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Shozo Yokoyama, a biologist at Emory University, says evolutionary biologists need to shift their focus from present-day molecules to synthesized, ancestral ones to truly understand the mechanisms of natural selection.

Yokoyama presented evidence to support his claim at the American Academy of Arts and Sciences (AAAS) meeting in Boston this week.

This is not just an evolutionary biology problem, its a science problem, says Yokoyama, a leading expert in the natural selection of color vision. If you want to understand the mechanisms of an adaptive phenotype, the function of a gene and how that function changes, you have to look back in time. That is the secret. Studying ancestral molecules will give us a better understanding of genes that could be applied to medicine and other areas of science.

Yokoyama notes positive Darwinian selection has been studied for years almost exclusively using comparative sequence analysis of present-day molecules, an approach fueled by increasingly fast and cheap genome sequencing techniques. Faster and easier, says Yokoyama, are not always best if you want to arrive at a true, quantitative result.

If you only study present-day molecules, youre only getting part of the picture, and that picture is often wrong, he says.

Studying fish and other vertebrates, Yokoyama has spent two decades teasing out secrets of the adaptive evolution of vision.

There are five classes of opsin genes that encode visual pigments. They are also responsible for dim-light and color vision. Since the available light at various ocean depths is well quantified, fish provide valuable clues for how environmental factors can lead to vision changes. For example, the common vertebrate ancestor possessed ultraviolet vision, suited to both shallow water and land.

As the environment of a species sinks deeper in the ocean, or rises closer to the surface and moves to land, bits and pieces of the opsin genes change and vision adapts, Yokoyama says. Im interested in exactly how that happens at the molecular level.

Molecular biologists construct a specific visual pigment by taking DNA from an animal, isolating and cloning its opsin genes, then using in vitro assays to create the pigment that can then be manipulated by changing the positions of the amino acids. This allows the scientists to study the regulation of the genes functions.

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