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Takaraha was found ashore in Marlborough with a severe wound to his flipper, likely inflicted by a seal or a shark, which meant he would never swim again.
Zoology PhD candidate Mel Young said she had hoped for a better result for Takaraha, but she was still looking for better outcomes for all yellow-eyed penguins.
The juvenile bird, the darling of a University of Otago study of 23 yellow-eyed penguin juveniles fitted with satellite tags for their fledgling journeys, was tracked all the way up the South Island's east coast after fledging from Penguin Bay, south of Owaka, on February 19.
Takaraha had not moved for about five days before Department of Conservation volunteer Harry Litchwark found him injured and underweight near Cape Campbell.
The bird was taken to Picton Veterinary Clinic and, in consultation with Dunedin Wildlife Hospital specialist penguin vet Lisa Argilla, euthanised yesterday.
Takaraha was one of four penguins in the study that fledged from Penguin Bay, his sibling was ''still going'' in the south Canterbury Bight area where the majority of the birds appeared to be foraging.
None of the other birds had travelled as far as Takaraha, the only named bird in the study, but now a second bird appeared to be heading north of Banks Peninsula.
''Seeing the condition that [Takaraha] was in just prior to fledging he was 6.2kg and I got sent a few photos and he was looking very, very lean, so he's obviously lost a lot of body condition. And has got himself into some trouble,'' Ms Young said.
''It's disheartening, but this is the reality - not all of them survive.''
Only 20% of the penguins survive their first year at sea.