. 2019 Dec 4;12(1):3615–3634. doi: 10.1093/gbe/evz266

Table 1.

Selection Analysis of Vertebrate TLRs

Taxa	Gene	Recognition Status^a	Sequences Number^b	aa Length^c	dN/dS^d	PSS^e	PSS/Ref.^f (‰)
Fish	TLR1	Nonviral	34	795	0.248	4	5.0
	TLR2	Nonviral	40	788	0.257	4	5.1
	TLR3	Viral	35	903	0.217	2	2.2
	TLR4	Nonviral	15	816	0.306	2	2.5
	TLR5	Nonviral	32	881	0.259	6	6.8
	TLR5S	Nonviral	21	641	0.264	4	6.2
	TLR7	Viral	39	1,036	0.144	8	7.7
	TLR8	Viral	49	1,019	0.250	7	6.9
	TLR9	Viral	37	1,057	0.216	5	4.7
	TLR13	—	4	—	—	—	—
	TLR18	Nonviral	38	854	0.128	0	0
	TLR19	Viral	8	958	0.189	1	1.0
	TLR20	Nonviral	9	950	0.379	16	16.8
	TLR21	Viral	38	989	0.236	4	4.0
	TLR22	Viral	49	947	0.306	6	6.3
	TLR23	—	29	941	0.399	32	34.0
	TLR25	Both	23	821	0.200	1	1.2
	TLR27	—	3	—	—	—	—
		—		14,396	—	102	7.1
Amphibian	TLR1	Nonviral	45	842	0.289	6	7.1
	TLR1L	Nonviral	28	796	0.260	1	1.3
	TLR2	Nonviral	56	780	0.287	5	6.4
	TLR3	Viral	38	895	0.239	1	1.1
	TLR4	Nonviral	8	872	0.281	1	1.1
	TLR5	Nonviral	28	879	0.270	4	4.6
	TLR5L	—	49	653	0.262	0	0
	TLR7	Viral	15	1,054	0.182	1	0.9
	TLR8	Viral	19	1,037	0.226	1	1.0
	TLR9	Viral	20	1,030	0.239	0	0
	TLR12	Nonviral	7	894	0.286	1	1.1
	TLR13	Viral	25	948	0.309	3	3.2
	TLR14	Both	38	835	0.225	0	0
	TLR19	Viral	21	950	0.325	4	4.2
	TLR21	Viral	28	937	0.273	3	3.2
	TLR22	Viral	17	944	0.268	1	1.1
		—		14,346	—	32	2.2
Reptile	TLR1	Nonviral	17	654	0.334	1	1.5
	TLR2	Nonviral	20	783	0.420	18	23.0
	TLR3	Viral	14	896	0.270	0	0
	TLR4	Nonviral	13	840	0.326	2	2.4
	TLR5	Nonviral	13	885	0.398	10	11.3
	TLR5L	—	9	654	0.236	0	0
	TLR7	Viral	13	1,059	0.284	2	1.9
	TLR8	Viral	11	1,049	0.338	0	0
	TLR9	—	2	—	—	—	—
	TLR13	Viral	9	948	0.322	1	1.1
	TLR14	Both	13	835	0.126	2	2.4
	TLR15	Both	8	823	0.341	5	6.1
	TLR21	Viral	11	956	0.153	1	1.0
	TLR22	Viral	11	952	0.395	1	1.1
		—		11,334	—	43	3.8
Bird	TLR1A	Nonviral	32	818	0.354	17	20.8
	TLR1B	Nonviral	29	652	0.385	28	42.9
	TLR2A	Nonviral	23	792	0.376	22	27.8
	TLR2B	Nonviral	30	732	0.337	21	28.7
	TLR3	Viral	37	896	0.334	20	22.3
	TLR4	Nonviral	35	843	0.417	27	32.0
	TLR5	Nonviral	34	861	0.414	33	38.3
	TLR7	Viral	39	1,059	0.306	24	22.7
	TLR15	Both	34	868	0.258	20	23.0
	TLR21	Viral	8	972	0.082	0	0
		—		8,493	—	212	25.0
Mammal	TLR1	Nonviral	16	786	0.413	6	7.6
	TLR2	Nonviral	24	784	0.325	8	10.2
	TLR3	Viral	23	904	0.240	6	6.6
	TLR4	Nonviral	22	839	0.414	21	25.0
	TLR5	Nonviral	23	858	0.317	10	11.7
	TLR6	Nonviral	22	796	0.383	5	6.3
	TLR7	Viral	22	1,049	0.257	12	11.4
	TLR8	Viral	23	1,038	0.286	24	23.1
	TLR9	Viral	22	1,032	0.162	11	10.7
	TLR10	Nonviral	17	811	0.346	1	1.2
	TLR11	Nonviral	11	931	0.434	14	15.0
	TLR12	Nonviral	14	906	0.416	19	21.0
	TLR13	Viral	9	991	0.332	1	1.0
		—		11,725	—	138	11.8
		—		60,294	—	527	8.7

Note.—Natural selective analysis was excluded for fish TLR13, TLR27, and reptile TLR9 because there are only a limited number of sequences for these genes.

^{^a}

TLR genes were classified into two groups (viral and nonviral) according to the microorganism ligands they recognize. “Both” indicate TLRs that can bind viral and nonviral ligands. The ligands for TLR5L and TLR23 remain unknown; we did not assign a viral/nonviral status. See Materials and Methods for detailed criteria of viral and nonviral classification.

^{^b}

Number of sequences for each TLR gene.

^{^c}

The protein sequence length in reference vertebrate TLRs (NCBI accession numbers are listed in supplementary table S6, Supplementary Material online).

^{^d}

Estimated mean dN/dS for each TLR gene using the codeml method. dN, number of nonsynonymous substitutions per nonsynonymous site; dS, number of synonymous substitutions per synonymous site.

^{^e}

Number of PSSs detected in the investigated species per TLR gene by any one of codeml (M7/M8) and FUBAR methods. See supplementary table S5, Supplementary Material online, for more details.

^{^f}

The percentage of PSS per entire TLR amino acid sequence.