Comparison of methods for detecting bottlenecks from microsatellite loci

  • Williamson-Natesan E
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Abstract

Abstract  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 wasnâ_tt 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

Author-supplied keywords

  • MICROSATELLITE LOCI
  • bottleneck
  • method
  • microsatellite
  • model
  • population

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Authors

  • Ellen Williamson-Natesan

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