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Science   Surprising genetic changes

Scientists created fruit flies with ancient genes to test evolution

Fruit fliesScientists at the University of Chicago have created the first genetically modified animals containing reconstructed ancient genes.

They used it to test the evolutionary effects of past genetic changes on the animals’ biology and fitness.

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The research, published online in Nature Ecology & Evolution on Jan. 13, is a major step forward for efforts to study the genetic basis of adaptation and evolution.

The specific findings, involving the fruit fly’s ability to break down alcohol in rotting fruit, overturn a widely held hypothesis about the molecular causes of one of evolutionary biology’s classic cases of adaptation.

“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 in ecology and evolution at the University of Chicago, one of the study’s lead scientists.

“We realized we could overcome this problem by combining two recently developed methods—statistical reconstruction of ancient gene sequences and engineering of transgenic animals,” he said.

Until recently, most studies of molecular adaptation have analyzed gene sequences to identify “signatures of selection”—patterns suggesting that a gene changed so quickly during its evolution that selection is likely to have been the cause.

The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted.

Siddiq and his adviser, Joe Thornton, professor of ecology and evolution and human genetics, wanted to directly test the effects of a gene’s evolution on adaptation.

Thornton has pioneered methods for reconstructing ancestral genes—statistically determining their sequences from large databases of present-day sequences, then synthesizing them and experimentally studying their molecular properties in the laboratory.

This strategy has yielded major insights into the mechanisms by which biochemical functions evolve.

Thornton and Siddiq reasoned that by combining ancestral gene reconstruction with techniques for engineering transgenic animals, they could study how genetic changes that occurred in the deep past affected whole organisms—their development, physiology and even their fitness.

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

For the first test case, we chose a classic example of adaptation—how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit. We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong.”

The fruit fly Drosophila melanogaster is one of the most studied organisms in genetics and evolution. In the wild, D. melanogaster lives in alcohol-rich rotting fruit, tolerating far higher alcohol concentrations than its closest relatives, which live on other food sources.

Twenty-five years ago at the University of Chicago, biologists Martin Kreitman and John McDonald invented a new statistical method for finding signatures of selection, which remains to this day one of the most widely used methods in molecular evolution.

They demonstrated it on the alcohol dehydrogenase (Adh) gene—the gene for the enzyme that breaks down alcohol inside cells—from this group of flies. Adh had a strong signature of selection, and it was already known that D. melanogaster flies break down alcohol faster than their relatives.

So, the idea that the Adh enzyme was the cause of the fruit fly’s adaptation to ethanol became the first accepted case of a specific gene that mediated adaptive evolution of a species.

Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies.

iddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago.

He synthesized these genes biochemically, expressed them and used biochemical methods to measure their ability to break down alcohol in a test tube.

The results were surprising: The genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein’s function.




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