Huff et al. BMC Genomics 2010, 11:8 http://www.biomedcentral.com/1471-2164/11/8 Page 4 of 9 Figure 2 Power to detect selection from single-site statistics for various demographic models with a constant recombination rate. All statistics perform well under all 4 population histories. The only statistic notably sensitive to population history was iHS, which performed particularly well in models with expansion and relatively worse in models with bottlenecks and migration. The simulated region was 1 Mb in length with an equal proportion of allele frequencies 0.2, 0.4, 0.6, and 0.8 for the favored allele at a significance level of 0.01. values for power, false positive rates, and false discovery rates (Figure 4). Here we distinguish between the false positive rate and the false discovery rate, with the first equal to the rate of false positives for each test, and the second equal to the rate of false positives among all of the statistically significant results. Since both tests were designed to identify candidate genes from a full genome scan, for this analysis we evaluated the statistical proper- ties of the tests at the gene level rather than the SNP level. For the iHS test, we make the simplifying assump- tion that each gene is contained in a single 100 Kb region. With one 100 Kb test statistic for each gene evaluated at the 0.01 level, the false positive rate per gene is at most 0.01. For ALnLHu, we treat the test sta- tistic for each SNP within a 200 Kb region as a separate (but not independent) test for each gene. While the false positive rate per SNP was 0.016 for ALnLHu [4], we estimate that the false positive rate per gene was between 0.05 and 0.13. Therefore, of those candidate genes identified by Wang et al., we estimate that a frac- tion between 0.74 and 0.96 are false positives (Figure 4b). In comparison, we estimate that the false discovery Figure 3 Effects of variable recombination rate on the power of selection statistics. The variable recombination rate reduced the power of iHS by 8% and the power of ALnLHp by 46%. The locus recombination rate for each simulation was set to an exponential random variate with mean equal to 1 cm/Mb. For other simulation parameters, see Figure 2.