Comparison of methods for detecting bottlenecks from microsatellite loci
- 1k Downloads
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.
Keywordsallele frequency distribution population size reduction effective population size extinction risk
Unable to display preview. Download preview PDF.
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.