UO researchers had role in international study of an ancient fish

Using an international database of zebrafish maintained at the University of Oregon, two UO researchers identified more than 50 genes still present in fish but potentially "left in the water" when fish began to walk on land.

These lost genes, says Ingo Braasch, a postdoctoral researcher in the Institute of Neuroscience laboratory of John Postlethwait, are not found today in tetrapods — four-legged land dwelling creatures that include, for example, frogs, lizards, chickens, mice and humans.

Braasch and Postlethwait were co-authors on a paper penned by a 91-member international team and published in April 18 issue of the journal Nature. The paper is described in a news release issued by the Broad Institute of the Massachusetts Institute of Technology and Harvard University.

The paper details the completion of the genome of the African coelacanth, a fish species thought to have been extinct for millions of years until found alive and well in 1938 off the coast of South Africa. "The coelacanth is important, because it is much more closely related to humans than it is to salmon and zebrafish, in terms of its historical lineage, but nevertheless it shares the aquatic habit of other fish," said Postlethwait, a professor of biology.

Thus, the coelacanth genome, researchers reported in their paper, provides new insights into the evolution of tetrapods, as well as the evolution of genes that stayed with fish.

The UO's part was the analysis of changes in genes and gene regulation during vertebrate adaptation to life on land.

Braasch and Postlethwait used the Zebrafish Model Organism Database that is maintained at the Zebrafish International Resource Center, a National Institutes of Health-funded center (grant P40 RR012546) based at the University of Oregon and led by Monte Westerfield. Zebra fish were first cloned and established as a model organism by UO biologist George Streisinger in the 1970s.

Braasch and Postlethwait compared the zebra fish data with genes found in stickleback, also a much-studied fish at the UO, and the African coelacanth, looking for genes still present in all three species of fish but absent from tetrapod genomes.

"Many of these genes we identified have functions in the development of fins, the tail, ears, eyes, the brain, and the kidney," Braasch said. "And these structures are exactly those that have been most dramatically changed during the evolution from land to water — as fins turned into limbs and the ears and eyes adapted to signal transmission through the air instead of water. This tells us that gene losses were an important component of the genomic remodeling that occurred in our earliest terrestrial ancestors and potentially contributed to the morphological adaptations to life on land.

"These genes were lost around the time of the water-to-land transition, because they are still found in the lobefin fish coelacanth but cannot be found in terrestrial vertebrates," Braasch said. "During the process of the conquest of land, these genes were lost from the genome, presumably, because they were no longer of any use to a terrestrial lifestyle or because they were even deleterious for life on land. We like to say that these genes were 'left in the water'."