Table 1.

Putative Targets of Balancing Selection

		Test 1		Test 2—ZFD				Test 2—FFD
Gene	Species	MK1 + TD	MK2 + TD	TajD0	FuF0	FuD0	π/dxy0	TajD4	FuF4	FuD4	π/dxy4
AQP9	Lm	0.28	NA	0.05	0.02*	0.11	<1E-4*	0.31	0.69	0.8	0.11
BCL3	Lm	0.03*	0.76	0.83	0.95	0.95	0.32	0.69	0.82	0.82	0.87
CYLD	Lm	0.02*	0.06	0.75	0.79	0.75	0.02*	0.46	0.8	0.85	0.94
ELK1	Lm	NA	NA	0.66	0.47	0.42	0.3	0.62	0.15	0.02*	0.02*
EPS8	Lm	0.25	0.03*	0.39	0.38	0.42	0.02*	0.90	0.84	0.73	0.57
IL17RD	Lm	0.02*	0.21	0.63	0.68	0.68	0.02*	0.50	0.09	0.02*	0.63
IL28RA	Lm	NA	NA	0.22	0.03*	0.02*	0.22	0.20	0.05*	0.05*	0.03*
NBN	Lm	0.1	0.03*	0.56	0.52	0.49	0.48	0.51	0.52	0.52	0.88
NFE2L2	Lm	0.17	0.01*	0.83	0.97	0.98	0.18	0.43	0.4	0.43	0.7
PAFAH1B1	Lm	4E-3*	0.04*	0.84	0.87	0.83	<1E-4*	0.14	0.21	0.38	0.24
PRDX6	Lm	0.04*	4E-4*	0.67	0.68	0.63	0.08	0.40	0.29	0.3	0.46
PRELID1	Lm	0.23	0.45	0.93	0.39	0.04*	0.01*	0.95	0.83	0.7	0.45
RNF41	Lm	5E-3*	0.22	0.52	0.8	0.82	NA	0.31	0.38	0.44	0.27
SEC61A1	Lm	0.01*	1	0.43	0.11	0.04*	<1E-4*	0.27	0.06	0.04*	0.01*
SIGLEC1	Lm	0.01*	0.51	0.88	0.76	0.63	0.02*	0.67	0.7	0.68	0.31
SOCS3	Lm	0.12	0.03*	0.64	0.68	0.68	0.65	0.26	0.18	0.21	0.96
SOD1	Lm	0.01*	0.11	0.71	0.72	0.66	0.71	0.81	0.65	0.5	0.96
TAX1BP1	Lm	0.82	0.35	0.10	0.03*	0.06	0.04*	0.23	0.24	0.35	0.07
UBA52	Lm	0.02*	1	0.33	0.06	0.01*	<1E-4*	0.26	0.02*	1E-3*	0.33
USP7	Lm	1E-3*	1	0.62	0.55	0.50*	0.01*	0.68	0.41	0.28	0.78
AAMP	Lvg	0.04*	NA	0.44	0.58	0.59	<1E-4*	0.73	0.38	0.21	0.7
AKIRIN2	Lvg	0.6	NA	0.05*	0.03*	0.14	<1E-4*	0.28	0.22	0.23	0.09
APP	Lvg	0.02*	1	0.75	0.7	0.63	NA	0.54	0.69	0.71	0.66
CANX	Lvg	0.35	0.05*	0.38	0.5	0.56	0.04*	0.25	0.11	0.1	0.22
CD40LG	Lvg	0.09	0.04*	0.65	0.66	0.64	0.11	0.71	0.37	0.25	0.86
CEBPG	Lvg	0.04*	0.56	0.94	0.97	0.96	NA	0.70	0.85	0.85	0.3
GP5	Lvg	0.02*	0.12	0.33	0.16	0.15	0.11	0.31	0.2	0.2	0.74
HSF1	Lvg	0.03*	0.07	0.70	0.62	0.54	0.07	0.85	0.54	0.31	0.86
ITFG1	Lvg	0.01*	NA	0.62	0.65	0.63	<1E-4*	0.52	0.52	0.51	0.72
KLHL6	Lvg	0.03*	0.3	0.85	0.66	0.51	NA	0.23	0.08	0.09	0.02*
OTUD5	Lvg	0.05*	0.01*	0.46	0.48	0.46	0.36	0.22	0.39	0.5	0.83
PAMR1	Lvg	0.02*	0.45	0.80	0.96	0.96	0.06	0.65	0.51	0.43	0.78
PRDX6	Lvg	0.22	0.02*	0.29	0.58	0.67	0.07	0.35	0.27	0.29	0.22
SEC61A1	Lvg	1E-3*	0.51	0.76	0.28	0.11	<1E-4*	0.73	0.42	0.25	0.1
SIGLEC1	Lvg	4E-3*	0.13	0.93	0.96	0.95	0.05*	0.68	0.55	0.46	0.62
SQSTM1	Lvg	0.57	0.02*	0.16	0.23	0.32	0.31	0.62	0.68	0.65	0.83
TAP1	Lvg	0.02*	0.2	0.79	0.85	0.82	0.01*	0.44	0.14	0.08	0.03*
TRIM32	Lvg	0.01*	0.03*	0.89	0.96	0.95	0.01*	0.68	0.71	0.67	0.3
UBA52	Lvg	4E-4*	<1E-4*	0.74	0.96	0.96	<1E-4*	0.94	0.95	0.87	0.93
USP7	Lvg	1E-4*	1	0.76	0.79	0.74	<1E-4*	0.78	0.68	0.56	0.95

Note.—List of genes identified with composite tests 1 or 2 as targets of balancing selection in L. montandoni (Lm) and L. v. graecus (Lvg). Test 1 identified genes showing an excess of nonsynonymous polymorphisms segregating at intermediate frequencies: a combination of significant McDonald–Kreitman test conducted on ungenotyped (MK1) or genotyped (MK2) data and not significant or significantly positive Tajima’s D (TD). Test 2 identified genes with high ratio of polymorphism to divergence showing an excess of polymorphisms segregating at high frequencies: a combination of increased polymorphism-to-divergence ratio (π/dxy) and significantly positive Tajima’s D (TajD) or Fu and Li’s F (FuF) or Fu and Li’s D (FuD). Test 2 was performed for 0-fold degenerate (ZFD, 0) and 4-fold degenerate (FFD, 4) sites.

P values in bold indicate test combinations determining inclusion of a particular gene as candidate. Symbols of genes which were confirmed as single-copy are in bold.

NA, not applicable.