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.Fil: Pan, Hailin. Bgi-shenzhen; ChinaFil: Cole, Theresa L. University Of Otago; CanadáFil: Bi, Xupeng. Bgi-shenzhen; ChinaFil: Fang, Miaoquan. Bgi-shenzhen; ChinaFil: Zhou, Chengran. Bgi-shenzhen; ChinaFil: Yang, Zhengtao. Bgi-shenzhen; ChinaFil: Ksepka, Daniel T. Bruce Museum; Estados UnidosFil: Hart, Tom. University of Oxford; Reino UnidoFil: Bouzat, Juan L.. Bowling Green State University; Estados UnidosFil: Boersma, P. Dee. University of Washington; Estados UnidosFil: Bost, Charles-André. Centre Detudes Biologiques de Chizé; FranciaFil: Cherel, Yves. Centre Detudes Biologiques de Chizé; FranciaFil: Dann, Peter. Phillip Island Nature Parks; AustraliaFil: Mattern, Thomas. University of Otago; Nueva ZelandaFil: Ellenberg, Ursula. Global Penguin Society; Estados Unidos. La Trobe University; AustraliaFil: Garcia Borboroglu, Jorge Pablo. University of Washington; Estados Unidos. Global Penguin Society; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Argilla, Lisa S.. Otago Polytechnic; Nueva ZelandaFil: Bertelsen, Mads F.. Copenhagen Zoo; Dinamarca. University of Copenhagen; DinamarcaFil: Fiddaman, Steven R.. University of Oxford; Reino UnidoFil: Howard, Pauline. Hornby Veterinary Centre; Nueva Zelanda. South Island Wildlife Hospital; Nueva ZelandaFil: Labuschagne, Kim. National Zoological Garden; SudáfricaFil: Miller, Gary. University of Western Australia; Australia. University of Tasmania; AustraliaFil: Parker, Patricia. University of Missouri St. Louis; Estados UnidosFil: Phillips, Richard A.. Natural Environment Research Council; Reino UnidoFil: Quillfeldt, Petra. Justus-Liebig-Universit ̈ at Giessen; AlemaniaFil: Ryan, Peter G.. University of Cape Town; SudáfricaFil: Taylor, Helen. Vet Services Hawkes Bay Ltd; Nueva Zelanda. Wairoa Farm Vets; Nueva ZelandaFil: Zhang, De-Xing. Chinese Academy of Sciences; República de ChinaFil: Zhang, Guojie. BGI-Shenzhen; China. Chinese Academy of Sciences; República de China. University of Copenhagen; DinamarcaFil: McKinlay, Bruce. Department of Conservation; Nueva Zeland

High-coverage genomes to elucidate the evolution of penguins

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

An investigation of the causes of mortality in yellow-eyed penguins (Megadyptes antipodes) across their range with specific emphasis on the role played by Leucocytozoon : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Science in Wildlife Health at Massey University, Palmerston North, New Zealand

Over the past 40 years, there have been frequent mass mortality events documented in yellow-eyed penguins (Megadyptes antipodes). In most cases, these mortality events have resulted in significant adult or chick mortality resulting in a population decline. Previous studies in yellow-eyed penguin mortality have been attributed to events such as unidentified phytotoxins, starvation, poor nutrition, climatic events and infectious causes. However, the full impact of these factors on yellow-eyed penguin population decline and mortality events is not well understood. During the Austral summer of 2008/09, there were mortality events documented in both the subantarctic and mainland yellow-eyed penguin populations with different patterns of mortality and different factors associated with the mortality between both locations. A high overall prevalence of Leucocytozoon spp. in association with a high incidence of chick mortality was observed during this period on Enderby Island. Despite its endemic nature in this population, statistical analysis demonstrated that infection with Leucocytozoon did not play a significant role in mass mortality of Enderby Island chicks, other than as a cause of sporadic individual mortality. The Leucocytozoon spp. sequences detected lead to the conclusion that the Leucocytozoon parasite is endemic in yellow-eyed penguins and has a higher prevalence in penguins from Enderby Island than those from Campbell Island and the mainland of New Zealand. The Enderby Island yellow-eyed penguins are infected with a Leucocytozoon spp. that is genetically distinct from that found in other yellow-eyed penguin populations. The role of Leucocytozoon in the high levels of chick mortality in the yellow-eyed penguins remains unclear. A very low mortality was observed in the Catlins population despite there being a high level of human impact at some nest regions within this location. A high level of mortality was described in the Otago Peninsula population with this population affected by high human disturbance from tourism, reduced quality of breeding habitat, diphtheritic stomatitis as well as increased environmental temperatures during the study season. All of these factors played a significant role in mortality of chicks at this location. Results from this research provide the foundation for future investigations into the risk factors for mortality in yellow-eyed penguins across their range as well as providing a basis for sound management and veterinary advice to assist with conservation of this endangered species

Correction to: High-coverage genomes to elucidate the evolution of penguins

In the original version of the article “High-coverage genomes to elucidate the evolution of penguins” by Hailin Pan et al. [1], the authors received a request to make some clarifications and changes in the acknowledgements, the following is the modified version:“We thank the following: John Cockrem, Scott Flemming, Helen McConnell, Chris Rickard, Sarah Fraser, Otto Whitehead, Kyle Morrison, and Amy Van Buren for help collecting samples; Jonathan Banks, Kirsten Rodgers, and Jo Hiscock for sample information; Manuel Paredes Oyarzún and Hernán Rivera Meléndez for facilitating permits and sample collection; Lauren Tworkowski, Richard O\u27Rorke, and Joanna Sumner for facilitating sample collection; Adrian Smith for providing laboratory support to extract 2 DNA samples; Peter Dearden, Neil Fowke, Michael Knapp, Hoani Langsbury, Claire Porima, Nic Rawlence, Paul Scofield, Jonathan Waters, Janet Wilmshurst, and Jamie Wood for informal discussions regarding the New Zealand indigenous consultation; The New Zealand Department of Conservation for facilitating New Zealand indigenous consultation and approving permits, particularly Neil Fowke and Jesse Mason for facilitating permits and/or obtaining past permit details; Brett Gartrell and Pauline Nijman for providing animal ethics details; and the China National Genebank for contributing the sequencing resources for this project. The Penguin Genome Consortium welcomes participation and collaboration for our ongoing work regarding comparative and evolutionary genomics of penguins.