High-coverage genomes to elucidate the evolution of penguins

Hailin Pan; Theresa L. Cole; Xupeng Bi; Miaoquan Fang; Chengran Zhou; Zhengtao Yang; Daniel T. Ksepka; Tom Hart; Juan L. Bouzat; Lisa S. Argilla; Mads F. Bertelsen; P. Dee Boersma; Charles André Bost; Yves Cherel; Peter Dann; Steven R. Fiddaman; Pauline Howard; Kim Labuschagne; Thomas Mattern; Gary Miller; Patricia Parker; Richard A. Phillips; Petra Quillfeldt; Peter G. Ryan; Helen Taylor; David R. Thompson; Melanie J. Young; Martin R. Ellegaard; M. Thomas P. Gilbert; Mikkel Holger S. Sinding; George Pacheco; Lara D. Shepherd; Alan J.D. Tennyson; Stefanie Grosser; Emily Kay; Lisa J. Nupen; Ursula Ellenberg; David M. Houston; Andrew Hart Reeve; Kathryn Johnson; Juan F. Masello; Thomas Stracke; Bruce McKinlay; Pablo García Borboroglu; De Xing Zhang; Guojie Zhang

doi:10.1093/gigascience/giz117

High-coverage genomes to elucidate the evolution of penguins

Hailin Pan, Theresa L. Cole, Xupeng Bi, Miaoquan Fang, Chengran Zhou, Zhengtao Yang, Daniel T. Ksepka, Tom Hart, Juan L. Bouzat, Lisa S. Argilla, Mads F. Bertelsen, P. Dee Boersma, Charles André Bost, Yves Cherel, Peter Dann, Steven R. Fiddaman, Pauline Howard, Kim Labuschagne, Thomas Mattern, Gary MillerPatricia Parker, Richard A. Phillips, Petra Quillfeldt, Peter G. Ryan, Helen Taylor, David R. Thompson, Melanie J. Young, Martin R. Ellegaard, M. Thomas P. Gilbert, Mikkel Holger S. Sinding, George Pacheco, Lara D. Shepherd, Alan J.D. Tennyson, Stefanie Grosser, Emily Kay, Lisa J. Nupen, Ursula Ellenberg, David M. Houston, Andrew Hart Reeve, Kathryn Johnson, Juan F. Masello, Thomas Stracke, Bruce McKinlay, Pablo García Borboroglu, De Xing Zhang, Guojie Zhang

Ecology and Evolution

3 Citations (Scopus)

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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.

Original language	English
Journal	GigaScience
Volume	8
Issue number	9
Pages (from-to)	1-17
ISSN	2047-217X
DOIs	https://doi.org/10.1093/gigascience/giz117
Publication status	Published - 18 Sept 2019

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/gigascience/giz117Licence: CC BY

High-coverage genomes to elucidate the evolution of penguinsFinal published version, 1.78 MBLicence: CC BY

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Pan, H., Cole, T. L., Bi, X., Fang, M., Zhou, C., Yang, Z., Ksepka, D. T., Hart, T., Bouzat, J. L., Argilla, L. S., Bertelsen, M. F., Boersma, P. D., Bost, C. A., Cherel, Y., Dann, P., Fiddaman, S. R., Howard, P., Labuschagne, K., Mattern, T., ... Zhang, G. (2019). High-coverage genomes to elucidate the evolution of penguins. GigaScience, 8(9), 1-17. https://doi.org/10.1093/gigascience/giz117

Pan, H, Cole, TL, Bi, X, Fang, M, Zhou, C, Yang, Z, Ksepka, DT, Hart, T, Bouzat, JL, Argilla, LS, Bertelsen, MF, Boersma, PD, Bost, CA, Cherel, Y, Dann, P, Fiddaman, SR, Howard, P, Labuschagne, K, Mattern, T, Miller, G, Parker, P, Phillips, RA, Quillfeldt, P, Ryan, PG, Taylor, H, Thompson, DR, Young, MJ, Ellegaard, MR, Gilbert, MTP , Sinding, MHS , Pacheco, G, Shepherd, LD, Tennyson, AJD, Grosser, S, Kay, E, Nupen, LJ, Ellenberg, U, Houston, DM, Reeve, AH, Johnson, K, Masello, JF, Stracke, T, McKinlay, B, Borboroglu, PG, Zhang, DX & Zhang, G 2019, 'High-coverage genomes to elucidate the evolution of penguins', GigaScience, vol. 8, no. 9, pp. 1-17. https://doi.org/10.1093/gigascience/giz117

