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Gene Switches Help “Nemo” Fish Adapt to Life on the Coral Reef

Two clown fish.
Credit: David Clode / Unsplash.
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A new study has found extraordinary genetic changes in reef fish as they transition from hatched larvae living in the open ocean to becoming juvenile reef-dwellers.

Dr Adam Downie from the Australian Research Council Centre of Excellence for Coral Reef Studies at James Cook University led a study examining the development of cinnamon anemonefish as they moved from the open ocean to living on reefs.

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“Fish larvae living in the open ocean must be elite swimmers to overcome currents, but once settling onto the reef, larvae undergo metamorphosis – like a caterpillar to a butterfly.

“At this point, juveniles transition to endure hypoxia – very low oxygen levels that are typical of coral reefs during night-time hours.

“Hypoxia occurs on reefs because corals and plants shift from producing oxygen via photosynthesis during the day to consuming oxygen via respiration at night, therefore creating low oxygen conditions,” said Dr Downie.

“This means coral reef fish larvae must rapidly and dramatically shift their physiology over a very short period of time, as the larval phase may only last for 9 days,” says Professor Jodie Rummer, senior author on the study, also based at JCU.

The scientists took daily measurements of swimming speeds, oxygen uptake rates, and hypoxia tolerance in newly hatched anemonefish over their entire early development.

“The measurements show larval anemonefish initially have very high oxygen uptake rates for their small size and are some of the fastest swimmers that have ever been studied,” said Dr Downie.

“However, oxygen uptake rates decrease midway through the larval phase, meaning larvae may be more efficient and need less energy in preparation for moving to and settling down on coral reefs. This may also mean they can’t easily leave the reef once they settle.”

Dr Downie, Professor Rummer and the team also examined changes in gene expression patterns over this entire period of early development.

They found over 4,000 genes were changing during this short window of time. However, they were most interested in the genes that code for oxygen transport proteins, such as haemoglobin, myoglobin, cytoglobin, and neuroglobin.

The shifts in these genes may be what allow anemonefish larvae to transition from being elite athletes in the open ocean to coping with night-time hypoxia on the reef.

“Our research shows changes in oxygen uptake rates and gene expression patterns of the various proteins responsible for oxygen transport correspond perfectly to this transition from open ocean to reef habitats,” said Professor Rummer.

She said this genetic flexibility may be what allows coral reef fishes to swim great distances and disperse widely during these first couple of weeks of life before settling onto a reef where they need to tolerate very different conditions.

“All of this may be key to enhancing genetic diversity and protecting biodiversity in a changing world,” said Dr Downie.

Reference: Downie AT, Lefevre S, Illing B, et al. Rapid physiological and transcriptomic changes associated with oxygen delivery in larval anemonefish suggest a role in adaptation to life on hypoxic coral reefs. PLOS Biology. 2023;21(5):e3002102. doi: 10.1371/journal.pbio.3002102

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