Science Literature

Shallow water light ranges from the ultraviolet to red (wavelengths 360 nm - 650 nm). Going deeper, the extremes disappear and the spectrum narrows to a blue (approx 480 nm). Of the fish species whose colour vision has been tested to date, all except one can see in the ultraviolet (UV). The exception is the scabbardfish, which is the subject of a new research paper. The authors find that the fish that are sensitive to UV have a pigment that absorbs UV light, but the scabbardfish lacks this pigment and has, instead, a pigment that is violet-sensitive.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University) (Source ScienceDaily)

The researchers have looked at the molecular structure of the relevant pigments and their absorption spectra.

"[T]hey used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.
"Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted," Yokoyama says."

The hypothesis is that the shift from UV to violet vision was adaptive. Since the lampfish is also a benthopelagic marine fish, the adaptation explanation must also address why the lampfish has retained UV vision.

"Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light."

The researchers found several other amino acid sequence variants that could not be linked to any change in function. This stimulated some salutary comments from the authors:

"It is very common that evolutionary biologists infer the possibility of adaptive evolution of various genes by using computer programs, which compare the nonsynonymous and synonymous nucleotide substitutions per site. However, these analyses not only predict a significant number of false-positives but also fail to predict many positively selected sites; consequently, the positively selected amino acid changes inferred by the statistical methods must be tested by using experimental methods."

In the Press Release, Yokoyama is quoted as saying: "Evolutionary biology is filled with arguments that are misleading, at best". The research team is to be commended for connecting changes in amino acid sequences with changes in phenotypes and then relating all to the living environments. This is good science and a big contrast from the story-telling approach. Adaptation can be studied in a rigorous way, and analyses like this are a demonstration of what is possible.

The words "evolutionary" and "evolution" are used by the authors in their paper. It is strange that evolutionary biology has a fixation of the e-word when there are so many different meanings given to it. In this case, we have a study of adaptive change involving the change of a single amino acid in the opsin protein. This can be understood as a means of the organism becoming fine-tuned to its environment. Darwinian mechanisms appear to be adequate for understanding the data. It should not be necessary to point out that 'fine-tuning' is qualitatively different from 'constructing' the visual apparatus of the organism. Fine-tuning is only possible when the eye is functioning. This point can be better appreciated when the change involves the deletion of existing biological information - as it is in this case. Adaptation is not the route to create biological novelties: microevolution is not macroevolution.

There is a design-orientated way of approaching these data. What if organisms are designed to vary so that they can adapt to changes in their environment? In such cases, mechanisms for fine-tuning can be understood as designed mechanisms, thereby shifting the focus away from the biological world being the product of chance + necessity and towards a world resulting from purposeful intelligent agency.

Evolutionary replacement of UV vision by violet vision in fish
Takashi Tada, Ahmet Altun and Shozo Yokoyama
Proceedings of the National Academy of Sciences, October 13, 2009, 106(41), 17457-17462 | DOI: 10.1073/pnas.0903839106

Abstract: The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally ([lamda]max) at approximately 360 and 390-440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a [lamda]max of 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.

See also:

Seeing Blue: Fish Vision Discovery Makes Waves In Evolutionary Biology, ScienceDaily (17 October 2009)

Tyler, D. Adaptations affecting dim-light vision in vertebrates, ARN Literature blog (10 September 2008)