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Gigascience. 2019 Sep 1;8(9). pii: giz117. doi: 10.1093/gigascience/giz117.

High-coverage genomes to elucidate the evolution of penguins.

Author information

1
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
2
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
3
Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
4
Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, Canterbury 7640, New Zealand.
5
Department of Zoology, University of Otago, PO Box 56, Dunedin, Otago 9054, New Zealand.
6
China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.
7
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
8
Bruce Museum, Greenwich, CT 06830, USA.
9
Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
10
Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
11
The Wildlife Hospital Dunedin, School of Veterinary Nursing, Otago Polytechnic, Dunedin, Otago 9016, New Zealand.
12
Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark.
13
Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
14
Center for Ecosystem Sentinels, Department of Biology, University of Washington, Seattle, WA 98195, USA.
15
Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France.
16
Research Department, Phillip Island Nature Parks, PO Box 97, Cowes, Phillip Island, Victoria, 3922, Australia.
17
Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK.
18
Hornby Veterinary Centre, 7 Tower Street, Hornby, Christchurch, Canterbury 8042, New Zealand.
19
South Island Wildlife Hospital, Christchurch, Canterbury, New Zealand.
20
National Zoological Garden, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa.
21
Division of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia.
22
Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia.
23
Department of Biology, University of Missouri St. Louis, St Louis, MO 63121, USA.
24
British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, UK.
25
Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.
26
FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa.
27
Vet Services Hawkes Bay Ltd, 801 Heretaunga Street, Hastings, New Zealand.
28
Wairoa Farm Vets, 77 Queen Street, Wairoa 4108, New Zealand.
29
National Institute of Water and Atmospheric Research Ltd., Private Bag 14901, Kilbirnie, Wellington 6241, New Zealand.
30
Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen, Denmark.
31
NTNU University Museum, Trondheim, Norway.
32
Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington 6140, New Zealand.
33
Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany.
34
Wildbase, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
35
Wellington Zoo, 200 Daniell St, Newtown, Wellington 6021, New Zealand.
36
National Zoological Gardens of South Africa, Pretoria, South Africa.
37
Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia.
38
Global Penguin Society, University of Washington, Seattle, WA, USA.
39
Biodiversity Group, Department of Conservation, Auckland, New Zealand.
40
Department of Biology, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
41
Biodiversity Group, Department of Conservation, Dunedin, New Zealand.
42
Global Penguin Society, Puerto Madryn 9120, Argentina.
43
CESIMAR CCT Cenpat-CONICET, Puerto Madryn 9120, Chubut, Argentina.
44
Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing 100101, China.

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.

KEYWORDS:

Antarctica; Sphenisciformes; biogeography; climate change; comparative evolution; demography; evolution; genomics; phylogenetics; speciation

PMID:
31531675
DOI:
10.1093/gigascience/giz117

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