Conservation Genetics

, Volume 6, Issue 4, pp 551-562

First online:

Comparison of methods for detecting bottlenecks from microsatellite loci

  • Ellen G. Williamson-NatesanAffiliated withDepartment of Integrative Biology, University of CaliforniaAAAS Risk Policy Fellow National Center for Environmental Assessment, Office of Research and Development US Environmental Protection Agency Email author 

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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