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New Zealanders have never been particularly enamored with their native shags. Anglers blamed the cormorants for —an introduced species—and many colonies were destroyed to protect sports fisheries. One 1945 treatise, “The Shag Menace,” called for wholesale slaughter of the birds, with focused efforts during nesting and breeding seasons.

Perhaps that’s why, compared with kiwis and other island birds, New Zealand’s dozen or so shag species have not been well studied. For many years, scientists couldn’t even decide how many shag species lived in New Zealand. One species, the , exemplifies the confusion. First described in 1845, by British zoologist George Robert Gray, the Stewart Island Shag was listed as having two distinct populations, as well as bronze and pied morphs. While some ornithologists considered these one species, others dubbed them separate species or subspecies.

Recent research finally resolved the century-old debate. Scientists analyzed the birds’ genes and concluded that the Stewart Island Shag is actually two separate species: the Foveaux Shag (Leucocarbo stewarti), which lives on both sides of the Foveaux Strait between Stewart Island and South Island, and the Otago Shag (Leucocarbo chalconotus), which lives further to the east on South Island.

Nic Rawlence, lead author of a study published in the in February, and a postdoctoral fellow at the University of Otago, said the team used ancient DNA from museum samples and sub-fossil remains to show that the two species have been separate for centuries. “The Otago species was spread around the entire eastern South Island,” he says. “It never interacted with the Foveaux Shag.”

The research revealed another key difference: One of the species is in serious trouble.

Uncertain Futures

Though they differ in appearance only slightly, the two species suffered disproportionately at the hands of humans. Settlers who arrived 700 to 1,000 years ago did far more damage than the trout-inspired hysteria of the past century, Rawlence says. He estimates that as many as 99 percent of the Otago Shag disappeared within 100 years of Polynesian settlement. A resulted, and the species now has almost no genetic variation. The Foveaux Shag avoided this fate because it mostly lives on inaccessible rock islands just offshore where settlers could not disturb them.

The Stewart Island Shag, which numbers around 5,000 birds, had already been considered vulnerable to extinction. But the split into two species creates new conservation priorities. Another study, underway now, will get accurate population counts of the Otago and Foveaux species. Rawlence says initial estimates suggest roughly equal numbers of each, which likely means both will be recategorized as endangered. The Otago Shag’s limited genetics, however, put it in worse shape.

“The Foveaux Shag still has a lot of diversity, so as long as you stop predators from getting to the islands where they live, they should be okay,” he says. “But the Otago shag needs tailored conservation.” He suggested that establishing new colonies in parts of the species’ former range may be an effective way to boost their population, although it would not solve the problem of their genetic diversity.

Meanwhile, both species benefit from efforts by the New Zealand Department of Conservation to preserve their coastal ecosystems. Because shags are commonly killed as fisheries bycatch, they benefit from efforts to mitigate that, too.

For his part, Rawlence doesn’t plan to limit his research to shags, although his team is also looking at the genetic lineage of South American and Antarctic shags. Rather, he says, the work that revealed the two new species is part of a broader effort to study the impact of Polynesian settlement on New Zealand’s coastal and marine fauna. He likens shags to “sentinels of how humans can affect species in the marine realm,” adding that we need to understand this impact in order to conserve species. “There’s still so much we don’t know about New Zealand birds and their history,” he says.