TABLE 2.

Tests of positive selection and positively selected codons in the three transposase data sets of C. watsonii according to neutral models (M1 and M7) and selection models (M2 and M8) of PAML

Model	Data set	Likelihooda	Tree lengthb	Kappa	Parametersc,d	Codon	Amino acide	Probability for positive selection (BEB)f	dN/dS codon and SE
M1	I	2,230.86	0.13	1.27	ω0 = 0.00, ω1 = 1.00, p0 = 0.67, p1 = 0.33
	IA	2,129.05	0.11	1.1	ω0 = 0.00, ω1 = 1.00, p0 = 0.69, p1 = 0.31
	II	1,315.87	0.32	2.32	ω0 = 0.00, ω1 = 1.00, p0 = 0.54, p1 = 0.46
M2	I	2,196.17	0.14	1.91	ω0 = 0.67, ω1 = 1.00, ω2 = 53.90, p0 = 0.98, p1 = 0.00, p2 = 0.02	24	P	1.00	10.13 ± 0.68
62	P	1.00	10.12 ± 0.73
						128	S	1.00	10.13 ± 0.67
						184	K	0.99	10.02 ± 1.20
	IA	2,092.65	0.12	1.75	ω0 = 0.75, ω1 = 1.00, ω2 = 71.43, p0 = 0.97, p1 = 0.00, p2 = 0.03	24	P	1.00	10.21 ± 0.58
47	P	0.97	9.96 ± 1.61
						62	T	1.00	10.18 ± 0.73
						128	R	1.00	10.21 ± 0.58
						136	V	0.98	9.99 ± 1.53
						259	M	1.00	10.18 ± 0.75
						305	A	0.97	9.95 ± 1.62
						421	F	1.00	10.18 ± 0.75
	II	1,289.29	0.33	3.14	ω0 = 0.77, ω1 = 1.00, ω2 = 29.41, p0 = 0.98, p1 = 0.00, p2 = 0.02	24	P	1.00	9.98 ± 0.81
128	R	1.00	9.98 ± 0.82
						137	V	0.99	9.72 ± 1.70
M7	I	2,230.93	0.13	1.23	B(p = 0.01, q = 0.01)
	IA	2,130.19	0.11	0.99	B(p = 0.005, q = 0.02)
	II	1,316.12	0.32	2.27	B(p = 0.02, q = 0.02)
M8	I	2,196.17	0.14	1.91	B(p = 99, q = 47.61), p0 = 0.98, p1 = 0.02, ω2 = 53.92	24	P	1.00	10.12 ± 0.70
62	P	1.00	10.12 ± 0.73
						128	S	1.00	10.12 ± 0.70
						184	K	0.99	10.04 ± 1.11
	IA	2,092.66	0.12	1.75	B(p = 0.02, q = 0.01), p0 = 0.97, p1 = 0.03, ω2 = 71.96	24	P	1.00	10.21 ± 0.57
47	P	0.99	10.09 ± 1.22
						62	T	1.00	10.20 ± 0.64
						128	R	1.00	10.21 ± 0.57
						136	V	0.99	10.10 ± 1.16
						259	M	1.00	10.20 ± 0.65
						305	A	0.99	10.09 ± 1.23
						421	F	1.00	10.20 ± 0.64
	II	1,289.33	0.33	3.11	B(p = 0.02, q = 0.02), p0 = 0.98, p1 = 0.02, ω2 = 20.83	24	P	1.00	9.96 ± 0.83
128	R	1.00	9.96 ± 0.83
						137	V	0.98	9.80 ± 1.47
						184	Q	0.95	9.55 ± 2.07

^aThe likelihood indicates the fit of the data to the different models.

^bTree length is measured as the number of mutations per codon.

^cKappa is the transversion/transition ratio. Pi denotes the proportion of sites falling in site class ωi.

^dParameters p and q are the shape parameters of the beta distribution which underlies M7 and M8.

^eThe reference sequence for the amino acid designation is ZP_00519072.

^fThe probability that codons were under positive selection was determined using Bayes empirical Bayes (BEB), with the ω and its standard error indicated per codon.