Table 2. Details of the data sets used for estimation of nucleotide substitution rate and time to the most recent common ancestor for Cauliflower mosaic virus.
| Parameter | Open reading frame | |
| I–V | VI | |
| Best-fit substitution model | GTR+I+Γ4 | GTR+I+Γ4 |
| Best-fit molecular clock model | Relaxed Uncorrelated Exponential | Relaxed Uncorrelated Exponential |
| Best-fit population growth model | Exponential growth | Constant size |
| Sequence length (nt) | 5106 | 1269 |
| No. of sequences | 66 | 97 |
| Sampling date range | 1960–2010 | 1960–2012 |
| Chain length (in millions) | 100 | 100 |
| TMRCAa (years) | 491 (86–1270) | 431 (113–886) |
| Substitution rate (nt/site/year) | 1.71×10−4 (1.45×10−5–3.87×10−4) | 5.81×10−4 (2.47×10−4–9.47×10−4) |
| dN/dSb | 0.069 | 0.201 |
| No. of variable sites | 1074 | 448 |
a
Time to the most recent common ancestor.
b
Nonsynomymous (dN) and synonymous (dS) substitution (dN/dS) ratios were calculated for seven ORFs using the Pamilo-Bianchi-Li (PBL) method in MEGA v5 [56].