Table 2.

Branches of gene trees under positive selection as determined using HyPhy branch site random effects likelihood model [51]

Gene	Branch	Mean Ω	Ω1	p1	Ω2	p2	Ω3	p3	LRT	p-value	Corrected p-value
IR143a	H. timareta*H. melpomene	0.151	0	0.963	0	0.035	10000	0.002	11.309	0.000	0.008
IR60a1a	H. erato*H. telesiphe*H. clysonymus*H. sapho*H. sara	0.196	0.165	0.994	0.167	0.001	3333	0.005	11.042	0.000	0.009
IR60a1a	H. sapho*H. sara	0.178	0.151	0.983	0.149	0.013	10000	0.004	8.989	0.001	0.027
IR60a2a	H. sapho	0.434	0.055	0.942	0.163	0.026	22	0.032	19.785	0.000	0.000
IR60a2a	H. sara	0.839	0.762	0.975	0.763	0.015	199	0.010	14.949	0.000	0.001
IR60a2a	H. timareta*H. melpomene	0.501	0.402	0.984	0.401	0.000	5197	0.016	36.954	0.000	0.000
IR68a	H. hecuba	0.244	0.206	0.992	0.204	0.005	263	0.003	8.198	0.002	0.044
IR75d	H. timareta*H. melpomene	0.155	0.091	0.971	0.151	0.025	2181	0.004	14.184	0.000	0.002
IR7d1	H. sara	0.498	0.463	0.973	0.462	0.025	10000	0.002	9.936	0.001	0.017
IR7d4	H. timareta	0.079	0.033	0.994	0.032	0.002	5447	0.004	13.677	0.000	0.002
IR93a	H. clysonymus	0.131	0.079	0.991	0.080	0.005	80	0.004	12.607	0.000	0.004
IR93a	H. doris	0.287	0	0.950	0	0.001	8	0.049	10.858	0.000	0.010

IR gene name and phylogenetic branch showing positive selection is reported in the first two columns. Values obtained from HyPhy for positive selection are shown only for the IR genes supported by a significant p-value obtained from the likelihood ratio test (LRT) and corrected for multiple testing with the Holm formula