Table 2. Parameter estimates for each clonal complex.
| Parameter | ST-21 complex | ST-45 complex | ST-828 complex |
|---|---|---|---|
| Substitution rate (10−3 per site per τ) | 2.815 (1.950, 3.560) | 3.715 (2.315, 5.158) | 9.582 (8.019, 11.534) |
| TMRCA | |||
| Coalescent time, τ | 1.022 (0.442, 3.068) | 0.709 (0.288, 2.583) | 0.159 (0.110, 0.232) |
| Yearsa | 89.069 (38.521, 267.381) | 81.545 (33.124, 297.085) | 47.168 (32.632, 68.824) |
| Host switching rate | |||
| Per τ | 54.078 (10.089,97.519) | 61.634 (14.540, 98.069) | 23.491 (6.802, 85.357) |
| Per yeara | 0.621 (0.116, 1.119) | 0.536 (0.126, 0.853) | 0.079 (0.023, 0.287) |
| Number of migrations | 588.89 (109.80, 1325.90) | 468.67 (105.70, 1264.48) | 117.691 (36.558, 456.318) |
| Estimated host frequencies | |||
| Chicken | 0.614 (0.388, 0.809) | 0.498 (0.311, 0.685) | 0.425 (0.136, 0.691) |
| Cattle | 0.386 (0.191, 0.612) | 0.348 (0.185, 0.540) | 0.282 (0.095, 0.562) |
| Wild bird | — | 0.140 (0.0429, 0.313) | — |
| Pig | — | — | 0.270 (0.103, 0.545) |
| Relative migration rates between host species | |||
| Chicken–cattle | 0.695 (0.023, 3.705) | 0.820 (0.051, 3.779) | 0.303 (0.010, 2.139) |
| Chicken–wild bird | — | 0.592 (0.021, 3.282) | — |
| Chicken–pig | — | — | 0.581 (0.024, 3.129) |
| Cattle–wild bird | — | 0.728 (0.031, 3.643) | — |
| Cattle–pig | — | — | 1.367 (0.192, 4.783) |
Abbreviation: TMRCA, time to most recent common ancestor.
a
Using the mutation rate 3.23 × 10−5 substitutions per site per year for calibration with the median evolutionary rate from the BEAST analysis, one unit of coalescent time (τ) is equal to: 87.151 years in the ST-21 complex, 115.015 years in ST-45 complex and 296.656 years in ST-828 complex. The median value was used for estimating all other parameters in years.