Argilla, L. | bioRxiv Science

bioRxiv2025

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

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the worlds rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease called respiratory distress syndrome (RDS), contributing to a decline to fewer than 143 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 from the New Zealand mainland (Northern range) and subantarctic Enderby and Campbell Islands (Southern). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, 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 ka. Genome scans for local adaptation revealed regions of strong differentiation, and genome-wide association analyses identified candidate immune and respiratory genes linked to RDS. In partnership with Ng[a]i 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 Auckland and Campbell Island populations.

genomics↗

bioRxiv2024

Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered kakapo (Strigops habroptilus)

The k[a]k[a]p[o] is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine k[a]k[a]p[o] affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased k[a]k[a]p[o]. We identified three bacterial species - Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli - as significantly more abundant in diseased k[a]k[a]p[o] compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased k[a]k[a]p[o] suggests that these bacteria originate from exogenous sources rather than from k[a]k[a]p[o]-to-k[a]k[a]p[o] transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased k[a]k[a]p[o] population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggests that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.

microbiology↗