Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

doi:10.1186/1471-2148-12-39

Table 2 Positive selection at amino acid sites of cetacean TLR4

From: Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

AA Positions^a	PAML Site Model (M8) p> 0.9	PAML Branch-Site Model^c	FEL^d p< 0.2	REL^d BF > 50	AA Changes	Parallel Changes	Property Changes^e	Protein Domain	Functional Information^f	Clade^g
25					Ser-Arg	Yes	SM, P, NEU-P.POS	LRR3		B, C
28			0.07		Leu-Trp		NP, NEU-P, NEU	LRR3		A, D
					Leu-Pro		NP, NEU-SM, NP, NEU
45			0.16		Thr-Ile	Yes	SM, P, NEU-NP, NEU	LRR4		A, F
104			0.17		Leu-Val		NP, NEU-NP, NEU	LRR6
					Leu-Ser		NP, NEU-SM, P, NEU
128		0.875			Glu-Pro		P, NEG-SM, NP, NEU	LRR7		D
133		0.723			Asn-Lys		SM, P, NEU-P, POS	LRR7		G
139		0.708			Gly-Glu		SM, NP, NEU-P, NEG	LRR8	Adjacent to site involved in interaction with MD2	G
149		0.565			Ser/Leu -Thr		SM, P, NEU/NP, NEU -SM, P, NEU	LRR8		G
150	0.995			228.23	His-Arg	Yes	P, POS-P, POS	LRR8		A, B, C
					His-Asp		P, POS-SM, P, NEG
177				61.94	Asn-Thr Asn/Thr -Ile Asn-Lys Ile-Asn		SM, P, NEU-SM, P, NEU SM, P, NEU/SM, P, NEU -NP, NEU SM, P, NEU-P, POS NP, NEU-SM, P, NEU	LRR9	Adjacent to site involved in ligand binding and interaction with MD2	A, C, G
179	0.992		0.07	647.96	Lys-Glu Glu-Gln Glu/Lys- Gln	Yes	P, POS-P, NEG P, NEG-P, NEU P, NEG/P, POS-P, NEU	LRR9		A, C, F
183			0.12	51.06	Arg-Ser Arg-Thr		P, POS-SM, P, NEU P, POS-SM, P, NEU	LRR9		C, D
204					Glu-His	Yes	P, NEG-P, POS	LRR10		A, D
207	1.000		0.08	1563.58	Gly/Lys -Arg Arg-Lys Arg-Thr Lys-Arg		SM, NP, NEU/P, POS -P, POS P, POS-P, POSP, POS-SM, P, NEU P, POS-P, POS	LRR10		A, G, C, E
212					Leu-Val	Yes	P, POS-NP, NEU	LRR10		A, B
221			0.1		Val-Met	Yes	NP, NEU-NP, NEU	LRR11		C, D, F
228	0.994		0.15	544.88	Asp/Ser/Cys -Asn Asp-Asn		SM, P, NEG/SM, P, NEU/SM, NP, NEU -SM, P, NEU SM, P, NEG-SM, P, NEU	LRR11		A, G
230	0.978				Gly/Glu/Asp -Arg Asp-His		SM, NP, NEU/P, NEG/SM, P, NEG -P.POS SM, P, NEG-P, POS	LRR11		A, E
239				50.32	Cys-Tyr	Yes	SM, NP, NEU-P, NEU	LRR12		B, D, G
247			0.14	86.14	Ile-Thr Thr-Ile		NP, NEU-SM, P, NEU SM, P, NEU-NP, NEU	LRR12	Adjacent to site involved in interaction with ligand binding	C, G
250 ^b	0.936				Asp/Ala -Lys Asp/Lys/Ala -Asn Asn-Lys		SM, P, NEG/SM, NP, NEU -P, POS SM, P, NEG/P, POS/SM, NP, NEU -SM, P, NEU SM, P, NEU-P, POS	LRR12	Ligand binding	A, E, G
265					Phe-Leu	Yes	NP, NEU-NP, NEU	LRR13		B, E
272	0.997		0.13	188.28	Gly/Asp- His Gly-His His-Gly		SM, NP, NEU/SM, P, NEG-P, POS SM, NP, NEU-P, POS P, POS-SM, NP, NEU	LRR13	Adjacent to site involved in interaction with ligand binding	A, C
