Table 3.
Parametric bootstrap estimates of the branch lengths based on ND5 codon position 2 under the independence and correlated rates assumptions. Sequences with 600 sites were simulated based on the phylogeny shown in Figure 1 using the branch lengths specified in parentheses in the first column. For the correlated rate case, B = 27, ρmax = 0.73, and in both cases, ξ = 1.26. The total number of simulations = 6,000. Of these, 76.1% produced a tree topology identical to the given tree for both independence and correlated cases.
| Branch (Length) | Correlation Type | Mean (Se) | Se Increase (%) | Median (95% CI) |
|---|---|---|---|---|
| 1, 2 (0.0050) | IND | 0.0061 (0.0032) | - | 0.0057 (0.0016,0.0120) |
| CORR B27 | 0.0062 (0.0035) | 9.0 | 0.0056 (0.0015,0.0126) | |
| 1, Orangutan (0.0533) | IND | 0.0488 (0.0095) | - | 0.0486 (0.0339,0.0649) |
| CORR B27 | 0.0496 (0.0132) | 38.8 | 0.0487 (0.0294,0.0730) | |
| 2, 3 (0.0084) | IND | 0.0084 (0.0039) | - | 0.0081 (0.0030,0.0154) |
| CORR B27 | 0.0084 (0.0040) | 3.1 | 0.0079 (0.0029,0.0158) | |
| 2, Gorilla (0.0252) | IND | 0.0240 (0.0066) | - | 0.0238 (0.0137,0.0353) |
| CORR B27 | 0.0242 (0.0079) | 19.6 | 0.0237 (0.0119,0.0379) | |
| 3, 4 (0.0076) | IND | 0.0076 (0.0035) | - | 0.0070 (0.0025,0.0140) |
| CORR B27 | 0.0076 (0.0040) | 11.9 | 0.0069 (0.0017,0.0149) | |
| 3, Human (0.0217) | IND | 0.0208 (0.0062) | - | 0.0205 (0.0116,0.0316) |
| CORR B27 | 0.0210 (0.0073) | 17.2 | 0.0204 (0.0101,0.0343) | |
| 4, Chimpanzee (0.0068) | IND | 0.0067 (0.0035) | - | 0.0067 (0.0017,0.0131) |
| CORR B27 | 0.0068 (0.0036) | 5.3 | 0.0067 (0.0017,0.0135) | |
| 4, Pygmy Chimp (0.0100) | IND | 0.0098 (0.0041) | - | 0.0097 (0.0034,0.0170) |
| CORR B27 | 0.0099 (0.0046) | 11.3 | 0.0098 (0.0033,0.0182) | |
| 5, 1 (0.0133) | IND | 0.0127 (0.0051) | - | 0.0123 (0.0050,0.0217) |
| CORR B27 | 0.0130 (0.0056) | 9.8 | 0.0125 (0.0050,0.0232) | |
| 5, Gibbon (0.0302) | IND | 0.0282 (0.0073) | - | 0.0278 (0.0170,0.0408) |
| CORR B27 | 0.0285 (0.0089) | 22.1 | 0.0280 (0.0151,0.0436) | |
| 6, 5 (0.0252) | IND | 0.0235 (0.0072) | - | 0.0231 (0.0122,0.0361) |
| CORR B27 | 0.0240 (0.0086) | 19.9 | 0.0233 (0.0113,0.0392) | |
| 6, 7 (0.0491) | IND | 0.0428 (0.0097) | - | 0.0425 (0.0273,0.0589) |
| CORR B27 | 0.0430 (0.0123) | 27.4 | 0.0421 (0.0247,0.0647) | |
| 7, Lemur (0.0474) | IND | 0.0433 (0.0093) | - | 0.0429 (0.0284,0.0590) |
| CORR B27 | 0.0442 (0.0124) | 32.4 | 0.0435 (0.0252,0.0661) | |
| 7, Tarsier (0.0626) | IND | 0.0561 (0.0109) | - | 0.0556 (0.0392,0.0747) |
| CORR B27 | 0.0569 (0.0149) | 37.0 | 0.0555 (0.0344,0.0832) | |
| 8, 6 (0.0456) | IND | 0.0404 (0.0091) | - | 0.0400 (0.0262,0.0560) |
| CORR B27 | 0.0409 (0.0116) | 27.6 | 0.0400 (0.0236,0.0613) | |
| 8, Baboon (0.0267) | IND | 0.0255 (0.0071) | - | 0.0252 (0.0145,0.0376) |
| CORR B27 | 0.0258 (0.0086) | 21.4 | 0.0252 (0.0126,0.0409) | |
| 8, Barbary Ape (0.0302) | IND | 0.0285 (0.0076) | - | 0.0281 (0.0168,0.0412) |
| CORR B27 | 0.0288 (0.0093) | 22.3 | 0.0282 (0.0149,0.0451) |