Table 1.
Ages Calculated for the Entire JT Phylogeny with the Use of ML and ρ Estimates
| Clade | n |
ML Estimates (ka) |
ρ Estimates (ka) |
|
|---|---|---|---|---|
| Complete Sequencea | Complete Sequencea | Coding Regionb | ||
| JT | 902 | 58.0 ± 7.5 | 56.2 ± 7.4 | 55.8 ± 8.8 |
| J | 451 | 43.3 ± 6.1 | 34.5 ± 4.9 | 30.3 ± 5.0 |
| >J1 | 337 | 33.3 ± 6.2 | 25.0 ± 4.0 | 21.5 ± 3.7 |
| > > J1b | 74 | 23.1 ± 3.1 | 21.9 ± 3.3 | 24.2 ± 4.7 |
| > > > J1b1 | 39 | 20.5 ± 2.9 | 22.9 ± 4.5 | 22.6 ± 5.5 |
| > > > > J1b1a | 25 | 14.2 ± 2.8 | 12.9 ± 2.7 | 11.8 ± 2.1 |
| > > > > J1b1b | 14 | 18.2 ± 3.2 | 17.6 ± 3.9 | 17.1 ± 4.6 |
| > > > J1b2 | 13 | 9.3 ± 4.2 | 6.0 ± 2.1 | 7.1 ± 3.2 |
| > > > J1b3 | 5 | 11.8 ± 5.6 | 7.4 ± 2.5 | 5.5 ± 2.6 |
| > > J1c | 234 | 16.4 ± 2.0 | 13.5 ± 1.4 | 14.1 ± 1.5 |
| > > > J1c1 | 30 | 11.1 ± 1.9 | 11.1 ± 1.9 | 13.2 ± 2.8 |
| > > > J1c2 | 63 | 9.5 ± 1.4 | 9.4 ± 1.3 | 10.9 ± 1.7 |
| > > > J1c3 | 41 | 11.1 ± 2.5 | 10.5 ± 1.6 | 11.1 ± 1.8 |
| > > > J1c4 | 14 | 7.9 ± 2.4 | 5.2 ± 1.3 | 5.3 ± 1.7 |
| > > > J1c5 | 14 | 9.0 ± 2.2 | 8.1 ± 1.6 | 10.2 ± 2.4 |
| > > > J1c7 | 36 | 13.6 ± 3.7 | 12.3 ± 3.0 | 11.9 ± 3.9 |
| > > > J1c8 | 9 | 5.8 ± 2.3 | 4.6 ± 1.2 | 3.1 ± 1.3 |
| > > > J1c12 | 7 | 15.3 ± 2.1 | 18.6 ± 3.5 | 21.1 ± 4.7 |
| > > J1d | 28 | 19.9 ± 5.9 | 16.5 ± 2.4 | 16.6 ± 2.8 |
| > > > J1d1 | 11 | 15.6 ± 4.8 | 12.6 ± 3.4 | 13.8 ± 4.2 |
| > > > J1d2 | 17 | 19.9 ± 5.9 | 17.2 ± 2.5 | 18.4 ± 3.4 |
| >J2 | 114 | 36.8 ± 5.5 | 32.9 ± 5.0 | 33.4 ± 6.0 |
| > > J2a | 54 | 31.9 ± 5.1 | 33.9 ± 6.0 | 30.6 ± 6.4 |
| > > > J2a1 | 29 | 16.4 ± 5.1 | 13.9 ± 4.1 | 14.6 ± 5.1 |
| > > > > J2a1a | 27 | 10.9 ± 2.4 | 8.4 ± 1.9 | 9.6 ± 3.0 |
| > > > J2a2 | 25 | 20.3 ± 3.5 | 18.7 ± 3.0 | 19.9 ± 3.6 |
| > > J2b | 60 | 20.2 ± 4.3 | 15.3 ± 3.1 | 18.5 ± 4.5 |
| > > > J2b1 | 55 | 15.6 ± 2.4 | 12.4 ± 1.7 | 13.5 ± 1.6 |
| > > > > J2b1a | 27 | 11.3 ± 1.8 | 9.3 ± 1.3 | 10.1 ± 1.9 |
| > > > J2b2 | 5 | 11.2 ± 3.8 | 9.0 ± 2.5 | 9.2 ± 3.9 |
| T | 451 | 28.8 ± 6.4 | 27.8 ± 4.5 | 26.1 ± 5.3 |
