Evolution of a fish vision protein

How do genetic mutations, which occur in single molecules of DNA, lead to changes that help an organism of 10²³ or so molecules adapt to its environment? To answer that fundamental question, Shozo Yokoyama of Emory University and his colleagues looked at proteins called opsins, which help fish and other animals see in dim light. The molecule ultimately responsible for vision is retinal. Isolated retinal absorbs in the UV, but when it’s swaddled by an opsin, the pigment’s peak absorption shifts redward. Depending on its amino acid sequence, an opsin can shift the peak all the way to the IR. Fish exploit that tuning to evade predators during a particularly dangerous time of day, twilight. In shallow, clear water, the twilight spectrum peaks broadly between 400 nm (violet) and 500 nm (green). In deep water, the spectrum narrows around a peak at 480 nm (blue). And in shallow, muddy water, the spectrum shifts to the red. As you might expect, fish that swim in those different environments have opsins that engender an appropriate, survival-enhancing shift. To find evidence that those shifts arose through evolution, the Emory team first applied a statistical technique called phylogenetic reconstruction to the genetic sequences of 38 opsins drawn from various fish and other vertebrates. The result was an opsin family tree whose trunk springs from the first ancestral fish. Each node of the tree, downstream of the trunk and upstream of the present-day vertebrates, represents the opsin of an extinct species. The Emory team reconstructed those ancestral opsins in the lab, equipped them with retinal molecules, and measured their peak absorption. The combination of spectral measurements and genetic sequences revealed which DNA mutations—that is, amino acid substitutions—were responsible for the shift in peak wavelength. The results were surprising: Identical substitutions didn’t always produce the same shift; substitutions that produce a significant shift didn’t have to take place in amino acids that lie close to retinal; quite different substitutions yielded the same shift. The results show how hard it is to identify productive mutations and to predict their effect. Showing conclusively how the survival of the fittest plays out on the molecular level would require reconstructing not only the protein, but also the whole animal and its long-lost habitat. Still, the Emory researchers did find one piece of reassuring evidence: The opsin of the first fish tuned retinal to absorb at 501 nm, which is consistent with the shallow-water habitat of its fossilized remains. (S. Yokoyama et al., Proc. Natl. Acad. Sci. USA, in press.) — Charles Day