Table 2.
Detection and Age of WGD Peaks for Distributed Duplication and Loss Rates with Estimated Node Ks
| WGD Age | Retention | Exp+Norm Replicates with Optimal k = 2 | Exp+LogNorm Replicates with Optimal k = 2 | Norm Replicates with Optimal k = 2 | Exp+Norm Mean for k = 2 | Exp+LogNorm Mean for k = 2 | Norm Mean for k = 2 |
|---|---|---|---|---|---|---|---|
| 0.15 | 0 | 0 | 0.19 | 0 | 2.92±0.22 | 3.82±0.12 | 2.17±0.24 |
| 0.01 | 0 | 0.18 | 0 | 2.86±0.22 | 3.22±0.17 | 2.13±0.24 | |
| 0.05 | 0 | 0.63 | 0 | 2.66±0.23 | 2.59±0.22 | 1.94±0.24 | |
| 0.1 | 0 | 0.42 | 0 | 2.49±0.23 | 2.40±0.24 | 1.85±0.24 | |
| 0.3 | 0 | 0.19 | 0 | 2.29±0.23 | 2.27±0.25 | 1.77±0.25 | |
| 0.5 | 0.02 | 0.01 | 0 | 2.25±0.23 | 2.25±0.25 | 1.72±0.25 | |
| 1 | 0.2 | 0 | 0 | 2.23±0.24 | 2.02±0.27 | 1.64±0.24 | |
| 0.5 | 0 | 0.51 | 0.43 | 0 | 3.12±0.21 | 3.58±0.16 | 2.15±0.24 |
| 0.01 | 0.72 | 0.74 | 0 | 3.17±0.20 | 3.68±0.15 | 2.16±0.24 | |
| 0.05 | 0.79 | 0.99 | 0 | 3.28±0.19 | 3.77±0.14 | 2.17±0.24 | |
| 0.1 | 0.86 | 1 | 0 | 3.33±0.19 | 3.77±0.14 | 2.15±0. 24 | |
| 0.3 | 0.29 | 0.68 | 0 | 3.43±0.18 | 3.71±0.14 | 2.12±0. 24 | |
| 0.5 | 0.02 | 0.24 | 0 | 2.40±0.12 | 3.70±0.13 | 2.08±0.23 | |
| 1 | 0 | 0 | 0 | 0.49±0.03 | 0.81±0.17 | 2.01±0.23 | |
| 1 | 0 | 0.1 | 0.82 | 0 | 3.39±0.18 | 4.14±0.09 | 2.13±0.24 |
| 0.01 | 0.13 | 0.87 | 0 | 3.50±0.17 | 4.18±0.08 | 2.15±0.24 | |
| 0.05 | 0.34 | 0.93 | 0 | 3.74±0.14 | 4.18±0.08 | 2.38±0.24 | |
| 0.1 | 0.41 | 0.98 | 0 | 3.91±0.11 | 4.20±0.08 | 2.55±0.23 | |
| 0.3 | 0.01 | 0.82 | 0 | 3.64±0.08 | 3.70±0.07 | 2.63±0.23 | |
| 0.5 | 0 | 0.45 | 0 | 1.22±0.05 | 2.46±0.07 | 2.65±0.22 | |
| 1 | 0 | 0 | 0 | 1.03±0.06 | 1.28±0.18 | 2.61±0.22 | |
| 2 | 0 | 0.63 | 0.52 | 0 | 5.46±0.39 | 7.52±0.19 | 3.70±0.42 |
| 0.01 | 0.64 | 0.48 | 0 | 5.48±0.39 | 7.57±0.18 | 3.71±0.42 | |
| 0.05 | 0.79 | 0.28 | 0 | 5.80±0.36 | 7.36±0.20 | 3.74±0.41 | |
| 0.1 | 0.67 | 0.15 | 0 | 6.51±0.30 | 7.85±0.17 | 3.82±0.42 | |
| 0.3 | 0.2 | 0.03 | 0 | 6.91±0.18 | 7.82±0.16 | 3.99±0.42 | |
| 0.5 | 0.32 | 0.11 | 0 | 2.60±0.09 | 5.43±0.26 | 4.13±0.42 | |
| 1 | 0.02 | 1 | 0 | 1.89±0.09 | 2.41±0.34 | 4.30±0.42 | |
| 3 | 0 | 0.42 | 0.92 | 0 | 4.68±0.37 | 3.96±0.40 | 3.18±0.39 |
| 0.01 | 0.37 | 0.93 | 0 | 4.66±0.37 | 3.95±0.40 | 3.16±0.39 | |
| 0.05 | 0.24 | 0.96 | 0 | 4.51±0.35 | 3.90±0.39 | 3.14±0.38 | |
| 0.1 | 0.08 | 0.93 | 0 | 4.31±0.31 | 3.79±0.39 | 3.12±0.38 | |
| 0.3 | 0 | 0.93 | 0 | 3.95±0.20 | 4.36±0.39 | 3.54±0.41 | |
| 0.5 | 0 | 0.98 | 0 | 3.38±0.20 | 3.62±0.37 | 3.02±0.37 | |
| 1 | 0 | 1 | 0 | 3.21±0.19 | 3.59±0.36 | 3.00±0.36 | |
| 5 | 0 | 0.06 | 0.37 | 0 | 4.91±0.37 | 5.54±0.29 | 3.37±0.40 |
| 0.01 | 0.04 | 0.37 | 0 | 4.97±0.37 | 5.43±0.30 | 3.41±0.40 | |
| 0.05 | 0.04 | 0.36 | 0 | 4.98±0.37 | 5.48±0.31 | 3.47±0.40 | |
| 0.1 | 0.15 | 0.38 | 0 | 5.00±0.37 | 5.22±0.32 | 3.55±0.41 | |
| 0.3 | 0.55 | 0.71 | 0 | 5.06±0.38 | 5.27±0.33 | 3.77±0.42 | |
| 0.5 | 0.03 | 0.71 | 0 | 5.08±0.38 | 5.32±0.33 | 3.88±0.42 | |
| 1 | 0 | 0.68 | 0 | 5.11±0.38 | 5.42±0.32 | 4.02±0.43 |
Note.—The proportion of replicates with and optimal number of 2 components (k) and the mean Ks when k is constrained to 2 is displayed. 95% confidence intervals are given for WGD peak means.