TABLE 5.
False positive rates under bottlenecks
| Onset time
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
t = 0.002
|
t = 0.02
|
t = 0.2
|
||||||||||
| Depth (severity) | HMMA | HMMB | CLsw | SF | HMMA | HMMB | CLsw | SF | HMMA | HMMB | CLsw | SF |
| Duration δ = 0.04 | ||||||||||||
| 0.5 (0.08) | 0.02 | 0.02 | 0.01 | 0.02 | 0.07 | 0.06 | 0.04 | 0.08 | 0.05 | 0.02 | 0.08 | 0.05 |
| 0.1 (0.4) | 0.22 | 0.38 | 0.33 | 0.26 | 0.40 | 0.60 | 0.57 | 0.48 | 0.29 | 0.32 | 0.53 | 0.31 |
| 0.02 (2) | 0.33 | 0.25 | 0.93 | 0.73 | 0.28 | 0.13 | 1.00 | 0.60 | 0.14 | 0.04 | 0.43 | 0.29 |
| Duration δ = 0.2 | ||||||||||||
| 0.5 (0.4) | 0.10 | 0.13 | 0.12 | 0.10 | 0.12 | 0.15 | 0.18 | 0.14 | 0.11 | 0.08 | 0.16 | 0.10 |
| 0.1 (2) | 0.17 | 0.07 | 0.48 | 0.46 | 0.21 | 0.04 | 0.80 | 0.33 | 0.04 | 0.01 | 0.19 | 0.12 |
| 0.02 (10) | 0.00 | 0.00 | 0.14 | 0.02 | 0.00 | 0.00 | 0.63 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
False positive rates obtained with HMMA, HMMB, CLsw, and SweepFinder for various population bottleneck scenarios are shown. Parameters are n = 30, L = 100 kb. Type I error is 5% for simulations with constant population size. Time is in units of 2N generations. The depth of a bottleneck is the factor by which the population size is reduced.