Table 2.
Timescale analysis of ORF sequences using different BEAST programs.
| Parameter | ||||
|---|---|---|---|---|
| Demographic model | Constant population size | Expansion growth | Exponential growth | Bayesian skyline plot |
| Path sampling (BF) | 141.31 | 99.47 | 107.51 | 179.87 |
| Stepping-stone sampling (BF) | 152.94 | 260.15 | 110.3 | 185.96 |
| TMRCA (95% CI) | 1873 (1,090–2,608) | 1841 (1,157–2,622) | 1663 (1,071–2,384) | 1879 (1,192–2,659) |
| TMRCA effective sample size | 239 | 238 | 247 | 261 |
| Substitution rate (nt/site/year) | 9.66 × 10−5 (7.10 × 10−5–1.23 × 10−4) | 9.30 × 10−5 (6.79 × 10−5–1.18 × 10−4) | 9.89 × 10−5 (7.40 × 10−5–1.25 × 10−4) | 9.16 × 10−5 (6.90 × 10−5–1.15 × 10−4) |
Number of sequences: 162, sequence length: 8,913 nucleotides (nts), best-fit substitution model: GTR + I + Γ4, Best-fit clock model: relaxed uncorrelated lognormal. Best-fit population growth models were expansion growth and Bayesian skyline plot supported by the best Bayes factors (BFs) (italics) of path sampling and stepping-stone sampling, respectively (BEAST 1.8.2 and Tracer v1.6). The data sets passed date-randomization tests for temporal structure. Effective sample size of substitution rates was 128–167. TMRCA; years before 2016.