TABLE 6.

Maximum-likelihood codon-based analysis of positive selection in the repleta species group

Data set	M1	M2	LRT	P	P(s)	ω	BEB selected sites
Full alignment	−7424.47	−7388.35	72.24	1.91E-17	0.08	2.80	68, 132, 133, 135, 253
Exclude D. mettleri-1,	−6642.72	−6619.94	45.55	1.49E-11	0.07	2.63	68, 132, 133, 135, 253
D. mettleri-2
Exclude D. mettleri-1, D. mettleri-2,	−5726.11	−5703.86	44.49	2.55E-11	0.08	2.79	68, 132, 133, 135, 253
Dmoj\GLEANR_897, D. arizonae-4,
D. arizonae-5, Dvir\GLEANR_2181
Exclude D. mettleri-1, D. mettleri-2,	−5265.49	−5258.06	14.88	1.15E-04	0.03	3.02	253
Dmoj\GLEANR_896,
Dmoj\GLEANR_898,
Dmoj\NEW_PARALOG,
D. arizonae-1, D. arizonae-2,
D. arizonae-5, D. mayaguana-1
Data set	M7	M8	LRT	P	P(s)	ω	BEB selected sites
Full alignment	−7426.01	−7376.89	98.23	3.72E-23	0.13	2.11	68, 73, 112, 113, 132, 133, 135, 179, 184, 187, 204, 208, 211, 209, 253
Exclude D. mettleri-1, D. mettleri-2	−6643.22	−6608.53	69.37	8.16E-17	0.13	1.92	68, 73, 112, 132, 133, 135, 179, 187, 204, 253
Exclude D. mettleri-1, D. mettleri-2,	−5734.58	−5698.60	71.96	2.19E-17	0.14	2.08	68, 73, 112, 113, 132, 133, 135, 179, 187, 204, 208, 209, 253, 257
Dmoj\GLEANR_897, D. arizonae-4,
D. arizonae-5, Dvir\GLEANR_2181
Exclude D. mettleri-1, D. mettleri-2,	−5269.09	−5253.85	30.48	3.38E-08	0.11	1.70	68, 112, 113, 133, 135, 179, 187, 253
Dmoj\GLEANR_896, Dmoj\GLEANR_898,
Dmoj\NEW_PARALOG, D. arizonae-1,
D. arizonae-2, D. arizonae-5, D. mayaguana-1

M1, M2, M7, and M8 denote codon models implemented in PAML (Yang 1997). LRT, the value of the likelihood ratio test between nested models. P, the probability of the LRT under a χ² distribution. P(s), proportion of sites in the positively selected site class. ω, estimated d_N/d_S of the positively selected site class. BEB selected sites, Bayes empirical Bayes predicted selected sites for the given selection model (Yang et al. 2005).