Skip to main content
. 2023 Oct 4;40(10):msad206. doi: 10.1093/molbev/msad206

Table 2.

Results From Site and Branch-site Selection Analyses.

Gene Known spectral tuning sites in vertebrates Codon number
(bovine RH1 numbering)a 		Nearby spectral tuning site Location Selection test P-value/Posterior Probability Number of branches (MEME only)
LWS 100, 164, 181, 214, 217, 261, 269, 292, 293 49b None TMD I MEME P < 0.01 3
CODEML PP = 1.00 −
59 None TMD I MEME P = 0.02 1
FEL (−) P = 0.04 −
162 164 TMD IV MEME P < 0.01 7
166b 164 TMD IV MEME P < 0.01 1
FUBAR PP = 0.99 −
CODEML PP = 0.97 −
176 None TMD IV MEME P < 0.01 2
FEL (−)c P < 0.01 −
205 None TMD V MEME P = 0.04 8
206 None TMD V MEME P < 0.01 1
209 None TMD V MEME P = 0.02 2
217b 217 TMD V MEME P = 0.04 0
231 None TMD V MEME P = 0.02 1
FEL (−) P < 0.01 −
262 261 TMD VI MEME P < 0.01 3
SWS1 46, 49, 52, 81, 86, 90, 91, 93, 97, 108, 109, 113, 114, 116, 118, 207 50 49, 52 TMD I MEME P = 0.04 0
FEL (+) P = 0.03 −
FUBAR PP = 0.97 −
120b 118 TMD III MEME P = 0.04 0
FEL (+) P = 0.02 −
159b None TMD IV MEME P = 0.01 6
221 None TMD V MEME P < 0.01 5
SWS2 (Only sites up to 129 were analyzed) 44, 46, 49, 52, 91, 93, 94, 97, 99, 109, 116, 117, 118, 122, 164, 207, 261, 265, 269, 275, 292, 295 −1 None N-T FUBAR PP = 0.90 −
8 None N-T FUBAR PP = 0.98 −
56 None TMD I FUBAR PP = 0.98 −
106 None ECD I MEME P = 0.02 1
FEL (−) P = 0.01 −
RH1 83, 90, 96, 102, 118, 122, 124, 125, 132, 164, 183, 189, 194, 195, 207, 208, 211, 253, 261, 265, 269, 289, 292, 295, 299, 300, 308 37 None TMD I CODEML PP = 1.00 −
39b None TMD I MEME P = 0.03 0
FEL (+) P = 0.02 −
FUBAR PP = 0.97 −
82 83 TMD II MEME P < 0.01 2
87 None TMD II MEME P = 0.03 7
FEL (+) P = 0.03 −
FUBAR PP = 0.95 −
97b 96 TMD II FEL (+) P = 0.05 −
FUBAR PP = 0.95 −
103 102 ECD I CODEML PP = 1.00 −
107b None ECD I MEME P = 0.04 9
111 None TMD III MEME P < 0.01 2
124 122, 124, 125 TMD III MEME P = 0.03 8
FEL (−) P = 0.04 −
159 None TMD IV MEME P < 0.01 2
164 164 TMD IV CODEML PP = 1.00 −
168 None TMD IV MEME P = 0.03 3
169b None TMD IV MEME P < 0.01 12
FEL (+) P < 0.01 −
FUBAR PP = 1.00 −
213b 211 TMD V MEME P < 0.01 9
FUBAR PP = 0.97 −
260 261 TMD VI MEME P < 0.01 1
262 261 TMD VI MEME P = 0.01 1
FEL (−) P = 0.01 −
277b None TMD VI MEME P = 0.01 3
281 None ECD III CODEML PP = 1.00 −
290 289, 292 TMD VI MEME P = 0.02 2
FUBAR PP = 0.95 −

Amino acid sites in four opsin genes that were detected to be under positive selection by site (FEL, FUBAR, CODEML) or branch-site combinations (MEME). We aligned sequences against bovine rhodopsin (NP_001014890.1) to make comparisons with known spectral tuning sites (see supplementary table S3, Supplementary Material online for references). More details regarding the phylogenetic patterns of selection can be reviewed in figure 1 and supplementary S1, Supplementary Material online. We report all significant FEL results that correspond to sites identified by MEME or FUBAR and note each FEL result as indicative of positive (+) or negative (−) selection. Sites identified to be under positive selection in CODEML analyses are reported as posterior probabilities from Bayes Empirical Bayes analysis of M8 models. N-T, N-terminus; C-T, C-terminus; ECD I, extracellular domain I; TMD I–VII, transmembrane domains I–VII; −, does not apply. Reported P-values for MEME have been corrected for multiple testing using Holm–Bonferroni. Input files and results are available in supplementary Data S1, Supplementary Material online.

a

The numbering system used in our alignments can be determined by adding 17 to the bovine RH1 number for LWS, adding 9 for SWS2, and subtracting 5 for SWS1.

b

Amino acid sites reported by Schott et al. (2022) as under positive selection.