Dr Alexander said getting small tissue samples from free-swimming and elusive underwater aquatic mammals was "tricky", meaning pulling together a quality genome using their DNA had been challenging up until now.
"We’re really lucky that in New Zealand, when whales and dolphins get stranded, the Department of Conservation takes a small tissue sample with the permission of iwi, and they send it to the New Zealand Cetacean Tissue Archive, at the University of Auckland.
"One of our Maui dolphin samples came from that archive, and our Hector’s dolphin sample came from an animal that was sampled while free-swimming at Cloudy Bay, on the South Island.
"The way that these samples were stored was really great for genetics back in the day, but now we’ve got all these fancy genome techniques that have come on board, and they need really high-quality tissue.
"They needed to be snap frozen at the point of collection."
Unfortunately, these samples were not stored in optimal conditions, leading to DNA degradation, she said.
The researchers used high-quality genomes from closely related whales and dolphins — particularly the bottlenose dolphin and vaquita — to create a reference framework to properly assemble and organise the fragmented DNA pieces from Hector’s and Māui dolphins.
The result was the development of an innovative genome assembly process (a pipeline) that leveraged ‘‘synteny’’ — similarities in the order of genes between related species and the structure of their chromosome, Dr Alexander said.
‘‘The analogy I would use is that doing a genome is like doing a puzzle with three billion pieces and you don’t know where any of them go.
‘‘What using these other whales and dolphins did was kind of give us the picture on the front of the jigsaw puzzle box, so that we had a good idea about where those different bits of DNA should be placed, so that we could stitch together genomes for these species.’’
The technique is a first and has had proved remarkably successful.
More than 99% of the genome has been successfully mapped to chromosomes, despite the team working with degraded DNA samples.
Their small size and inshore distribution makes these dolphins very vulnerable to fisheries bycatch, pollution, marine traffic and disease.
As a result, the Hector’s dolphin is endangered with about 15,000 distributed around the South Island, and the Māui dolphin is critically endangered with only 48 individuals older than 1-year-old.
Mr Alvarez-Costes said there were concerns for Māui dolphins because the study indicated the species might now be at risk of inbreeding.
‘‘What’s also particularly concerning is their reduced genetic diversity may hamper their ability to adapt to other emerging threats like climate change,’’ he said.
Despite the great challenges, the new genomic information would give conservationists a deeper understanding of each population’s genetic health and evolutionary history.
That in turn would allow them to contribute to better-informed decisions about protection measures.
Dr Alexander said it had been ‘‘a long journey’’ and the team was excited to see the project completed.
Scientists around the world were now looking to see if the same technique could be used on other species, she said.
