BOTTLENECK : A Computer Program for Detecting Recent Reductions in the Effective Population Size Using Allele Frequency Data

BOTTLENECK (current version 1.2) is a population genetics computer program that conducts four tests for identifying populations that have recently experienced a severe reduction in effective population size (Ne). ‘‘Recently’’ is defined as within approximately the past 2Ne–4Ne generations, depending on several factors such as the severity of the bottleneck and the mutation rate of the loci being studied (Cornuet and Luikart 1996). The program runs on Windows 95y. It requires allele frequency data obtained from one sample of individuals (e.g., 20–30 diploid individuals) and at least four polymorphic loci. Significant deviations from population mutation-drift equilibrium (e.g., bottlenecks) are important to detect because equilibrium is an assumption required for numerous analyses of population genetics data (e.g., see Nei 1987, p. 251). Bottlenecks are important to detect in conservation biology because they can increase the risk of population extinction. Founderflush events (i.e., short but severe bottlenecks) are important to detect because they may play a role in some modes of speciation [for reviews see Harrison (1991) and Howard (1993)].