"These were once reliable cues for prey-rich waters, but climate change and industrial fishing have depleted forage fish stocks in this system," said Sherley.
"These signs can now lead them to places where these fish, the penguins' main prey, are scarce."
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Researchers used satellites to track newly fledged African penguins from eight sites across their breeding range.
They found that many penguins were getting trapped in the Benguela Current Large Marine Ecosystem (BCLME), an area that stretches from southern Angola to Cape Point in South Africa's Western Cape.
The region has suffered from decades of overfishing and environmental changes, reducing the number of fish.
"The penguins still move to where the plankton are abundant, but the fish are no longer there," Sherley said.
Young penguins that wind up there often starve to death.
"Their breeding numbers are about 50 percent lower than they would be if they found their way to other waters, where the human impact has been less severe," said the study.