Genetic ‘supergenes’ power explosive evolution in some fish

In the waters of Lake Malawi, a single group of fish has evolved into over 800 different species in just a few million years. This rapid and concentrated evolutionary explosion has long puzzled scientists.

Now, researchers have uncovered a powerful genetic mechanism that may explain how such extreme biodiversity can arise so quickly.

A recent study led by scientists from the Universities of Cambridge and Antwerp reveals that large chunks of reversed, or “flipped,” DNA in cichlid fish act like evolutionary accelerators.

These chromosomal inversions preserve key genetic traits across generations and help fish adapt swiftly to new habitats – fueling the formation of new species at remarkable speed.

The shortcut in our genes

“Why are there so many different kinds of animals and plants on Earth?” is a question that has guided evolutionary biology for centuries.

In the case of Malawi’s cichlids, all 800-plus species share a common ancestor. Yet they’ve diversified into everything from algae-grazers to sand-sifters to open-water predators – all within the confines of one lake.

To understand this phenomenon, the researchers examined the genomes of over 1,300 individual cichlids. Some species had flipped DNA sections across five chromosomes – a genetic anomaly called a chromosomal inversion.

“We discovered that, in some species, large chunks of DNA on five chromosomes are flipped – a type of mutation called a chromosomal inversion,” said senior author Hennes Svardal from the University of Antwerp.

Ordinarily, recombination reshuffles DNA each generation by mixing genetic material from both parents.

But inside these chromosomal inversions, the structure blocks recombination. As a result, organisms inherit linked gene sets together, preserving adaptations that function effectively as a group.

Fish supergenes lock in traits

“It’s sort of like a toolbox where all the most useful tools are stuck together, preserving winning genetic combinations that help fish adapt to different environments,” said Moritz Blumer from Cambridge’s Department of Genetics.

These preserved gene clusters, or supergenes, help explain how diverse cichlid fish evolve while sharing the same lake. In sandy lake beds, inversions limit gene mixing, helping preserve each species’ unique adaptations despite a lack of barriers.

The supergenes govern traits essential to survival: vision, hearing, feeding behavior, and more. For instance, fish that live in the lake’s deep waters – some as far down as 655 feet (200 meters) – require specialized vision to navigate dim light.

They also need unique diets to survive in the nutrient-poor depths and physiology to withstand high pressure. Their supergenes lock in those abilities.

Supergenes in fish interbreeding

Another advantage of these DNA inversions is that they can transfer wholesale between species when different cichlids interbreed. This spreads entire suites of beneficial traits in one stroke.

“When different cichlid species interbred, entire inversions can be passed between them – bringing along key survival traits, like adaptations to specific environments, speeding up the process of evolution,” Blumer said.

This genetic mechanism lets adaptations transfer between species, speeding evolution without needing to evolve traits independently each time.

Researchers found these inversions often act as sex chromosomes, determining whether a fish develops as male or female. Because sex chromosomes drive speciation, this finding adds complexity to how cichlids diversify so rapidly.

Going beyond fish

“While our study focused on cichlids, chromosomal inversions aren’t unique to them,” said co-senior author Richard Durbin, a professor at Cambridge’s Department of Genetics.

“They’re also found in many other animals – including humans – and are increasingly seen as a key factor in evolution and biodiversity.”

These findings reveal new ways to study the genetics of speciation. This applies not just to fish, but across all branches of the tree of life. Supergenes and inversions may be more than just quirks of DNA – they could be among evolution’s most powerful tools for generating new forms and functions.

“We have been studying the process of speciation for a long time,” Svardal said. “By understanding how these supergenes evolve and spread, we’re getting closer to answering one of science’s big questions: how life on Earth becomes so rich and varied.”

The study shows how a DNA twist can speed evolution, offering a key clue to the mystery of biodiversity. It also reveals that sometimes, nature hides its most elegant solutions in its smallest structures.

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