Engineered Flies Upend Classic Adaptation Theory

(CN) – Scientists have disproved a classic, commonly accepted theory within evolutionary biology after creating the first animals genetically modified with reconstructed genes from millions of years ago.

In a new study published in the journal Nature Ecology & Evolution, researchers from the University of Chicago describe the genetic changes to the fruit fly’s ability to break down alcohol in rotting fruit and, in the process, testing a widely supported hypothesis about one of the must studied organisms in genetics and evolution.

“We chose a classic example of adaptation,” study co-author and University of Chicago professor Joe Thornton said. “We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong.”

To test whether specific genes helped certain species adapt to various environmental threats, the team combined statistical reconstructions of ancient gene sequences with transgenic animal engineering – two new methods that helped the researchers test how the fruit fly Drosophila melanogaster adapted to ethanol.

“One of the major goals of modern evolutionary biology is to identify the genes that caused species to adapt to new environments, but it’s been hard to do that directly because we’ve had no way to test the effects of ancient genes on animal biology,” said Mo Siddiq, a graduate student at the University of Chicago and one of the study’s lead scientists.

The team tested the findings of two University of Chicago biologists, Martin Kreitman and John McDonald, who 25 years ago invented a new statistical model for finding signatures for selection – a tool that is still widely used within molecular evolution. Using this method, the team analyzed the alcohol dehydrogenase (Adh) for the enzyme that breaks down alcohol inside cells.

Adh has a strong signature of selection, and it was known that D. melanogaster break down alcohol faster than related species. So the theory that the Adh enzyme allowed the fruit fly to adapt to ethanol became the first accepted case of a specific gene sparking adaptive evolution of a species.

Thornton and Siddiq realized this hypothesis could be tested using modern technologies, which helped them infer the sequences of ancient Adh genes from just before and after D. melanogaster evolved its ethanol tolerance two to four million years ago.

Siddiq then synthesized the genes biochemically, and used biochemical methods to measure their ability to break down alcohol in a test tube.

The team found the genetic changes had no detectable effect on the enzyme’s function.

Working with collaborators David Loehlin from the University of Wisconsin and Kristi Montooth at the University of Nebraska, Siddiq then created transgenic flies containing the reconstructed ancestral forms of Adh. The researchers bred thousands of “ancestralized” flies, tested their ability to break down alcohol, and measured how well the larvae and adult flies were able to adapt when raised on food with high alcohol content.

The team found that the transgenic flies carrying the more recent Adh genes were no better at metabolizing alcohol than flies carrying the older form of the gene. Even more surprisingly, the flies with the more recent Adh genes were no better at growing or surviving on increased alcohol concentrations. The findings invalidated the classic theory and suggest that D. melanogaster adapted to high-alcohol food sources during its evolution, independent of changes in the Adh enzyme.

“The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction,” Thornton said. “But three lines of circumstantial evidence don’t make an airtight case.”

Kreitman, who is still a professor of ecology and evolution at the University of Chicago, has been supportive of the team’s research – advising Siddiq on the project and sharing his expertise on Drosophila genetics and molecular evolution.

“From the beginning, Marty was excited about our experiments, and he was just as supportive when our results overturned well-known conclusions based on his past work,” Siddiq said.

For their part, Thornton and Siddiq hope the use of ancestralized transgenics will become the gold standard in the field.

“This strategy of engineering ‘ancestralized animals’ could be applied to many evolutionary questions,” Thornton said.