Genetic research revealed four distinct gentoo penguin species, including a newly identified species from the Kerguelen Islands. Scientists warn climate change may endanger several isolated island populations.
The emperor penguin, which can grow to about 4 feet (1.2 meters) tall, is the best-known penguin species, but 17 other penguin species live across the Southern Hemisphere. Many inhabit remote islands that scientists rarely visit, making them difficult to study.
That isolation may explain why researchers overlooked an entirely new species of gentoo penguin on the Kerguelen Islands, also known in French as the Desolation Islands. The islands sit nearly 2,000 miles (3,220 kilometers) from the nearest permanently inhabited landmass.
An international research team led by scientists from Chile and the University of California, Berkeley, announced the discovery in a paper published in Communications Biology. It marks the first newly named penguin species in more than a century.
Genetic evidence revealed that what scientists once considered a single widespread gentoo species is actually made up of four distinct species. One of them remained hidden because it closely resembles other gentoo penguins, with the same black back and white underside that help the birds avoid predators and hunt efficiently in the ocean.
Aside from small differences in body size and vocalizations, the newly identified penguin appeared almost identical to other gentoos. Researchers classify it as a cryptic species because of those subtle physical differences despite major genetic separation.
Four Distinct Gentoo Penguin Species Identified
Researchers also determined that three previously recognized gentoo subspecies are genetically unique enough to qualify as full species.
The future of the newly identified southeastern gentoo penguin, Pygoscelis kerguelensis, along with two other gentoo species, remains uncertain as climate change reshapes Antarctic and sub-Antarctic habitats. Only the southern gentoo, now called Pygoscelis ellsworthi, appears likely to avoid major harm and could even benefit from an expanding range in Antarctica.
“In Antarctica, of course, other species, not the gentoo, are threatened by climate change,” said Juliana Vianna, one of the paper’s senior authors and a professor of ecosystems and environment at Andrés Bello National University in Santiago, Chile. “But the gentoo is of most concern in the sub-Antarctic region,” an area of widely separated islands north of Antarctica governed by numerous countries, including Chile, South Africa, France, the Netherlands, Australia, and New Zealand.
“It’s very important that conservation institutions in all the different countries involved recognize and take appropriate action to save these three gentoo penguin species,” she added.
Genomic Analysis Resolves Penguin Taxonomy Debate
Vianna and fellow senior authors Rauri Bowie of UC Berkeley and Elie Poulin of the University of Chile brought together penguin specialists from several countries to carry out a new genomic study of gentoo penguins. Some of the scientists had previously proposed as many as six gentoo subspecies, although researchers had long disagreed over the classification.
The new study represents a broad scientific consensus based on whole-genome sequences from 64 penguins collected across 10 breeding colonies. For the first time, the sampling covered nearly the entire geographic range of gentoo penguins. Researchers also compared physical traits such as coloration, vocalizations, breeding schedules, diet, and feeding behavior.
“There’s probably no species of penguin where the taxonomy has been more debated than the gentoo penguin,” said Bowie, a curator in UC Berkeley’s Museum of Vertebrate Zoology. “For over 100 years it’s been controversial as to how many species or how many subspecies there are. What this paper does is try to address that question using cutting-edge integrative approaches.”
Penguin Evolution and Antarctic Expansion
Bowie and Vianna have collaborated for nearly a decade to study penguin evolution and diversity. In 2019, they published research showing that penguins first emerged around Australia and New Zealand roughly 22 million years ago. Emperor and king penguins later split into separate groups that occupied Antarctica and sub-Antarctic regions.
About 12 million years ago, the development of the circumpolar current helped spread other penguin species throughout the sub-Antarctic. Penguins eventually colonized isolated islands and expanded as far north as parts of Africa and South America.
Gentoo penguins differ from many other penguin species because they eat a highly varied diet, feeding on almost anything they can catch underwater. That flexibility has become an advantage as krill populations decline. Penguins with more specialized diets, such as emperor and Adélie penguins, are experiencing population declines, while gentoo populations on the Antarctic Peninsula continue to grow.
