• Energy Research

Abstract 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.

The Magellanic penguin breeds in coastal Argentina, Chile and the Falkland Islands. Nests are built under bushes or in burrows, and they lay eggs in warm places when the temperature remains over 20. Magellanic penguins travel in large flocks when hunting for food. The International Union for Conservation of Nature (IUCN) classifies the Magellanic penguin as near threatened.We sequenced the genome of an adult Magellanic penguin from Chiloe Island, Chile (provided by Juan Bouzat) to a depth of approximately 171x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.2Gb, with the contig and scaffold N50 values of 40.48Kb and 12.09Mb respectively. We identified 16795 protein-coding genes.

The African penguin (also known as jackass penguin and black-footed penguin) is endemic to southern African coasts. The pink gland above the eyes helps to adjust to changing temperatures: when it's hotter, more blood is sent to these glands to be cooled by the surrounding air. It is a charismatic species and is popular with tourists. The African penguin has declined rapidly and the International Union for Conservation of Nature (IUCN) classifies it as endangered.We sequenced the genome of an adult African penguin from Luderitz, Namibia (provided by Kim Labuschagne) to a depth of approximately 115x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 99.03Kb and 14.67Mb respectively. We identified 16134 protein-coding genes.