Fish vision makes waves in natural selection

Emory researchers have identified the first fish known to have switched from ultraviolet vision to violet vision, or the ability to see blue light. The discovery is also the first example of an animal deleting a molecule to change its visual spectrum.

Their findings on scabbardfish, linking molecular evolution to functional changes and the possible environmental factors driving them, are in the current issue of the Proceedings of the National Academy of Sciences.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says evolutionary geneticist Shozo Yokoyama, who led the study. “Building on this framework will take studies of natural selection to the next level.”

The research team included Takashi Tada, a post-doctoral fellow in biology, and Ahmet Altun, a post-doctoral fellow in biology and computational chemistry.

For two decades, Yokoyama has done groundbreaking work on the adaptive evolution of vision in vertebrates. Vision serves as a good study model, since it is the simplest of the sensory systems. For example, only four genes are involved in human vision.

"It's amazing, but you can mix together this small number of genes and detect a whole color spectrum," Yokoyama says. "It's just like a painting."

The common vertebrate ancestor possessed UV vision. However, many species, including humans, have switched from UV to violet vision, or the ability to sense the blue color spectrum.


Fish provide clues for how environmental factors can lead to such vision changes, since the available light at various ocean depths is well quantified. All fish previously studied have retained UV vision, but the Emory researchers found that the scabbardfish has not. To tease out the molecular basis for this difference, they 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 finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” he adds. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet 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.

"Evolutionary biology is filled with arguments that are misleading, at best," Yokoyama says. "To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment." 

Last year, Yokoyama and collaborators completed a comprehensive project to track changes in the dim-light vision protein opsin in nine fish species, chameleons, dolphins and elephants, as the animals spread into new environments and diversified over time. The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes.

Their results provided a reference framework for further research, and helped bring to light the limitations of studies that rely on statistical analysis of gene sequences alone to identify adaptive mutations in proteins.

Related stories:
A fish-eye view of natural selection

Averting the next food crisis

While the United States battles an obesity epidemic, people in some areas of the globe face a daily struggle to find nutritionally adequate and safe foods. Emory anthropologists Craig Hadley and Kenneth Maes wrote an article for The Lancet, proposing a new global monitoring system for food insecurity:

"The theme of this year's World Food Day on Oct 16, 'Achieving food security in times of crisis,' reflects the tremendous interest in food insecurity raised by the 2008 food crisis. Yet, as the world confronts the links between global food insecurity and crises, we still have little systematic knowledge about who was affected by the 2008 food crisis and to what extent. The lack of timely data, and the failure to account for heterogeneity in human responses, have led to general predictions that are surely inaccurate and have prevented a nuanced understanding of the crisis. This lack of knowledge is rooted in methodological and conceptual shortcomings."

Read the whole article.

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Get a masters in sustainable development

Dancing with the scientists

Will Chemistry Chair David Lynn wow the campus with an interpretive dance on DNA?

Sorry, folks, Lynn will not be performing. However, he did put his toe in the world of dance through collaborations with New York choreographer David Neumann and Seattle’s Lelavision Physical Music group.

Lynn and Neumann will hold a discussion on “Where Dance and Science Meet,” Thursday, Oct. 15 at 4 pm. This weekend, the science-art experiments take the stage in the form of Neumann’s “Big Eater” and “The Accumulation of Change,” combining Lelavision’s kinetic musical sculpture with Lynn’s research on molecular evolution.

Click here for details of all these events.

Watch a video of last spring's initial collaboration with Emory scientists and artists:

Richard Gere on Emory, Tibet and shyness

From a couple of flirtatious reporters at Washington's POLITICO:

"Who would have guessed that a man who makes a living on the big screen would actually be camera shy?

"Richard Gere proved he can get as nervous in front of the lens as the rest of us when POLITICO spoke with him at an Emory University-hosted reception at the Mayflower Hotel on Friday, where he was on a panel discussing the connection between science and spirituality.

'"This is scary,' the star once voted the 'sexiest man alive' said when he came face to face with a flip-cam."

The ripple effect of a Nobel in Economics

Tracy Yandle was vacationing in the Smoky Mountains when Elinor Ostrom won the Nobel Prize in Economics. “I had the radio on in the cabin, and when I heard the news I went outside and started jumping up and down,” says Yandle, associate professor in environmental studies. “Intellectually, and personally, it’s just a wonderful thing to me.”

Ostrom, a leading scholar of how communities can effectively regulate common resources, was Yandle’s dissertation advisor at Indiana University. Yandle focused on the market forces of fisheries in New Zealand – one of the only systems in the world that had privatized to allow fishermen to buy and sell the rights to catch a certain amount.

After she began her research, in 1999, the fishermen started using their fishing rights as leverage. “They realized, ‘If we have catching rights, we own a part of the fishery and we want a say in it,’” Yandle recalls.

In a panic, Yandle called Ostrom to report: “I’m doomed, the entire system is changing. It’s not a market system anymore.”

Ostrom advised her to go with the flow. “She said, ‘This is exciting, a self-governing organization is forming before your eyes,’” Yandle says. “She helped me to see that clearly, and to figure out a way to study it.”

After joining Emory in 2001, Yandle continued to dig deeper into this new angle of research. She is currently studying the quantity and quality of property rights required to get people involved in managing a natural resource.

Ostrom “is a wonderful example of an interdisciplinary thinker,” Yandle says. “She’s one of the key people in forming natural resource economics, through her work at the boundaries of economics, political science and organizational thinking."

The Nobel laureate’s mentees in the Emory environmental studies department also include Lore Ruttan, who was a post-doctoral fellow under Ostrom.

In his NYT column, John Tierney describes Elinor Ostrom's work disputing "the tragedy of the commons" theory.