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Two oaks, a New Zealand beech and a common beech had to come down because their condition was becoming a safety issue, Dunedin Botanic Garden curator Alan Matchett said.
Park staff had been monitoring the health of the trees for years, in particular a 120-year-old common beech in a row of beech trees near the southern entrance to the garden.
The row of trees suffered from years of tractors and people working around their base when a lawn ran right up to it.
A camellia bed had been extended to run under the row of trees and staff had been treating them with tea compost to stimulate soil activity and improve root systems and uptake of nutrients, but the particular tree had not responded.
It was taken down in chunks, cut up and removed. A local woodturning group took some of the wood, while the 4.5 tonne butt might become a feature elsewhere in the garden, Mr Matchett said.
The other three trees had also been treated for years, but branches had started splitting and the trees were becoming a safety issue.
''We don't take losing a tree lightly. We try and maintain the integrity of the garden, but there comes a time when these decisions just have to be made.''