
Branches Model	on branch 1, w = 999.0	23	−1674.69	on branch 2, w = 0.4652	21	−2396.97	on branch 6, w = 999.00	21	−2257.38
				on branch 3, w = 999.00	21	−2396.98	on branch 7, w = 0.1539	21	−2263.12
				on branch 4, w = 999.00	21	−2397.41
				on branch 5, w = 0.0001	21	−2397.85

Likelihood ratio test statistics		2(Δl)	df	P value		2(Δl)	df	P value		2(Δl)	df	P value
Null Model vs branches-sites null Model		5.492	2	0.0642		4.743	2	0.0933		21.394	2	< 0.0001
Null Model vs Free ratio Model		48.001	19	0.0003		15.602	17	0.5522		46.830	17	0.0001
Branches-sites Model vs Null Model	on branch 1	12.096	3	0.0071	on branch 2	6.480	3	0.0905	on branch 6	86.362	3	< 0.0001
					on branch 3	8.665	3	0.0341	on branch 7	22.519	3	< 0.0001
					on branch 4	5.760	3	0.1239
					on branch 5	4.743	3	0.1916
Branches-sites Model vs Branches-sites null Model	on branch 1	6.604	2	0.0368	on branch 2	1.737	2	0.4196	on branch 6	64.967	2	< 0.0001
					on branch 3	3.923	2	0.1407	on branch 7	1.124	2	0.5700
					on branch 4	1.017	2	0.6015
					on branch 5	0.006	2	0.9970
Branches Model vs Null Model	on branch 1	4.162	1	0.0413	on branch 2	1.756	1	0.1851	on branch 6	11.574	1	0.0007
					on branch 3	1.737	1	0.1876	on branch 7	0.092	1	0.7620
					on branch 4	0.879	1	0.3486
					on branch 5	0.000	1	0.9980