While most fruit flies are known for their attraction to fermenting fruit, one species has evolved to hunt in fast-moving streams in Africa, taking on the role of a predator.
A team of researchers from Lund University has mapped the genome of Drosophila enhydrobia, a fruit fly with a unique life cycle. Its larvae develop underwater in fast-flowing streams, where they prey on black fly and midge larvae. The study, published in Current Biology, reveals how a lineage that was once considered a household nuisance transitioned into a new ecological world and identifies the genetic changes that supported this shift.
“We’re talking about a fruit fly that has completely turned its lifestyle upside down,” said Marcus Stensmyr, biology researcher at Lund University and lead author of the study. “From feeding on yeast and rotting fruit, it has become a specialized predator in running water.”
Museomics Provides an Answer
D. enhydrobia has not been observed in the wild since 1981. To obtain genetic material, the research team located a single pinned specimen in a natural history museum in Zurich and used modern DNA techniques to extract an almost complete genome without damaging the specimen.
This method, called museomics, is part of a wider effort to recover genetic information from museum collections that wasn’t accessible when the specimens were first collected. The Zurich specimen, preserved for about 40 years, still contained enough intact DNA for the researchers to conduct both phylogenetic and comparative genomic studies. Earlier technology could not have achieved this result.
Not an Evolutionary Loner
One of the main findings is that D. enhydrobia is not as biologically isolated as once believed. Genomic analysis shows it belongs to a group of flies linked to water-adjacent habitats, mostly in South Asia. Its relatives already possess traits that have evolved into an extreme aquatic lifestyle in this species.
“What at first looked like an evolutionary mystery turned out to be an extreme elaboration of something that already existed,” Stensmyr said. “That makes the story both more understandable and, in a way, even more fascinating.”
A Genome Trimmed for a Different Life
Genomic analysis reveals evidence of genetic trade-offs associated with adaptation to an aquatic environment. The analysis shows that the species has lost several gene families involved in smell, taste, and metabolism, which fruit flies that feed on fermenting food typically rely on. For a species whose relatives rely on chemosensory detection to find food and mates, these losses are significant. The remaining sensory genes display signs of intensified selection, suggesting adaptation to new ecological pressures.
“It’s as if it has fewer tools in the toolbox, but the tools that remain are all the more finely tuned for this particular environment,” said Hamid Ghanavi, a biology researcher at Lund University and co-author of the study.
The findings suggest that major evolutionary shifts can involve losing functions that no longer serve a species, while refining those that do.
The Potential of Museum Collections
In addition to its evolutionary findings, the study is a prime example of the value of natural history collections worldwide. Specimens collected many years ago can now provide new genetic insights thanks to modern sequencing technology.
For species that have disappeared from the wild or gone unobserved for years, museum archives may offer the only source of available biological material. The D. enhydrobia specimen examined in this study serves as an example of this; without it, the genetic history of this unusual fruit fly would have remained unknown.
Stensmyr said his team has only scratched the surface of what those collections might contain. Continued advances in ancient DNA recovery could make museum archives a significant resource for tracking how species have evolved over time and how they might respond to future environmental shifts.
Austin Burgess is a writer and researcher with a background in sales, marketing, and data analytics. He holds an MBA, a Bachelor of Science in Business Administration, and a data analytics certification. His work focuses on breaking scientific developments, with an emphasis on emerging biology, cognitive neuroscience, and archaeological discoveries.