Conservation Genetics

, Volume 6, Issue 4, pp 551–562 | Cite as

Comparison of methods for detecting bottlenecks from microsatellite loci

  • Ellen G. Williamson-NatesanEmail author


This paper describes simulation tests to compare methods for detecting recent bottlenecks using microsatellite data. This study considers both type I error (detecting a bottleneck when there wasn’t one) and type II error (failing to detect a bottleneck when there was one) under a variety of scenarios. The two most promising methods were the range in allele size conditioned on the number of alleles, M k , and heterozygosity given the number of alleles, H k , under a two-phase mutation model; in most of the simulations one of these two methods had the lowest type I and type II error relative to other methods. M k was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large. On the other hand H k was most likely to correctly identify a bottleneck when a bottleneck was more recent and less severe and when mutation rates were low or pre-bottleneck population sizes were small. Both methods were prone to type I errors when assumptions of the model were violated, but it may be easier to design a conservative heterozygosity test than a conservative ratio test.


allele frequency distribution population size reduction effective population size extinction risk 


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This study was supported by NIH grant GM40282 to M. Slatkin. I would like to thank J.C. Garza, C. Muirhead, R.D. Schnabel, M. Slatkin, and T.J. Ward for many helpful comments and suggestions.


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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  1. 1.Department of Integrative BiologyUniversity of CaliforniaBerkeleyUSA
  2. 2.AAAS Risk Policy Fellow National Center for Environmental AssessmentOffice of Research and Development US Environmental Protection AgencyWashingtonUSA
  3. 3.RockvilleUSA

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