TABLE 1.
Mycobacterium tuberculosis complex L4.4.1.1 sublineage substitution rate and time to most recent common ancestor (TMRCA) estimates.
| Clock model | Demographic model | Substitution rate (×10–8) | L4.4.1.1 TMRCA | CS clade TMRCA | Rangipo TMRCA | Otara TMRCA |
| Strict | Constant | 6.63 (4.34–9.06) | 1513 (1301–1673) | 1671 (1529–1777) | 1978 (1965–1987) | 1827 (1744–1886) |
| Strict | Exponential | 6.63 (4.37–9.08) | 1513 (1299–1672) | 1672 (1530–1781) | 1978 (1965–1986) | 1827 (1745–1887) |
| Strict | Skyline | 6.28 (4.54–8.10) | 1492 (1325–1629) | 1652 (1535–1741) | 1980 (1969–1988) | 1813 (1746–1868) |
| UCLD | Constant | 6.49 (4.23–8.93) | 1500 (1277–1667) | 1665 (1518–1774) | 1977 (1964–1986) | 1824 (1741–1887) |
| UCLD | Exponential | 6.64 (4.37–8.98) | 1511 (1294–1667) | 1673 (1528–1772) | 1977 (1965–1986) | 1828 (1748–1888) |
| UCLD | Skyline | 6.15 (4.39–7.98) | 1480 (1300–1624) | 1645 (1524–1743) | 1980 (1968–1988) | 1809 (1739–1867) |
Median values are reported and 95% HPD interval shown in brackets. Substitution rate is in substitutions per site per year. The best fitting model and estimates reported in the text are shown in bold. The GTR model of substitution was used for all analyses.