Abstract
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.