Abstract

Range shift is the primary short-term species response to rapid climate change, but it is often hampered by natural or anthropogenic habitat fragmentation. Different critical areas of a species’ niche may be exposed to heterogeneous environmental changes and modelling species response under such complex spatial and ecological scenarios presents well-known challenges. Here, we use a biophysical ecological niche model validated through population genomics and palaeodemography to reconstruct past range shifts and identify future vulnerable areas and potential refugia of the king penguin in the Southern Ocean. Integrating genomic and demographic data at the whole-species level with specific biophysical constraints, we present a refined framework for predicting the effect of climate change on species relying on spatially and ecologically distinct areas to complete their life cycle (for example, migratory animals, marine pelagic organisms and central-place foragers) and, in general, on species living in fragmented ecosystems.

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Acknowledgements

This work was conducted within the framework of the Programme 137 of the Institut Polaire Français Paul-Emile Victor (IPEV; CLB), with additional support from the French National Research Agency (ANR) ‘PICASO’ grant (ANR-2010-BLAN-1728-01; Y.L.M.), Marie Curie Intra European Fellowships (FP7-PEOPLE-IEF-2008, European Commission; project no. 235962 to C.L.B. and FP7-PEOPLE-IEF-2010, European Commission; project no. 252252 to E.T.), the Centre Scientifique de Monaco through the budget allocated to the Laboratoire International Associé 647 BioSensib (CSM/CNRS-University of Strasbourg; C.L.B., Y.L.M.), the Centre National de la Recherche Scientifique (Programme Zone Atelier de Recherches sur l’Environnement Antarctique et Subantarctique), South African National Antarctic Programme (P.P.) and the IPEV Programme 109 (Y.C.). Logistic and field costs of research were supported by the IPEV Programme 137 (C.L.B.), the South African Department of Environmental Affairs and the National Research Foundation (P.P.). This work was performed on the Abel Cluster, owned by the University of Oslo and the Norwegian Metacenter for High Performance Computing (NOTUR), and operated by the Department for Research Computing at USIT, the University of Oslo. We are very grateful to M. Skage, A. Tooming-Klunderud, M. Selander-Hansen and the Norwegian Sequencing Center for their very valuable help in the laboratory, as well as L. Nederbragt and M. Matschiner for their assistance with the Abel cluster, and M. Fumagalli and T. Korneliussen for their precious advice regarding ngsTools and ANGSD. We thank G. Bertorelle, L. Fusani, A. Mazzarella and D. Fordham for useful comments and advice. We acknowledge the World Climate Research Programme’s Working Group on Coupled Modelling, which is responsible for CMIP, and we thank the climate modelling groups (listed in Supplementary Table 1) for producing and making available their model output. For CMIP, the US Department of Energy’s Program for Climate Model Diagnosis and Intercomparison provides coordinating support and led development of software infrastructure in partnership with the Global Organization for Earth System Science Portals.

Author information

Author notes

    • Virginie Raybaud

    Present address: Université Côte d’Azur, CNRS, ECOMERS, Nice, France

  1. These authors contributed equally: Céline Le Bohec and Emiliano Trucchi.

  2. These authors jointly supervised this work: Céline Le Bohec and Emiliano Trucchi.

Affiliations

  1. Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Strasbourg, France

    • Robin Cristofari
    • , Yvon Le Maho
    •  & Céline Le Bohec
  2. Département de Biologie Polaire, Centre Scientifique de Monaco (CSM), Monaco, Monaco

    • Robin Cristofari
    • , Yvon Le Maho
    •  & Céline Le Bohec
  3. Laboratoire International Associé (LIA-647 BioSensib, CSM-CNRS-Unistra), Monaco, Monaco

    • Robin Cristofari
    • , Yvon Le Maho
    •  & Céline Le Bohec
  4. Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway

    • Robin Cristofari
    • , Nils Christian Stenseth
    •  & Emiliano Trucchi
  5. Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA

    • Xiaoming Liu
  6. Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France

    • Francesco Bonadonna
  7. Centre d’Etudes Biologiques de Chizé (CEBC), CNRS-Université de La Rochelle, Villiers-en-Bois, France

    • Yves Cherel
  8. DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, South Campus, Port Elizabeth, South Africa

    • Pierre Pistorius
  9. Département de Biologie Marine, Centre Scientifique de Monaco (CSM), Monaco, Monaco

    • Virginie Raybaud
  10. Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria

    • Emiliano Trucchi
  11. Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy

    • Emiliano Trucchi

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Contributions

C.L.B. and E.T. conceived and supervised the study. C.L.B., F.B., Y.C. and P.P. collected the samples. R.C. performed DNA extraction, library preparation, and prepared and performed the genomic and demographic analyses and the climate modelling. X.L. and E.T. participated in the genomic and demographic analyses. V.R. and C.L.B. participated in climate modelling. N.C.S. hosted the project. R.C., C.L.B. and E.T. wrote the manuscript. F.B., N.C.S., P.P., Y.C., Y.L.M. and V.R. commented the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Céline Le Bohec or Emiliano Trucchi.

Supplementary information

  1. Supplementary Information

    Supplementary Notes 1–5, Supplementary Figures 1–9, Supplementary Tables 1–4, Supplementary References

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https://doi.org/10.1038/s41558-018-0084-2

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