Conservation Genetics

, Volume 11, Issue 3, pp 1043–1049 | Cite as

Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure

  • Romane CristescuEmail author
  • William Bruce Sherwin
  • Kathrine Handasyde
  • Valma Cahill
  • Desmond W. Cooper
Research Article


Reduced, or bottlenecked, populations are more prone to adverse events. Thus, the detection of genetic bottleneck signatures in wildlife is an important issue for conservation. BOTTLENECK 1.2.02 is a software commonly used for detecting genetic characteristics of past bottlenecks. Here we test the efficiency with which this software detects bottlenecks in two koala populations of known history. The sign test performed well for both populations, particularly under the infinite alleles model for mutation. This suggests this model could be the more realistic for marsupial microsatellites than other mutation models. Under the allele frequency distribution test, the two populations falsely appeared to be at mutation/drift equilibrium. However, this test could detect the bottleneck when only imperfect repeat microsatellites were included in the analysis. We thus recommend further investigation of imperfect repeat microsatellites, which could be more powerful for bottleneck detection. These results underline the cautious approach researchers and conservationists should take when studying the past of unknown populations.


Bottleneck Infinite alleles model Marsupial Perfect and imperfect repeat microsatellites 



Infinite alleles model


Stepwise mutation model


Two phase model



This worked has been funded by ARC linkage grant (LPO560344). We thank K. Carlyon for providing koala samples, B. L. Carlsson and A. Wilton for technical assistance. We also thank the Rangers from French Island National Park (Parks Victoria) and the members of the Koala Management Program (Department for Environment and Heritage) for their support and assistance in the field. We would also like to thank two anonymous reviewers for their most helpful comments.


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Romane Cristescu
    • 1
    Email author
  • William Bruce Sherwin
    • 1
  • Kathrine Handasyde
    • 2
  • Valma Cahill
    • 3
  • Desmond W. Cooper
    • 1
  1. 1.Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesKensingtonAustralia
  2. 2.Department of ZoologyUniversity of MelbourneMelbourneAustralia
  3. 3.Dubbo CollegeDubboAustralia

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