Conservation Genetics

, Volume 11, Issue 2, pp 539–546 | Cite as

Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin

  • Sanne Boessenkool
  • Bastiaan Star
  • Philip J. Seddon
  • Jonathan M. Waters
Research Article


There is an increasing awareness that the long-term viability of endemic island populations is negatively affected by genetic factors associated with population bottlenecks and/or persistence at small population size. Here we use contemporary samples and historic museum specimens (collected 1888–1938) to estimate the effective population size (N e) for the endangered yellow-eyed penguin (Megadyptes antipodes) in South Island, New Zealand, and evaluate the genetic concern for this iconic species. The South Island population of M. antipodes—constituting almost half of the species’ census size—is thought to be descended from a small number of founders that reached New Zealand just a few hundred years ago. Despite intensive conservation measures, this population has shown dramatic fluctuations in size over recent decades. We compare estimates of the harmonic mean N e for this population, obtained using one moment and three likelihood based-temporal methods, including one method that simultaneously estimates migration rate. Evaluation of the N e estimates reveals a harmonic mean N e in the low hundreds. Additionally, the inferred low immigration rates (m = 0.003) agree well with contemporary migration rate estimates between the South Island and subantarctic populations of M. antipodes. The low N e of South Island M. antipodes is likely affected by strong fluctuations in population size, and high variance in reproductive success. These results show that genetic concerns for this population are valid and that the long-term viability of this species may be compromised by reduced adaptive potential.


Museum specimens Temporal method Megadyptes antipodes New Zealand Island Microsatellites 



We are very grateful to the Auckland Museum, American Museum of Natural History, Australian Museum, Canterbury Museum, Museum of Comparative Zoology, Natural History Museum Geneva, Natural History Museum Tring, Natural History Museum Paris, Museum of New Zealand Te Papa Tongarewa, Natural History Museum Vienna, Swedish Museum of Natural History, Otago Museum, South Australian Museum, Smithsonian Institution, Museum für Naturkunde Berlin and Craig Millar for supplying tissue samples of historic specimens. We thank the New Zealand Department of Conservation for help with collecting contemporary samples. We are indebted to Tania King for guidance and advice in the laboratory and we thank Stein Are Sæther for helpful discussions about analyses. We would further like to thank the ESF Science Networking Programme ConGen for organising the Conservation Genetics conference in Trondheim in May 2009 and for this special issue of Conservation Genetics. This research was supported by the Department of Zoology, University of Otago, including PBRF Research Enhancement Grants to PJS and JMW. Samples were collected under Department of Conservation permits SO-17933-FAU and OT-19097-RES and University of Otago Animal Ethics Approval 69/06.

Supplementary material

10592_2009_9988_MOESM1_ESM.pdf (103 kb)
Supplementary material 1 (PDF 103 kb)


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Sanne Boessenkool
    • 1
    • 3
  • Bastiaan Star
    • 2
  • Philip J. Seddon
    • 1
  • Jonathan M. Waters
    • 1
  1. 1.Department of ZoologyUniversity of OtagoDunedinNew Zealand
  2. 2.Centre for Ecological and Evolutionary Synthesis, Department of BiologyUniversity of OsloOsloNorway
  3. 3.National Centre for Biosystematics, Natural History MuseumUniversity of OsloOsloNorway

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