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Recent catches in the harbour had been skinny and the heaviest fish at the recent salmon-fishing competition weighed 6.01kg, which was usually the average size caught not the biggest, New Zealand Salmon Anglers' Otago branch chairman Wayne Olsen said.
''It's a bit of a concern. Something is happening in the food chain, as they don't have a lot in their stomachs.''
Normally, signs of sprats and krill were noticeable around the harbour and at Taiaroa Head but this year ‘‘there hasn't been that food to make the salmon grow big'', he said.
Given yellow-eyed penguins were starving, the lack of condition on sea-run salmon was further evidence of a gap in the food chain, he believed.
The cause of the problems could be as simple as weather patterns and it was too soon to say if there was an ongoing problem, Mr Olsen said.
‘‘It could be just a poor season.''
There were signs other fish were doing well in the harbour and he had even seen kahawai, a species he had not seen in the harbour in about 15 years.
University of Otago ecologist Prof Steve Wing said salmon and yellow-eyed penguins were important marine sentinel species for the health of the ocean.
As both species needed to find food from the sea every day, coming back skinny was a direct measure of what the ocean was doing, he said.
Oceans were extremely variable in their productivity and those patterns were not fully understood.
‘‘The only thing we can really say is if conditions are warm or cold we can expect productivity to be different than normal.''