Fig. 3 The most probable pattern of the amino acid replacements during amphibian pigment evolution. The evolutionary tree of frog-423 and orthologous amphibian pigments, where the divergence times at the three nodes were obtained from the TimeTree of Life web server (www.timetree.org). Six functionally critical amino acid replacements are shown above, where the numbers are the products of the PPs of the two amino acids inferred and indicate the likelihoods that these changes occur at a specific evolutionary stage. The PPs are taken from the maximum likelihood–based Bayesian method (35) with the JTT model, and the logos of amino acids at 12 critical sites for the three ancestral amphibian pigments indicate their support values, where amino acids in red have PPs >0.95 (table S1). Branches and boxes in black and blue indicate UV and violet sensitivities, respectively. Sharing only T118, I207, and T277 among the 12 critical amino acids of frog-423, the bullfrog SWS1 pigment must have achieved its violet sensitivity (55) using an entirely different mechanism. (For the sequence of mutation accumulations, see the “Evolutionary trajectories” section. MYA, million years ago.)
- Table 1 Abbreviations and explanation of key terms with examples.
SWS1
pigmentThe short wavelength–sensitive type 1
visual pigmentλmax The wavelength of maximal absorption Δλmax The magnitude of λmax shift TM Transmembrane helix of a visual pigment PP Posterior probability of an amino acid inferred SBN Schiff base nitrogen—when it is unprotonated, a pigment
is UV-sensitive; otherwise, it is violet-sensitiveA2F The chimeric pigment, in which the TM II of AncAmphibian-359
was replaced by the corresponding segment of frog-423A24F The chimeric pigment, in which the TM II and IV
of AncAmphibian-359 were replaced by the corresponding
segments of frog-423E113 Amino acid glutamic acid (E) at site 113 E113D Amino acid change from glutamic acid (E) to aspartic
acid (D) at site 113F1.086I0.52 Phenylalanine (F) is replaced by isoleucine (I) at site 86,
where F and I have PPs of 1.0 and 0.52, respectively.ζ86 The Δλmax of AncAmphibian-359 caused by an
amino acid change, F86Mζ86×93 The Δλmax of AncAmphibian-359 caused by the epistatic
interaction between F86M and T93Pθ2 The λmax shift of AncAmphibian-359 caused by replacing
its TM II by the corresponding segment of frog-423θ23 The λmax shift of AncAmphibian-359 caused by the epistatic
interaction between the TM II and III of frog-423 - Table 2 The effects of amino acid replacements on the λmax shift in AncAmphibian-359.*
TM II TM III λmax (nm) λmax shift F86M V91I T93P V109A E113D L116V S118T Δλmax (nm) Wavelength ± SE (nm) 0 0 0 0 0 0 0 359 1 0 0 0 0 0 0 361 ζ86 2 ± 1.41 0 1 0 0 0 0 0 362† ζ91 3 ± 1.41 0 0 1 0 0 0 0 359 ζ93 0 ± 1.41 1 0 1 0 0 0 0 394 ζ86×93 33 ± 2.0 1 1 1 0 0 0 0 380 ζ86×91×93 −17 ± 2.8 0 0 0 1 0 0 0 360 ζ109 1 ± 1.41 0 0 0 0 1 0 0 355 ζ113 −4 ± 1.41 0 0 0 0 0 1 0 359 ζ116 0 ± 1.41 0 0 0 0 0 0 1 361 ζ118 2 ± 1.41 0 0 0 1 1 0 0 370 ζ109×113 14 ± 2.0 0 0 0 1 0 1 0 359 ζ109×116 −1 ± 2.0 0 0 0 1 0 0 1 361 ζ109×118 −1 ± 2.0 0 0 0 0 1 1 0 356† ζ113×116 1 ± 2.0 0 0 0 0 1 0 1 357 ζ113×118 0 ± 2.0 0 0 0 0 0 1 1 360 ζ116×118 −1 ± 2.0 0 0 0 1 1 1 0 391 ζ109×113×116 21 ± 2.8 0 0 0 1 1 0 1 391 ζ109×113×118 20 ± 2.8 0 0 0 1 0 1 1 360 ζ109×116×118 1 ± 2.8 0 0 0 0 1 1 1 359† ζ113×116×118 2 ± 2.8 0 0 0 1 1 1 1 408 ζ109×113×116×118 −6 ± 2.8 *Numbers 0 and 1 indicate the amino acid of AncAmphibian S1 and that of frog S1, respectively.
†These data are newly obtained; others are taken from (34).
Supplementary Materials
Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/1/8/e1500162/DC1
Fig. S1. The amino acid sequences of AncAmphibian-359 and frog-423.
Fig. S2. A composite phylogenetic tree of 14 representative SWS1 pigments.
Fig. S3. The tertiary structure of AncAmphibian-359.
Fig. S4. Evolutionary patterns of TM replacements in AncAmphibian-359.
Table S1. Ancestral amino acids with PPs (in parentheses) inferred using PAML with JTT and WAG models.
Table S2. TM changes and associated λmax, Δλmax, θ, and θ0 (Δλmax values at the highest levels of epistatic interactions without individual effects) in AncAmphibian-359.
Table S3. The λmax shifts of chimeric mutants caused by various TM replacements that were preceded by other TM replacements.
Table S4. Epistatic evolution of A251643F.
Additional Files
Supplementary Materials
This PDF file includes:
- Fig. S1. The amino acid sequences of AncAmphibian-359 and frog-423.
- Fig. S2. A composite phylogenetic tree of 14 representative SWS1 pigments.
- Fig. S3. The tertiary structure of AncAmphibian-359.
- Fig. S4. Evolutionary patterns of TM replacements in AncAmphibian-359.
- Table S1. Ancestral amino acids with PPs (in parentheses) inferred using PAML with JTT and WAG models.
- Table S2. TM changes and associated λmax, Δλmax, θ, and θ0 (Δλmax values at the highest levels of epistatic interactions without individual effects) in AncAmphibian-359.
- Table S3. The λmax shifts of chimeric mutants caused by various TM replacements that were preceded by other TM replacements.
- Table S4. Epistatic evolution of A251643F.
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