Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

nature ecology & evolution Article https://doi.org/10.1038/s41559-026-03062-w Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome Received: 19 October 2025 A list of authors and their affiliations appears at the end of the paper Accepted: 27 March 2026 Published online: xx xx xxxx Check for updates Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the world’s rarest penguins and considered taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease, respiratory distress syndrome, contributing to a decline to fewer than 115 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including New Zealand mainland (Northern range) and sub-Antarctic Enderby (Auckland Islands) and Campbell Islands (Southern range). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, which is consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5–16 thousand years. Genome scans for local adaptation revealed regions of strong differentiation, while genome-wide association analyses identified candidate immune and respiratory genes linked to respiratory distress syndrome. In partnership with Ngāi Tahu, who hold Indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies and the need for immediate population size and trend assessments for the Auckland and Campbell Island populations. Yellow-eyed penguins (Megadyptes antipodes) are an endangered species endemic to Aotearoa New Zealand1. They are regarded as taonga (treasured) by Māori, the Indigenous peoples of New Zealand, who named them hoiho or takaraka. As one of the rarest penguin species in the world, yellow-eyed penguins serve as an important indicator of ecosystem health, with their population trajectories reflecting broader ecosystem change1–3. Therefore, protecting yellow-eyed penguins is critical for biodiversity conservation and maintaining the integrity e-mail: Nature Ecology & Evolution of coastal ecosystems. They are also an icon of the regional wildlife tourism industry, substantially contributing to the local economy4. Therefore, their decline represents a biodiversity crisis and a cultural and economic loss. Yellow-eyed penguins have been delineated into two management groups: the Northern population found on the New Zealand mainland (throughout Te Waipounamu/South Island and Rakiura/Stewart Island) and the Southern population distributed across the Maukahuka/Motu Article Maha/Auckland Islands, including Enderby Island, and Motu Ihupuku/ Campbell Island (Fig. 1a). The Department of Conservation estimates that fewer than 3,000 individuals remain, with approximately 115 breeding pairs remaining within the Northern distribution, and fewer than 20% of Northern chicks surviving to adulthood5. As the sole surviving species of the Megadyptes genus, the yellow-eyed penguin is not only endangered6,7, but also at risk of extinction within its Northern range within the next two decades because of threats of habitat loss, dietary change8–11, disease12–18, bycatch19–21 and climate change22,23. Since 2019, a deadly neonatal respiratory disease known as respiratory distress syndrome (RDS) has presented an additional threat to the persistence of the Northern population. RDS results in severe breathing difficulties, with necropsies revealing lung congestion and haemorrhage along with lymphoid depletion24. The causative agent is probably a non-enveloped DNA virus in the Anelloviridae family known as yellow-eyed penguin gyrovirus (YPGV)24. In contrast, although YPGV is endemic across all regions, the Southern population shows no clinical signs consistent with RDS, and YPGV can be detected in apparently healthy individuals, including both adults and chicks, throughout the species range. Whether the Northern population is genetically more susceptible to developing RDS, or the differences in disease presentation are due to other causes (such as environmental variables or differences in viral lineages), remains an open question requiring species-wide genomic studies. Previous genetic studies have suggested that yellow-eyed penguins migrated to their Northern range approximately 500 years ago, after the extinction of the closely related Megadyptes antipodes waitaha, coincident with human arrival on the mainland25–28. In this recent-immigrant model, the mainland population is viewed as having established via a peripheral northward range expansion of the species and is potentially maladapted to warmer conditions. Under this hypothesis, conservation strategies for the Northern population could involve replacement, translocation or genetic rescue from Southern populations, noting that at the present time, no such strategies have been proposed29. Yet, before such interventions can be realistically considered, the genetic basis of the populations’ apparent differential susceptibility to developing RDS must be resolved because this remains a key knowledge gap that could directly inform conservation decision-making. In this study, deep sequencing of 249 yellow-eyed penguin genomes further resolved the species demographic history and allowed us to investigate the genetic basis of susceptibility to developing RDS. We combined phylogenetic molecular dating, genome-wide association studies30, selective sweep scans31 and ancestral recombination graph (ARG) inference32,33 to capture both long-term and recent evolutionary dynamics. Among these, ARGs were particularly suited to our aims because they enabled the estimation of the time to the most recent common ancestor both within and between populations. This fine-scale approach offers substantially greater resolution of divergence, migration and adaptation over the last few dozen generations than traditional population genetic methods34,35. Through this framework, we revealed the presence of three genetically distinct populations of yellow-eyed penguins. These lineages are characterized by deep divergence, minimal genomic evidence of ongoing migration and signatures of local adaptation. The scale of genomic differentiation strongly supports their recognition as three genomically and geographically distinct subspecies, with the split between the Northern and Southern populations occurring much earlier than previously considered25. We identified genetic variants that underlie differential responses to infection with YPGV, highlighting the role of host genetics (...truncated)