280	0.952		0.18	191.07	Glu-Ala Gln/Glu- Ala	Yes	P, NEG-SM, NP, NEU P, NEU/P, NEG-SM, NP, NEU	LRR13		A, B, E
302		0.624			His-Arg		P, POS-P.POS	LRR14		D
304				55.05	Asp-Asn Asn-Pro		SM, P, NEG-SM, P, NEU SM, P, NEU-SM, NP, NEU	LRR14		G
324	0.996			301.87	Asn-Ser Asn-Lys Gly-Asn		SM, P, NEU-SM, P, NEU SM, P, NEU-P, POS SM, NP, NEU-SM, P, NEU	LRR15	Adjacent to site involved in interaction with ligand binding (hydrogen bond)	C, E, G
342				53.56	Asn-Ser Asn/Ser- Thr		SM, P, NEU-SM, P, NEU SM, P, NEU/SM, P, NEU-SM, P, NEU	LRR16	Adjacent to site involved in interaction with ligand binding (hydrogen bond)	A
351				0.17	Ile/Ala-Val		NP, NEU/SM, NP, NEU-NP, NEU	LRR16	Adjacent to site involved in interaction with ligand binding (hydrophobic interaction)	G
368		0.576			Ile-Thr		NP, NEU-SM, P, NEU	LRR17	Adjacent to site involved in interaction with ligand binding (hydrophobic interaction)	G
404				0.08	Leu-Met		NP, NEU-NP, NEU	LRR18		C
408					Ile-Thr	Yes	NP, NEU-SM, P, NEU	LRR19		A, G
409				0.19	Leu/Ile/Phe -Val		NP, NEU/NP, NEU/NP, NEU -NP, NEU	LRR19		A
482				0.16	Ser/Trp- Phe Phe/Ser/Trp -Leu		SM, P, NEU/P, NEU-NP, NEU NP, NEU/SM, P, NEU/P, NEU -NP, NEU	LRR22		A
542	0.903				Met-Thr	Yes	NP, NEU-SM, P, NEU	LRRCT		A, D
551	0.938				Ile-Val Val-Ile	Yes	NP, NEU-NP, NEU NP, NEU-NP, NEU	Transmembrane		B, F
559				0.16	Val-Ala		NP, NEU-SM, NP, NEU	Transmembrane		G
690		0.564			Arg-Gln		P, POS-P, NEU	TIR		D
740		0.790			Glu-Asp		P, NEG-SM, P, NEG	TIR		G
742		0.697			Asn-Arg		SM, P, NEU-P, POS	TIR		G
743				0.18	Gln-Glu		P, NEU-P, NEG	TIR		A, F

^a Codons identified by more than one ML method were in bold and underlined.
^b Site 250 in italic was mapped onto the 3D structure of TLR4, since it directly participates in binding of LPS to TLR4.
^c Codons were identified by branch-site model in PAML. Details were in Materials and Methods and Additional file 2: Table S2.
^d Codons were estimated in DATAMONKEY.
^e SM, small; NP, nonpolar; P, polar; NEU, neutral; POS, positively charged; NEG, negatively charged.
^f Codons were in the functional regions predicted by the three-dimensional structure in Shishido et al. 2010. LRR = Leucine-rich repeat, CT = C-terminal, TIR = cytoplasmic Toll/IL-1 receptor
^g Amino acid substitutions occurred in the following clades: A = even-toed ungulates, B = river dolphins, C = oceanic dolpins, D = porpoises and white whales, E = sperm whales, F = baleen whales, G = more than one equally parsimonious reconstruction

Back to article page

ISSN: 2730-7182

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Ecology and Evolution

Contact us