Abstract
BackgroundPenguins (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.ResultsHere 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.ConclusionsWe 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.
Highlights
Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere
With ∼20 species among 6 genera, penguins range from the tropical Galapagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica
The genomics era has been boosted by global research consortiums, which bring together contextual, technical, and analytical skills spanning a network of international collaborations [123,124,125,126]
Summary
Library construction, and sequencing While it is possible to recover genome sequences from historical museum samples [75], such genomes are often of low quality and/or fragmented [76], limiting the ability of downstream analyses. Protein sequences from human (hg38) and avian transcripts were mapped to each penguin genome and the annotated gene models (as above). We first applied rigorous filtering steps to obtain 7,235 high-quality orthologs This was achieved by filtering ∼13,214 orthologs (BLAST reciprocal best hits [RBHs]) that were present in the Taeniopygia guttata genome and the 21 penguins/5 avian outgroup genomes (described above), retaining orthologs with no missing data, and removing sequences containing internal stop codons. We generated Taonga genomes encompassing hoiho (yellow-eyed penguin, Megadyptes antipodes antipodes), korora (little penguin, Eudyptula spp.), pokotiwha (Snares-crested penguin, E. robustus), tawaki (Fiordland-crested penguin, E. pachyrhynchus), and erect-crested penguin (Eudyptes sclateri) These genomes were obtained following rigorous Department of Conservation permitting procedures (including collection, holding, and exporting permits) and following Department of Conservation Iwi, Runanga, Whanau, or Hapuconsultation (Supplementary Table 1). While this work is still underway we have published these 19 penguin genomes to provide early access, while requesting researchers intending to use these data for similar cross-species comparisons to continue to follow the long-running Fort Lauderdale and Toronto rules
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