Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment

Mol Biol Evol. 2016 Feb;33(2):323-36. doi: 10.1093/molbev/msv217. Epub 2015 Oct 20.


Cetaceans have undergone a remarkable evolutionary transition that was accompanied by many sensory adaptations, including modification of the visual system for underwater environments. Recent sequencing of cetacean genomes has made it possible to begin exploring the molecular basis of these adaptations. In this study we use in vitro expression methods to experimentally characterize the first step of the visual transduction cascade, the light activation of rhodopsin, for the killer whale. To investigate the spectral effects of amino acid substitutions thought to correspond with absorbance shifts relative to terrestrial mammals, we used the orca gene as a background for the first site-directed mutagenesis experiments in a cetacean rhodopsin. The S292A mutation had the largest effect, and was responsible for the majority of the spectral difference between killer whale and bovine (terrestrial) rhodopsin. Using codon-based likelihood models, we also found significant evidence for positive selection in cetacean rhodopsin sequences, including on spectral tuning sites we experimentally mutated. We then investigated patterns of ecological divergence that may be correlated with rhodopsin functional variation by using a series of clade models that partitioned the data set according to phylogeny, habitat, and foraging depth zone. Only the model partitioning according to depth was significant. This suggests that foraging dives might be a selective regime influencing cetacean rhodopsin divergence, and our experimental results indicate that spectral tuning may be playing an adaptive role in this process. Our study demonstrates that combining computational and experimental methods is crucial for gaining insight into the selection pressures underlying molecular evolution.

Keywords: absorption spectra; adaptive evolution; cetacean vision; clade model; codon substitution model; dN/dS; dim-light vision; evolution of protein structure and function; opsins; site-directed mutagenesis; visual ecology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological*
  • Animals
  • Biological Evolution
  • Evolution, Molecular
  • Gene Expression
  • Light
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Phylogeny
  • Protein Conformation
  • Retinal Pigments / genetics*
  • Retinal Pigments / metabolism
  • Rhodopsin / chemistry
  • Rhodopsin / genetics*
  • Rhodopsin / metabolism
  • Selection, Genetic*
  • Structure-Activity Relationship
  • Whale, Killer / genetics*
  • Whale, Killer / metabolism


  • Retinal Pigments
  • Rhodopsin