Table 3.
Simulation Results—Ancestral Effective Population Size and Divergence Time.
| Ancestral Nef, ×06 (1 million) |
Divergence Time, ×106 (1 million) |
|||||||
| Model | MLE | HPD90 | # Completea | # Trueb | MLE | HPD90 | # Completea | # Trueb |
| Baseline—IS | 0.96 | 0.16–4.26 | 5 | 5 | 0.88 | 0.46–7.53 | 1 | 5 |
| Baseline—HKY | 0.82 | 0.15–4.50 | 5 | 5 | 1.06 | 0.48–6.46 | 2 | 5 |
| Recombination, ρ = 0.005 | 0.55 | 0.10–1.36 | 5 | 4 (1,0) | 1.93 | 0.93–3.34 | 4 | 3 (0,2) |
| Recombination, ρ = 0.01 | 0.60 | 0.23–1.25 | 5 | 4 (1,0) | 1.78 | 1.01–2.77 | 5 | 3 (0,2) |
| Recombination, ρ = 0.02 | 0.52 | 0.16–1.07 | 5 | 4 (1,0) | 1.76 | 1.18–2.72 | 5 | 1 (0,4) |
| Recombination, ρ = 0.03 | 0.53 | 0.19–1.07 | 5 | 3 (2,0) | 2.00 | 1.48–2.75 | 5 | 0 (0,5) |
| Recombination, ρ = 0.04 | 0.61 | 0.27–1.15 | 5 | 3 (2,0) | 1.99 | 1.48–2.63 | 5 | 0 (0,5) |
| Recombination, ρ = 0.05 | 0.54 | 0.24–0.99 | 5 | 3 (2,0) | 1.95 | 1.54–2.45 | 5 | 0 (0,5) |
| NR blocks, ρ = 0 | 0.75 | 0.01–5.87 | 5 | 4 (1,0) | 1.16 | 0.55–8.34 | 1 | 5 |
| NR blocks, ρ = 0.005 | 0.48 | 0.01–6.67 | 5 | 5 | 1.12 | 0.65–11.52 | 1 | 4 (0,1) |
| NR blocks, ρ = 0.01 | 0.45 | 0.01–7.99 | 5 | 5 | 1.13 | 0.41–13.19 | 0 | 5 |
| NR blocks, ρ = 0.02 | 0.20 | 0.02–6.22 | 5 | 3 (2,0) | 1.30 | 0.55–11.24 | 2 | 5 |
| NR blocks, ρ = 0.03 | 0.27 | 0.01–5.07 | 5 | 3 (2,0) | 1.20 | 0.54–12.78 | 2 | 5 |
| NR blocks, ρ = 0.04 | 0.25 | 0.02–6.34 | 5 | 3 (2,0) | 1.16 | 0.42–13.41 | 2 | 5 |
| NR blocks, ρ = 0.05 | 0.20 | 0.01–7.97 | 5 | 5 | 1.09 | 0.39–20.78 | 0 | 5 |
| Third species g.f., Nefm = 0.1 | 1.49 | 0.27–5.99 | 5 | 4 (0,1) | 0.96 | 0.49–8.00 | 0 | 5 |
| Third species g.f., Nefm = 0.2 | 1.34 | 0.25–9.42 | 5 | 5 | 1.35 | 0.89–9.09 | 0 | 3 (0,2) |
| Third species g.f., Nefm = 0.3 | 1.65 | 0.21–5.41 | 5 | 5 | 1.11 | 0.79–7.27 | 0 | 4 (0,1) |
| Third species g.f., Nefm = 0.5 | 1.01 | 0.01–3.84 | 5 | 5 | 0.94 | 0.70–7.27 | 0 | 5 |
| Third species g.f., Nefm = 1.0 | 1.68 | 0.01–6.03 | 5 | 5 | 1.01 | 0.59–9.09 | 0 | 3 (0,2) |
| Pop. structure, Nefm = 2.0 | 0.86 | 0.17–5.14 | 5 | 5 | 0.91 | 0.47–6.00 | 2 | 5 |
| Pop. structure, Nefm = 1.0 | 1.07 | 0.19–5.39 | 5 | 5 | 1.05 | 0.49–7.02 | 1 | 5 |
| Pop. structure, Nefm = 0.5 | 0.88 | 0.08–5.50 | 5 | 5 | 1.45 | 0.77–7.66 | 1 | 4 (0,1) |
| Pop. structure, Nefm = 0.2 | 1.03 | 0.35–2.40 | 5 | 5 | 0.94 | 0.51–4.42 | 3 | 4 (1,0) |
| Pop. structure, Nefm = 0.1 | 0.83 | 0.05–6.13 | 5 | 4 (1,0) | 1.19 | 0.63–7.63 | 1 | 5 |
| Linkage, r = 0.1 | 1.74 | 0.67–9.43 | 5 | 4 (0,1) | 0.91 | 0.52–9.09 | 0 | 5 |
| Linkage, r = 0.05 | 1.36 | 0.39–8.89 | 3 | 4 (0,1) | 0.95 | 0.55–9.09 | 0 | 5 |
| Linkage, r = 0.02 | 2.23 | 1.04–6.83 | 5 | 1 (0,4) | 1.25 | 0.44–7.65 | 2 | 5 |
| Linkage, r = 0.01 | 1.59 | 0.49–8.88 | 3 | 4 (0,1) | 1.03 | 0.62–7.50 | 1 | 4 (0,1) |
| Linkage, r = 0.005 | 2.13 | 0.69–9.76 | 5 | 3 (0,2) | 1.44 | 0.59–8.97 | 0 | 5 |
| Selection—early weak | 0.56 | 0.02–3.09 | 5 | 3 (2,0) | 1.27 | 0.76–5.09 | 3 | 3 (0,2) |
| Selection—early strong | 0.75 | 0.10–4.02 | 5 | 5 | 1.07 | 0.62–7.65 | 1 | 5 |
| Selection—late weak | 0.81 | 0.07–6.05 | 5 | 5 | 1.02 | 0.52–7.24 | 0 | 4 (0,1) |
| Selection—late strong | 0.69 | 0.01–6.08 | 5 | 5 | 1.10 | 0.60–8.51 | 0 | 4 (0,1) |
Values listed for MLE and HPD90 interval are averages over five independent simulated data sets. Numbers in parentheses next to parameters are values used in simulations.
a
Number of runs for which the posterior probability distribution has zero density at the prior upper bound.
b
Number of runs for which the HPD interval contains the true value. Numbers in parentheses are the number of simulated values that were significantly lower and higher than the true value, respectively.