Article open access publication

High-coverage genomes to elucidate the evolution of penguins

GigaScience, Oxford University Press (OUP), ISSN 2047-217X

Volume 8, 9, 2019

DOI:10.1093/gigascience/giz117, Dimensions: pub.1121090165, PMC: PMC6904868, PMID: 31531675,



  1. (1) University of Copenhagen, grid.5254.6, KU
  2. (2) Beijing Genomics Institute, grid.21155.32
  3. (3) Kunming Institute of Zoology, grid.419010.d
  4. (4) Landcare Research, grid.419186.3
  5. (5) University of Otago, grid.29980.3a
  6. (6) Chinese Academy of Sciences, grid.9227.e
  7. (7) Bruce Museum, Greenwich, CT 06830, USA
  8. (8) University of Oxford, grid.4991.5
  9. (9) Bowling Green State University, grid.253248.a
  10. (10) Otago Polytechnic, grid.462693.c
  11. (11) Copenhagen Zoo, grid.480666.a
  12. (12) University of Washington, grid.34477.33
  13. (13) Centre d'Etudes Biologiques de Chizé, grid.452338.b
  14. (14) Research Department, Phillip Island Nature Parks, PO Box 97, Cowes, Phillip Island, Victoria, 3922, Australia
  15. (15) Hornby Veterinary Centre, 7 Tower Street, Hornby, Christchurch, Canterbury 8042, New Zealand
  16. (16) South Island Wildlife Hospital, Christchurch, Canterbury, New Zealand
  17. (17) South African National Biodiversity Institute, grid.452736.1
  18. (18) University of Tasmania, grid.1009.8
  19. (19) University of Western Australia, grid.1012.2
  20. (20) University of Missouri–St. Louis, grid.266757.7
  21. (21) British Antarctic Survey, grid.478592.5
  22. (22) University of Giessen, grid.8664.c
  23. (23) University of Cape Town, grid.7836.a
  24. (24) Vet Services Hawkes Bay Ltd, 801 Heretaunga Street, Hastings, New Zealand
  25. (25) Wairoa Farm Vets, 77 Queen Street, Wairoa 4108, New Zealand
  26. (26) National Institute of Water and Atmospheric Research, grid.419676.b
  27. (27) Norwegian University of Science and Technology, grid.5947.f
  28. (28) Museum of New Zealand Te Papa Tongarewa, grid.488640.6
  29. (29) Ludwig-Maximilians-Universität München, grid.5252.0
  30. (30) Massey University, grid.148374.d
  31. (31) Wellington Zoo, 200 Daniell St, Newtown, Wellington 6021, New Zealand
  32. (32) National Zoological Gardens of South Africa, grid.507757.7
  33. (33) La Trobe University, grid.1018.8
  34. (34) Biodiversity Group, Department of Conservation, Auckland, New Zealand
  35. (35) Natural History Museum of Denmark, grid.507616.3
  36. (36) Biodiversity Group, Department of Conservation, Dunedin, New Zealand
  37. (37) Centro Científico Tecnológico Patagónico, grid.507427.3
  38. (38) Global Penguin Society, Puerto Madryn 9120, Argentina
  39. (39) Institute of Zoology, grid.458458.0


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.


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