| >T1 | 144 | 21.0 ± 6.6 | 20.3 ± 4.9 | 13.8 ± 2.6 |
| > > T1a | 126 | 17.2 ± 2.9 | 15.6 ± 3.4 | 14.3 ± 3.0 |
| > > > T1a1 | 102 | 15.5 ± 2.8 | 13.1 ± 3.1 | 14.0 ± 3.6 |
| > > > > T1a1a | 78 | 11.0 ± 3.9 | 9.0 ± 2.7 | 13.1 ± 4.6 |
| > > > > > T1a1a1 | 75 | 6.8 ± 0.9 | 6.4 ± 0.7 | 8.5 ± 1.2 |
| > > > T1a2 | 7 | 6.5 ± 4.1 | 6.0 ± 2.9 | 5.3 ± 3.5 |
| > > > T1a3 | 5 | 15.1 ± 2.9 | 14.5 ± 2.9 | 18.4 ± 4.1 |
| > > T1b | 16 | 10.8 ± 2.6 | 7.7 ± 1.5 | 10.1 ± 2.4 |
| >T2 | 307 | 21.3 ± 2.3 | 19.8 ± 2.6 | 20.5 ± 3.4 |
| > > T2a | 38 | 17.1 ± 3.9 | 16.0 ± 3.8 | 21.5 ± 6.1 |
| > > > T2a1 | 35 | 14.5 ± 3.0 | 13.6 ± 3.0 | 18.2 ± 4.7 |
| > > > > T2a1a | 23 | 6.3 ± 1.5 | 6.5 ± 1.4 | 8.2 ± 2.1 |
| > > > > T2a1b | 9 | 13.5 ± 1.8 | 17.4 ± 3.6 | 23.6 ± 5.6 |
| > > T2b | 146 | 9.7 ± 1.1 | 10.3 ± 1.0 | 9.8 ± 1.2 |
| > > > T2b1 | 5 | 6.2 ± 2.0 | 5.2 ± 1.7 | 6.5 ± 2.4 |
| > > > T2b2 | 12 | 7.6 ± 1.9 | 9.0 ± 2.9 | 6.1 ± 1.7 |
| > > > T2b3 | 18 | 8.8 ± 2.6 | 13.1 ± 3.5 | 4.4 ± 1.6 |
| > > > T2b4 | 21 | 8.2 ± 1.8 | 8.7 ± 1.6 | 8.6 ± 1.7 |
| > > > T2b5 | 7 | 6.4 ± 2.5 | 6.4 ± 2.4 | 5.3 ± 2.3 |
| > > > T2b23 | 5 | 3.3 ± 1.8 | 15.8 ± 3.6 | 17.5 ± 4.8 |
| > > T2c | 28 | 20.3 ± 2.4 | 26.6 ± 5.7 | 24.5 ± 5.9 |
| > > > T2c1 | 27 | 18.5 ± 2.7 | 21.2 ± 4.0 | 20.7 ± 3.8 |
| > > T2d | 10 | 20.4 ± 2.4 | 30.4 ± 5.7 | 32.3 ± 6.4 |
| > > > T2d1 | 7 | 17.1 ± 3.4 | 24.0 ± 5.2 | 27.0 ± 6.1 |
| > > T2e | 32 | 11.1 ± 2.3 | 10.4 ± 1.8 | 8.9 ± 1.3 |
| > > > T2e1 | 10 | 9.1 ± 2.4 | 9.0 ± 1.8 | 10.1 ± 2.3 |
| > > T2f | 18 | 17.1 ± 4.0 | 18.7 ± 4.9 | 21.0 ± 6.5 |
| > > > T2f1 | 12 | 12.1 ± 3.7 | 16.2 ± 5.8 | 20.0 ± 8.4 |
| > > > T2f2 | 3 | 7.0 ± 3.3 | 6.1 ± 2.3 | 7.7 ± 3.4 |
| > > T2g | 8 | 11.3 ± 4.5 | 8.2 ± 2.2 | 6.9 ± 4.2 |
| > > T2h | 5 | 15.5 ± 3.4 | 12.3 ± 2.8 | 15.7 ± 4.0 |
Ages are shown for all J and T subclades until the fourth hierarchical level and, in general, only when encompassing at least five individuals.
a
According to the time-dependent clock of Soares et al.;46 ML and ρ used for calculations.