Table 2.
Substitution Rate and Divergence Time Estimates with Highest Probability Density (HPD) in Thousands of Years Ago (kya) Inferred for HPV16 Complete (Full) or Selection-Filtered Genome Alignment (Neutral), under the HHS or the ROOA Scenarios, and Considering Different Priors.
| Model | Calibration | Rate uniform prior | Data | ×10−9 (subs/site/yr) |
Log marginal |
2lnBF | tmrca ABCD (kya) |
tmrca A1–4 (kya) |
tmrca BCD (kya) |
tmrca CD (kya) |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ×10−9 (subs/site/yr) | µ | (95% HPD) | likelihood | mean | (95% HPD) | mean | (95% HPD) | mean | (95% HPD) | mean | (95% HPD) | ||||
| HHS | HHS 2 calib | PVs estímate [13.2–24.7] a | Neutral | 18.4 | (14.5–22.1) | −12476.94 | Ref | 461 | (365–561) | 87 | (48–133) | 197 | (121–293) | 105 | (82–129) |
| HHS | HHS 2 calib | Human mtDNA [17.6–32.3]b | Neutral | 20.3 | (16–25.1) | −12480.34 | 6.8 | 456 | (358–553) | 78 | (42–123) | 184 | (109–273) | 101 | (76–124) |
| HHS | HHS 2 calib | PVs estimate [5.5–13.6]c | Neutral | 12.8 | (11.1–14.3) | −12484.91 | 15.9 | 484 | (396–580) | 130 | (80–190) | 250 | (158–360) | 122 | (100–144) |
| HHS | HHS 2 calib | Mammal genome [2.0–2.4]d | Neutral | 3.6 | (3.1–4.1) | −12567.19 | 180.5 | 571 | (488–655) | 423 | (284–578) | 408 | (267–575) | 180 | (158–201) |
| HHS | HHS 2 calib | 4.5-4.5E–11 | Neutral | 20.2 | (14.0–26.8) | −12482.18 | 10.5 | 457 | (357–5559) | 79 | (40–128) | 185 | (105–280) | 101 | (75–128) |
| HHS | HHS 1 calib 500 kya | 4.5-4.5E–11 | Neutral | 13.6 | (8.1–20.3) | −12482.41 | 10.9 | 490 | (389–587) | 125 | (55–206) | 311 | (157–471) | 197 | (95–312) |
| HHS | HHS 1 calib 90 kya | 4.5-4.5E–11 | Neutral | 32.1 | (17.0–49.6) | −12483.21 | 12.5 | 210 | (92–346) | 54 | (23–91) | 134 | (72–203) | 85 | (53–115) |
| ROOA | 90 kya | 4.5-4.5E–11 | Neutral | 80.5 | (40.3–128) | −12481.41 | 8.9 | 85 | (54–115) | 22 | (9–38) | 54 | (24–87) | 34 | (14–56) |
| HHS | HHS 2 calib | PVs estímate [13.2–24.7]a | Full | 22.9 | (20.3–25.3) | −19313.69 | 4.7 | 476 | (387–568) | 147 | (101–200) | 246 | (164–343) | 127 | (106–148) |
| HHS | HHS 2 calib | Human mtDNA [17.6–32.3]b | Full | 27.5 | (23.5–31.0) | −19311.33 | Ref | 459 | (364–551) | 120 | (79–166) | 216 | (140–300) | 116 | (95–138) |
| HHS | HHS 2 calib | PVs estimate [5.5–13.6]c | Full | 14.4 | (13.1–15.8) | −19333.81 | 44.9 | 519 | (431–607) | 240 | (167–324) | 330 | (212–455) | 152 | (8131–173) |
| HHS | HHS 2 calib | Mammal genome [2.0–2.4]d | Full | 4.6 | (4.0–5.2) | −19502.91 | 383.1 | 650 | (571–727) | 616 | (518–705) | 411 | (320–498) | 214 | (8189–232) |
| HHS | HHS 2 calib | 4.5-4.5E–11 | Full | 33.9 | (24.4–43.4) | −19314.23 | 5.8 | 446 | (346–544) | 95 | (53–142) | 186 | (110–271) | 105 | (80–132) |
| HHS | HHS 1 calib 500 kya | 4.5-4.5E–11 | Full | 22.0 | (13.2–31.2) | −19311.87 | 1.1 | 490 | (390–586) | 156 | (78–240) | 320 | (176–473) | 209 | (111–319) |
| HHS | HHS 1 calib 90 kya | 4.5-4.5E–11 | Full | 55.0 | (31.8–82.9) | −19311.82 | 1 | 199 | (99–322) | 63 | (31–100) | 130 | (73–193) | 84 | (54–115) |
| ROOA | 90 kya | 4.5-4.5E–11 | Full | 130.6 | (71.8–206.0) | −19311.94 | 1.2 | 84 | (54–115) | 27 | (12–44) | 55 | (27–88) | 36 | (17–58) |
Note.—Likelihood values in bold are the best-supported models, taken as reference (Ref) for the path sampling Bayes factor (2lnBF) comparison.