TABLE 3

Simulation results: simulated data violate assumptions of the analysis model

Mean parameter estimates (SD)
Simulated βSimulated N3E(s)N1 assumedβN3E(s)
a. Mild bottleneck followed by population expansion
0.210200.20 (0.057)15.2 (14.6)
1000.20 (0.058)15.0 (14.8)
1201.16 (0.31)9.8 (3.13)
1001.17 (0.31)9.7 (2.97)
5205.4 (1.14)9.8 (0.64)
1005.6 (1.56)11.6 (2.60)
b. Severe bottleneck followed by population expansion
0.210200.25 (0.083)8.2 (3.12)
1000.27 (0.091)7.7 (3.05)
1201.08 (0.28)9.7 (2.71)
1001.11 (0.31)9.7 (2.43)
5205.6 (2.40)9.6 (0.69)
1006.4 (3.25)9.3 (0.67)
c. Two phases of accelerating population expansion
0.210200.22 (0.081)10.6 (7.61)
1000.24 (0.10)10.3 (8.52)
1201.1 (0.22)10.1 (1.84)
1001.2 (0.31)9.4 (1.83)
5205.6 (2.00)9.7 (0.88)
1007.0 (3.09)9.2 (0.99)
  • Replicate data sets were generated by Monte Carlo simulation for three values of β and E(s) = 0.1 under demographic models involving three epochs that violated the assumptions of the model simulated: (a) N1 = 100, N2 = 25, N3 = 100, t2 = 5, t3 = 100; (b) N1 = 100, N2 = 10, N3 = 100, t2 = 10, t3 = 100; and (c) N1 = 25, N2 = 50, N3 = 100, t2 = 100, t3 = 100. The parameter f0 = 0.95. The data sets consisted of 40 alleles sampled for 10,000 neutral sites and 2000 selected sites. Each data set was analyzed separately assuming two different N1's (20 and 100), and estimates of N2, t, β, E(s), and f0 were obtained. There were 5 replicates for β = 1 and β = 5 and 10 replicates for β = 0.2.