Fish Vision Discovery Makes Waves in Natural Selection

Emory University 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, were published Oct. 13 in 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.

Vision ‘like a painting'

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.

From the ocean depths

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.

More examples likely

"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.

A framework for evolutionary biology

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.

"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."

From eScienceCommons

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Warnell researchers help discover smallest salamander in U.S.

Researchers from the University of Georgia Warnell School of Forestry and Natural Resources weren’t looking for anything new when they went exploring in the northeast part of the state. But they ended up making a big discovery of a tiny animal, finding a new species of salamander that could change what scientists know about some amphibians.

The newly discovered salamander, which is the second-smallest salamander species in the U.S. and one of the smallest in the world at just two inches long, is now under study by a diverse group of researchers from several U.S. colleges. The team is searching for more of the salamanders, which are detailed in a new paper appearing in the Journal of Zoology.

The discovering research team consists of Carlos Camp, professor at Piedmont College; Joe Milanovich, Warnell graduate student; Bill Peterman, University of Missouri graduate student; Trip Lamb, professor at East Carolina University; John Maerz, assistant wildlife professor at Warnell; and David Wake, professor at the University of California Berkeley.

The initial discovery came in spring 2007 near Toccoa, Ga., when Peterman and Milanovich stumbled across it while collecting another species of salamander in Stephens County. They knew they’d found an animal not known in that region but did not yet know it was a new species. Milanovich works with Maerz, a Warnell assistant professor of wildlife, and called him. Maerz advised them to take the salamander to Camp at Piedmont College, who recognized it as a new species. Lamb, a professor at East Carolina University, used genetics to confirm the new species and establish its relationship to other species in the region.

After the students found the first salamander, a female with eggs, in a creek, researchers went back repeatedly looking for others. That is when Maerz’s then 10-year-old son Jack and Milanovich found the first male specimen. The research team has found several individuals at the original site, including larvae, and they have found the new species at two other nearby locations in Georgia. Collaborators also found the species at a nearby site in South Carolina.

This discovery, according to Maerz, could yield exciting new information on the evolution of stream salamanders in this region.

“Whenever you find something new, it has the potential to change what we know about a range of related species,” he said. There are more than 560 species of salamanders worldwide, and approximately 10 percent are found in Georgia.”

But that’s not the only reason Maerz is excited. The new species was found in a well-traveled area in the middle of a creek right next to a road, almost hidden in plain sight.

To make such a find in an area with extensive human activity, Maerz said, proves that “there are still things out there to discover. It makes you wonder, what else is out there?”

With funding from The Environmental Resources Network (TERN), Milanovich and Camp are leading research efforts to describe the ecology of the tiny creatures.

“It is truly a once-in–a-lifetime opportunity to be involved in such a big find, particularly one right in our backyard,” Milanovich said. “The fact that it is such a unique animal makes it all the better and gives us more opportunity to continue to learn about the species. One of the best parts of being involved with this project is the collaboration that has come out of the species description, so I am excited to continue working with the other coauthors as we keep unpeeling the onion of U. brucei.”

The research team’s suggested common name is patch-nosed salamander, based on the lighter coloring on the tiny salamander’s nose. The formal Latin name is Urspelerpes brucei for Richard Bruce, professor emeritus at Western Carolina University and a well-respected, longtime salamander researcher who has connections to many members of the research team.

“Dr. Bruce has done much of the foundational work on stream salamander ecology in the region and on the evolution of miniaturization in salamanders, so naming this species after him is a good fit,” Maerz said.

Camp marveled at the find.

“This animal is so distinct that it belongs in its own genus, a taxonomic level used for grouping closely related species,” he said.“The real significance of this find is that it represents the first new genus of four-footed creature discovered in the United States in 50 years.”

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The Most Important Jurassic Discovery Ever Made in the Arctic!

/PRNewswire/ -- On the remote archipelago of Svalbard, just 800 miles from the North Pole, a team of paleontologists has made a remarkable discovery. Led by Jorn Hurum from the University of Oslo Natural History Museum they have unearthed the fossilized remains of a huge sea creature from the distant past - which they believe is the most important Jurassic discovery ever made in the Arctic. PREDATOR X is the story of this major Arctic discovery of an entirely new species, 150 million years old. It is a new species of pliosaur, a massive and powerful marine predator estimated to be at least 50 feet long... weighing 45 tons - six times the weight of a Tyrannosaurus Rex - and with powerful jaws that killed with an amazing 33,000-pound bite - four times as powerful as a T Rex.

The two-hour special PREDATOR X premieres on HISTORY(TM) on Sunday, March 29 at 8pm ET/PT.

PREDATOR X follows Jorn Hurum and his team of paleontologists every step of the way, from field work through cutting edge research of this amazing dinosaur-age reptile - one of the most incredible Jurassic ocean discoveries in modern history.

Hurum and team member Patrick Druckenmiller, an Alaskan paleontologist and extreme adventurer, must excavate the find from the ice, transport it back to the lab and bring it back to life using advanced scientific techniques. They travel the globe breaking new ground to scientifically understand and recreate Predator X. Their results are astounding and only now can they fully understand the beast they unearthed. Analysis usually reserved for precision engineering of modern machines, reveals the secrets of Predator X. Their quest takes them from wind tunnels to CT scanners to bio-mechanic and robotic laboratories. In analyzing its body, delving into its brain and witnessing its hunting strategy, the team conclude that they have found a perfectly designed killing machine - the most terrifying beast to patrol the planet's oceans.

As a child, Dr. Hurum had visited the Oslo Natural History Museum, well known for its treasure trove of fossils, and gazed in awe at the fossilized flipper of a prehistoric sea predator. A quarter of a century later, Dr. Hurum was in Svalbard, one of the most inhospitable places on Earth, leading a team of paleontologists committed to finding what they all believed was there. Because of its extreme polar conditions, few paleontologists have ever explored Svalbard's fertile fossil hunting ground; and Dr. Hurum's group along with Dr. Druckenmiller are the first to document this diverse assembly of marine reptiles.

With modern forensic technology, Dr. Hurum and team work to unlock the secrets of the monster. CGI will help bring Predator X to life, in an environment like the one all those years ago. Its anatomy, physiology and hunting technique all point to it being the ultimate predator - the ferocious pliosaur they are calling Predator X. Pliosaurs were a short-necked form of plesiosaur, a group of extinct reptiles that inhabited the world's oceans in the age of dinosaurs. The team is able to determine that their find, Predator X, is indeed a new species based on its incredible size and bone morphology - specifically: the flipper bones, the breast plate, and the neck vertebrae.

Predator X is produced for History(TM) by Atlantic Productions. Executive Producer for Atlantic Productions is Anthony Geffen. Executive Producer for History is Dirk Hoogstra.

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