For decades, scientists have studied the yellow-eyed penguin (Megadyptes antipodes). Previously thought to consist of two large populations, new genomic research has unveiled three distinct lineages of this endangered species that have been isolated for thousands of years, well before humans arrived in New Zealand (Aotearoa).
Geographical distribution of yellow-eyed penguins. Image credit: Guhlin et al., doi: 10.1038/s41559-026-03062-w.
In 1841, Jacques-Bernard Ombron and Honoré Jaquinot first described the yellow-eyed penguin as an endangered species endemic to New Zealand.
The indigenous Maori people of New Zealand consider these penguins taonga (cherished things) and refer to them as huiho or takaraka.
Since 2019, respiratory distress syndrome has affected chicks in mainland New Zealand, significantly reducing the number of breeding pairs to under 115.
“As one of the world’s rarest penguin species, the yellow-eyed penguin is an essential indicator of ecosystem health. Its population trends mirror broader ecological changes,” stated Professor Gemma Geoghegan from the University of Otago.
“Conserving yellow-eyed penguins is vital for biodiversity and the health of coastal ecosystems.”
“They also play a crucial role in local wildlife tourism, significantly contributing to the economy.”
“Their decline indicates a biodiversity crisis, leading to cultural and economic losses.”
In a recent study, Professor Geoghegan and collaborators sequenced the complete genomes of 249 yellow-eyed penguins from mainland New Zealand (Northern Ranges), the sub-Antarctic Enderby (Auckland Islands), and the Campbell Islands (Southern Ranges).
Rather than observing two simple population structures, the researchers were surprised to discover three genetically distinct groups with minimal interbreeding.
These findings suggest that each group warrants formal recognition as a separate subspecies due to significant genetic variations.
“In this study, we utilized population genomics to explore the evolutionary history and disease susceptibility of the endangered yellow-eyed penguin,” said Professor Geoghegan.
“Supported by Genomics Aotearoa, we generated comprehensive genomic data from these 249 penguins, enabling us to understand the reasons behind the severe respiratory disease affecting mainland chicks.”
Unexpectedly, we found that the yellow-eyed penguin consists of three distinct subspecies, showing no evidence of migration among them.
Our analysis indicates these populations have been separated for thousands of years, much earlier than previously believed.
This means the endangered northern population is not merely a recent offshoot of the southern lineage, but rather a unique evolutionary group.
We have identified potential genes related to immune function and respiratory biology, which may contribute to the northern populations’ vulnerability to respiratory distress syndrome.
“These findings shed light on the role of host genetics in wildlife diseases and have significant implications for conservation management.”
After discussions with Ngāi Tahu, the species’ kaitiaki (guardians), the authors suggest new subspecies names based on Māori geography: Megadyptes antipodes Murihiku (Hoiho Murihiku) for the northern residents, Megadyptes antipodes Motu Maha (Hoiho Motu Maha) for Enderby Island in the Auckland Islands, and Megadyptes antipodes Motu Ifupuku (Hoiho Motu Ifupuku) for Campbell Island.
“Collaborating with Ngāi Tahu, the Kaitiaki of Hoiho, we aim for this research to support urgent conservation efforts for each subspecies, particularly the declining northern lineage with fewer than 115 breeding pairs,” stated Professor Geoghegan.
The team’s research paper is published in the journal Nature Ecology and Evolution.
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J. Gurin et al. Population genomics of yellow-eyed penguins reveals subspecies divergence and candidate genes associated with respiratory distress syndrome. Nat Ecol Evol, published online May 12, 2026. doi: 10.1038/s41559-026-03062-w
Source: www.sci.news
