Table 1

Simulation results for a population with constant size and standard microsatellite mutations
Ne Vk Ne/Nc He (SD) K (SD) Fis (SD) M-ratio (SD) %P FPR
M-ratioft M-ratiosim Het excess MSVAR
50
2 1 0.11 (0.17) 1.53 (0.59) 0.00 (0.09) 1.00 (0.03) 48 0.01 0.02 0.01 0.00
40 0.1 0.07 (0.14) 1.30 (0.52) -0.03 (0.12) 1.00 (0.00) 27 0.0 0.04 0.02 0.00
400 0.01 0.05 (0.14) 1.24 (0.45) -0.01 (0.11) 1.00 (0.03) 23 0.01 0.04 0.10 0.00
2000 0.002 0.07 (0.13) 1.25 (0.35) -0.15 (0.17) 0.97 (0.06) 25 0.00 0.17 0.11 0.00
500
2 1 0.44 (0.16) 3.08 (0.72) -0.02 (0.12) 1.00 (0.03) 100 0.0 0.09 0.04 0.00
40 0.1 0.42 (0.20) 2.74 (0.81) -0.07 (0.21) 0.98 (0.07) 96 0.03 0.36 0.32 0.62
400 0.01 0.43 (0.23) 2.91 (1.10) -0.17 (0.29) 0.87 (0.18) 89 0.21 1.00 0.53 0.97
2000 0.002 0.44 (0.21) 3.17 (1.20) -0.19 (0.31) 0.71 (0.21) 88 0.43 1.00 0.54 1.00
2500
2 1 0.71 (0.06) 6.3 (1.3) 0.01 (0.05) 0.95 (0.08) 100 0.0 0.03 0.06 0.06
40 0.1 0.69 (0.1) 5.7 (1.8) -0.08 (0.11) 0.89 (0.13) 100 0.07 0.51 0.20 0.66
400 0.01 0.64 (0.09) 4.5 (1.2) -0.19 (0.13) 0.82 (0.15) 99 0.35 1.00 0.39 0.99
2000 0.002 0.61 (0.12) 4.2 (1.4) -0.20 (0.12) 0.69 (0.18) 99 0.49 1.00 0.42 1.00
5000
2 1 0.76 (0.08) 7.70 (1.60) -0.016 (0.08) 0.94 (0.09) 100 0.0 0.05 0.07 0.14
40 0.1 0.72 (0.09) 6.06 (1.76) -0.11 (0.17) 0.81 (0.19) 100 0.23 0.93 0.22 0.97
400 0.01 0.66 (0.13) 4.80 (1.51) -0.22 (0.16) 0.68 (0.23) 100 0.50 1.00 0.40 1.00
2000 0.002 0.67 (0.11) 4.90 (1.66) -0.24 (0.14) 0.66 (0.20) 99 0.58 1.00 0.43 1.00

Mean values of summary statistics (with standard deviations) across 100 replicates are given. The last four columns report the rate of false positives (FPR = type I error) estimated as the fraction of replicates with an M-ratio smaller than the commonly used threshold of 0.68 (M-ratioft), with a M-ratio smaller and the critical value computed by simulation using the same parameter θ = 4Neμ used to generate the data (M-ratiosim), where a significant (P< 0.05) heterozygoty excess was detected using the program BOTTLENECK, and where a significant difference between ancestral and current population size is detected by MSVAR, respectively. Ne = effective population size; Nc = census population size; He = expected heterozygosity; F = inbreeding coefficient, estimated as 1-Ho/He, where Ho is the observed heterozygosity; M = M-ratio; %P = fraction of replicates producing a polymorphic locus; the starting values, in the log10 scale, for the mean and variance of the prior distributions in MSVAR, are as follows: ancestral size (3,1), current size (3,1), mutation rate ( -3.3,1), time since the decline (2,0.5); means and variances (and their means and variances) of the hyperprior distributions used in MSVAR are as follows: ancestral size (3,1,0,0.5), current size (3,1,0,0.5), mutation rate (-3.3,0.25,0,0.5), time since the decline (2,0.5,0,0.5).

Hoban et al.

Hoban et al. BMC Bioinformatics 2013 14:309   doi:10.1186/1471-2105-14-309

Open Data