High-coverage genomes to elucidate the evolution of penguins.

BACKGROUND: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. RESULTS: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. CONCLUSIONS: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.

DIPHTHERITIC STOMATITIS IN YELLOW-EYED PENGUINS (MEGADYPTES ANTIPODES) IN NEW ZEALAND.

Diphtheritic stomatitis is a seasonal disease that has been recognized as a syndrome in Yellow-eyed Penguin ( Megadyptes antipodes ) chicks in New Zealand for >10 yr. It was present in about 50% of 234 chicks examined since 2002 and is characterized by a thick serocellular exudate in the oral cavity of 1-4-wk-old chicks. The syndrome includes inanition, weight loss, and death in many affected birds. Microscopically, the lesions varied in severity. Most affected chicks had severe, locally extensive, ulcerative stomatitis with large amounts of exudate containing numerous bacteria; a smaller number had mild focal lesions with smaller amounts of exudate and bacteria. Although Corynebacterium amycolatum has been consistently isolated from the oral lesions, it was also present in the oral cavity of 34% of normal adult penguins and their chicks and is not known to possess diphtheritic toxins. A primary viral pathogen was therefore suspected, and intracytoplasmic inclusion bodies were occasionally seen in oral mucosal epithelial cells. No herpesvirus DNA was detected with PCR. Avipoxvirus DNA and an unidentified virus-like agent were detected in some early oral lesions, but could not be confirmed in subsequent testing. Electron microscopy on early affected epithelium with intracytoplasmic inclusion bodies was unrewarding. Our findings raise the possibility that the disease is caused by an unknown primary virus infection followed by secondary Corynebacterium invasion, but this requires confirmation. The means of transmission has not been established but insect vectors are suspected.