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Research article - Peer-reviewed, 2021

Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation

Frugone, Maria Jose; Cole, Theresa L.; Lopez, Maria Eugenia; Clucas, Gemma; Matos-Maravi, Pavel; Lois, Nicolas A.; Pistorius, Pierre; Bonadonna, Francesco; Trathan, Phil; Polanowski, Andrea; Wienecke, Barbara; Raya-Rey, Andrea; Putz, Klemens; Steinfurth, Antje; Bi, Ke; Wang-Claypool, Cynthia Y.; Waters, Jonathan M.; Bowie, Rauri C. K.; Poulin, Elie; Vianna, Juliana A.


Aim Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus Eudyptes comprise three broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome) and eastern rockhopper (E. filholi). Their taxonomic status has been controversial for decades, with researchers disagreeing about whether E. chrysocome and E. filholi are distinct species or conspecific. Our goal is to evaluate genome-wide patterns of divergence to evaluate genetic differentiation and species delimitation in rockhopper penguins, and to assess which mechanisms may underlie previous discordance among nuclear versus mitochondrial analyses. Location Sub-Antarctic and temperate coastal regions of the Southern Hemisphere. Methods We generated reduced-representation genomic libraries using double digest restriction-site associated DNA (ddRAD) sequencing to evaluate genetic differentiation, contemporary migration rates and admixture among colonies of rockhopper penguins. Results The extent of genetic differentiation among the three taxa was consistently higher than population-level genetic differentiation found within these and other penguin species. There was no evidence of admixture among the three taxa, suggesting the absence of ongoing gene flow among them. Species delimitation analyses based on molecular data, along with other lines of evidence, provide strong support for the taxonomic distinction of three species of rockhopper penguins. Main conclusions Our results provide strong support for the existence of three distinct species of rockhopper penguins. The recognition of this taxonomic diversity is crucial for the management and conservation of this widely distributed species group. This study illustrates that widespread dispersive seabird lineages lacking obvious morphological differences may nevertheless have complex evolutionary histories and comprise cryptic species diversity.


Eudyptes; genomics; rockhopper penguins; species delimitation

Published in

Diversity and Distributions
2021, volume: 27, number: 11, pages: 2277-2296
Publisher: WILEY

Authors' information

Frugone, Maria Jose
Universidad Austral de Chile
Frugone, Maria Jose
Universidad de Chile
Cole, Theresa L.
University of Copenhagen
Cole, Theresa L.
University of Otago
López, Maria-Eugenia (López, María-Eugenia)
Swedish University of Agricultural Sciences, Department of Aquatic Resources
Clucas, Gemma
Cornell University
Matos-Maravi, Pavel
Czech Academy of Sciences
Lois, Nicolas A.
University of Buenos Aires
Lois, Nicolas A.
Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)
Pistorius, Pierre
Nelson Mandela University
Bonadonna, Francesco
Universite Paul-Valery
Trathan, Phil
UK Research and Innovation (UKRI)
Polanowski, Andrea
Australian Antarctic Division
Wienecke, Barbara
Australian Antarctic Division
Raya-Rey, Andrea
Univ Nacl Tierra Fuego
Raya-Rey, Andrea
Wildlife Conservation Society
Raya-Rey, Andrea
Consejo Nacl Invest Cient and Tecn CADIC CON
Putz, Klemens
Antarctic Res Trust
Steinfurth, Antje
Royal Society for Protection of Birds
Steinfurth, Antje
University of Cape Town

UKÄ Subject classification

Biological Systematics

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