Isolation and Diet Drove Gentoo Speciation
Researchers believe this adaptable feeding behavior also contributed to the evolution of the new species. Because gentoo penguins usually feed close to their nesting sites and return to the same breeding colonies each year, isolated populations gradually developed unique behavioral and ecological traits.
Over the past 300,000 to 500,000 years, those isolated island populations evolved into separate species. Scientists say the Antarctic Polar Front, which creates strong differences in ocean temperature and salinity, also limited animal movement and reinforced that separation.
North of the Polar Front, warmer and saltier waters are home to the eastern lineage, Pygoscelis taeniata, found on the Crozet, Marion, and Macquarie Islands, as well as the northern lineage, Pygoscelis papua, which inhabits the Falkland/Malvinas and Martillo Islands near South America.
The newly identified southeastern lineage, Pygoscelis kerguelensis, evolved on Kerguelen Island and likely nearby Heard Island near the Polar Front. South of the front lives the southern lineage, Pygoscelis ellsworthi, the largest gentoo population, which occupies the Antarctic Peninsula, coastal Antarctica, and South Georgia Island.
Genetic Adaptations Across Gentoo Populations
The genomic study, led by University of Chile graduate student Daly Noll, analyzed a broader range of genes than earlier research and examined thousands of single nucleotide polymorphisms (SNPs). The results showed how each species adapted genetically to its environment.
For instance, southern gentoo penguins living in Antarctica possess more genes associated with heat production, fat storage, and light perception. Researchers believe these traits help them survive extreme cold, seasonal daylight shifts, and the reflective ice environment.
Eastern gentoo penguins showed more genes related to efficient carbohydrate metabolism and improved diving ability. These genetic traits are linked to oxygen transport, blood vessel growth, mitochondrial function, and lung development, all of which may support longer dives in nutrient-poor oceans.
Meanwhile, the northern gentoo population in South America displayed genetic patterns tied to digestion, heart function, and muscle activity. Researchers say these changes likely help sustain extended foraging in the water.
Climate Change Threatens Sub-Antarctic Penguins
To predict how climate change may affect gentoo penguins, scientists used climate models to estimate where suitable habitat could exist by 2050. Under a moderate warming scenario, the sub-Antarctic island species could lose all habitable conditions on their current islands, with few nearby alternatives available.
The Antarctic species, however, may expand farther into Antarctica as emperor, Adélie, and chinstrap penguins decline due to shrinking sea ice and falling krill populations.
Vianna noted that many non-Antarctic penguins also face growing threats from warming oceans, habitat destruction, predators such as rats and dogs, competition with commercial fishing operations, and accidental capture in fishing nets.
“In terms of climate change, island species that have really low population sizes could be compared with the sub-Antarctic gentoo penguins,” she said. “Galapagos and other island penguin species, because they’re endemic to these islands, will find no place to go after a change in their environment. Those islands are very isolated, and these penguins cannot adapt easily to colonize any other region.”
Whole Genome Sequencing Boosts Conservation Research
Bowie said the massive genomic dataset collected for the study could support additional conservation research. Vianna is already using penguin genomes to search for genetic traits linked to surviving avian influenza, which is currently affecting penguins, birds, and mammals around the world. The findings could help scientists identify populations most vulnerable to the disease.
“Whole genome sequencing has transformed our ability to not only look at adaptation from a perspective of how things diversify, but it has really important conservation value,” Bowie said.
Reference: “Integrative evidence reveals adaptive divergence and speciation in gentoo penguins” by Daly Noll, Jane Younger, Luis R. Pertierra, Michelle Greve, Eduardo J. Pizarro, Fabiola León, Debora Y. C. Brandt, Joshua Tyler, Gemma Clucas, Hila Levy, W. Brian Simison, Julie McInnes, Pierre Pistorius, Céline Le Bohec, Francesco Bonadonna, Phil N. Trathan, Andrés Barbosa, Andrea Raya Rey, Gisele P. M. Dantas, Rauri C. K. Bowie, Elie Poulin and Juliana A. Vianna, 23 April 2026, Communications Biology.
DOI: 10.1038/s42003-026-10081-7
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