That isolation may help explain why all gentoo penguin populations were not recognized as separate species until now. An international research team led by scientists from Chile and the University of California, Berkeley, has determined that gentoo penguins comprise four distinct species. One population, found on the remote Kerguelen Islands, is being recognized as a species for the first time.

The Kerguelen Islands, also known as the Desolation Islands in French, lie nearly 3,000 miles from any permanent landmass. The findings, based on whole-genome analysis and comparisons of physical and behavioral traits, were published in Communications Biology.

DNA reveals four species of gentoo penguin

Genetic evidence shows that what scientists previously treated as one widely distributed gentoo penguin species is actually a group of four genetically distinct species.

One of the four had never been officially recognized. Although it closely resembles other gentoos, with the familiar black back and white underside that help penguins hunt and avoid predators at sea, it differs in subtle body-size and vocalization traits. Its genetic differences are much more pronounced.

Species that look almost identical to closely related species but are genetically distinct are sometimes called cryptic species.

The researchers also determined that three gentoo populations previously classified as subspecies are distinct enough to be recognized as full species. The newly recognized southeastern gentoo penguin, Pygoscelis kerguelensis, may face an uncertain future. Two other newly defined species could also become vulnerable as global warming alters the Antarctic and sub-Antarctic regions where they live.

Only one of the four gentoo species lives in Antarctica. Climate projections suggest that its suitable habitat may expand as conditions change, while island-dwelling species could lose habitat.

“In Antarctica, of course, other species are under threat from climate change, not just gentoos,” said Juliana Viana, one of the study’s senior authors and a professor of ecosystems and environment at Andrés Bello National University in Santiago, Chile. “But gentoos are of greatest concern in the subantarctic region.”

The sub-Antarctic region consists of widely separated islands governed by several countries, including Chile, South Africa, France, the Netherlands, Australia and New Zealand.

“It is very important that conservation agencies in all countries involved are aware of these three species of gentoo penguins and take appropriate measures,” Viana added.

A century of debate over gentoo penguin classification

To resolve the long-running disagreement over gentoo penguin taxonomy, Viana collaborated with co-senior authors Lauri Bowie, a professor of integrative biology at the University of California, Berkeley, and Ellie Poulin, a professor at the University of Chile in Santiago. The researchers worked with penguin experts around the world to conduct an extensive genomic study.

Earlier researchers had proposed as many as six gentoo variants, but there was no universal agreement about how many species and subspecies existed. The new study sought to settle the question using an integrative approach that combined genetics, anatomy and behavior.

The team analyzed whole-genome sequences from 64 penguins collected from 10 breeding colonies. For the first time, the sampling covered nearly the entire geographic range of gentoo penguins.

Researchers also compared coloration, vocalizations, breeding schedules, diet and feeding behavior.

“There is probably no other species of penguin whose taxonomy is as controversial as the gentoo penguin,” said Bowie, curator of the Museum of Vertebrate Zoology at the University of California, Berkeley. “For more than 100 years, there has been debate about how many species and subspecies there are. This paper attempts to address that question using a cutting-edge integrative approach.”

How penguins spread across the Southern Hemisphere

Bowie and Viana have studied penguin evolution and diversification for nearly a decade. In 2019, they published research indicating that penguins originated near Australia and New Zealand about 22 million years ago.

Emperor and king penguins later diverged from other penguin lineages. Emperor penguins became associated with Antarctica, while king penguins became associated with the sub-Antarctic region.

About 12 million years ago, the development of circumpolar currents helped other penguin groups spread into the sub-Antarctic region. Over time, they colonized remote islands and archipelagos, eventually reaching as far north as Africa and South America.

Gentoo penguins have an important advantage over some of their relatives: a flexible diet. Rather than relying heavily on one type of prey, they consume a wide range of food that they can catch in the water.

Gentoos eat fish, krill, squid and cuttlefish. Their varied diet may become increasingly valuable as krill populations decline. Penguins with narrower diets, including emperor and Adélie penguins, are declining in some areas, while gentoo populations are increasing in parts of the Antarctic Peninsula.

How a flexible diet may have helped create new species

Ironically, the gentoo’s broad diet may also have contributed to the evolution of its distinct species.

