TABLE 5

Number of outlier loci under standard neutral and bottleneck models

DHHfwKKd
SNMBNSNMBNSNMBNSNMBNSNMBN
Embedded ImageBSBSBSBSBSBSBSBSBSBS
1081780028280000001101060027*27*00
7807812027250100001061010024*24*00
1552800131100000055550014*11500
0110071220000393000575700
  • Outlier loci were determined by the calculation of two-sided P-values and then by controlling the false discovery rate (FDR) at 0.05. The FDR method implemented in qvalue (Storey 2002) can use either a bootstrapping or a smoothing method while estimating parameters. The results of both methods are presented here (B and S, respectively). SNM, standard neutral model; BN, bottleneck. The bottlenecks are simulated from the joint posterior distributions obtained with the values of Embedded Image indicated. In some cases, the distribution of P-values is too skewed, resulting in a negative point estimate of the fraction of P-values that come from the null model. In this case, a Bonferroni correction is applied instead, reporting the number of loci with a P-value of ≤0.05/115. Such values are marked with an asterisk.