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However, in the short-term, the research will not have an effect on the Department of Conservation's Kaki (black stilt) Recovery Programme at Twizel, but will be incorporated into a review of the project due to be carried out next year.
"It has proved what we thought all along, but were never quite sure because of the small population whether it [inter-breeding] had impacted," programme manager Dean Nelson said yesterday.
Over the past three years, the breeding programme has released about 110 juvenile kaki into the wild a year.
Yesterday, University of Canterbury announced its scientists had found evidence the kaki was a genetically distinct species and therefore worthy of protection.
The research found that, contrary to popular belief, New Zealand's rarest and critically endangered wading bird did not represent a hybrid swarm.
Conservation geneticist Dr Tammy Steeves, who led the research team, said the introduction of predators, widespread habitat loss and degradation had driven the species close to extinction, with only 98 adult birds in the current population.
"It has also been suggested that breeding, or hybridisation, with the self-introduced pied stilt, or poaka, also contributed to the species' decline and that kaki will eventually hybridise to extinction," she said.
The extinction risk associated with hybridisation between native kaki and non-native poaka was, until now, unknown. It was unclear whether birds with all black plumage, classified as kaki, were indeed kaki or merely kaki-poaka hybrids in disguise.
The research team carried out a genetic census of nearly every individual kaki and showed that birds classified as kaki based on plumage were genetically kaki - excluding one individual - and none of the birds had poaka DNA.
"These results are both surprising and exciting," Dr Steeves said. "Because kaki-poaka hybrids can breed with either kaki or poaka, we expected to find many more cryptic hybrids, or birds that appear to be one species but actually have DNA from both species."
Since 1999, kaki had been actively prevented from breeding with non-kaki and the research team said this management strategy should continue to maintain the genetic integrity of kaki.
"The best thing we can do to ensure the recovery and survival of kaki is to continue using innovative conservation management strategies to increase the population size of this iconic species," she said.
Mr Nelson said it would be "business as usual" for the kaki programme, which had existed in one form or another since the 1980s.
The last review of the programme was 11 years ago, and another was planned for next year when the research results would be taken into consideration.
"We had an idea of the findings that the kaki were unique. It supports the kind of management programme we have had in place," he said.