Table 2.

TLR5 Amino Acid Sites under Positive Selection Identified Using Different Methods

AA positiona	Amino Acid Change (No. of Parallel Changes)	Protein Domainb	Maximum Likelihood Method				Parallel Change	Uf, g	Clade g
			PAML M8c	SLAC	FELd	RELe
14	Val-Met (2)	Signal P.					Yes	0.986	A, N
29	Arg-Gln (2)	LRRNT					Yes	1.045	A, O
104	Asp-Ser	LRR3	0.908		0.158	63		*	A, O, amb.
	Ser-Gly							1.360
	Ser-Asn							2.053
158	Arg-His (3)	LRR5			0.173	22	Yes	1.317	A, O, N
168	Lys-Glu (2)	LRR5					Yes	0.548	N, amb
[181]	Gln-Lys	LRR6			0.192			1.466	O, N
	Gln-Arg					1.045
[197]	Thr-Met (2)	LRR6					Yes	1.007	O, N
[207]	Asn-Ser (2)	LRR7					Yes	2.053	A, N
[230]	Thr-Ileu (2)	LRR8					Yes	0.750	A, N
[262]	His-Tyr (2)	LRR9					Yes	0.665	O, N
[268]	Gly-Ser or Gly-Thr	LRR9	0.883					1.36 or *	N, amb
	Ser-Thr							2.49
[280]	Asn-Ser (2)	LRR9					Yes	2.053	A, N
[292]	His-Arg (3)	LRR10	0.925		0.102	86	Yes	1.317	A, N, amb
	His-Leu or Arg-Leu							0.56 or 0.414
[312]	Gln-Arg	LRR10	0.990		0.069	113	Yes	1.045	A, N, amb
	Arg-Gly (2)							0.534
	Gln-Lys							1.466
[354]	Ser-Trp or Ser-Leu	LRR12	0.972			28	Yes	0.375 or 0.725	A, N, amb
	Trp-Leu (2)							0.793
	Ser-Ala							2.38
[363]	Ala-Thr (2)	LRR13					Yes	1.587	N, amb
[400]	His-Tyr (2)	LRR14					Yes	0.665	O, amb
407	Asp-Ala (2)	LRR15	0.897				Yes	0.657	O, amb
	Asp-Asn (1 or 2)							1.015
416	Ala-Val (2)	LRR15					Yes	1.017	N, amb
446	Arg-Gln or Arg-Glu	LRR16			0.187			1.045 or *	N, amb
	Gln-Glu							1.634
460	Leu-Phe	LRR17			0.185			0.732	A
482	Glu-Gly (3)	LRR18			0.185	22	Yes	0.553	O
492	Glu-Gln (3)	LRR18	0.951				Yes	1.634	A, O
	Glu-Ala							0.906
496	Asp-Asn (2)	LRR18					Yes	1.015	A, O
523	Ser-Lys (2 or 3)	LRR19	0.995		0.110	166	Yes	*	O
530	Gly-Arg (3)	LRR20	0.968	0.181	0.108	73	Yes	0.534	A, O, N
	Gly-Ala							1.379
564	Asp-Asn (2)	LRR21					Yes	1.015	A
567	Leu-Val (3)	LRR21	0.971		0.160	36	Yes	1.329	A, O, N
	Leu-Phe							0.732
586	Glu-Ala	LRR22			0.172	22	Yes	0.906	O
	Ala-Thr (2)							1.587
592	Asn-His	LRR22	0.906					1.382	A, O
	Asn-Ser							2.053
	Asn-Lys							1.075
	His-Arg							1.317
616	Leu-Phe (1–2)	LRRCT					Yes	0.732	A, amb
628	Asp-Gly (2)	LRRCT	0.924				Yes	0.548	A, O, amb
	Asp-Ala or Gly-Ala							0.657 or 1.379
	Ala-Val							1.015
634	Ileu-Val (2)	LRRCT					Yes	2.415	N, amb
644	Ileu-Val (2)	Transm.					Yes	2.415	O, N
650	Val-Leu	Transm.			0.153			1.329	O
680	Lys-Arg (2)	Intracel.					Yes	1.583	O
690	Thr-Met (2)	Intracel.					Yes	1.007	O, amb
847	Ser-Asn (3)	TIR	0.916		0.130	74	Yes	2.053	N, amb
	Asn-Asp							1.015
854	Val-Ileu (2)	TIR					Yes	2.415	O, N

For the codons identified as candidates for positive selection, posterior probabilities, P values or Bayes factors are given (see below). Codons identified by more than one ML method are underlined.

^a Amino acids between brackets fall within the 228 amino acid region identified by Andersen-Nissen et al. (2007) as important for flagellin recognition.

^b Signal P = Signal Peptide, LLR = Leucine-rich repeat, NT = N-terminal, CT = C-terminal, Transm. = Transmembrane, Intracel. = Intracellular, and TIR = Toll-IL-1 Receptor Domain.

^c Posterior probabilities of the BEB analysis.

^d P values.

^e Bayes factor.

^f U is an empirically derived index that measures the likelihood of a nonsynonymous fixation (Tang et al. 2004). * indicates that more than 1-nt change is needed for the amino acid change.

^g Clade in which amino acid substitution occurred (O = Old World Monkeys, N = New World Monkeys, A = Apes and Humans, amb = more than one equally parsimonious reconstruction).