Fragments of humpback whale skin no bigger than a thumbnail, gathered from the remote waters of Raoul Island, could help solve one of the great migration mysteries of the South Pacific.

New Zealand scientists are trying to unravel the reasons behind their slow recovery rate, and understand why these whales make unusual detours in their annual migration south to the waters of Antarctica.

Playing a part in the latest research was Bhakti Patel, the environmental programme manager for the Sir Peter Blake Trust, who earlier this month joined the expedition to the Kermadec Islands on board the Royal New Zealand Navy ship, HMNZS Wellington.

Armed with a net and camera, Patel collected data on humpbacks who visit Raoul Island from September to November every year.

She then passed on the tubes of sloughed skin and photographs of whale flukes to Dr Rochelle Constantine, a cetacean scientist and senior lecturer at the University of Auckland. Constantine has been studying humpback whales throughout the South Pacific since 1995, and is intrigued by the mysteries of Oceania’s threatened humpback group.

Patel, who has a Master’s degree in marine science but had never seen a humpback whale before, was in for a staggering introduction.

“Rochelle had told me that as soon as I got to Raoul Island, I’d see the whales from the ship. I didn’t believe her – I thought she was exaggerating. Then sure enough, when I woke up on the morning we arrived, there were so many whales around us – spouting, breaching, and fin slapping – it was ridiculous!” she says.

“Sometimes it was chaotic – there would be 30 bottlenose dolphins and nine whales in front of you, and you wouldn’t know where to drive.”

Raoul, the largest island in the Kermadecs, 1000km northeast of New Zealand, is a regular pitstop along the “humpback highway”. Every spring, after the breeding season, the Oceania humpbacks leave their South Pacific islands – including Tonga, Niue and the Cooks – and head to Antarctica for the summer to feast on krill.

No one knows exactly why they always call in at Raoul, but Patel says most don’t stop for long. “There’s no other congregation of humpback whales quite like it in the Pacific. They generally spend a couple of days there before heading off again. The longest time a whale has been observed hanging around has been 21 days,” she says.

They tend to travel in pairs. A trio of humpbacks is usually a mother, calf and nurse whale.

But when they leave Raoul, they don’t head directly south past New Zealand to Antarctic waters, like their east Australian humpback cousins do. Instead, their south-east diagonal path has scientists baffled.

In 2015, Constantine was part of an international research team who went to Raoul Island to put satellite tracker tags on the humpbacks. The whales all headed south-east, taking a much longer route to reach the icy continent; one whale swimming 7000km over nine weeks to get there. When the whales arrived, they then spread out over a 3000km area of Antarctica.

“They’re adding thousands of kilometres to their journey by going that way, when the Australian whales make a beeline straight down,” Patel says. “The researchers think the extra mileage may be part of the reason the Oceania humpbacks are recovering slower.”  The Australian whale population, incidentally, is recovering much faster.

And so the research continues. Next year Constantine will travel with NIWA to Antarctica to find the humpbacks feeding, and hopefully tag them to track their path home.

The whales will probably be happy to see her. Patel says the humpbacks around Raoul were a curious bunch, seemingly unafraid of human interaction. “They were spy-hopping [poking their heads out of the water] to check us out, rolling around, lying on their backs and giving us a wave. They were once-in-a-lifetime moments,” she says.

Gathering the sloughed skin after the whales breached was an interesting mission for Patel. In data collections in the past two years, scientists used biopsy guns and crossbows to take skin and blubber samples for genetic analysis.

This time Patel, on board a Navy RHIB, had to “head full-throttle to the breach spot” and beat the seabirds to scoop up the tiny remnants of whale before they sunk.

When driving around whales, the general rule is to stay clear of the giants by 200m. A research permit allowed her within 50m.

The skin samples from 17 different whales were then carefully removed from the net with tweezers and stored in ethanol to preserve them for analysing back in Auckland. The DNA in the shed skin cells can reveal a host of information including the whale’s parentage, sex and health.

It was also Patel’s task to take photos of the whales’ tail flukes – the scars, colours and shapes are unique to each whale, and are used to identify them for a population database. The dorsal fins of Raoul Island’s resident bottlenose dolphins were also recorded.

She was also gleaning inside information before next year’s Young Blake Expedition to the Kermadecs. Twenty college students will sail on the HMNZS Canterbury on a science mission in February.  Leading the science team will be Dr Libby Liggins, the first Blake Ambassador to Antarctica, who is now a lecturer in marine ecology at Massey University.

“The overall theme will be looking at the Kermadecs as a way of modelling what could potentially happen to New Zealand’s marine ecosystems when they are subjected to climate change,” says Patel, who will also return.

“The students will look at the composition of plankton and fish species – there are a mixture of tropical and subtropical species there. They’ll do underwater video work, and hopefully some oceanography to learn more about mapping the seafloor.

“If climate change were to warm up New Zealand waters, even by a couple of degrees, what could happen around our local coastlines could be potentially reflected in what we see in the Kermadecs.”