Table 3.

Significant likelihood ratio tests of selection on transformer in Drosophila and the Tephritidae

Test	Line	Alternative Ma	Null Ma	2ΔL	df	Pb	Sitesc
1	a	Nearly Neutral	One ratio	13.75	1	0.0002	4
2	b	Local relaxation	Uniform Selection	5.39	2	0.02	0
3-D	c	Local relaxation	Uniform Selection	64.89	2	< 0.0001	16
3-T	d	Local relaxation	Uniform Selection	15.79	2	< 0.0001	1

^a Alternative and null models, see Additional File 6, Table S3 for more information on models and Log-likelihood values, ^b P value calculated from a χ² distribution, ^c number of sites significant in Bayesian post-hoc tests (P < 0.05). The alignment, after deleting gaps, was composed of 122 codons. Tests that we deemed weakly significant because Bayesian post-hoc tests did not detect relevant AA are shown in italics.