Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches.

Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches.  A striking array of phenotypes exhibited by contemporary animals is assumed to have evolved by accumulating a series of selectively advantageous mutations, but the experimental test of such adaptive events has been remarkably difficult. Genetically engineering 11 ancestral rhodopsins, which regulate dim-light vision, we have shown that early ancestral rhodopsins absorbed light maximally (max) at 500 nm, from which contemporary rhodopsins with variable maxs of 480–525 nm evolved on at least 18 separate occasions.  These highly environment-specific adaptations have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 (~94%) sites have undergone neutral evolution.  The comparison between these results and those inferred by commonly-used statistical methods demonstrates that statistical tests of positive selection can be misleading without experimental support and that the molecular basis of spectral tuning in rhodopsins should be elucidated by mutagenesis analyses using ancestral pigments.  In deep-sea environments, three genera of dragonfishes are unique by emitting bioluminescence with peaks at 465-485 and 500-710 nm.  These fishes can discriminate small wavelength differences between 470-580 nm using rhodopsins (or RH11 pigments) and porphyropsins (RH12), which use vitamin A1 and vitamin A2, respectively, and they also discriminate wavelengths within 430-470 and 580-720 nm using “rhodopsin-like” RH21 and RH22 pigments and long wavelength-sensitive LWS1 and LWS2 pigments, respectively.  Researchers have argued that dragonfishes have invented the new color vision system to visualize their new environment generated by bioluminescence, but the data show that dragonfishes have recreated the light environments of shallow water in the deep-sea by inventing blue, green, and far-red bioluminescence.