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title = "High-coverage genomes to elucidate the evolution of penguins",

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 Gal{\'a}pagos 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, biogeography, climate change, comparative evolution, demography, evolution, genomics, phylogenetics, speciation, Sphenisciformes",

author = "Hailin Pan and Cole, {Theresa L.} and Xupeng Bi and Miaoquan Fang and Chengran Zhou and Zhengtao Yang and Ksepka, {Daniel T.} and Tom Hart and Bouzat, {Juan L.} and Argilla, {Lisa S.} and Bertelsen, {Mads F.} and Boersma, {P. Dee} and Bost, {Charles Andr{\'e}} and Yves Cherel and Peter Dann and Fiddaman, {Steven R.} and Pauline Howard and Kim Labuschagne and Thomas Mattern and Gary Miller and Patricia Parker and Phillips, {Richard A.} and Petra Quillfeldt and Ryan, {Peter G.} and Helen Taylor and Thompson, {David R.} and Young, {Melanie J.} and Ellegaard, {Martin R.} and Gilbert, {M. Thomas P.} and Sinding, {Mikkel Holger S.} and George Pacheco and Shepherd, {Lara D.} and Tennyson, {Alan J.D.} and Stefanie Grosser and Emily Kay and Nupen, {Lisa J.} and Ursula Ellenberg and Houston, {David M.} and Reeve, {Andrew Hart} and Kathryn Johnson and Masello, {Juan F.} and Thomas Stracke and Bruce McKinlay and Borboroglu, {Pablo Garc{\'i}a} and Zhang, {De Xing} and Guojie Zhang",

year = "2019",

month = sep,

day = "18",

doi = "10.1093/gigascience/giz117",

language = "English",

volume = "8",

pages = "1--17",

journal = "GigaScience",

issn = "2047-217X",

publisher = "BioMed Central Ltd.",

number = "9",

}

TY - JOUR

T1 - High-coverage genomes to elucidate the evolution of penguins

AU - Pan, Hailin

AU - Cole, Theresa L.

AU - Bi, Xupeng

AU - Fang, Miaoquan

AU - Zhou, Chengran

AU - Yang, Zhengtao

AU - Ksepka, Daniel T.

AU - Hart, Tom

AU - Bouzat, Juan L.

AU - Argilla, Lisa S.

AU - Bertelsen, Mads F.

AU - Boersma, P. Dee

AU - Bost, Charles André

AU - Cherel, Yves

AU - Dann, Peter

AU - Fiddaman, Steven R.

AU - Howard, Pauline

AU - Labuschagne, Kim

AU - Mattern, Thomas

AU - Miller, Gary

AU - Parker, Patricia

AU - Phillips, Richard A.

AU - Quillfeldt, Petra

AU - Ryan, Peter G.

AU - Taylor, Helen

AU - Thompson, David R.

AU - Young, Melanie J.

AU - Ellegaard, Martin R.

AU - Gilbert, M. Thomas P.

AU - Sinding, Mikkel Holger S.

AU - Pacheco, George

AU - Shepherd, Lara D.

AU - Tennyson, Alan J.D.

AU - Grosser, Stefanie

AU - Kay, Emily

AU - Nupen, Lisa J.

AU - Ellenberg, Ursula

AU - Houston, David M.

AU - Reeve, Andrew Hart

AU - Johnson, Kathryn

AU - Masello, Juan F.

AU - Stracke, Thomas

AU - McKinlay, Bruce

AU - Borboroglu, Pablo García

AU - Zhang, De Xing

AU - Zhang, Guojie

PY - 2019/9/18

Y1 - 2019/9/18

N2 - 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.

AB - 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.

KW - Antarctica

KW - biogeography

KW - climate change

KW - comparative evolution

KW - demography

KW - evolution

KW - genomics

KW - phylogenetics

KW - speciation

KW - Sphenisciformes

U2 - 10.1093/gigascience/giz117

DO - 10.1093/gigascience/giz117

M3 - Journal article

C2 - 31531675

AN - SCOPUS:85072283600

SN - 2047-217X

VL - 8

SP - 1

EP - 17

JO - GigaScience

JF - GigaScience

IS - 9

ER -

High-coverage genomes to elucidate the evolution of penguins

Abstract

Keywords

UN SDGs

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