Table 4.

Positive selection for bat TLR3, TLR7, TLR8, and TLR9 under site-specific models

Gene	PSSa	Site in alignmentb	P (ω > 1)		Domain
			M2a	M8
TLR7	238K	234	0.662	0.962*	LRR7
	282V	278	0.794	0.978*	LRR8
	303N c	299	0.949	0.994**	LRR9
	385Q	381	0.563	0.951*	LRR12
	387Y	383	0.799	0.978*	LRR12
	394N	390	0.620	0.957*	LRR12
	453A	449	0.710	0.966*	LRR14
	461Q	457	0.645	0.960*	LRR14
	493L	488	0.797	0.978*	LRR14
	737C	732	0.797	0.978*	LRR24
TLR8	419K d	15	0.989*	0.996**	LRR14
	479T d	72	0.983*	0.994**	LRR14
	545S	137	0.899	0.962*	LRR17
	606V d	198	0.996**	0.998**	LRR19
	675R c	267	0.997**	0.999**	LRR22
	697Y d	289	0.984*	0.994**	LRR23
	721R	312	0.904	0.961*	LRR24
TLR9	270R d	60	0.966**	0.992**	LRR8
	277R	67	0.871	0.961*	LRR8
	298H	88	0.894	0.971*	LRR9
	301I	91	0.862	0.958*	LRR9
	325T c	115	0.951*	0.987*	LRR10
	326R c	116	0.969*	0.992**	LRR10
	331K	121	0.915	0.977*	LRR10
	355S d	145	0.999**	1.000**	LRR11
	358P	148	0.898	0.971*	LRR11
	364H d	154	0.968*	0.992**	LRR11
	382D d	172	0.984*	0.997**	LRR12
	392E d	182	0.991**	0.998**	LRR12
	405Q c	195	0.973*	0.994**	LRR13
	407Q	197	0.913	0.977*	LRR13
	416R c	206	0.971*	0.993**	LRR13
	418C	208	0.866	0.960*	LRR14
	431P	220	0.866	0.960*	LRR14
	434R c	223	0.960*	0.990**	LRR14
	447G	236	0.838	0.950	LRR14
	451S	240	0.934	0.983*	LRR14
	461A	250	0.928	0.981*	LRR14
	547Q	333	0.921	0.978*	LRR17
	602R d	388	0.973*	0.993**	LRR20
	651K c	437	0.956*	0.989*	LRR21
	658V d	444	0.976*	0.994**	LRR22
	727K d	513	0.972*	0.993**	LRR24
	735A	521	0.936	0.983*	LRR25

*P (ω > 1) > 0.95; **P (ω > 1) > 0.99

^aPositively selected sites detected by models M2a or M8 with P (ω > 1) ≥ 0.95 (scored by BEB). Sites both selected by models M2a and M8 are in bold. The amino acids refer to Rhinolophus affinis

^bThe alignments of bat TLR3, TLR7, TLR8, and TLR9 can be found in the top of mlc files (result files from PAML)

^cThe sites only selected in bats

^dThe sites both selected in bats and mammals