Because gentoos can eat many types of prey, they do not need to travel especially far from their breeding colonies to find food. They also tend to return to the same nesting sites year after year.

Over long periods, isolated populations on remote islands became increasingly adapted to their local environments. These behavioral and ecological differences were reinforced by natural selection across the genome.

Researchers estimate that the four gentoo species diverged between 300,000 and 500,000 years ago. Geographic isolation played a major role, particularly the Antarctic Polar Front. This boundary separates waters with rapidly changing temperatures and salinity and can restrict the movement of marine animals.

The eastern lineage lives north of the polar front, where water temperatures and salinity are relatively high. Pygoscelis taeniata is found on Crozet Island, Marion Island and Macquarie Island.

The northern lineage, Pygoscelis papua, is restricted to the Falkland Islands, also known as the Malvinas Islands, and the Martillo Islands in South America.

The newly recognized southeastern gentoo, Pygoscelis kerguelensis, lives near the polar front. This relatively small population evolved around Kerguelen Island and may also occur near Heard Island.

Farther south, Pygoscelis elswatii inhabits the Antarctic Peninsula, the Antarctic coast and South Georgia Island.

Penguin genomes reveal local adaptation

The genomic analysis was led by Daley Noll, a graduate student at the University of Chile and the study’s first author. Compared with earlier studies, the researchers examined a much broader portion of the genome and analyzed thousands of genetic differences known as single-nucleotide polymorphisms, or SNPs.

These data revealed how each gentoo species has adapted to its specific environment.

The southern gentoo, which thrives in Antarctica, has genetic changes associated with life in extreme polar conditions. Researchers found more genes linked to heat production, fat and lipid storage, and light perception.

Changes related to light perception may help these penguins cope with dramatic seasonal shifts in sunlight and intense reflections from ice.

Eastern gentoos, by contrast, have more genes associated with efficient carbohydrate metabolism and diving ability. These include genes involved in oxygen transport and use, blood-vessel formation, mitochondrial activity and lung development.

Those adaptations may allow eastern gentoos to stay underwater longer while foraging in oceans where biological productivity is relatively low.

The northern gentoo of South America showed a different genetic pattern. Its genome contained more genes involved in digestion, heart contraction and muscle excitation. The researchers said these changes may support the sustained physical activity required for prolonged underwater feeding.

Climate change could leave island penguins stranded

The research team also used climate models to estimate where suitable gentoo penguin habitat may remain in 2050.

Under moderate climate-change scenarios, sub-Antarctic species living on islands could lose suitable habitat across all of the islands they currently inhabit. In many cases, there may be few or no nearby islands with suitable conditions.

Antarctic gentoos could face a very different future. Their suitable range is projected to extend farther into the continent as conditions change.

At the same time, emperor, Adélie and chinstrap penguins are expected to decline as sea ice disappears and the krill populations that depend on ice are affected.

Climate change is not the only danger facing penguins outside Antarctica. Ocean warming, habitat destruction, predation by rats and dogs, competition with commercial fisheries and accidental capture in fishing nets also threaten many penguin populations.

“In terms of climate change, island species with very low populations could be comparable to sub-Antarctic gentoo penguins,” Viana said. “Penguin species in the Galápagos and other islands are endemic to these islands, so they cannot find a place to go when the environment changes.”

Because these islands are highly isolated, the penguins cannot easily adapt by colonizing new areas.

Genomics could help protect penguins

The unusually large and diverse dataset assembled for the study could be valuable beyond resolving gentoo penguin classification.

Viana is already examining penguin genomes for genetic differences associated with survival after exposure to bird flu. Avian influenza is currently affecting penguin, bird and mammal populations around the world.

Identifying genetic traits linked to resistance or vulnerability could help conservationists determine which populations face the greatest risk.

“Whole-genome sequencing has not only changed our ability to think about adaptation in terms of how things diversify, but it has really important conservation value,” Bowie said.

In addition to Bowie and Viana, the study involved biologists from Australia, Spain, Venezuela, South Africa, the United Kingdom, France, Argentina, Monaco and Brazil. Daley Noll of the University of Chile in Santiago was the paper’s lead author.